Data Types

2026-09-24T13:36:27Z

Himanshusaxena: I've added a new Anaplerotic Carbon Fixation method under Primary Production heading.

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>
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"/>.

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>
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.

If you would like to add a data type page, please use the [[Data wiki template | Data wiki template]].

== Data Type Sections ==

''Expand a section below to browse methods by type.''


<div id="Primary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;">
<div style="background:#d5e8d4; padding:8px 14px; font-weight:bold; font-size:1.1em;">Primary Production</div>
<div class="mw-collapsible-content" style="padding:8px 14px;">

<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Photoautotrophy]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
; Incubation | Discrete
* [[14-Carbon uptake (NPP)]]
* [[18O-labelled water (GOP)]]
* [[Winkler light-dark dissolved O2 bottle]]
* [[Phytoplankton carbon biomass (Cphyto) x growth rate (µ)]]
* [[13-Carbon uptake]]
* [[Gross Primary Production (GPP) - triple oxygen]]
* [[Net community production (NCP)]]
; ''In situ | Continuous''
* [[Net community production (NCP) - O₂/Ar]]
* [[Continuous dissolved oxygen (DO) optodes]]
; Optics-based
* [[Single Turnover Chlorophyll Fluorescence]]
* [[Remote Sensing NPP]]
* [[BGC-Argo NPP]]
; Omics-based
* [[RT-qPCR/ddPCR]]
* [[rcbL gene expression/quant]]
* [[psbA]]
* [[Rubisco protein]]
* [[PSII/PSI quantification]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Nitrogen Fixation]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Bulk uptake 15N2]]
* [[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)|Single cell uptake techniques]]
* [[Acetylene Reduction Assays (ARA)]]
* [[NifH detection/quantification (qPCR, RT-qPCR; nifH database)|nifH detection/quantification]]
* [[nifH amplicon sequence]]
* [[H2 supersaturation]]
* [[Nitrogenase quantification]]
* [[Other diazotroph marker genes: nifD, nifK|Other diazotroph marker genes]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Phytoplankton C/N-Based Growth Rates]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Carbon content]]
* [[Nitrogen content]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Chemoautotrophy]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Mass balance approach]]
* [[Dark 14C-bicarbonate fixation]]
* [[Nano SIP]]
* [[Black smoker]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #b0d0ae; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[Anaplerotic Carbon Fixation]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Dark 14C-bicarbonate fixation]]
* [[Dark 13C-bicarbonate fixation]]
</div>
</div>

</div>
</div>


<div id="Secondary_Production" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;">
<div style="background:#fff2cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Secondary Production</div>
<div class="mw-collapsible-content" style="padding:8px 14px;">

<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Enzyme Activity]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Enzyme assay with fluoresceinamine labeled biopolymers]]
* [[Enzyme assay with RBB labeled polysaccharides]]
* [[Enzyme assay with DNS]]
* [[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Growth Rate]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Growth rate from biomass observation]]
* [[Radiolabeled tracer method]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #e0c86a; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Respiration]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Respiration from BGC-Argo floats and AOU]]
* [[Respiration from oxygen consumption: optodes]]
* [[Respiration from activity of respiratory chain: enzymatic assays]]
* [[Respiration from activity of respiratory chain: redoxsensor green]]
* [[Respiration from oxygen consumption]]
</div>
</div>

</div>
</div>


<div id="Nutrient_Fluxes" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;">
<div style="background:#ddeeff; padding:8px 14px; font-weight:bold; font-size:1.1em;">Nutrient Fluxes</div>
<div class="mw-collapsible-content" style="padding:8px 14px;">

