OceanWiki - User contributions [en]

Model Types

2026-05-27T21:53:08Z

Hagi BucknWise:

Models integrate our understanding of ocean carbon cycling, proposing hypothesized mechanisms and trade-offs, and generating predictions. Biogeochemical models represent the conversion of elements, such as carbon, nitrogen, and phosphorus, from inorganic substrates to organic compounds through photosynthesis by phytoplankton and ultimately back into inorganic form through heterotrophic activity. For each of the model pools, a set of equations express how the pool changes over time, describing our best understanding of the dynamics at play in the physics, biogeochemistry, and ecology of the ocean. The ecosystem and biogeochemical components are derived from food web models, and are embedded into physical fluid dynamic models that represent the transport and conservation of water, salt, and heat, as well as carbon, nutrients, and plankton. Thus, ocean biogeochemical models inherently account for interactions between marine organisms and the dynamic fluid environment in which they live<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>.<br>
Current state-of-the-art models represent a range of different microbial functional types including multiple phytoplankton groups, mixotrophs, grazers, viruses, detrital pools, and bacteria and archaea that consume the dead organic matter<ref>Follows MJ, Dutkiewicz S, Ward B, Follett CN. 2018. Theoretical interpretations of subtropical plankton biogeography. In Microbial Ecology of the Oceans, ed. JM Gasol, DL Kirchman , pp. 467–94. Hoboken, NJ:: Wiley & Sons, http://ndl.ethernet.edu.et/bitstream/123456789/33641/1/pdf.52#page=484</ref>.

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

=== Cellular scale ===

*[[Flux Balance Analysis]] <span style="color: red;">- needs creation</span>
*[[Proteome Allocation Models]]
*[[Particle Simulation]] <span style="color: red;">- needs creation</span>
*[[Bio Particle Simulation]] <span style="color: red;">- needs creation</span>

=== Biome scale ===

*[[Community Flux Balance Analysis]] <span style="color: red;">- needs creation</span>
*[[GENOME]] <span style="color: red;">- needs creation</span>

=== Global scale ===

*[[CMIP]]
*[[MARBL]] <span style="color: red;">- needs creation</span>
*[[Darwin]]
*[[AWESOME-OCIM]]
*[[PISCES]]

== References ==
<references />

Data Types

2026-05-27T21:32:02Z

Hagi BucknWise:

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;">
; Laboratory-based
* [[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''
* [[Net community production (NCP) - O₂/Ar]]
* [[Continuous dissolved oxygen (DO) optodes]]
; Global 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>
</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]]
; 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 (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]]
* [[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]]
* [[Gut-fluorescence]]
; Bacterivory & Mixotrophy
* [[Fluorescently labeled prey surrogates]]
* [[Radioactively labeled prey surrogates]]
* [[Pulse-chase labeling of bacterial prey]]
* [[Stable isotope-labelled prey]]
; Omics
* [[Bulk RNA-sequencing (whole transcriptome)]]
</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 />

Data Types

2026-05-27T21:28:06Z

Hagi BucknWise:

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;">
* [[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)]]
* [[Net community production (NCP) - O₂/Ar]]
* [[Continuous dissolved oxygen (DO) optodes]]
* [[Single Turnover Chlorophyll Fluorescence]]
* [[Remote Sensing NPP]]
* [[BGC-Argo NPP]]
* [[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>
</div>


<div id="Secondary_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;">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:#f2faf1;">[[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 #b0d0ae; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[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 #b0d0ae; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[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:#fff2cc; 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:#fffbe6;">[[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]]
; 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 #e0c86a; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Phosphorus]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[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]]
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]
* [[32-P incorporation]]
</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;">[[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 #e0c86a; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[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 #e0c86a; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[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]]
* [[Gut-fluorescence]]
; Bacterivory & Mixotrophy
* [[Fluorescently labeled prey surrogates]]
* [[Radioactively labeled prey surrogates]]
* [[Pulse-chase labeling of bacterial prey]]
* [[Stable isotope-labelled prey]]
; Omics
* [[Bulk RNA-sequencing (whole transcriptome)]]
</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 />

Data Types

2026-05-27T21:21:11Z

Hagi BucknWise:

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:#ddeeff; 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 #cee0f2; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[Photoautotrophy]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[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)]]
* [[Net community production (NCP) - O₂/Ar]]
* [[Continuous dissolved oxygen (DO) optodes]]
* [[Single Turnover Chlorophyll Fluorescence]]
* [[Remote Sensing NPP]]
* [[BGC-Argo NPP]]
* [[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:#f0f7ff;">[[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 #cee0f2; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[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 #cee0f2; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f0f7ff;">[[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>
</div>


<div id="Secondary_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;">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:#f2faf1;">[[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 #b0d0ae; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[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 #b0d0ae; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#f2faf1;">[[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:#fff2cc; 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:#fffbe6;">[[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]]
; 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 #e0c86a; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[Phosphorus]]</div>
<div class="mw-collapsible-content" style="padding:4px 10px 6px 24px;">
* [[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]]
* [[Reduction of phosphite to phosphate for growth (ptxABCD)|ptxABCD]]
* [[32-P incorporation]]
</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;">[[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 #e0c86a; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[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 #e0c86a; margin:4px 0;">
<div style="padding:5px 10px; font-weight:bold; background:#fffbe6;">[[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]]
* [[Gut-fluorescence]]
; Bacterivory & Mixotrophy
* [[Fluorescently labeled prey surrogates]]
* [[Radioactively labeled prey surrogates]]
* [[Pulse-chase labeling of bacterial prey]]
* [[Stable isotope-labelled prey]]
; Omics
* [[Bulk RNA-sequencing (whole transcriptome)]]
</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 />

Fluorescent in situ hybridization microscope counts

2026-05-14T02:02:17Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Life cycle stage abundance (FISH) |- | '''Approach:''' fluorescence in situ hybridisation (FISH) with life-stage-specific or species-specific probes |- | '''Context:''' ''in situ'', lab |- | '''Spa..."

Light or electron microscopic counts of life cycle stages/transitions

2026-05-14T01:59:48Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Life cycle stage abundance (microscopy) |- | '''Approach:''' light or electron microscopy counts of morphologically distinct life stages |- | '''Context:''' ''in situ'', lab |- | '''Spatial scale:'..."

{{BreadcrumbsInteractions}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Life cycle stage abundance (microscopy)
|-
| '''Approach:''' light or electron microscopy counts of morphologically distinct life stages
|-
| '''Context:''' ''in situ'', lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' days
|-
| '''Units:''' cells L<sup>-1</sup>; % of population
|-
| '''Community captured:''' specific species with morphologically recognizable life stages
|-
| '''Co-measurements:''' species-specific duration of recognizable life stages (transition times)
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Fixed water samples (e.g. Lugol's iodine, glutaraldehyde, or formalin) are concentrated by settling or centrifugation and examined by light microscopy (LM) or transmission electron microscopy (TEM). Cells are identified and counted by their morphological characteristics, with individual life stages — resting cysts (hypnozygotes), spores, auxospores, vegetative cells, gametes, or temporary cysts — distinguished by their shape, size, wall structure, and pigmentation. Absolute abundances (cells L<sup>-1</sup>) and relative proportions (% of total population in each stage) are calculated from the counts. Time-series sampling reveals when life cycle transitions occur in natural populations<ref name="Crawford1995">Crawford, R. M. (1995). The role of sex in the sedimentation of a marine diatom bloom. ''Limnology and Oceanography'', 40(1), 200–204. https://doi.org/10.4319/lo.1995.40.1.0200</ref>.

=== Scale of measurement ===

Point samples; days between sample collection points. Some life cycle stages (e.g., gametes, auxospores) may be short-lived and require high-frequency sampling to capture.

=== Data generated ===

Abundances and proportions of distinct life cycle stages (cells L<sup>-1</sup> and %). Time-series data reveal the timing, duration, and environmental triggers of life cycle transitions.

=== Units & currency ===

Units are cells L<sup>-1</sup> or % of cells in each life stage. The currency is measured absolute or relative abundance of each life cycle stage.

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

Many life cycle stages are morphologically cryptic or indistinguishable from the vegetative cell by LM alone, requiring specialist knowledge or molecular markers. Short-lived stages (e.g., gametes, temporary cysts) may be underrepresented if sampling intervals are long. Fixation can alter cell morphology and mask diagnostic features. Knowledge of species-specific life stage durations is required to convert counts to transition rates.

== Example Applications & Protocols ==

=== Classic examples ===
* Crawford (1995) ''The role of sex in the sedimentation of a marine diatom bloom'' <ref name="Crawford1995" />
* Rynearson et al. (2013) ''Major contribution of diatom resting spores to vertical flux in the sub-polar North Atlantic'' <ref name="Rynearson2013">Rynearson, T. A., Richardson, K., Lampitt, R. S., Sieracki, M. E., Poulton, A. J., Lyngsgaard, M. M., & Perry, M. J. (2013). Major contribution of diatom resting spores to vertical flux in the sub-polar North Atlantic. ''Deep-Sea Research Part I'', 82, 60–71. https://doi.org/10.1016/j.dsr.2013.07.013</ref>

=== Recent applications ===
* Šupraha et al. (2016) ''Coccolithophore life-cycle dynamics in a coastal Mediterranean ecosystem'' <ref name="Supraha2016">Šupraha, L., Gerecht, A. C., Probert, I., & Henderiks, J. (2016). Coccolithophore life-cycle dynamics in a coastal Mediterranean ecosystem: seasonality and species-specific patterns. ''Journal of Plankton Research'', 38, 1178–1193. https://doi.org/10.1093/plankt/fbw061</ref>

=== Common calculations/conversions ===
* Life stage transition rate = change in stage abundance / known stage duration (from literature or lab experiments).

== References ==

[[Category:Main Pages|Model types]]

Size-fractionated extract spiking

2026-05-14T01:57:56Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Allelopathy (size-fractionated extract spiking) |- | '''Approach:''' size-fractionated culture extracts added to target species; growth or Fv/Fm response measured |- | '''Context:''' lab |- | '''Sp..."

