https://biogeoscapes.net//wiki/api.php?action=feedcontributions&feedformat=atom&user=RStrzepek
OceanWiki - User contributions [en]
2026-10-11T00:52:58Z
User contributions
MediaWiki 1.45.0
https://biogeoscapes.net//wiki/index.php?title=14-Carbon_uptake_(NPP)&diff=947
14-Carbon uptake (NPP)
2026-09-24T14:05:11Z
<p>RStrzepek: </p>
<hr />
<div>{{DISPLAYTITLE:14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)}}<br />
{{BreadcrumbsPrimaryProduction}}<br />
<br />
* [[Page authors|Page authors]]: [[User:RStrzepek|Robert Strzepek]]<br />
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]<br />
----<br />
<br />
__TOC__<br />
<div class="model-box"><br />
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"<br />
! Net primary production<br />
|-<br />
| '''Approach:''' radiotracer (<sup>14</sup>C) uptake<br />
|-<br />
| '''Context:''' incubation, simulated ''in situ''<br />
|-<br />
| '''Spatial scale:''' point sample<br />
|-<br />
| '''Temporal scale:''' 2–24 h<br />
|-<br />
| '''Units:''' µmol C L<sup>-1</sup> d<sup>-1</sup>; (x)mol C biomass<sup>-1</sup> d<sup>-1</sup><br />
|-<br />
| '''Community captured:''' all (usually > 0.2 µm); size fractions are typically 0.2-2.0, 2.0-20, and >20 µm<br />
|-<br />
| '''Co-measurements:''' temperature, PAR (simulated ''in situ''), DIC, biomass (Chl, cells, POC, cell volume)<br />
|}<br />
</div><br />
<div style="clear:both"></div><br />
<br />
== Method Overview ==<br />
<br />
Radioactive bicarbonate (NaH<sup>14</sup>CO<sub>3</sub>) is added to seawater samples incubated under simulated ''in situ'' conditions of temperature and photosynthetically active radiation (PAR). Phytoplankton incorporate <sup>14</sup>C into organic matter during photosynthesis. At the end of the incubation, samples are filtered onto membrane filters, acidified to remove dissolved inorganic <sup>14</sup>C, and the organically fixed <sup>14</sup>C is quantified by liquid scintillation counting. Incubation duration determines the balance between Gross Primary Productivity (GPP) and Net Primary Productivity (NPP) captured: short incubations (e.g. 2h) approach GPP, while 24 h incubations approach NPP as some of the fixed carbon is respired back to CO<sub>2</sub> during the incubation period<ref name="Nielsen1952">Steemann Nielsen, E. (1952). The use of radio-active carbon (C<sup>14</sup>) for measuring organic production in the sea. ''ICES Journal of Marine Science'', 18(2), 117–140. https://doi.org/10.1093/icesjms/18.2.117</ref>.<br />
<br />
The method can be applied to bulk community samples, size-fractionated fractions, or individual sorted cells, and is routinely performed across depth profiles to characterize the vertical distribution of NPP.<br />
<br />
=== Scale of measurement ===<br />
<br />
Each incubation provides a point measurement in space. For daily-integrated NPP estimates, standard incubation durations of 12–24 h integrate photosynthetic activity over a full light cycle. Depth profiles require separate incubations at each target depth under the appropriate irradiance level.<br />
<br />
=== Data generated ===<br />
<br />
The method yields GPP or NPP expressed as carbon fixed per unit volume and time. When normalized to biomass (chlorophyll, cell carbon, or POC), it gives the carbon-specific production rate. The fraction of fixed carbon released as dissolved organic carbon (DOC) is not captured by standard filtration and requires additional measurements.<br />
<br />
=== Units & currency ===<br />
<br />
Units are µmol C L<sup>-1</sup> d<sup>-1</sup>, or (x)mol C biomass<sup>-1</sup> d<sup>-1</sup> when normalized to biomass. <br />
<br />
=== Sample size ===<br />
<br />
Typical samples are 0.5-1 L in volume; multiple replicate bottles are incubated at each depth.<br />
<br />
=== Repositories & databases ===<br />
<br />
== Limitations ==<br />
<br />
Bottle confinement excludes larger grazers and alters the physico-chemical environment relative to ambient conditions. Excretion of labelled dissolved organic carbon is not retained on the filter and is lost from the measured rate. Small bottle volumes discriminate against larger, less abundant phytoplankton taxa.<br />
<br />
== Example Applications & Protocols ==<br />
<br />
=== Classic examples ===<br />
* Steemann Nielsen (1952) ''The use of radio-active carbon (C<sup>14</sup>) for measuring organic production in the sea'' <ref name="Nielsen1952" /><br />
<br />
=== Recent applications ===<br />
*<br />
<br />
=== Common calculations/conversions ===<br />
* NPP (µmol C L<sup>-1</sup> d<sup>-1</sup>) = (<sup>14</sup>C<sub>POC</sub> / <sup>14</sup>C<sub>added</sub>) × DIC<sub>initial</sub> × (1.05/incubation time) ; the factor 1.05 corrects for isotopic discrimination against <sup>14</sup>C relative to <sup>12</sup>C.<br />
<br />
== References ==<br />
<br />
[[index.php?title=Category:Main Pages|Model types]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=User:RStrzepek&diff=946
User:RStrzepek
2026-09-24T14:02:47Z
<p>RStrzepek: </p>
<hr />
<div>Hi!<br />
<br />
Robert Strzepek<br />
<br />
https://orcid.org/0000-0002-6442-7121<br />
<br />
[[File:DSC5437.jpg]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=User:RStrzepek&diff=945
User:RStrzepek
2026-09-24T14:01:57Z
<p>RStrzepek: </p>
<hr />
<div>Hi!<br />
[[File:DSC5437.jpg]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=File:DSC5437.jpg&diff=944
File:DSC5437.jpg
2026-09-24T14:01:09Z
<p>RStrzepek: </p>
<hr />
<div>yet another cat</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=File:DSC5437_1_1.jpg&diff=943
File:DSC5437 1 1.jpg
2026-09-24T13:55:32Z
<p>RStrzepek: Blanked the page</p>
<hr />
<div></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=User:RStrzepek&diff=942
User:RStrzepek
2026-09-24T13:51:35Z
<p>RStrzepek: Created page with "Hi! thumb"</p>
<hr />
<div>Hi!<br />
[[File:DSC5437 1 1.jpg|thumb]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=File:DSC5437_1_1.jpg&diff=941
File:DSC5437 1 1.jpg
2026-09-24T13:50:39Z
<p>RStrzepek: </p>
<hr />
<div>Tongue</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Photoautotrophy&diff=916
Photoautotrophy
2026-09-22T04:12:03Z
<p>RStrzepek: </p>
<hr />
<div>=== Incubation | Discrete ===<br />
*[[14-Carbon uptake (NPP)|<sup>14</sup>Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
*[[18O-labelled water (GOP)]]<br />
*[[Winkler light-dark dissolved O2 bottle|Winkler light-dark dissolved O<sub>2</sub> bottle]]<br />
*[[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
*[[13-Carbon uptake|<sup>13</sup>Carbon uptake]]<br />
*[[Continuous dissolved oxygen (DO) optodes]]<br />
<br />
=== ''In situ'' | Continuous ===<br />
*[[Gross Primary Production (GPP) - triple oxygen]]<br />