<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Nitrogen]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
; Nitrogen Uptake
* [[(15N-ρNO3-) uptake New Production]]
* [[Size-fractionated (15N-ρNO3-) uptake New Production]]
* [[15N-ρNO3/chl a (N assimilation rate)]]
* [[Size-fractionated 15N-ρNO3/chl a (N assimilation rate)]]
* [[(15N-ρNH4+) uptake Regenerated Production]]
* [[Size-fractionated (15N-ρNH4+) uptake Regenerated Production]]
* [[(15N-ρurea) uptake Regenerated Production]]
* [[Size-fractionated (15N-ρurea) uptake Regenerated Production]]
; Nitrogen Assimilation
* [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]
; Nitrification
* [[DIN inventory with inhibitors]]
* [[Inhibitors with 14 or 13CO2 uptake]]
* [[Nitrite oxidation (Nxr)]]
* [[amoA gene or transcript abundance]]
* [[Natural abundance of N and O isotopes in nitrate, nitrite and ammonium]]
* [[15N tracers]]
; Denitrification
* [[Acetylene-block proxy for denitrifcation enzyme activity]]
* [[15N tracer-based method]]
* [[N2:Ar ratio quantification]]
* [[Mass Balance]]
* [[Stoichiometric approach]]
* [[Natural Abundances of 15N and 18O]]
; Other Processes (DNRA, Anammox, DON)
* [[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation|Isotopic measurements of 15NH4+ accumulation (DNRA)]]
* [[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)|15N tracers for anaerobic ammonium oxidation]]
* [[Functional gene quantification (hzs, hzo)]]
* [[FISH staining of anammox bacteria]]
* [[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)|13C- and 15N-labeled algal exudates with nanoSIMS]]
* [[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity|Leucine-aminopeptidase activity measurement]]
* [[Degradation of dissolved organic nitrogen: Endopeptidase activity|Endopeptidase activity measurement]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Phosphorus]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
; Degradation of dissolved organic phosphorus
* [[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)|Alkaline phosphatase activity (APA)]]
* [[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)|Phosphodiesterase activity (PDE)]]
* [[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)|C-P lyase activity (CLA)]]
* [[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity|5'NT/5PN activity]]
; P nutrition
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]
* [[32-P incorporation]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Sulfur]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[DMS/P/O cycling]]
* [[Rates of DMSO reduction to DMS]]
* [[Rates of DMS and DMSP oxidation to DMSO]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Trace Metals]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[55-Iron uptake]]
* [[54-Manganese uptake]]
* [[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake|67-Copper & 64-Cu uptake]]
* [[Cobalamin uptake with 57Cobalt-B12]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #cee0f2; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Biomineralization]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
; Silicon
* [[Silicon uptake]]
* [[Kinetics of silicon uptake]]
* [[Silica production]]
* [[Silica production - PDMPO]]
* [[Biogenic silica accumulation]]
; Calcification
* [[Calcification (13-Carbon uptake)]]
</div>
</div>

</div>
</div>


<div id="Interactions" class="mw-collapsible mw-collapsed" style="border:1px solid #a2a9b1; margin:0.5em 0;">
<div style="background:#ffe6cc; padding:8px 14px; font-weight:bold; font-size:1.1em;">Interactions</div>
<div class="mw-collapsible-content" style="padding:8px 14px;">

<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Grazing]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
; Microzooplankton on Phytoplankton
* [[Incubation dilution experiments]]
* [[Size-fractionated incubation dilution experiments]]
* [[Cell abundance]]
; Mesozooplankton
* [[Gut-fluorescence]]
; Bacterivory & Mixotrophy
* [[Fluorescently labeled prey surrogates]]
* [[Radioactively labeled prey surrogates]]
* [[Pulse-chase labeling of bacterial prey]]
* [[Stable isotope-labelled prey]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Mixotrophy]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[LysoTracker Green Incorporation]]
* [[15N/13C-labelled DOM/cells]]
* [[Bead consumption rates by cells with chloroplasts]]
* [[BrdU-labeled prey incorporation into things with chloroplasts]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Viruses]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Electron microscopy of cells]]
* [[Quantification of virus particles]]
* [[Dilution incubation experiments]]
* [[Bulk RNA marker-gene PCR analysis]]
* [[Bulk RNA-sequencing (whole transcriptome)]]
* [[Single-cell RNA-sequencing (population)]]
* [[Single-cell RNA-sequencing (community)]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Allelopathy]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Filtrate cross-culturing]]
* [[Size-fractionated extract spiking]]
</div>
</div>

<div class="mw-collapsible mw-collapsed" style="border:1px solid #f0c080; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fff8f0;">[[Life cycles]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[Light or electron microscopic counts of life cycle stages/transitions]]
* [[Fluorescent in situ hybridization microscope counts]]
* [[Bulk RNA marker-gene PCR analysis]]
* [[Bulk RNA-sequencing (whole transcriptome)]]
</div>
</div>

</div>
</div>

== References ==
<references />

Chemoautotrophy

2026-09-24T13:16:23Z

Himanshusaxena:

*[[mass balance approach|Mass balance approach]]
*[[Dark 14C-bicarbonate fixation]]
*[[nano SIP|Nano SIP]]
*[[black smoker|Black smoker]]

OceanWiki - User contributions [en]

Data Types

Chemoautotrophy