Filtrate cross-culturing

2026-05-14T01:55:56Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Allelopathy (filtrate cross-culturing) |- | '''Approach:''' cell-free filtrate of candidate allelopathic species added to target species culture; growth or motility response measured |- | '''Contex..."

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<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Allelopathy (filtrate cross-culturing)
|-
| '''Approach:''' cell-free filtrate of candidate allelopathic species added to target species culture; growth or motility response measured
|-
| '''Context:''' lab
|-
| '''Spatial scale:''' culture flask (point)
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' cells L<sup>-1</sup> d<sup>-1</sup>; Fv/Fm; settling rate
|-
| '''Community captured:''' individual target species
|-
| '''Co-measurements:''' temperature, PAR; sometimes pH and salinity
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

The filtrate cross-culturing approach tests for allelopathic effects — inhibitory compounds produced and released by one organism affecting the physiology or behavior of another. Cell-free filtrate (0.2 µm or 0.45 µm filtered) from a potentially allelopathic species (the donor) is added to cultures of a target (recipient) species. The donor filtrate is assumed to contain any secreted allelopathic compounds without cells; controls receive equal volumes of filtered seawater. Target species growth rate, photosynthetic efficiency (Fv/Fm from variable fluorescence), or motility (settling rate in motile flagellates) are monitored over hours to days. Inhibition of growth or photosynthesis relative to the seawater control indicates allelopathic activity<ref name="Kearns2001">Kearns, K. D., & Hunter, M. D. (2001). Toxin-producing Anabaena flos-aquae induces settling of Chlamydomonas reinhardtii, a competing motile alga. ''Microbial Ecology'', 42(1), 80–86. https://doi.org/10.1007/s002480000086</ref>.

=== Scale of measurement ===

Laboratory culture; no direct ''in situ'' spatial scale. Incubations of hours to days.

=== Data generated ===

Growth rate, Fv/Fm, or settling rate of the target species in the presence vs. absence of the filtrate. A significant inhibition indicates allelopathic potential of the donor species.

=== Units & currency ===

Units are cells L<sup>-1</sup> d<sup>-1</sup> (growth) or Fv/Fm (photosynthesis). The currency is phytoplankton/cyanobacteria cell abundance or motility behavior.

=== Sample size ===

Typical samples are < 1 L in volume per treatment.

=== Repositories & databases ===

== Limitations ==

The method assumes that no competition for resources (nutrients, light) occurs between donor compounds and target growth; in practice, carrier media differences can confound results. The concentration of allelopathic compound in the filtrate may differ substantially from ''in situ'' conditions, leading to overestimation if natural donor densities are lower than in culture. Bottle effects may arise.

== Example Applications & Protocols ==

=== Classic examples ===
* Kearns & Hunter (2001) ''Toxin-producing Anabaena flos-aquae induces settling of Chlamydomonas reinhardtii, a competing motile alga'' <ref name="Kearns2001" />
* Arzul et al. (1999) ''Comparison of allelopathic properties in three toxic Alexandrium species'' <ref name="Arzul1999">Arzul, G., Seguel, M., Guzman, L., & Erard-Le Denn, E. (1999). Comparison of allelopathic properties in three toxic Alexandrium species. ''Journal of Experimental Marine Biology and Ecology'', 232(2), 285–295. https://doi.org/10.1016/S0022-0981(98)00120-8</ref>

=== Recent applications ===
*

=== Common calculations/conversions ===
* % inhibition = (µ<sub>control</sub> − µ<sub>filtrate</sub>) / µ<sub>control</sub> × 100; positive values indicate allelopathic growth inhibition.

== References ==

[[Category:Main Pages|Model types]]

Single-cell RNA-sequencing (community)

2026-05-14T01:53:56Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Viral infection across the plankton community (scRNA-seq) |- | '''Approach:''' community-level single-cell RNA sequencing; viral transcripts detected in individually barcoded cells |- | '''Context:..."

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__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Viral infection across the plankton community (scRNA-seq)
|-
| '''Approach:''' community-level single-cell RNA sequencing; viral transcripts detected in individually barcoded cells
|-
| '''Context:''' ''in situ''
|-
| '''Spatial scale:''' single cell
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' % of cells with viral transcripts; molecule cell<sup>-1</sup>
|-
| '''Community captured:''' individual cells across the full plankton community
|-
| '''Co-measurements:''' host cell abundance
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Community-level single-cell RNA sequencing (scRNA-seq) captures the transcriptomes of individual cells across the entire planktonic community without prior cell type selection. Seawater is collected, cells are fixed or kept live, dissociated (if necessary), and encapsulated in microdroplets or nanowells with barcoded oligonucleotides (e.g., 10x Genomics Chromium, Drop-seq). Each cell's RNA is reverse-transcribed using the barcode, creating a library where each read is associated with a unique cell. After sequencing, reads are demultiplexed by barcode and assembled into per-cell transcriptomes. Viral transcripts detected in individual cell libraries, combined with host taxonomic assignment from eukaryotic or prokaryotic marker genes, reveal which community members are infected and the frequency of infection<ref name="Fromm2024">Fromm, A., Hevroni, G., Vincent, F., Schatz, D., Martinez-Gutierrez, C. A., Aylward, F. O., & Vardi, A. (2024). Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment. ''Nature Microbiology'', 9, 1619–1629. https://doi.org/10.1038/s41564-024-01669-y</ref>.

=== Scale of measurement ===

Single-cell resolution across taxonomically diverse community members. Thousands of cells can be profiled simultaneously, enabling statistically robust estimates of infection frequency.

=== Data generated ===

Per-cell transcriptomes enabling: (1) taxonomic classification of each cell; (2) detection of viral transcripts indicating active infection; (3) identification of which host taxa are infected by which viruses. The proportion of infected cells per taxon is a measure of virus–host specificity.

=== Units & currency ===

Units are % of cells with viral transcripts per taxon; molecule cell<sup>-1</sup>. The currency is transcript molecules.

=== Sample size ===

Typical samples are < 1 L in volume; thousands of individual cells are profiled per experiment.

=== Repositories & databases ===

Sequencing data deposited at NCBI SRA; viral and host reference databases.

== Limitations ==

Only ~5% of cellular transcripts are captured per cell in most droplet-based scRNA-seq protocols, limiting detection of low-abundance viral transcripts. Taxonomic assignment of viral and host transcripts depends on database completeness. Cell encapsulation can cause doublets (two cells captured together), complicating per-cell analyses.

== Example Applications & Protocols ==

=== Classic examples ===
* Fromm et al. (2024) ''Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment'' <ref name="Fromm2024" />

=== Recent applications ===
*

=== Common calculations/conversions ===
* Infection frequency per taxon = (cells of taxon X with viral reads / total cells assigned to taxon X) × 100.

== References ==

[[Category:Main Pages|Model types]]

Single-cell RNA-sequencing (population)

2026-05-14T01:50:57Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Viral infection in individual cells (scRNA-seq, population) |- | '''Approach:''' single-cell RNA sequencing of sorted populations; viral transcript detection per cell |- | '''Context:''' ''in situ'..."

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__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Viral infection in individual cells (scRNA-seq, population)
|-
| '''Approach:''' single-cell RNA sequencing of sorted populations; viral transcript detection per cell
|-
| '''Context:''' ''in situ'', lab
|-
| '''Spatial scale:''' single cell
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' % of cells with viral transcripts; molecule cell<sup>-1</sup>
|-
| '''Community captured:''' individual cells of a specific species or population
|-
| '''Co-measurements:''' host cell abundance
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Cells of a specific species or population of interest are isolated by flow cytometric sorting or microfluidic capture. Individual cells are subjected to single-cell RNA sequencing (scRNA-seq): each cell is lysed, its RNA reverse-transcribed, amplified, and sequenced. The transcriptome of each individual cell is scanned for viral transcripts by mapping reads to viral gene databases. Cells positive for viral gene expression are identified as actively infected. This approach reveals the heterogeneity in infection status within a defined host population — what proportion of cells are infected, at what stage, and how viral gene expression changes over the course of an infection<ref name="Ku2020">Ku, C., Sheyn, U., Sebé-Pedrós, A., Ben-Dor, S., Schatz, D., Tanay, A., Rosenwasser, S., & Vardi, A. (2020). A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. ''Science Advances'', 6(21), eaba4137. https://doi.org/10.1126/sciadv.aba4137</ref>.

=== Scale of measurement ===

Single-cell resolution; each cell's transcriptome is sequenced independently. Throughput is limited by the cell sorting and library preparation workflow (typically hundreds to thousands of cells per experiment).

=== Data generated ===

Per-cell transcriptome profiles; proportion of cells with detectable viral transcripts (% infected); stage-specific viral gene expression profiles revealing infection progression.

=== Units & currency ===

Units are % of cells with viral transcripts, or viral transcript molecules cell<sup>-1</sup>. The currency is transcript molecules.

=== Sample size ===

Typical samples are < 1 L in volume; the number of cells sequenced per sample is hundreds to thousands.

=== Repositories & databases ===

== Limitations ==

Only ~5% of total transcripts in a cell are captured in most scRNA-seq protocols, so low-abundance viral transcripts may be missed. Viral gene expression does not guarantee eventual cell lysis (e.g., in lysogenic or chronic infection). Sorting of population-specific cells requires prior knowledge of their optical properties or surface markers.

== Example Applications & Protocols ==

=== Classic examples ===
* Ku et al. (2020) ''A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states'' <ref name="Ku2020" />
* Hevroni et al. (2023) ''Daily turnover of active giant virus infection during algal blooms revealed by single-cell transcriptomics'' <ref name="Hevroni2023">Hevroni, G., Flores-Uribe, J., Béjà, O., & Philosof, A. (2023). Daily turnover of active giant virus infection during algal blooms revealed by single-cell transcriptomics. ''Science Advances'', 9(41), eadf7971. https://doi.org/10.1126/sciadv.adf7971</ref>

=== Recent applications ===
*

=== Common calculations/conversions ===
* % infected cells = (cells with viral transcript reads / total cells sequenced) × 100.