*[[Net community production (NCP)|Net community production (NCP)- Nitrate drawdown]]<br />
*[[Net community production (NCP) - O₂/Ar]]<br />
<br />
=== Optics-based ===<br />
*[[Single Turnover Chlorophyll Fluorescence]]<br />
*[[Remote Sensing NPP]]<br />
*[[BGC-Argo NPP]]<br />
<br />
=== Omics-based ===<br />
*[[RT-qPCR/ddPCR]]<br />
*[[rcbL gene expression/quant]]<br />
*[[psbA]]<br />
*[[Rubisco protein]]<br />
*[[PSII/PSI quantification]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Photoautotrophy&diff=915
Photoautotrophy
2026-09-22T04:10:24Z
<p>RStrzepek: </p>
<hr />
<div>=== Incubation | Discrete ===<br />
*[[14-Carbon uptake (NPP)|<sup>14</sup>Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
*[[18O-labelled water (GOP)]]<br />
*[[Winkler light-dark dissolved O2 bottle]]<br />
*[[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
*[[13-Carbon uptake|<sup>13</sup>Carbon uptake]]<br />
*[[Continuous dissolved oxygen (DO) optodes]]<br />
<br />
=== ''In situ'' | Continuous ===<br />
*[[Gross Primary Production (GPP) - triple oxygen]]<br />
*[[Net community production (NCP)|Net community production (NCP)- Nitrate drawdown]]<br />
*[[Net community production (NCP) - O₂/Ar]]<br />
<br />
=== Optics-based ===<br />
*[[Single Turnover Chlorophyll Fluorescence]]<br />
*[[Remote Sensing NPP]]<br />
*[[BGC-Argo NPP]]<br />
<br />
=== Omics-based ===<br />
*[[RT-qPCR/ddPCR]]<br />
*[[rcbL gene expression/quant]]<br />
*[[psbA]]<br />
*[[Rubisco protein]]<br />
*[[PSII/PSI quantification]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Photoautotrophy&diff=914
Photoautotrophy
2026-09-22T04:07:28Z
<p>RStrzepek: </p>
<hr />
<div>=== Incubation | Discrete ===<br />
*[[14-Carbon uptake (NPP)|<sup>14</sup>Carbon uptake - Net Primary Productivity (NPP)and Gross Primary Productivity (GPP)]]<br />
*[[18O-labelled water (GOP)]]<br />
*[[Winkler light-dark dissolved O2 bottle]]<br />
*[[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
*[[13-Carbon uptake]]<br />
*[[Continuous dissolved oxygen (DO) optodes]]<br />
<br />
=== ''In situ'' | Continuous ===<br />
*[[Gross Primary Production (GPP) - triple oxygen]]<br />
*[[Net community production (NCP)|Net community production (NCP)- Nitrate drawdown]]<br />
*[[Net community production (NCP) - O₂/Ar]]<br />
<br />
=== Optics-based ===<br />
*[[Single Turnover Chlorophyll Fluorescence]]<br />
*[[Remote Sensing NPP]]<br />
*[[BGC-Argo NPP]]<br />
<br />
=== Omics-based ===<br />
*[[RT-qPCR/ddPCR]]<br />
*[[rcbL gene expression/quant]]<br />
*[[psbA]]<br />
*[[Rubisco protein]]<br />
*[[PSII/PSI quantification]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Photoautotrophy&diff=913
Photoautotrophy
2026-09-22T04:07:13Z
<p>RStrzepek: </p>
<hr />
<div>=== Incubation | Discrete ===<br />
*[[14-Carbon uptake (NPP)|<sup>14</sup>-Carbon uptake - Net Primary Productivity (NPP)and Gross Primary Productivity (GPP)]]<br />
*[[18O-labelled water (GOP)]]<br />
*[[Winkler light-dark dissolved O2 bottle]]<br />
*[[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
*[[13-Carbon uptake]]<br />
*[[Continuous dissolved oxygen (DO) optodes]]<br />
<br />
=== ''In situ'' | Continuous ===<br />
*[[Gross Primary Production (GPP) - triple oxygen]]<br />
*[[Net community production (NCP)|Net community production (NCP)- Nitrate drawdown]]<br />
*[[Net community production (NCP) - O₂/Ar]]<br />
<br />
=== Optics-based ===<br />
*[[Single Turnover Chlorophyll Fluorescence]]<br />
*[[Remote Sensing NPP]]<br />
*[[BGC-Argo NPP]]<br />
<br />
=== Omics-based ===<br />
*[[RT-qPCR/ddPCR]]<br />
*[[rcbL gene expression/quant]]<br />
*[[psbA]]<br />
*[[Rubisco protein]]<br />
*[[PSII/PSI quantification]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Photoautotrophy&diff=912
Photoautotrophy
2026-09-22T04:06:06Z
<p>RStrzepek: /* Incubation | Discrete */</p>
<hr />
<div>=== Incubation | Discrete ===<br />
*[[14-Carbon uptake (NPP)|<sup>14</sup>-Carbon uptake - Net Primary Productivity (NPP)and Gross Primary Productivity (GPP)]]<br />
*[[18O-labelled water (GOP)]]<br />
*[[Winkler light-dark dissolved O2 bottle]]<br />
*[[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
*[[13-Carbon uptake]]<br />
*[[Continuous dissolved oxygen (DO) optodes]]<br />
<br />
=== ''In situ'' | Continuous ===<br />
*[[Gross Primary Production (GPP) - triple oxygen]]<br />
*[[Net community production (NCP)]]<br />
*[[Net community production (NCP) - O₂/Ar]]<br />
<br />
=== Optics-based ===<br />
*[[Single Turnover Chlorophyll Fluorescence]]<br />
*[[Remote Sensing NPP]]<br />
*[[BGC-Argo NPP]]<br />
<br />
=== Omics-based ===<br />
*[[RT-qPCR/ddPCR]]<br />
*[[rcbL gene expression/quant]]<br />
*[[psbA]]<br />
*[[Rubisco protein]]<br />
*[[PSII/PSI quantification]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Main_Page&diff=911
Main Page
2026-09-22T03:49:49Z
<p>RStrzepek: </p>
<hr />
<div>{{DISPLAYTITLE:Welcome to OceanWiki}}<br />
'''While still under development, these are some of the exciting entries on models and measurements recently added by community members:'''<br><br />
[[Respiration from oxygen consumption: optodes]]<br><br />
[[Single Turnover Chlorophyll Fluorescence]]<br><br />
[[NifH amplicon sequence]]<br><br />
[[Net community production (NCP) - O₂/Ar]]<br><br />
[[PISCES]]<br><br />
[[CMIP]]<br><br />
[[Proteome Allocation Models]]<br />
<br />
== Origin Story & Mission ==<br />
Marine biogeochemistry needs a shared vocabulary between experimentalists and modelers for cross-disciplinary work to advance the field. Yet, to integrate disciplines successfully, researchers need to be vocal about discrepancy and uncertainty, and realize caveats of how values are determined. This community-driven collection of biogeochemical output began at the [https://biogeoscapes.org/ BioGeoScapes] modelling workshop and the following [https://www.primoscorwg.org PRIMO] session at Woods Hole Oceanographic Institution in September 2025. To highlight cross-discipline implications like ''What data was particularly helpful to inform a model?'' or ''How can a model help constrain experimental parameters?'', the idea arose to create a Wiki that provided a central repository for basic information related to interdisciplinary biogeochemistry science. This emerged as a way to address needs that have arisen in conversations specifically: <br />
*defining key terms used across disciplines<br />
*explain types of data generated by different methods, assumptions, and potential biases<br />
*describe different types of models, required data inputs, computational demand, and limitations<br />
<br />
== Content ==<br />
'''OceanWiki''' is an encyclopedia of '''marine biogeochemistry''', and consists of three components:<br />
<br />
=== [[:Category:Lexicon|Lexicon]] ===<br />