== References ==

[[Category:Main Pages|Model types]]

Bulk RNA marker-gene PCR analysis

2026-05-14T01:47:27Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Viral infection marker gene expression (RT-qPCR) |- | '''Approach:''' RT-qPCR of virus-specific marker gene transcripts |- | '''Context:''' ''in situ'', lab |- | '''Spatial scale:''' point sample |..."

Dilution incubation experiments

2026-05-14T01:13:30Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Viral lysis rate (virus dilution method) |- | '''Approach:''' dilution of viruses with 0.2 µm filtered seawater; host abundance tracked by FCM |- | '''Context:''' incubation |- | '''Spatial scale:..."

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__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Viral lysis rate (virus dilution method)
|-
| '''Approach:''' dilution of viruses with 0.2 µm filtered seawater; host abundance tracked by FCM
|-
| '''Context:''' incubation
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours
|-
| '''Units:''' cell L<sup>-1</sup> d<sup>-1</sup>; d<sup>-1</sup>
|-
| '''Community captured:''' size-fractionated host populations (FCM-resolvable)
|-
| '''Co-measurements:''' time (h); host cell counts at t<sub>0</sub> and t<sub>f</sub>
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

The virus dilution method is analogous to the microzooplankton dilution method but targets viral lysis rather than grazing as the loss term. Whole seawater (containing both hosts and viruses) is diluted with 0.2 µm filtered seawater (containing the host community but no viruses). Lower dilutions reduce the virus-to-host encounter rate, reducing viral lysis. Any grazers are simultaneously removed by the filtration. By comparing host net growth rates across dilution levels, the viral lysis rate can be inferred from the regression of apparent growth rate vs. dilution factor<ref name="Wilhelm2002">Wilhelm, S. W., Brigden, S. M., & Suttle, C. A. (2002). A dilution technique for the direct measurement of viral production: a comparison in stratified and tidally mixed coastal waters. ''Microbial Ecology'', 43(1), 168–173. https://doi.org/10.1007/s00248-001-1021-9</ref>. Flow cytometry tracks specific host cell populations (e.g., Synechococcus, Prochlorococcus, picoeukaryotes) over the incubation period.

=== Scale of measurement ===

Discrete samples incubated for hours after collection.

=== Data generated ===

Viral lysis rate (d<sup>-1</sup>) for specific host populations. Combined with host growth rates from paired dilution experiments, the relative contributions of viral lysis and grazing to total phytoplankton mortality can be estimated.

=== Units & currency ===

Units are d<sup>-1</sup> (viral lysis rate) or cells L<sup>-1</sup> d<sup>-1</sup>. The currency is Chl-a or cell counts.

=== Sample size ===

Typical samples are 1–2 L per dilution treatment.

=== Repositories & databases ===

== Limitations ==

The method assumes that viral lysis is the only density-dependent process removed by dilution; if predation also scales with dilution, the two effects are confounded. Viral production during the incubation (from newly lysed cells) partially re-populates the viral pool at higher dilutions, potentially underestimating viral lysis rates. No other factors beyond viral infection should affect host cell abundance change over time.

== Example Applications & Protocols ==

=== Classic examples ===
* Wilhelm et al. (2002) ''A dilution technique for the direct measurement of viral production: a comparison in stratified and tidally mixed coastal waters'' <ref name="Wilhelm2002" />

=== Recent applications ===
* Cram et al. (2016) ''Dilution reveals how viral lysis and grazing shape microbial communities'' <ref name="Cram2016">Cram, J. A., Chow, C.-E. T., Sachdeva, R., Needham, D. M., Parada, A. E., Steele, J. A., & Fuhrman, J. A. (2016). Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ''Limnology and Oceanography'', 61(3), 889–905. https://doi.org/10.1002/lno.10259</ref>

=== Common calculations/conversions ===
* As for the microzooplankton dilution method: regression of k vs. dilution factor, but now the slope represents viral lysis rate rather than grazing.

== References ==

[[Category:Main Pages|Model types]]

Quantification of virus particles

2026-05-14T01:09:56Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Virus particle abundance |- | '''Approach:''' epifluorescence microscopy, flow cytometry, plaque assay, or MPN |- | '''Context:''' ''in situ'', incubation, lab |- | '''Spatial scale:''' point sampl..."

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__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Virus particle abundance
|-
| '''Approach:''' epifluorescence microscopy, flow cytometry, plaque assay, or MPN
|-
| '''Context:''' ''in situ'', incubation, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to days (changes in abundance)
|-
| '''Units:''' particles L<sup>-1</sup>; particles cell<sup>-1</sup> (burst size)
|-
| '''Community captured:''' bulk viral community
|-
| '''Co-measurements:''' host cell abundance
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Virus-like particle (VLP) concentrations in seawater are determined by one of several approaches: (1) Epifluorescence microscopy after staining with SYBR Green I or DAPI: filtered samples on anodisc or polycarbonate membranes are stained with a nucleic-acid-specific fluorescent dye and counted under the microscope. (2) Flow cytometry: samples are stained with SYBR Green I and run on a flow cytometer; VLPs are resolved as a distinct population based on their green fluorescence and side scatter<ref name="Marie1999">Marie, D., Brussaard, C. P. D., Thyrhaug, R., Bratbak, G., & Vaulot, D. (1999). Enumeration of marine viruses in culture and natural samples by flow cytometry. ''Applied and Environmental Microbiology'', 65(1), 45–52. https://doi.org/10.1128/aem.65.1.45-52.1999</ref>. (3) Plaque assays: serial dilutions of a water sample are applied to a lawn of susceptible host cells and plaques (clearings) are counted. (4) Most probable number (MPN) methods: serial dilution and host infection in multiwell plates.

=== Scale of measurement ===

Each measurement gives a snapshot of viral abundance at a single time point. Time-series measurements reveal viral production and decay rates.

=== Data generated ===

Virus-like particle concentration (VLPs L<sup>-1</sup>); virus-to-bacterium ratio (VBR). Changes in VLP concentration in dilution incubations can estimate viral production rates.

=== Units & currency ===

Units are particles L<sup>-1</sup>. The currency is virus particles.

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

All particle-counting methods quantify VLPs (virus-like particles) without distinguishing infective from non-infective viruses. Plaque and MPN assays only count viruses infective to the specific host cell line used, missing the majority of marine viral diversity. SYBR Green staining does not distinguish viruses from other small particles with nucleic acid. The assumption that all VLPs are bacteriophage or eukaryotic viruses (vs. gene transfer agents, membrane vesicles) introduces uncertainty.

== Example Applications & Protocols ==

=== Classic examples ===
* Marie et al. (1999) ''Enumeration of marine viruses in culture and natural samples by flow cytometry'' <ref name="Marie1999" />
* Hennes & Suttle (1995) ''Direct counts of viruses in natural waters and laboratory cultures by epifluorescence microscopy'' <ref name="Hennes1995">Hennes, K. P., & Suttle, C. A. (1995). Direct counts of viruses in natural waters and laboratory cultures by epifluorescence microscopy. ''Limnology and Oceanography'', 40(6), 1050–1055. https://doi.org/10.4319/lo.1995.40.6.1050</ref>

=== Recent applications ===
* Brussaard (2004) ''Optimisation of procedures for counting viruses by flow cytometry'' <ref name="Brussaard2004">Brussaard, C. P. D. (2004). Optimisation of procedures for counting viruses by flow cytometry. ''Applied and Environmental Microbiology'', 70(3), 1506–1513. https://doi.org/10.1128/aem.70.3.1506-1513.2004</ref>

=== Common calculations/conversions ===
* Virus-to-bacterium ratio (VBR) = VLP concentration / bacterial cell concentration; typically 10–100 in marine environments.
* Viral production rate (VP, VLPs L<sup>-1</sup> h<sup>-1</sup>) from dilution experiments: VP = ΔVLP / Δt corrected for virus decay.

== References ==

[[Category:Main Pages|Model types]]

Electron microscopy of cells

2026-05-14T01:07:30Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Viral infection prevalence (TEM) |- | '''Approach:''' transmission electron microscopy (TEM); scoring intracellular virions |- | '''Context:''' ''in situ'', lab |- | '''Spatial scale:''' point samp..."

BrdU-labeled prey incorporation into things with chloroplasts

2026-05-14T01:03:31Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Constitutive mixotrophy (BrdU-labelled prey) |- | '''Approach:''' BrdU-labelled bacteria ingested by pigmented cells; immunofluorescence detection |- | '''Context:''' field, lab |- | '''Spatial sca..."

Bead consumption rates by cells with chloroplasts

2026-05-14T01:01:20Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Phagotrophic mixotrophy (bead ingestion by pigmented cells) |- | '''Approach:''' fluorescent bead ingestion by FCM-identified autofluorescent cells; epifluorescence microscopy |- | '''Context:''' f..."

15N/13C-labelled DOM/cells

2026-05-14T00:59:16Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Osmotrophic mixotrophy (<sup>13</sup>C/<sup>15</sup>N DOM assimilation) |- | '''Approach:''' <sup>13</sup>C/<sup>15</sup>N-labelled dissolved or particulate organic matter; EA-IRMS or nanoSIMS |- |..."

LysoTracker Green Incorporation

2026-05-14T00:54:45Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Phagotrophic mixotroph detection (LysoTracker Green) |- | '''Approach:''' LysoTracker Green staining of food vacuoles; comparison to autofluorescence by FCM or imaging FCM |- | '''Context:''' field..."