A dictionary with definitions from both experimentalists, observationalists, and modelers.<br />
<br />
=== [[Data Types]] ===<br />
==== Primary Production ====<br />
[[Photoautotrophy]] | [[Nitrogen Fixation]] | [[Phytoplankton C/N-Based Growth Rates]] | [[Chemoautotrophy]]<br />
==== Secondary Production ====<br />
[[Enzyme Activity]] | [[Growth Rate]] | [[Respiration]]<br />
==== Nutrient Fluxes ====<br />
[[Nitrogen]] | [[Phosphorous]] | [[Sulfur]] | [[Trace Metals]] | [[Biomineralization]]<br />
==== Interactions ====<br />
[[Grazing]] | [[Mixotrophy]] | [[Viruses]] | [[Allelopathy]] | [[Life cycles]]<br />
<br />
=== [[Model Types]] ===<br />
==== [[Cellular scale]] ====<br />
[[Flux Balance Analysis]] | [[Proteome Allocation Models]] | [[Particle Simulation]] | [[Bio Particle Simulation]]<br />
==== [[Biome scale]] ====<br />
[[Community Flux Balance Analysis]] | [[GENOME]]<br />
==== [[Global scale]] ====<br />
[[CMIP]] | [[MARBL]] | [[Darwin]] | [[AWESOME-OCIM]] | [[PISCES]]<br />
<br />
=== Teaching material ===<br />
<br />
This was a suggestion from the BioGeoScapes leadership. If you are interested in leading the effort, please get in contact with one of us (see the bottom of [[How to contribute]]).</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Single_Turnover_Chlorophyll_Fluorescence&diff=910
Single Turnover Chlorophyll Fluorescence
2026-09-22T03:47:47Z
<p>RStrzepek: </p>
<hr />
<div>{{BreadcrumbsPhotoautotrophy}}<br />
<br />
* [[Page authors|Page authors]]: [[Michiel Perneel]], [[PRIMO]]<br />
* [[Responsible curator|Responsible curator]]: [[User:Kate Evans|Kate Evans]]<br />
----<br />
Photosynthetic primary productivity is the light-driven process of extracting reducing power from water to drive CO<sub>2</sub> reduction to carbohydrates (i.e. CO<sub>2</sub> ‘fixation’). Global primary productivity is a critical source of O<sub>2</sub> for the atmosphere and oceans. Marine primary productivity also plays an important role in carbon sequestration to the deep ocean through the biological pump, while providing a critical source of organic matter to support aquatic food webs and metabolism.<br />
<br />
__TOC__<br />
<div class="model-box"><br />
{| class="model-ib"<br />
! Active Chlorophyll Fluorescence<br />
|-<br />
| '''Photosynthetic electron transport'''<br />
|-<br />
| '''Approach:''' active chlorophyll fluorescence (single turnover), optical photophysiology<br />
|-<br />
| '''Context:''' ''in situ'', underway, incubation, autonomous platforms<br />
|-<br />
| '''Spatial scale:''' mL to km<sup>2</sup> (point measurements to transects)<br />
|-<br />
| '''Temporal scale:''' milliseconds to seasons (instantaneous to long-term monitoring)<br />
|-<br />
| '''Units:''' electrons m<sup>-3</sup> s<sup>-1</sup>, e<sup>-</sup> PSII<sup>-1</sup> s<sup>-1</sup>, derived C or O<sub>2</sub> units<br />
|-<br />
| '''Community captured:''' target species culture experiments, bulk phytoplankton community; taxon-weighted signal<br />
|-<br />
| '''Co-measurements:''' irradiance, temperature, salinity, nutrient concentrations, chlorophyll a, light history<br />
|}<br />
</div><br />
<div style="clear:both"></div><br />
<br />
== Method Overview ==<br />
Single Turnover Active Chlorophyll Fluorescence (ST-ChlF) is an optical technique used to quantify photosynthetic activity in aquatic primary producers by resolving rapid fluorescence induction and relaxation transients following short excitation flashes. These transients reflect the opening and closure of Photosystem II (PSII) reaction centres and downstream electron transport processes.<br />
<br />
By fitting photophysiological models to fluorescence transients, ST-ChlF enables estimation of photosynthetic electron transfer rates (ETR), which scale stoichiometrically with gross oxygen evolution and are closely linked to primary productivity. The method provides rapid, non-invasive measurements and can be applied across laboratory, ship-based, and autonomous observing platforms.<br />
<br />
== Output ==<br />
<br />
=== Scale of measurement ===<br />
*Cellular to community-integrated photosynthesis<br />
*Short- and long temporal scales<br />
<br />
=== Data generated ===<br />
*Raw fluorescence induction-relaxation transients<br />
*Primary photophysiological parameters (e.g. Fo, Fm, σPSII, τ)<br />
*Electron transfer rates (ETR)<br />
*Light-response (ETR–E) curves and derived parameters (α, Ek, ETRmax)<br />
*Ancillary stress and efficiency metrics (e.g. NPQ-related indices)<br />
<br />
=== Units & currency ===<br />
*ETR reported as electrons per unit volume or per PSII reaction centre per second<br />
*Can be converted to O<sub>2</sub> or carbon-based primary productivity using stoichiometric or empirical relationships<br />
*Represents gross photosynthetic activity on instantaneous time scales<br />
<br />
=== Sample size ===<br />
*Typically mL per measurement<br />
*Not necessarily needing sample destruction<br />
*Compatible with continuous flow-through systems<br />
<br />
=== Repositories & databases ===<br />
<br />
== Limitations ==<br />
*ETR is not a direct measure of carbon fixation and requires conversion assumptions<br />
*Relationships between ETR, O<sub>2</sub>, and carbon vary with taxonomy and environmental conditions<br />
*Sensitive to non-photochemical quenching (NPQ) and light history<br />
*Requires careful calibration, spectral correction, and baseline fluorescence treatment<br />
*Community-weighted signal may mask taxon-specific responses<br />
<br />
== Example Applications & Protocols ==<br />
<br />
=== Classic examples ===<br />
<br />
=== Recent applications ===<br />
<br />
=== Common calculations/conversions ===<br />
*Conversion of ETR to gross O<sub>2</sub> production (4 e- per O<sub>2</sub>)<br />
*Empirical ETR–C relationships calibrated against 14C incubations<br />
*Light-response curve fitting (ETR vs irradiance)<br />
<br />
<br />
== References ==<br />
SCOR Working Group 156 (2021). A User Guide for the Application of Single Turnover Active Chlorophyll Fluorescence for Phytoplankton Productivity Measurements. Version 1.0.<br />
<br />
[[Category:Main Pages|Model types]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=18O-labelled_water_(GOP)&diff=909
18O-labelled water (GOP)
2026-09-22T03:41:00Z
<p>RStrzepek: </p>
<hr />
<div>{{DISPLAYTITLE:<sup>18</sup>Oxygen-labelled water (GOP)}}<br />
{{BreadcrumbsPrimaryProduction}}<br />
<br />
* [[Page authors|Page authors]]: [[PRIMO]]<br />
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]<br />
----<br />
<br />
__TOC__<br />
<div class="model-box"><br />
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"<br />
! Gross oxygen production<br />
|-<br />
| '''Approach:''' stable isotope tracer (<sup>18</sup>O-water)<br />