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__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Phagotrophic mixotroph detection (LysoTracker Green)
|-
| '''Approach:''' LysoTracker Green staining of food vacuoles; comparison to autofluorescence by FCM or imaging FCM
|-
| '''Context:''' field, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours
|-
| '''Units:''' active mixotrophic cells L<sup>-1</sup>; % of phytoplankton community
|-
| '''Community captured:''' phagotrophic mixotrophs
|-
| '''Co-measurements:''' nutrient uptake measurements; imaging FCM for cell-level detail
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

LysoTracker Green (LTG) is an acidotropic fluorescent dye that selectively accumulates in acidic vacuoles within cells. In phagotrophic cells, food vacuoles become acidified after prey ingestion as part of the digestive process, and LTG stains these vacuoles brightly (excitation ~443 nm, emission ~505 nm). When added to seawater samples, cells with active phagosomes/food vacuoles stain green while autofluorescent phytoplankton emit red fluorescence from their plastids. Cells that are simultaneously green (LTG-positive: food vacuoles) and red (plastids) are identified as phagotrophic mixotrophs — organisms that combine photosynthesis with ingestion of prey. The proportion of such dual-fluorescent cells among the phytoplankton community is quantified by flow cytometry or imaging flow cytometry<ref name="Millette2024">Millette, N. C., Leles, S. G., Johnson, M. D., Maloney, A. E., Brownlee, E. F., Cohen, N. R., Duhamel, S., Poulton, N. J., Princiotta, S. D., Stamieszkin, K., Wilken, S., & Moeller, H. V. (2024). Recommendations for advancing mixoplankton research through empirical-model integration. ''Frontiers in Marine Science'', 11. https://doi.org/10.3389/fmars.2024.1392673</ref>.

=== Scale of measurement ===

Discrete samples collected and incubation of hours at in situ temperature required.

=== Data generated ===

Abundance of phagotrophically active mixotrophic cells (cells L<sup>-1</sup>) and their proportion within the total phytoplankton community (%). Imaging FCM additionally provides cell size and morphology data for each counted mixotroph.

=== Units & currency ===

Units are active mixotrophic cells L<sup>-1</sup>. The currency is number of phagotrophic versus phototrophic cells.

=== Sample size ===

Typical samples are ~1 L in volume.

=== Repositories & databases ===

== Limitations ==

Any acidic intracellular compartment — not only food vacuoles — will accumulate LTG, including contractile vacuoles, lysosomes, and chloroplast-associated acidic compartments. This means non-phagotrophic cells may stain green, leading to false-positive identification of mixotrophy. Distinguishing genuine food vacuoles from other acidic compartments requires additional confirmation (e.g., simultaneous FLB ingestion assay or imaging). Heterotrophic protists lacking plastids but with acidic vacuoles could in principle be misidentified as mixotrophs if their autofluorescence is above background.

== Example Applications & Protocols ==

=== Classic examples ===
* Millette et al. (2024) ''Recommendations for advancing mixoplankton research through empirical-model integration'' <ref name="Millette2024" />

=== Recent applications ===
*

=== Common calculations/conversions ===
* % mixotrophic cells = (LTG<sup>+</sup> and autofluorescent cells) / (total autofluorescent cells) × 100.

== References ==

[[Category:Main Pages|Model types]]

Stable isotope-labelled prey

2026-05-14T00:51:54Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Bacterivory and prey identity (stable isotope probing) |- | '''Approach:''' RNA/DNA-SIP with <sup>13</sup>C/<sup>15</sup>N-labelled prey; ultracentrifugation and amplicon sequencing of heavy fracti..."

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* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Bacterivory and prey identity (stable isotope probing)
|-
| '''Approach:''' RNA/DNA-SIP with <sup>13</sup>C/<sup>15</sup>N-labelled prey; ultracentrifugation and amplicon sequencing of heavy fraction
|-
| '''Context:''' incubation, field
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' 24 h
|-
| '''Units:''' actively feeding taxa (presence/absence; relative enrichment)
|-
| '''Community captured:''' taxon-specific consumers identified by amplicon sequencing
|-
| '''Co-measurements:''' cellular abundances
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Bacterial or algal prey are grown on <sup>13</sup>C- and/or <sup>15</sup>N-labelled substrates, producing cells whose nucleic acids carry a heavy isotope label. These labelled prey are added to natural seawater samples and allowed to be consumed by community members over ~24 h. After incubation, community RNA or DNA is extracted and separated by isopycnic ultracentrifugation into light (unlabelled) and heavy (isotopically enriched, i.e., from organisms that consumed labelled prey) fractions<ref name="Whiteley2007">Whiteley, A. S., Thomson, B., Lueders, T., & Manefield, M. (2007). RNA stable-isotope probing. ''Nature Protocols'', 2(4), 838–844. https://doi.org/10.1038/nprot.2007.115</ref>. Amplicon sequencing (16S, 18S, or ITS) of the heavy fraction identifies which community members consumed the labelled prey, revealing the taxonomic identity of active predators without prior culture.

=== Scale of measurement ===

The method provides qualitative and semi-quantitative information on which taxa are active predators under the incubation conditions. Incubations typically run 24 hours.

=== Data generated ===

Identities of actively feeding taxa (from 16S/18S amplicon sequencing of heavy RNA/DNA fraction). With quantitative SIP modifications, relative enrichment levels can be used to rank predator activity.

=== Units & currency ===

Units are actively feeding taxa (presence/relative abundance). The currency is actively feeding taxa identified by sequencing.

=== Sample size ===

Typical samples are ~1 L in volume.

=== Repositories & databases ===

== Limitations ==

Indirect routes of label incorporation — such as excretion and re-uptake of labelled compounds, or transfer of label through multiple trophic levels — can lead to false-positive identification of non-grazing organisms in the heavy fraction. Sufficient incubation time is required for detectable label incorporation, but this increases the risk of indirect labelling. The method identifies active grazers but does not directly quantify per-cell ingestion rates.

== Example Applications & Protocols ==

=== Classic examples ===
* Whiteley et al. (2007) ''RNA stable-isotope probing'' <ref name="Whiteley2007" />

=== Recent applications ===
* Wilken et al. (2023) ''Choanoflagellates alongside diverse uncultured predatory protists consume the abundant open-ocean cyanobacterium Prochlorococcus'' <ref name="Wilken2023">Wilken, S., Yung, C. C. M., Hamilton, M., Hoadley, K., Nzongo, J., Eckmann, C., Corrochano-Luque, M., Poirier, C., & Worden, A. Z. (2023). Choanoflagellates alongside diverse uncultured predatory protists consume the abundant open-ocean cyanobacterium Prochlorococcus. ''Proceedings of the National Academy of Sciences'', 120(27), e2302388120. https://doi.org/10.1073/pnas.2302388120</ref>
* Orsi et al. (2018) ''Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing'' <ref name="Orsi2018">Orsi, W. D., Wilken, S., del Campo, J., Heger, T., James, E., Richards, T. A., Keeling, P. J., Worden, A. Z., & Santoro, A. E. (2018). Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing. ''Environmental Microbiology'', 20(2), 815–827. https://doi.org/10.1111/1462-2920.14018</ref>

=== Common calculations/conversions ===
* Semi-quantitative enrichment: compare 16S/18S amplicon read relative abundance in heavy vs. light fraction to rank predator activity.

== References ==

[[Category:Main Pages|Model types]]

Pulse-chase labeling of bacterial prey

2026-05-14T00:49:43Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Bacterivory by mixotrophs (pulse-chase <sup>14</sup>C) |- | '''Approach:''' <sup>14</sup>C pulse labelling of bacterial prey; radioactivity in FCM-sorted pigmented cells |- | '''Context:''' incubat..."

Radioactively labeled prey surrogates

2026-05-14T00:47:15Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Bacterivory (radiolabelled prey surrogates) |- | '''Approach:''' <sup>3</sup>H or <sup>14</sup>C radiolabelled bacteria; filtration and scintillation counting |- | '''Context:''' incubation |- | ''..."

Fluorescently labeled prey surrogates

2026-05-14T00:41:36Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Bacterivory (fluorescently labelled prey surrogates) |- | '''Approach:''' fluorescently labelled bacteria (FLB) or beads added to seawater; ingestion counted by epifluorescence microscopy or FCM |-..."

Gut-fluorescence

2026-05-14T00:39:41Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Mesozooplankton ingestion (gut fluorescence) |- | '''Approach:''' fluorometric measurement of gut pigment content × gut evacuation rate |- | '''Context:''' ''in situ'', lab |- | '''Spatial scale:'..."

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* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Mesozooplankton ingestion (gut fluorescence)
|-
| '''Approach:''' fluorometric measurement of gut pigment content × gut evacuation rate
|-
| '''Context:''' ''in situ'', lab
|-
| '''Spatial scale:''' point sample (net tow)
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' mg Chl-a m<sup>-2</sup> d<sup>-1</sup>; mg C m<sup>-2</sup> d<sup>-1</sup>
|-
| '''Community captured:''' selected herbivorous species (> 0.5 mm; typically copepods, euphausiids)
|-
| '''Co-measurements:''' Chl-a, phaeopigments; gut evacuation rate (k'); C:Chl ratio
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

The gut fluorescence method estimates ingestion rates of herbivorous mesozooplankton (copepods, euphausiids, and other species > 0.5 mm) from the chlorophyll-a content of their digestive tracts. Freshly caught animals from net tows are immediately frozen or fixed in liquid nitrogen in the dark to halt pigment degradation. The gut contents are homogenized and extracted in acetone; chlorophyll-a and phaeopigment concentrations are quantified fluorometrically before and after acidification. The gut pigment content (G, µg Chl-a animal<sup>-1</sup>) is multiplied by the gut evacuation rate constant (k', h<sup>-1</sup>), which is determined from separate dark-bottle experiments tracking pigment loss from living animals over time: Ingestion (I) = G × k'. Depth-integration and multiplication by species abundance yields areal ingestion rates.

=== Scale of measurement ===

Net tows typically integrate over tens to hundreds of meters of water column, providing depth-averaged estimates. The integration time of the gut content varies with gut transit time, which is temperature dependent (typically 0.5–2 h at in situ temperatures).

=== Data generated ===

Per-animal ingestion rates (µg Chl-a animal<sup>-1</sup> d<sup>-1</sup>) and community ingestion rates (mg Chl-a m<sup>-2</sup> d<sup>-1</sup>). Conversion to carbon requires the C:Chl ratio, which must be measured or estimated for the prey community.