|-<br />
| '''Context:''' incubation, ''in situ''<br />
|-<br />
| '''Spatial scale:''' point sample<br />
|-<br />
| '''Temporal scale:''' hours to one day<br />
|-<br />
| '''Units:''' µmol O<sub>2</sub> L<sup>-1</sup> d<sup>-1</sup>; convertible to µmol C L<sup>-1</sup> d<sup>-1</sup><br />
|-<br />
| '''Community captured:''' all<br />
|-<br />
| '''Co-measurements:''' initial dissolved O<sub>2</sub> concentration; photosynthetic quotient (PQ) for C conversion; parallel O<sub>2</sub>/Ar measurement for respiration by difference<br />
|}<br />
</div><br />
<div style="clear:both"></div><br />
<br />
== Method Overview ==<br />
<br />
H<sub>2</sub><sup>18</sup>O is added to seawater incubations, enriching the water isotopically. During oxygenic photosynthesis, phytoplankton split water molecules, releasing O<sub>2</sub> that carries the <sup>18</sup>O label. The accumulation of <sup>18</sup>O<sub>2</sub> above natural abundance is measured by isotope ratio mass spectrometry (IRMS) at the end of the incubation, and the rate of <sup>18</sup>O<sub>2</sub> production is converted to gross oxygen production (GOP)<ref name="Bender1987">Bender, M., Grande, K., Johnson, K., Marra, J., Williams, P. J. le B., Sieburth, J., Pilson, M., Langdon, C., Hitchcock, G., Orchardo, J., Hunt, C., Donaghay, P., & Heinemann, K. (1987). A comparison of four methods for determining planktonic community production. ''Limnology and Oceanography'', 32(5), 1085–1098. https://doi.org/10.4319/lo.1987.32.5.1085</ref>.<br />
<br />
Unlike the <sup>14</sup>C method, the <sup>18</sup>O approach directly measures gross O<sub>2</sub> production before respiratory consumption. Combined with a simultaneous measurement of net O<sub>2</sub> exchange (e.g., via O<sub>2</sub>/Ar), community respiration can be estimated by difference.<br />
<br />
=== Scale of measurement ===<br />
<br />
Each incubation provides a point measurement. Standard incubations run for hours to one day. The small sample volume (~50 mL) limits the approach to discrete sampling rather than continuous deployment.<br />
<br />
=== Data generated ===<br />
<br />
The primary output is the gross O<sub>2</sub> production rate. Conversion to gross carbon fixation requires the photosynthetic quotient (PQ, mol O<sub>2</sub> produced per mol CO<sub>2</sub> fixed, typically 1.1–1.4 depending on substrate and nitrogen source).<br />
<br />
=== Units & currency ===<br />
<br />
Units are µmol O<sub>2</sub> L<sup>-1</sup> d<sup>-1</sup>, or µmol C L<sup>-1</sup> d<sup>-1</sup> after PQ conversion. The primary currency is oxygen; carbon is the derived currency.<br />
<br />
=== Sample size ===<br />
<br />
Typical samples are ~50 mL in volume.<br />
<br />
=== Repositories & databases ===<br />
<br />
== Limitations ==<br />
<br />
The method assumes that newly produced <sup>18</sup>O<sub>2</sub> mixes rapidly and uniformly with the dissolved O<sub>2</sub> pool in the incubation vessel. Light-dependent O<sub>2</sub> consumption (Mehler reaction, photorespiration) can cause overestimation of gross carbon fixation when rates are converted via PQ. Bottle confinement effects apply. Small sample volumes exclude larger, rarer phytoplankton.<br />
<br />
== Example Applications & Protocols ==<br />
<br />
=== Classic examples ===<br />
* Bender et al. (1987) ''A comparison of four methods for determining planktonic community production'' <ref name="Bender1987" /><br />
<br />
=== Recent applications ===<br />
*<br />
<br />
=== Common calculations/conversions ===<br />
* GOP (µmol O<sub>2</sub> L<sup>-1</sup> d<sup>-1</sup>) = (<sup>18</sup>O excess in POO / <sup>18</sup>O enrichment of water) × [O<sub>2</sub>]<sub>initial</sub> / incubation time.<br />
* Gross C fixation = GOP / PQ.<br />
<br />
== References ==<br />
<br />
[[Category:Main Pages|Model types]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Photoautotrophy&diff=908
Photoautotrophy
2026-09-22T03:35:34Z
<p>RStrzepek: </p>
<hr />
<div>=== Incubation | Discrete ===<br />
*[[14-Carbon uptake (NPP)]]<br />
*[[18O-labelled water (GOP)]]<br />
*[[Winkler light-dark dissolved O2 bottle]]<br />
*[[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
*[[13-Carbon uptake]]<br />
*[[Continuous dissolved oxygen (DO) optodes]]<br />
<br />
=== ''In situ'' | Continuous ===<br />
*[[Gross Primary Production (GPP) - triple oxygen]]<br />
*[[Net community production (NCP)]]<br />
*[[Net community production (NCP) - O₂/Ar]]<br />
<br />
=== Optics-based ===<br />
*[[Single Turnover Chlorophyll Fluorescence]]<br />
*[[Remote Sensing NPP]]<br />
*[[BGC-Argo NPP]]<br />
<br />
=== Omics-based ===<br />
*[[RT-qPCR/ddPCR]]<br />
*[[rcbL gene expression/quant]]<br />
*[[psbA]]<br />
*[[Rubisco protein]]<br />
*[[PSII/PSI quantification]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Photoautotrophy&diff=907
Photoautotrophy
2026-09-22T03:33:08Z
<p>RStrzepek: </p>
<hr />
<div>=== Incubation | Discrete ===<br />
*[[14-Carbon uptake (NPP)]]<br />
*[[18O-labelled water (GOP)]]<br />
*[[Winkler light-dark dissolved O2 bottle]]<br />
*[[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
*[[13-Carbon uptake]]<br />
<br />
<br />
=== ''In situ'' | Continuous ===<br />
*[[Gross Primary Production (GPP) - triple oxygen]]<br />
*[[Net community production (NCP)]]<br />
*[[Net community production (NCP) - O₂/Ar]]<br />
*[[Continuous dissolved oxygen (DO) optodes]]<br />
<br />
=== Optics-based ===<br />
*[[Single Turnover Chlorophyll Fluorescence]]<br />
*[[Remote Sensing NPP]]<br />
*[[BGC-Argo NPP]]<br />
<br />
=== Omics-based ===<br />
*[[RT-qPCR/ddPCR]]<br />
*[[rcbL gene expression/quant]]<br />
*[[psbA]]<br />
*[[Rubisco protein]]<br />
*[[PSII/PSI quantification]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=906
Data Types
2026-09-22T03:15:14Z
<p>RStrzepek: Undo revision 905 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation | Discrete<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Net community production (NCP)]]<br />
; ''In situ | Continuous''<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=905
Data Types
2026-09-22T03:14:24Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation | Discrete<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
; ''In situ | Continuous''<br />
* [[index.php?title=Gross Primary Production (GPP) - triple oxygen|Gross Primary Production (GPP) - triple oxygen]]<br />
* [[index.php?title=Net community production (NCP)|Net community production (NCP)]]<br />
* [[index.php?title=Net community production (NCP) - O₂/Ar|Net community production (NCP) - O₂/Ar]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Photoautotrophy&diff=904
Photoautotrophy
2026-09-22T01:40:03Z
<p>RStrzepek: relabelled subcategories</p>