=== Units & currency ===

Units are mg Chl-a m<sup>-2</sup> d<sup>-1</sup> or mg C m<sup>-2</sup> d<sup>-1</sup>. The currency is Chl-a.

=== Sample size ===

Typical catches of 20–200 individuals per species per sampling event.

=== Repositories & databases ===

== Limitations ==

The method assumes that gut evacuation rate (k') and assimilation efficiency are constant for a given species and temperature during the sampling period. The choice of phaeopigment index as a measure of gut fullness is somewhat arbitrary; phaeopigments are degradation products of chlorophyll and may not accurately reflect the true amount of chlorophyll ingested, particularly when animals feed on non-chlorophyll-containing prey. Converting gut pigment to absolute ingestion and then to carbon ingestion introduces multiple conversion factors, each with its own uncertainty.

== Example Applications & Protocols ==

=== Classic examples ===
* Mackas, D. & Bohrer, R. (1976) ''Fluorescence analysis of zooplankton gut contents and an investigation of diel feeding patterns'' <ref name="Mackas1976">Mackas, D., & Bohrer, R. (1976). Fluorescence analysis of zooplankton gut contents and an investigation of diel feeding patterns. ''Journal of Experimental Marine Biology and Ecology'', 25, 77–85.</ref>

=== Recent applications ===
*

=== Common calculations/conversions ===
* Ingestion rate I (µg Chl-a ind<sup>-1</sup> d<sup>-1</sup>) = G × k' × 24; where G is mean gut content (µg Chl-a) and k' is the evacuation rate constant (h<sup>-1</sup>).
* Carbon ingestion = I × C:Chl ratio (g C g Chl<sup>-1</sup>); typical values 30–100 g:g for marine phytoplankton.

== References ==

[[Category:Main Pages|Model types]]

Cell abundance

2026-05-14T00:37:50Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Phytoplankton net growth rate (cell counting) |- | '''Approach:''' FCM or microscopy cell counts in time-course incubations |- | '''Context:''' incubation |- | '''Spatial scale:''' point sample |-..."

Size-fractionated incubation dilution experiments

2026-05-14T00:36:07Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Microzooplankton grazing, size-fractionated |- | '''Approach:''' dilution method with FCM or HPLC tracking of size-class phytoplankton |- | '''Context:''' incubation |- | '''Spatial scale:''' point..."

Grazing

2026-05-14T00:34:45Z

Hagi BucknWise:

===Microzooplankton on phyto loss process===
*[[Incubation dilution experiments]]
*[[Size-fractionated incubation dilution experiments]]
*[[Cell abundance]]
*[[Gut-fluorescence]]

===Bacterivory & Mixotrophy===
*[[Fluorescently labeled prey surrogates]]
*[[Radioactively labeled prey surrogates]]
*[[Pulse-chase labeling of bacterial prey]]
*[[Stable isotope-labelled prey]]

===Life Cycles===
*[[Bulk RNA-sequencing (whole transcriptome)]]

Incubation dilution experiments

2026-05-14T00:33:50Z

Hagi BucknWise: Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Microzooplankton grazing (dilution method) |- | '''Approach:''' dilution of whole seawater with 0.2 µm filtered seawater; Chl-a or FCM tracking |- | '''Context:''' incubation |- | '''Spatial scale..."

{{BreadcrumbsInteractions}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Microzooplankton grazing (dilution method)
|-
| '''Approach:''' dilution of whole seawater with 0.2 µm filtered seawater; Chl-a or FCM tracking
|-
| '''Context:''' incubation
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours (one diel cycle)
|-
| '''Units:''' d<sup>-1</sup> (growth rate µ; grazing rate g)
|-
| '''Community captured:''' whole seawater (all phytoplankton)
|-
| '''Co-measurements:''' temperature, simulated or ''in situ'' PAR, depth of collection; Lagrangian sampling recommended; nutrient-amended bottles to delineate nutrient limitation
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

The dilution method estimates phytoplankton growth rates (µ) and microzooplankton grazing rates (g) simultaneously by exploiting the relationship between prey dilution and net growth rate. Whole seawater is diluted with particle-free (0.2 µm filtered) seawater to create a series of dilution levels (e.g., 100%, 75%, 50%, 25% of whole seawater). At lower dilutions, grazer-to-prey encounter rates are reduced proportionally while the intrinsic phytoplankton growth rate remains constant. By plotting the net phytoplankton growth rate — tracked by chlorophyll-a fluorometry or flow cytometry (FCM) — against the dilution factor, the y-intercept of the linear regression gives µ (d<sup>-1</sup>) and the negative slope gives the grazing rate g (d<sup>-1</sup>)<ref name="Chen2015">Chen, B. (2015). Assessing the accuracy of the "two-point" dilution technique. ''Limnology and Oceanography: Methods'', 13, 521–526. https://doi.org/10.1002/lom3.10044</ref>.

A simpler "two-point" variant uses only a single diluted and an undiluted treatment, sacrificing regression statistics for efficiency. Nutrient-amended parallel bottles allow the method to distinguish growth suppression by nutrient limitation from grazing effects.

=== Scale of measurement ===

Each dilution series provides a point measurement in space. Incubations are typically run for 24 h to integrate over the light cycle. Spatial context requires replicate sampling stations or Lagrangian sampling over multiple days.

=== Data generated ===

Phytoplankton growth rate µ (d<sup>-1</sup>) and microzooplankton grazing rate g (d<sup>-1</sup>) for the bulk chlorophyll community or, when FCM is used, for specific phytoplankton populations resolved by optical properties.

=== Units & currency ===

Units are d<sup>-1</sup>. The currency is Chl-a or cell abundance.

=== Sample size ===

Typical samples are 1–2 L per dilution treatment.

=== Repositories & databases ===

== Limitations ==

The method assumes that grazing rates scale linearly with dilution and that grazer community composition does not change during the incubation. Bottle effects can alter trophic interactions relative to ''in situ'' conditions. Nutrient depletion in unamended dilution bottles may suppress phytoplankton growth and bias µ estimates downward; paired nutrient-amended treatments address this but may introduce their own artifacts. The two-point variant can produce biased estimates when the growth–dilution relationship is non-linear.

== Example Applications & Protocols ==

=== Classic examples ===
* Landry et al. (2009) ''Lagrangian studies of phytoplankton growth and grazing relationships in a coastal upwelling ecosystem off Southern California'' <ref name="Landry2009">Landry, M. R., Ohman, M. D., Goericke, R., Stukel, M. R., & Tsyrklevich, K. (2009). Lagrangian studies of phytoplankton growth and grazing relationships in a coastal upwelling ecosystem off Southern California. ''Progress in Oceanography'', 83, 208–216. https://doi.org/10.1016/j.pocean.2009.07.026</ref>
* Chen (2015) ''Assessing the accuracy of the "two-point" dilution technique'' <ref name="Chen2015" />
* Morison & Menden-Deuer (2017) ''Doing more with less? Balancing sampling resolution and effort in measurements of protistan growth and grazing rates'' <ref name="Morison2017">Morison, F., & Menden-Deuer, S. (2017). Doing more with less? Balancing sampling resolution and effort in measurements of protistan growth and grazing rates. ''Limnology and Oceanography: Methods'', 15, 794–809. https://doi.org/10.1002/lom3.10200</ref>

=== Recent applications ===
* Marrec & Menden-Deuer (2024) ''Changes in phytoplankton size-structure alter trophic transfer in a temperate, coastal planktonic food web'' <ref name="Marrec2024">Marrec, P., & Menden-Deuer, S. (2024). Changes in phytoplankton size-structure alter trophic transfer in a temperate, coastal planktonic food web. ''Limnology and Oceanography Letters'', 9(5), 624–633. https://doi.org/10.1002/lol2.10410</ref>

=== Common calculations/conversions ===
* Net growth rate k (d<sup>-1</sup>) = ln(C<sub>final</sub>/C<sub>initial</sub>) / t; regression of k vs. dilution factor gives µ (y-intercept) and g (negative slope).
* Grazing in carbon units: g × [C<sub>phyto</sub>] gives µg C grazed L<sup>-1</sup> d<sup>-1</sup>.

== References ==

[[Category:Main Pages|Model types]]

Calcification (13-Carbon uptake)

2026-05-13T00:28:25Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Calcification rate (<sup>13</sup>C) |- | '''Approach:''' stable isotope (<sup>13</sup>C-bicarbonate) incubation; separation of PIC and POC fractions |- | '''Context:''' incubation, lab |- | '''Spatial..."

{{BreadcrumbsNutrients}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Calcification rate (<sup>13</sup>C)
|-
| '''Approach:''' stable isotope (<sup>13</sup>C-bicarbonate) incubation; separation of PIC and POC fractions
|-
| '''Context:''' incubation, lab
|-
| '''Spatial scale:''' point sample; single cell
|-
| '''Temporal scale:''' hours
|-
| '''Units:''' µmol C L<sup>-1</sup> d<sup>-1</sup>
|-
| '''Community captured:''' all (> 0.7 µm bulk); single-cell resolution available
|-
| '''Co-measurements:''' background δ<sup>13</sup>C (POC), DIC, Chl; <sup>13</sup>C:<sup>12</sup>C of POC and PIC before and after incubation
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

NaH<sup>13</sup>CO<sub>3</sub> is added to seawater samples incubated under simulated ''in situ'' conditions. After incubation, two subsamples are collected: one filtered for total particulate material (POC + PIC), and one where carbonate is dissolved by acidification before filtration (POC only). The <sup>13</sup>C enrichment in each fraction is measured by EA-IRMS. The difference in <sup>13</sup>C incorporation between the total and acidified fractions reflects incorporation into particulate inorganic carbon (PIC = CaCO<sub>3</sub>), i.e., calcification rate<ref name="Slawyk1977">Slawyk, G., Collos, Y., & Auclair, J.-C. (1977). The use of the <sup>13</sup>C and <sup>15</sup>N isotopes for the simultaneous measurement of carbon and nitrogen turnover rates in marine phytoplankton. ''Limnology and Oceanography'', 22(5), 925–932. https://doi.org/10.4319/lo.1977.22.5.0925</ref>. This approach avoids radioactive materials and can be coupled with <sup>15</sup>N uptake measurements in the same incubation.

=== Scale of measurement ===

Point samples after hours of incubation. At the single-cell level, nanoSIMS can measure per-cell calcification rates in individually identified coccolithophores.

=== Data generated ===

Calcification rates (µmol PIC C L<sup>-1</sup> d<sup>-1</sup>) and organic carbon fixation rates (µmol POC C L<sup>-1</sup> d<sup>-1</sup>), enabling direct calculation of the PIC:POC ratio (coccolithophore calcification ratio).

=== Units & currency ===

Units are µmol C L<sup>-1</sup> d<sup>-1</sup>. The currency is carbon.

=== Sample size ===

Typical samples range from 0.3 to 4 L for bulk; nanoSIMS requires mL volumes with cells sorted or identified by FISH.

=== Repositories & databases ===

== Limitations ==

Natural variability in background δ<sup>13</sup>C of the DIC pool must be accurately measured. Isotopic changes in the DIC pool during the incubation (from CO<sub>2</sub> invasion or outgassing) can bias rates. At the single-cell level, initial cellular carbon content must be estimated from biovolume, introducing uncertainty for cells with variable carbon densities. Bottle effects from incubation can arise.

== Example Applications & Protocols ==

=== Classic examples ===
* Slawyk et al. (1977) ''The use of the <sup>13</sup>C and <sup>15</sup>N isotopes for the simultaneous measurement of carbon and nitrogen turnover rates in marine phytoplankton'' <ref name="Slawyk1977" />

=== Recent applications ===
* Wu et al. (2022) ''Single-cell measurements and modelling reveal substantial organic carbon acquisition by Prochlorococcus'' <ref name="Wu2022">Wu, S., Huang, R., & Jiao, N. (2022). Single-cell measurements and modelling reveal substantial organic carbon acquisition by Prochlorococcus. ''Nature Microbiology'', 7, 2068–2077. https://doi.org/10.1038/s41564-022-01250-5</ref>
* Irion et al. (2021) ''Small phytoplankton contribute greatly to CO₂-fixation after the diatom bloom in the Southern Ocean'' <ref name="Irion2021">Irion, S., Jardillier, L., Sassenhagen, I., & Christaki, U. (2021). Small phytoplankton contribute greatly to CO₂-fixation after the diatom bloom in the Southern Ocean. ''The ISME Journal'', 15, 2509–2522. https://doi.org/10.1038/s41396-021-00915-z</ref>

=== Common calculations/conversions ===
* Calcification rate = [(<sup>13</sup>C<sub>total</sub> − <sup>13</sup>C<sub>POC</sub>) / <sup>13</sup>C<sub>DIC</sub>] × DIC / incubation time; where <sup>13</sup>C<sub>total</sub> and <sup>13</sup>C<sub>POC</sub> are the enrichments in total and acid-treated fractions respectively.

== References ==

[[Category:Main Pages|Model types]]

Biogenic silica accumulation

2026-05-13T00:26:26Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Biogenic silica accumulation (light–dark bottles) |- | '''Approach:''' change in BSi concentration in light vs. dark incubation bottles |- | '''Context:''' incubation, ''in situ'' and lab |- | '''Sp..."

{{BreadcrumbsNutrients}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Biogenic silica accumulation (light–dark bottles)
|-
| '''Approach:''' change in BSi concentration in light vs. dark incubation bottles
|-
| '''Context:''' incubation, ''in situ'' and lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' µmol BSi L<sup>-1</sup> d<sup>-1</sup>; (x)mol BSi cell<sup>-1</sup> d<sup>-1</sup>
|-
| '''Community captured:''' bulk or size-fractionated
|-
| '''Co-measurements:''' ambient [Si(OH)<sub>4</sub>], PAR, temperature
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Net biogenic silica (BSi) accumulation is measured as the change in BSi concentration in incubation bottles over time. Samples are incubated in both light and dark bottles; the difference between initial and final BSi concentrations in the light bottle reflects net BSi accumulation (gross production minus dissolution). In the dark bottle, the BSi change reflects only dissolution. Together, light and dark measurements can be used to estimate both gross BSi production and BSi dissolution rates. BSi concentration is typically measured by alkaline digestion (NaOH at 80°C) followed by colorimetric or ICP-OES determination of dissolved silicic acid.

=== Scale of measurement ===

The method integrates over the full incubation period rather than providing an instantaneous rate.

=== Data generated ===

Net BSi accumulation rate (µmol BSi L<sup>-1</sup> d<sup>-1</sup>); combined with dark bottle dissolution rates, gross BSi production can be estimated. Useful as an independent complement to <sup>32</sup>Si-based production measurements.

=== Units & currency ===

Units are µmol BSi L<sup>-1</sup> d<sup>-1</sup> or (x)mol BSi cell<sup>-1</sup> d<sup>-1</sup>. The currency is biogenic Si.

=== Sample size ===

Typical samples are 0.5–2.3 L in volume.

=== Repositories & databases ===

== Limitations ==

Bulk BSi measurements include both living cells and dead frustules (lithogenic contamination must also be subtracted), so rates normalized to BSi contain uncertainty. Non-steady state conditions during the incubation can cause the dissolution rate to change over time. Bottle effects may arise.

== Example Applications & Protocols ==

=== Classic examples ===
*

=== Recent applications ===
* Latour et al. (2023) ''Characterisation of a Southern Ocean deep chlorophyll maximum: response of phytoplankton to light, iron, and manganese enrichment'' <ref name="Latour2023">Latour, P., et al. (2023). Characterisation of a Southern Ocean deep chlorophyll maximum: response of phytoplankton to light, iron, and manganese enrichment. ''Limnology and Oceanography Letters'', 9(2), 145–154. https://doi.org/10.1002/lol2.10366</ref>

=== Common calculations/conversions ===
* Net BSi accumulation (µmol BSi L<sup>-1</sup> d<sup>-1</sup>) = ([BSi]<sub>final</sub> − [BSi]<sub>initial</sub>) / incubation time (light bottle).
* BSi dissolution = ([BSi]<sub>initial</sub> − [BSi]<sub>final</sub>) / incubation time (dark bottle).
* Gross production ≈ net accumulation + dissolution.

== References ==

[[Category:Main Pages|Model types]]

Silica production - PDMPO

2026-05-13T00:25:01Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Biogenic silica production (PDMPO) |- | '''Approach:''' fluorescent silica dye (PDMPO) incorporation |- | '''Context:''' incubation, ''in situ'' and lab |- | '''Spatial scale:''' point sample; single..."

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* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Biogenic silica production (PDMPO)
|-
| '''Approach:''' fluorescent silica dye (PDMPO) incorporation
|-
| '''Context:''' incubation, ''in situ'' and lab
|-
| '''Spatial scale:''' point sample; single cell
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' (x)mol Si cell<sup>-1</sup> d<sup>-1</sup>
|-
| '''Community captured:''' bulk, targeted size classes or taxa
|-
| '''Co-measurements:''' ambient [Si(OH)<sub>4</sub>], PAR, temperature, BSi, pH/pCO<sub>2</sub>
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole (PDMPO) is a fluorescent dye that partitions specifically into sites of active silica deposition in diatoms and other silicifying organisms. During incubation, PDMPO is added to the sample and becomes incorporated into newly forming frustule silica, where it fluoresces strongly (excitation ~415 nm, emission ~480 nm) due to the acidic environment of the silica deposition vesicle. The fluorescence intensity, measured by flow cytometry or confocal microscopy, is proportional to the amount of silica newly deposited during the incubation. Calibration against a fluorescence standard derived from uniformly PDMPO-labelled diatoms converts fluorescence to Si production rates<ref name="Shimizu2001">Shimizu, K., Del Amo, Y., Brzezinski, M. A., Stucky, G. D., & Morse, D. E. (2001). A novel fluorescent silica tracer for biological silicification studies. ''Chemistry & Biology'', 8(11), 1051–1060. https://doi.org/10.1016/S1074-5521(01)00072-2</ref>.

At the single-cell level, confocal microscopy resolves per-cell silica production rates and can identify individual silicifying cells within mixed communities.

=== Scale of measurement ===

Point samples requiring incubations of hours to days. At the single-cell level, production rates are resolved per individual cell.

=== Data generated ===

Per-cell and bulk BSi production rates (x)mol Si cell<sup>-1</sup> d<sup>-1</sup>. Can distinguish actively silicifying cells from non-silicifying cells in a community.

=== Units & currency ===

Units are (x)mol Si cell<sup>-1</sup> d<sup>-1</sup>. The currency is Si via calibrated fluorescence.

=== Sample size ===

Typical samples are ~60 mL in volume.

=== Repositories & databases ===

== Limitations ==

The BSi:PDMPO molar conversion ratio (established at ~2916 mol BSi per mol PDMPO) must be verified for each study, as it can vary between diatom taxa and measurement conditions. PDMPO fluorescence decreases over time in stored samples, potentially reducing quantitative comparability across sample collections. Calibration requires a uniformly labelled standard, which is difficult to prepare consistently.