<hr />
<div>=== Incubation | Discrete ===<br />
*[[14-Carbon uptake (NPP)]]<br />
*[[18O-labelled water (GOP)]]<br />
*[[Winkler light-dark dissolved O2 bottle]]<br />
*[[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
*[[13-Carbon uptake]]<br />
*[[Gross Primary Production (GPP) - triple oxygen]]<br />
*[[Net community production (NCP)]]<br />
<br />
=== ''In situ'' | Continuous ===<br />
*[[Net community production (NCP) - O₂/Ar]]<br />
*[[Continuous dissolved oxygen (DO) optodes]]<br />
<br />
=== Optics-based ===<br />
*[[Single Turnover Chlorophyll Fluorescence]]<br />
*[[Remote Sensing NPP]]<br />
*[[BGC-Argo NPP]]<br />
<br />
=== Omics-based ===<br />
*[[RT-qPCR/ddPCR]]<br />
*[[rcbL gene expression/quant]]<br />
*[[psbA]]<br />
*[[Rubisco protein]]<br />
*[[PSII/PSI quantification]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=903
Data Types
2026-09-22T01:39:01Z
<p>RStrzepek: </p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation | Discrete<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Net community production (NCP)]]<br />
; ''In situ | Continuous''<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=14-Carbon_uptake_(NPP)&diff=902
14-Carbon uptake (NPP)
2026-09-22T01:13:33Z
<p>RStrzepek: added info on typically used size fractions</p>
<hr />
<div>{{DISPLAYTITLE:14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)}}<br />
{{BreadcrumbsPrimaryProduction}}<br />
<br />
* [[Page authors|Page authors]]: [[PRIMO]]<br />
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]<br />
----<br />
<br />
__TOC__<br />
<div class="model-box"><br />
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"<br />
! Net primary production<br />
|-<br />
| '''Approach:''' radiotracer (<sup>14</sup>C) uptake<br />
|-<br />
| '''Context:''' incubation, simulated ''in situ''<br />
|-<br />
| '''Spatial scale:''' point sample<br />
|-<br />
| '''Temporal scale:''' 2–24 h<br />
|-<br />
| '''Units:''' µmol C L<sup>-1</sup> d<sup>-1</sup>; (x)mol C biomass<sup>-1</sup> d<sup>-1</sup><br />
|-<br />
| '''Community captured:''' all (usually > 0.2 µm); size fractions are typically 0.2-2.0, 2.0-20, and >20 µm<br />
|-<br />
| '''Co-measurements:''' temperature, PAR (simulated ''in situ''), DIC, biomass (Chl, cells, POC, cell volume)<br />
|}<br />
</div><br />
<div style="clear:both"></div><br />
<br />
== Method Overview ==<br />
<br />
Radioactive bicarbonate (NaH<sup>14</sup>CO<sub>3</sub>) is added to seawater samples incubated under simulated ''in situ'' conditions of temperature and photosynthetically active radiation (PAR). Phytoplankton incorporate <sup>14</sup>C into organic matter during photosynthesis. At the end of the incubation, samples are filtered onto membrane filters, acidified to remove dissolved inorganic <sup>14</sup>C, and the organically fixed <sup>14</sup>C is quantified by liquid scintillation counting. Incubation duration determines the balance between Gross Primary Productivity (GPP) and Net Primary Productivity (NPP) captured: short incubations (e.g. 2h) approach GPP, while 24 h incubations approach NPP as some of the fixed carbon is respired back to CO<sub>2</sub> during the incubation period<ref name="Nielsen1952">Steemann Nielsen, E. (1952). The use of radio-active carbon (C<sup>14</sup>) for measuring organic production in the sea. ''ICES Journal of Marine Science'', 18(2), 117–140. https://doi.org/10.1093/icesjms/18.2.117</ref>.<br />
<br />
The method can be applied to bulk community samples, size-fractionated fractions, or individual sorted cells, and is routinely performed across depth profiles to characterize the vertical distribution of NPP.<br />
<br />
=== Scale of measurement ===<br />
<br />
Each incubation provides a point measurement in space. For daily-integrated NPP estimates, standard incubation durations of 12–24 h integrate photosynthetic activity over a full light cycle. Depth profiles require separate incubations at each target depth under the appropriate irradiance level.<br />
<br />
=== Data generated ===<br />
<br />
The method yields GPP or NPP expressed as carbon fixed per unit volume and time. When normalized to biomass (chlorophyll, cell carbon, or POC), it gives the carbon-specific production rate. The fraction of fixed carbon released as dissolved organic carbon (DOC) is not captured by standard filtration and requires additional measurements.<br />
<br />
=== Units & currency ===<br />
<br />
Units are µmol C L<sup>-1</sup> d<sup>-1</sup>, or (x)mol C biomass<sup>-1</sup> d<sup>-1</sup> when normalized to biomass. <br />
<br />
=== Sample size ===<br />
<br />
Typical samples are 0.5-1 L in volume; multiple replicate bottles are incubated at each depth.<br />
<br />
=== Repositories & databases ===<br />
<br />
== Limitations ==<br />
<br />
Bottle confinement excludes larger grazers and alters the physico-chemical environment relative to ambient conditions. Excretion of labelled dissolved organic carbon is not retained on the filter and is lost from the measured rate. Small bottle volumes discriminate against larger, less abundant phytoplankton taxa.<br />
<br />
== Example Applications & Protocols ==<br />
<br />
=== Classic examples ===<br />
* Steemann Nielsen (1952) ''The use of radio-active carbon (C<sup>14</sup>) for measuring organic production in the sea'' <ref name="Nielsen1952" /><br />
<br />
=== Recent applications ===<br />
*<br />
<br />
=== Common calculations/conversions ===<br />
* NPP (µmol C L<sup>-1</sup> d<sup>-1</sup>) = (<sup>14</sup>C<sub>POC</sub> / <sup>14</sup>C<sub>added</sub>) × DIC<sub>initial</sub> × (1.05/incubation time) ; the factor 1.05 corrects for isotopic discrimination against <sup>14</sup>C relative to <sup>12</sup>C.<br />
<br />
== References ==<br />
<br />
[[index.php?title=Category:Main Pages|Model types]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=901
Data Types
2026-09-22T01:07:29Z
<p>RStrzepek: Undo revision 900 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Laboratory-based<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Net community production (NCP)]]<br />
; ''In situ''<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=900
Data Types
2026-09-22T01:05:53Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Laboratory-based<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[index.php?title=Continuous dissolved oxygen (DO) optodes|Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ''<br />
<br />
*[[index.php?title=Net community production (NCP)|Net community production (NCP)]]<br />
*[[index.php?title=Net community production (NCP) - O₂/Ar|Net community production (NCP) - O₂/Ar]]<br />
* [[index.php?title=Gross Primary Production (GPP) - triple oxygen|Gross Primary Production (GPP) - triple oxygen]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=899