== Example Applications & Protocols ==

=== Classic examples ===
* Shimizu et al. (2001) ''A novel fluorescent silica tracer for biological silicification studies'' <ref name="Shimizu2001" />
* Leblanc & Hutchins (2005) ''New applications of a biogenic silica deposition fluorophore in the study of oceanic diatoms'' <ref name="Leblanc2005">Leblanc, K., & Hutchins, D. A. (2005). New applications of a biogenic silica deposition fluorophore in the study of oceanic diatoms. ''Limnology and Oceanography: Methods'', 3, 462–476. https://doi.org/10.4319/lom.2005.3.462</ref>
* McNair et al. (2015) ''Quantifying diatom silicification with the fluorescent dye PDMPO'' <ref name="McNair2015">McNair, H. M., Brzezinski, M. A., & Krause, J. W. (2015). Quantifying diatom silicification with the fluorescent dye PDMPO. ''Limnology and Oceanography: Methods'', 13, 587–599. https://doi.org/10.1002/lom3.10049</ref>

=== Recent applications ===
* Maniscalco et al. (2022) ''Diminished carbon and nitrate assimilation drive changes in diatom elemental stoichiometry independent of silicification in an iron-limited assemblage'' <ref name="Maniscalco2022">Maniscalco, M., McNair, H. M., Brzezinski, M. A., & Krause, J. W. (2022). Diminished carbon and nitrate assimilation drive changes in diatom elemental stoichiometry independent of silicification in an iron-limited assemblage. ''ISME Communications'', 2, 6. https://doi.org/10.1038/s43705-022-00136-1</ref>

=== Common calculations/conversions ===
* ρSi (fmol Si cell<sup>-1</sup> h<sup>-1</sup>) = (RFU<sub>cell</sub> / RFU<sub>standard</sub>) × Si<sub>standard</sub> / incubation time; where Si<sub>standard</sub> is the known Si content of the labelled diatom standard.

== References ==

[[Category:Main Pages|Model types]]

Silica production

2026-05-13T00:23:21Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Biogenic silica production (<sup>32</sup>Si) |- | '''Approach:''' radiotracer (<sup>32</sup>Si) incubation; gross biogenic silica production |- | '''Context:''' incubation, ''in situ'' and lab |- | ''..."

{{BreadcrumbsNutrients}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Biogenic silica production (<sup>32</sup>Si)
|-
| '''Approach:''' radiotracer (<sup>32</sup>Si) incubation; gross biogenic silica production
|-
| '''Context:''' incubation, ''in situ'' and lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' µmol Si cell<sup>-1</sup> d<sup>-1</sup>; µmol Si L<sup>-1</sup> d<sup>-1</sup>
|-
| '''Community captured:''' bulk
|-
| '''Co-measurements:''' ambient [Si(OH)<sub>4</sub>], PAR, temperature, BSi
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Biogenic silica (opal) production rates are measured by the same <sup>32</sup>Si tracer incubation approach as silicon uptake, but are reported as gross production rates in µmol Si L<sup>-1</sup> d<sup>-1</sup> or per-cell equivalents, reflecting the total rate of silica deposition into diatom frustules and other silicified structures. The rate encompasses both net frustule growth and the replacement of lost silica from dissolution during the incubation. <sup>32</sup>Si(OH)<sub>4</sub> is added at tracer concentration, cells are incubated under ''in situ'' or simulated conditions, filtered onto polycarbonate membranes, and the incorporated radioactivity is measured by low-energy beta counting<ref name="Brzezinski1997">Brzezinski, M. A., & Phillips, D. R. (1997). Evaluation of <sup>32</sup>Si as a tracer for measuring silica production rates in marine waters. ''Limnology and Oceanography'', 42(5), 856–865. https://doi.org/10.4319/lo.1997.42.5.0856</ref>.

=== Scale of measurement ===

Point samples requiring hours to days incubation. Depth profiles require incubations at each depth.

=== Data generated ===

Gross BSi production rates (µmol Si L<sup>-1</sup> d<sup>-1</sup>); can be depth-integrated to give areal rates (mmol Si m<sup>-2</sup> d<sup>-1</sup>). Together with BSi dissolution rate estimates, net BSi accumulation can be inferred.

=== Units & currency ===

Units are µmol Si L<sup>-1</sup> d<sup>-1</sup> or µmol Si cell<sup>-1</sup> d<sup>-1</sup>. The currency is biogenic Si.

=== Sample size ===

Typical samples are 100–300 mL in volume.

=== Repositories & databases ===

== Limitations ==

As for [[Silicon uptake]]: non-steady state conditions, bottle effects, and BSi normalization uncertainty. Silica dissolution during the incubation releases <sup>32</sup>Si back into solution and can cause underestimation of gross production if the dissolution rate is high.

== Example Applications & Protocols ==

=== Classic examples ===
* Brzezinski & Phillips (1997) ''Evaluation of <sup>32</sup>Si as a tracer for measuring silica production rates in marine waters'' <ref name="Brzezinski1997" />

=== Recent applications ===
* Krause et al. (2011) ''Application of low-level beta counting of <sup>32</sup>Si for the measurement of silica production rates in aquatic environments'' <ref name="Krause2011">Krause, J. W., Brzezinski, M. A., Landry, M. R., Baines, S. B., Nelson, D. M., Selph, K. E., Taylor, A. G., & Twining, B. S. (2011). Application of low-level beta counting of <sup>32</sup>Si for the measurement of silica production rates in aquatic environments. ''Marine Chemistry'', 127, 40–47. https://doi.org/10.1016/j.marchem.2011.07.001</ref>

=== Common calculations/conversions ===
* ρSi (µmol Si L<sup>-1</sup> d<sup>-1</sup>) = (<sup>32</sup>Si<sub>BSi</sub> / <sup>32</sup>Si<sub>total added</sub>) × [Si(OH)<sub>4</sub>] / incubation time.

== References ==

[[Category:Main Pages|Model types]]

Kinetics of silicon uptake

2026-05-13T00:21:29Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Silicon uptake kinetics (V<sub>max</sub>, K<sub>s</sub>) |- | '''Approach:''' <sup>32</sup>Si incubations at multiple ambient silicic acid concentrations; Michaelis–Menten fitting |- | '''Context:''..."

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* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Silicon uptake kinetics (V<sub>max</sub>, K<sub>s</sub>)
|-
| '''Approach:''' <sup>32</sup>Si incubations at multiple ambient silicic acid concentrations; Michaelis–Menten fitting
|-
| '''Context:''' incubation, ''in situ'' and lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' V<sub>max</sub> (d<sup>-1</sup>); K<sub>s</sub> (µmol Si L<sup>-1</sup> or µmol Si cell<sup>-1</sup>)
|-
| '''Community captured:''' bulk
|-
| '''Co-measurements:''' ambient [Si(OH)<sub>4</sub>], PAR, temperature, BSi
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Silicon uptake kinetics are determined by conducting <sup>32</sup>Si tracer incubations across a range of silicic acid concentrations spanning from near-ambient to saturating levels. At each substrate concentration, the uptake rate is measured as for the standard silicon uptake assay, and the resulting uptake rate vs. [Si(OH)<sub>4</sub>] relationship is fitted to the Michaelis–Menten equation to derive the maximum specific uptake rate (V<sub>max</sub>, d<sup>-1</sup>) and the half-saturation constant for silicic acid (K<sub>s</sub>, µmol Si L<sup>-1</sup> or per-cell equivalent)<ref name="Brzezinski1997">Brzezinski, M. A., & Phillips, D. R. (1997). Evaluation of <sup>32</sup>Si as a tracer for measuring silica production rates in marine waters. ''Limnology and Oceanography'', 42(5), 856–865. https://doi.org/10.4319/lo.1997.42.5.0856</ref>. These kinetic parameters characterize the community's capacity to access silicic acid at varying concentrations and indicate whether the community is silicon-limited.

=== Scale of measurement ===

Point sample following hours to days of incubation across multiple substrate concentrations.

=== Data generated ===

V<sub>max</sub> (d<sup>-1</sup>) and K<sub>s</sub> (µmol Si L<sup>-1</sup>); these kinetic parameters characterize the community's affinity for silicic acid and maximum uptake capacity. When ambient [Si(OH)<sub>4</sub>] < K<sub>s</sub>, the community is silicon-limited.

=== Units & currency ===

Units are V<sub>max</sub> (d<sup>-1</sup>) and K<sub>s</sub> (µmol Si L<sup>-1</sup> or µmol Si cell<sup>-1</sup>). The currency is Si.

=== Sample size ===

Typical samples are 100–300 mL per substrate concentration, with multiple replicates.

=== Repositories & databases ===

== Limitations ==

Kinetic parameters derived from short incubations may not represent steady-state values; acclimation to substrate additions can shift V<sub>max</sub> and K<sub>s</sub> over longer timescales. Normalization to BSi introduces the same uncertainty as for bulk uptake (inclusion of dead frustules). V<sub>max</sub> and K<sub>s</sub> represent the integrated response of all silicifying organisms in the community and cannot be attributed to individual species without additional fractionation.

== Example Applications & Protocols ==

=== Classic examples ===
* Brzezinski & Phillips (1997) ''Evaluation of <sup>32</sup>Si as a tracer for measuring silica production rates in marine waters'' <ref name="Brzezinski1997" />

=== Recent applications ===
* Giesbrecht & Varela (2021) ''Summertime biogenic silica production and silicon limitation in the Pacific Arctic Region'' <ref name="Giesbrecht2021">Giesbrecht, K. E., & Varela, D. E. (2021). Summertime biogenic silica production and silicon limitation in the Pacific Arctic Region from 2006 to 2016. ''Global Biogeochemical Cycles'', 35, e2020GB006629. https://doi.org/10.1029/2020GB006629</ref>

=== Common calculations/conversions ===
* V<sub>Si</sub> = V<sub>max</sub> × [Si(OH)<sub>4</sub>] / (K<sub>s</sub> + [Si(OH)<sub>4</sub>]); rearranged as a Lineweaver–Burk or Eadie–Hofstee plot to obtain V<sub>max</sub> and K<sub>s</sub>.

== References ==

[[Category:Main Pages|Model types]]

Silicon uptake

2026-05-13T00:19:37Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Silicon uptake (<sup>32</sup>Si) |- | '''Approach:''' radiotracer (<sup>32</sup>Si) incubation |- | '''Context:''' incubation, ''in situ'' and lab |- | '''Spatial scale:''' point sample |- | '''Tempor..."