Data Types
2026-09-22T01:03:27Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Laboratory-based<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Net community production (NCP)]]<br />
; ''In situ''<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=898
Data Types
2026-09-22T00:59:33Z
<p>RStrzepek: Undo revision 861 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Laboratory-based<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Net community production (NCP)]]<br />
; ''In situ''<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Global optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=897
Data Types
2026-09-22T00:59:19Z
<p>RStrzepek: Undo revision 864 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Laboratory-based<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[14_Carbon uptake (GPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Net community production (NCP)]]<br />
; ''In situ''<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Global optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=896
Data Types
2026-09-22T00:58:53Z
<p>RStrzepek: Undo revision 865 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[14_Carbon uptake (GPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Global optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=895
Data Types
2026-09-22T00:58:39Z
<p>RStrzepek: Undo revision 867 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[14_Carbon uptake (GPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Global optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=894
Data Types
2026-09-22T00:58:18Z
<p>RStrzepek: Undo revision 868 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[14_Carbon uptake (GPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; [[''In situ'' and Discrete]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=893
Data Types
2026-09-22T00:58:03Z
<p>RStrzepek: Undo revision 869 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[14-Carbon uptake (GPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; [[''In situ'' and Discrete]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=892
Data Types
2026-09-22T00:57:35Z
<p>RStrzepek: Undo revision 870 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[<sup>14<\sup>-Carbon uptake (NPP)]]<br />
* [[14-Carbon uptake (GPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=891
Data Types
2026-09-22T00:57:19Z
<p>RStrzepek: Undo revision 871 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[<sup>14</sup>-Carbon uptake (NPP)]]<br />
* [[14-Carbon uptake (GPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=890
Data Types
2026-09-22T00:57:05Z
<p>RStrzepek: Undo revision 872 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[ <sup>14</sup>-Carbon uptake (NPP)]]<br />
* [[14-Carbon uptake (GPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=889
Data Types
2026-09-22T00:56:52Z
<p>RStrzepek: Undo revision 874 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake (NPP)]]<br />
* [[14-Carbon uptake (GPP)]]<br />
* [[18O-labelled water (GOP)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=888
Data Types
2026-09-22T00:56:35Z
<p>RStrzepek: Undo revision 875 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake (Net Primary Production (NPP) and Gross Primary Production (GPP))]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O<,sub>2</sub> bottle]]<br />
* [[Phytoplankton carbon biomass (C<sub>phyto</sub>) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=887
Data Types
2026-09-22T00:56:05Z
<p>RStrzepek: Undo revision 876 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake (Net Primary Production (NPP) and Gross Primary Production (GPP))]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O<sub>2</sub> bottle]]<br />
* [[Phytoplankton carbon biomass (C<sub>phyto</sub>) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=886
Data Types
2026-09-22T00:55:48Z
<p>RStrzepek: Undo revision 877 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Production (NPP) and Gross Primary Production (GPP)]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O<sub>2</sub> bottle]]<br />
* [[Phytoplankton carbon biomass (C<sub>phyto</sub>) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=885
Data Types
2026-09-22T00:55:00Z
<p>RStrzepek: Undo revision 879 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=884
Data Types
2026-09-22T00:54:30Z
<p>RStrzepek: Undo revision 880 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=883
Data Types
2026-09-22T00:53:05Z
<p>RStrzepek: Undo revision 882 by RStrzepek (talk)</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
* [[18Oxygen-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=882
Data Types
2026-09-22T00:38:21Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
* [[18-Oxygen-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=881
Data Types
2026-09-22T00:37:27Z
<p>RStrzepek: </p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRIMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
* [[18Oxygen-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=880
Data Types
2026-09-22T00:36:47Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRiMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
* [[18Oxygen-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=879
Data Types
2026-09-22T00:36:11Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRiMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Continuous_dissolved_oxygen_(DO)_optodes&diff=878
Continuous dissolved oxygen (DO) optodes
2026-09-22T00:28:08Z
<p>RStrzepek: </p>
<hr />
<div>{{BreadcrumbsPrimaryProduction}}<br />
<br />
* [[Page authors|Page authors]]: [[PRIMO]]<br />
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]<br />
<br />
----<br />
<br />
__TOC__<br />
<div class="model-box"><br />
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"<br />
! O<sub>2</sub> optode method<br />
|-<br />
| '''Approach:''' continuous O<sub>2</sub> measurement by luminescent optode, light and dark bottles<br />
|-<br />
| '''Context:''' incubation, simulated ''in situ''<br />
|-<br />
| '''Spatial scale:''' point sample<br />
|-<br />
| '''Temporal scale:''' hours to one day<br />
|-<br />
| '''Units:''' µmol O<sub>2</sub> L<sup>-1</sup> d<sup>-1</sup>; convertible to µmol C L<sup>-1</sup> d<sup>-1</sup><br />
|-<br />
| '''Community captured:''' all<br />
|-<br />
| '''Co-measurements:''' temperature, PAR, salinity, pressure; photosynthetic quotient (PQ) for C conversion<br />
|}<br />
</div><br />
<div style="clear:both"></div><br />
<br />
== Method Overview ==<br />
<br />
Luminescent optical oxygen sensors (optodes) are mounted inside incubation bottles, allowing dissolved O<sub>2</sub> to be logged continuously throughout the incubation rather than at a single endpoint. The same light-dark bottle design as the Winkler method is used: light bottles capture NCP (net O<sub>2</sub> production); dark bottles capture community respiration (CR). GPP = NCP + CR. Because O<sub>2</sub> is measured continuously, the method can resolve short-term dynamics and diel patterns within a single incubation, and non-linear responses in the dark bottles can be detected and accounted for.<br />
<br />
Optodes respond to the partial pressure of dissolved O<sub>2</sub> via a luminescence lifetime that decreases as O<sub>2</sub> quenches a fluorescent dye embedded in the sensor membrane. Temperature and salinity corrections are required for accurate O<sub>2</sub> concentration calculations.<br />
<br />
=== Scale of measurement ===<br />
<br />
As a bottle-based incubation, the method provides a point measurement in space. Larger bottle volumes (> 1 L) compared to Winkler bottles reduce the relative contribution of wall effects and increase the signal-to-noise ratio for low-productivity waters.<br />
<br />
=== Data generated ===<br />
<br />
The method yields time-resolved O<sub>2</sub> concentration trajectories, from which GPP, NCP, and CR are estimated as linear rates over selected time windows. Conversion to carbon requires PQ (for GPP and NCP) and RQ (for CR).<br />
<br />
=== Units & currency ===<br />
<br />
Units are µmol O<sub>2</sub> L<sup>-1</sup> d<sup>-1</sup>, or µmol C L<sup>-1</sup> d<sup>-1</sup> after conversion. The currency is oxygen (carbon is derived).<br />
<br />
=== Sample size ===<br />
<br />
Typical samples are > 1 L in volume.<br />
<br />
=== Repositories & databases ===<br />
<br />
== Limitations ==<br />
<br />
Sensor drift over longer incubations must be monitored and corrected. Response times of optodes can lag behind rapidly changing O<sub>2</sub> concentrations. Gas permeability of some incubation vessel materials can introduce artefacts in the O<sub>2</sub> mass balance. The same biological bottle effects (grazer exclusion, altered physico-chemical environment) apply as in the Winkler method. Light-dependent O<sub>2</sub> consumption reactions can cause overestimation of GPP.<br />
<br />
== Example Applications & Protocols ==<br />
<br />
=== Classic examples ===<br />
*<br />
<br />
=== Recent applications ===<br />
*<br />
<br />
=== Common calculations/conversions ===<br />
* GPP (µmol O<sub>2</sub> L<sup>-1</sup> d<sup>-1</sup>) = rate of O<sub>2</sub> increase in light bottle − rate of O<sub>2</sub> decrease in dark bottle.<br />
* GPP (µmol C L<sup>-1</sup> d<sup>-1</sup>) = GPP<sub>O2</sub> / PQ.<br />
<br />
== References ==<br />
<br />
[[Category:Main Pages|Model types]]</div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=877
Data Types
2026-09-22T00:10:55Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRiMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Productivity (NPP) and Gross Primary Productivity (GPP)]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O2 bottle]]<br />
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=876
Data Types
2026-09-22T00:09:34Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRiMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake - Net Primary Production (NPP) and Gross Primary Production (GPP)]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O<sub>2</sub> bottle]]<br />
* [[Phytoplankton carbon biomass (C<sub>phyto</sub>) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=875
Data Types
2026-09-22T00:02:38Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRiMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake (Net Primary Production (NPP) and Gross Primary Production (GPP))]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O<sub>2</sub> bottle]]<br />
* [[Phytoplankton carbon biomass (C<sub>phyto</sub>) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek
https://biogeoscapes.net//wiki/index.php?title=Data_Types&diff=874
Data Types
2026-09-21T23:58:51Z
<p>RStrzepek: /* Data Type Sections */</p>
<hr />
<div>Oceanographers measuring bulk rates of carbon fixation and respiration as well as elemental composition, i.e. how much particulate carbon, nitrogen, or phosphorus is present in a given volume of water, provide foundational information about ocean biogeochemical cycles. These bulk measurements can be coupled with targeted methods to further assess rates of transformation<ref name="Levine et al. 2025">Naomi M. Levine, Harriet Alexander, Erin M. Bertrand, Victoria J. Coles, Stephanie Dutkiewicz, Suzana G. Leles and Emily J. Zakem. 2025. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models.Annual Review of Earth and Planetary Science, Vol. 53:595-624, https://doi.org/10.1146/annurev-earth-040523-020630</ref>. More recently, new tools in analytical chemistry, molecular microbiology, and bioinformatics are enhancing our ability to integrate process-based mechanisms and biomass estimates of functional groups of interest into the study of ocean biogeochemistry<ref> Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, et al. 2016. Deciphering ocean carbon in a changing world. PNAS 113:(12):3143–51, https://doi.org/10.1073/pnas.1514645113</ref>. <br><br />
In addition, advances in sequencing and mass spectrometry technologies over the last decades have accelerated the study of microbial communities. These high-throughput, data-rich approaches enable assessment of community taxonomic and functional composition, metabolic potential and diversity, and phylogeny and evolutionary history across the global oceans<ref name="Levine et al. 2025"/>.<br />
<br />
This literature review, initiated by [https://www.primoscorwg.org PRiMO], covers well-established physiological metrics routinely used in biological oceanography, as well as novel metrics being developed to determine physiological rates at both the cellular and community level. The entries include information about the methods (currencies, units, assumptions, uncertainties). We also provide key references to facilitate discovery.<br><br />
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.<br />
<br />
If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].<br />
<br />
== Data Type Sections ==<br />
<br />
''Expand a section below to browse methods by type.''<br />
<br />
<!-- ═══════════════ PRIMARY PRODUCTION ═══════════════ --><br />
<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Incubation-based | Discrete<br />
* [[14-Carbon uptake (Net Primary Production (NPP) and Gross Primary Production (GPP))]]<br />
* [[18O-labelled water (Gross Oxygen Production)]]<br />
* [[Winkler light-dark dissolved O<,sub>2</sub> bottle]]<br />
* [[Phytoplankton carbon biomass (C<sub>phyto</sub>) x growth rate (µ)]]<br />
* [[13-Carbon uptake]]<br />
* [[Gross Primary Production (GPP) - triple oxygen]]<br />
* [[Continuous dissolved oxygen (DO) optodes]]<br />
; ''In situ'' | Continuous<br />
* [[Net community production (NCP)- Nitrate drawdown]]<br />
* [[Net community production (NCP) - O₂/Ar]]<br />
; Optics-based<br />
* [[Single Turnover Chlorophyll Fluorescence]]<br />
* [[Remote Sensing NPP]]<br />
* [[BGC-Argo NPP]]<br />
; Omics-based<br />
* [[RT-qPCR/ddPCR]]<br />
* [[rcbL gene expression/quant]]<br />
* [[psbA]]<br />
* [[Rubisco protein]]<br />
* [[PSII/PSI quantification]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Bulk uptake 15N2]]<br />
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]<br />
* [[Acetylene Reduction Assays (ARA)]]<br />
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]<br />
* [[nifH amplicon sequence]]<br />
* [[H2 supersaturation]]<br />
* [[Nitrogenase quantification]]<br />
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Carbon content]]<br />
* [[Nitrogen content]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Mass balance approach]]<br />
* [[Dark 14C-bicarbonate fixation]]<br />
* [[Nano SIP]]<br />
* [[Black smoker]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ SECONDARY PRODUCTION ═══════════════ --><br />
<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]<br />
* [[Enzyme assay with RBB labeled polysaccharides]]<br />
* [[Enzyme assay with DNS]]<br />
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Growth rate from biomass observation]]<br />
* [[Radiolabeled tracer method]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Respiration from BGC-Argo floats and AOU]]<br />
* [[Respiration from oxygen consumption: optodes]]<br />
* [[Respiration from activity of respiratory chain: enzymatic assays]]<br />
* [[Respiration from activity of respiratory chain: redoxsensor green]]<br />
* [[Respiration from oxygen consumption]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ NUTRIENT FLUXES ═══════════════ --><br />
<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Nitrogen Uptake<br />
* [[(15N-ρNO3-) uptake New Production]]<br />
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]<br />
* [[15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]<br />
* [[(15N-ρNH4+) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]<br />
* [[(15N-ρurea) uptake Regenerated Production]]<br />
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]<br />
; Nitrogen Assimilation<br />
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]<br />
; Nitrification<br />
* [[DIN inventory with inhibitors]]<br />
* [[Inhibitors with 14 or 13CO2 uptake]]<br />
* [[Nitrite oxidation (Nxr)]]<br />
* [[amoA gene or transcript abundance]]<br />
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]<br />
* [[15N tracers]]<br />
; Denitrification<br />
* [[Acetylene-block proxy for denitrifcation enzyme activity]]<br />
* [[15N tracer-based method]]<br />
* [[N2:Ar ratio quantification]]<br />
* [[Mass Balance]]<br />
* [[Stoichiometric approach]]<br />
* [[Natural Abundances of 15N and 18O]]<br />
; Other Processes (DNRA, Anammox, DON)<br />
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]<br />
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]<br />
* [[Functional gene quantification (hzs, hzo)]]<br />
* [[FISH staining of anammox bacteria]]<br />
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]<br />
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]<br />
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Degradation of dissolved organic phosphorus<br />
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]<br />
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]<br />
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]<br />
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]<br />
; P nutrition<br />
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]<br />
* [[32-P incorporation]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[DMS/P/O cycling]]<br />
* [[Rates of DMSO reduction to DMS]]<br />
* [[Rates of DMS and DMSP oxidation to DMSO]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[55-Iron uptake]]<br />
* [[54-Manganese uptake]]<br />
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]<br />
* [[Cobalamin uptake with 57Cobalt-B12]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Silicon<br />
* [[Silicon uptake]]<br />
* [[Kinetics of silicon uptake]]<br />
* [[Silica production]]<br />
* [[Silica production - PDMPO]]<br />
* [[Biogenic silica accumulation]]<br />
; Calcification<br />
* [[Calcification (13-Carbon uptake)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
<!-- ═══════════════ INTERACTIONS ═══════════════ --><br />
<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;"><br />
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div><br />
<div class="mw-collapsible-content" style="padding:8px 14px;"><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
; Microzooplankton on Phytoplankton<br />
* [[Incubation dilution experiments]]<br />
* [[Size-fractionated incubation dilution experiments]]<br />
* [[Cell abundance]]<br />
* [[Gut-fluorescence]]<br />
; Bacterivory & Mixotrophy<br />
* [[Fluorescently labeled prey surrogates]]<br />
* [[Radioactively labeled prey surrogates]]<br />
* [[Pulse-chase labeling of bacterial prey]]<br />
* [[Stable isotope-labelled prey]]<br />
; Life Cycles<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[LysoTracker Green Incorporation]]<br />
* [[15N/13C-labelled DOM/cells]]<br />
* [[Bead consumption rates by cells with chloroplasts]]<br />
* [[BrdU-labeled prey incorporation into things with chloroplasts]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Electron microscopy of cells]]<br />
* [[Quantification of virus particles]]<br />
* [[Dilution incubation experiments]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
* [[Single-cell RNA-sequencing (population)]]<br />
* [[Single-cell RNA-sequencing (community)]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Filtrate cross-culturing]]<br />
* [[Size-fractionated extract spiking]]<br />
</div><br />
</div><br />
<br />
<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;"><br />
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div><br />
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;"><br />
* [[Light or electron microscopic counts of life cycle stages/transitions]]<br />
* [[Fluorescent in situ hybridization microscope counts]]<br />
* [[Bulk RNA marker-gene PCR analysis]]<br />
* [[Bulk RNA-sequencing (whole transcriptome)]]<br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
<br />
== References ==<br />
<references /></div>
RStrzepek