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* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Silicon uptake (<sup>32</sup>Si)
|-
| '''Approach:''' radiotracer (<sup>32</sup>Si) incubation
|-
| '''Context:''' incubation, ''in situ'' and lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' µmol Si L<sup>-1</sup> h<sup>-1</sup>; µmol Si cell<sup>-1</sup> h<sup>-1</sup>
|-
| '''Community captured:''' bulk (primarily diatoms)
|-
| '''Co-measurements:''' ambient silicic acid [Si(OH)<sub>4</sub>], PAR, temperature, biogenic silica (BSi)
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Silicon uptake rates are measured using <sup>32</sup>Si, a low-energy beta-emitting radiotracer with a half-life of ~140 years. Silicic acid (<sup>32</sup>Si(OH)<sub>4</sub>) is added at tracer concentrations to seawater samples incubated under simulated ''in situ'' or ''in situ'' light and temperature conditions. Diatoms and other silicifying organisms incorporate the labelled silicic acid into their frustules at rates proportional to the ambient silicic acid uptake rate. At the end of the incubation, cells are filtered onto polycarbonate membranes; the filter is placed on a scintillator-coated Mylar film, and the beta emission from <sup>32</sup>Si incorporated into BSi is counted by a low-energy beta counter. The uptake rate is calculated from the fraction of added <sup>32</sup>Si incorporated relative to total available silicic acid<ref name="Brzezinski1997">Brzezinski, M. A., & Phillips, D. R. (1997). Evaluation of <sup>32</sup>Si as a tracer for measuring silica production rates in marine waters. ''Limnology and Oceanography'', 42(5), 856–865. https://doi.org/10.4319/lo.1997.42.5.0856</ref>.

=== Scale of measurement ===

Point samples after incubations of hours to days depending on ambient Si uptake rates. Depth profiles require incubations at each target depth or under the appropriate simulated irradiance.

=== Data generated ===

Silicon uptake rates (µmol Si L<sup>-1</sup> h<sup>-1</sup>), equivalent to biogenic silica production when steady state is assumed. Normalization to BSi concentration yields the specific uptake rate (V<sub>Si</sub>, d<sup>-1</sup>), which reflects the community's silicification rate relative to standing stock.

=== Units & currency ===

Units are µmol Si L<sup>-1</sup> h<sup>-1</sup> or µmol Si cell<sup>-1</sup> h<sup>-1</sup> (cell-specific). The currency is Si.

=== Sample size ===

Typical samples are 100–300 mL in volume.

=== Repositories & databases ===

== Limitations ==

The method assumes Michaelis–Menten kinetics and that the tracer is taken up at the same rate as ambient silicic acid. Bottle confinement and changes in light or mixing can alter uptake rates relative to ''in situ'' conditions (non-steady state). When uptake rates are normalized to BSi, bulk BSi measurements include both living cells and dead frustules, inflating the denominator and underestimating specific rates.

== Example Applications & Protocols ==

=== Classic examples ===
* Brzezinski & Phillips (1997) ''Evaluation of <sup>32</sup>Si as a tracer for measuring silica production rates in marine waters'' <ref name="Brzezinski1997" />

=== Recent applications ===
* Krause et al. (2011) ''Application of low-level beta counting of <sup>32</sup>Si for the measurement of silica production rates in aquatic environments'' <ref name="Krause2011">Krause, J. W., Brzezinski, M. A., Landry, M. R., Baines, S. B., Nelson, D. M., Selph, K. E., Taylor, A. G., & Twining, B. S. (2011). Application of low-level beta counting of <sup>32</sup>Si for the measurement of silica production rates in aquatic environments. ''Marine Chemistry'', 127, 40–47. https://doi.org/10.1016/j.marchem.2011.07.001</ref>
* Giesbrecht & Varela (2021) ''Summertime biogenic silica production and silicon limitation in the Pacific Arctic Region'' <ref name="Giesbrecht2021">Giesbrecht, K. E., & Varela, D. E. (2021). Summertime biogenic silica production and silicon limitation in the Pacific Arctic Region from 2006 to 2016. ''Global Biogeochemical Cycles'', 35, e2020GB006629. https://doi.org/10.1029/2020GB006629</ref>

=== Common calculations/conversions ===
* Uptake rate ρSi (µmol Si L<sup>-1</sup> h<sup>-1</sup>) = (<sup>32</sup>Si<sub>incorporated</sub> / <sup>32</sup>Si<sub>added</sub>) × [Si(OH)<sub>4</sub>] / incubation time.
* Specific uptake rate V<sub>Si</sub> (d<sup>-1</sup>) = ρSi / [BSi].

== References ==

[[Category:Main Pages|Model types]]

Cobalamin uptake with 57Cobalt-B12

2026-05-13T00:14:38Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Cobalamin uptake (<sup>57</sup>Co-B12) |- | '''Approach:''' radiotracer (<sup>57</sup>Co-labelled cobalamin) incubation |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- |..."

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* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Cobalamin uptake (<sup>57</sup>Co-B12)
|-
| '''Approach:''' radiotracer (<sup>57</sup>Co-labelled cobalamin) incubation
|-
| '''Context:''' incubation, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' 4–24 h
|-
| '''Units:''' mol cell<sup>-1</sup> d<sup>-1</sup>; mol L<sup>-1</sup> d<sup>-1</sup>; mol mol C<sup>-1</sup> d<sup>-1</sup>
|-
| '''Community captured:''' all (usually > 0.2 or 0.7 µm)
|-
| '''Co-measurements:''' biomass (Chl, cells, POC, cell volume)
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Cobalamin (vitamin B<sub>12</sub>) uptake rates are measured using <sup>57</sup>Co-labelled cyanocobalamin (<sup>57</sup>Co-B12; half-life ~271 days, gamma emitter). The radiolabelled cobalamin is added to seawater at tracer concentrations under trace-metal-clean conditions and equilibrated with the sample. After incubation (4–24 h), cells are collected on filters, rinsed to remove surface-adsorbed cobalamin, and counted by gamma spectrometry. Uptake rates are calculated from the fraction of <sup>57</sup>Co-B12 incorporated relative to total dissolved <sup>57</sup>Co-B12<ref name="Bertrand2011">Bertrand, E. M., Saito, M. A., Rose, J. M., Riesselman, C. R., Lohan, M. C., Noble, A. E., Lee, P. A., & DiTullio, G. R. (2011). Vitamin B<sub>12</sub> and iron colimitation of phytoplankton growth in the Ross Sea. ''Limnology and Oceanography'', 56(4), 1079–1091. https://doi.org/10.3389/fmicb.2011.00160</ref>.

Cobalamin is an essential cofactor that many phytoplankton cannot synthesize and must obtain from cobalamin-producing bacteria, making uptake rate measurements central to understanding phytoplankton–bacteria vitamin interactions.

=== Scale of measurement ===

Point sample after 4–24 h of incubation under trace-metal-clean conditions.

=== Data generated ===

Cobalamin uptake rates (mol cell<sup>-1</sup> d<sup>-1</sup> or mol L<sup>-1</sup> d<sup>-1</sup>). Combined with cellular B<sub>12</sub> quotas, the community's vitamin B<sub>12</sub> demand and turnover can be characterized.

=== Units & currency ===

Units are mol cell<sup>-1</sup> d<sup>-1</sup>, mol L<sup>-1</sup> d<sup>-1</sup>, or mol mol C<sup>-1</sup> d<sup>-1</sup>. The currency is Co (as cobalamin).

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

The method assumes that <sup>57</sup>Co remains associated with the intact cobalamin molecule throughout the incubation (no degradation of cobalamin to other Co-containing compounds). In practice, some B<sub>12</sub> degradation can occur, leading to uptake of <sup>57</sup>Co in non-cobalamin forms. Natural cobalamin-binding proteins in seawater can compete with cellular uptake, and their effect must be considered when estimating bioavailable cobalamin.

== Example Applications & Protocols ==

=== Classic examples ===
* Bertrand et al. (2011) ''Vitamin B<sub>12</sub> and iron colimitation of phytoplankton growth in the Ross Sea'' <ref name="Bertrand2011" />

=== Recent applications ===
*

=== Common calculations/conversions ===
* B<sub>12</sub> uptake rate = (cpm<sub>cells</sub> / cpm<sub>dissolved</sub>) × [B<sub>12,dissolved</sub>] / incubation time.

== References ==

[[Category:Main Pages|Model types]]

67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake

2026-05-13T00:13:00Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Copper uptake (<sup>67/64</sup>Cu) |- | '''Approach:''' radiotracer (<sup>67</sup>Cu for ''in situ''; <sup>64</sup>Cu for lab) incubation |- | '''Context:''' incubation, lab |- | '''Spatial scale:'''..."

{{BreadcrumbsNutrients}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Copper uptake (<sup>67/64</sup>Cu)
|-
| '''Approach:''' radiotracer (<sup>67</sup>Cu for ''in situ''; <sup>64</sup>Cu for lab) incubation
|-
| '''Context:''' incubation, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' 4–24 h
|-
| '''Units:''' (x)mol Cu biomass<sup>-1</sup> d<sup>-1</sup>; (x)mol Cu L<sup>-1</sup> d<sup>-1</sup>
|-
| '''Community captured:''' all (usually > 0.2 or 0.7 µm)
|-
| '''Co-measurements:''' biomass (Chl, cells, POC, cell volume)
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Copper uptake rates are measured using radioactive copper isotope tracers. Two isotopes are available depending on context: <sup>67</sup>Cu (half-life 61.8 h, gamma emitter; suitable for shipboard incubations of up to ~3 days) and <sup>64</sup>Cu (half-life 12.7 h, positron/gamma emitter; suitable for short lab incubations). The tracer (CuCl<sub>2</sub>) is added to seawater samples under trace-metal-clean conditions, equilibrated with the ambient copper-ligand pool, and samples are incubated for 4–24 h. Cells are collected by filtration, rinsed with a chelating wash to remove surface-adsorbed copper, and counted by gamma spectrometry. Uptake rates are calculated from the fraction of radiolabelled Cu incorporated relative to total dissolved radiolabelled Cu<ref name="Semeniuk2016">Semeniuk, D. M., Bundy, R. M., Bhatt, S., Landry, M. R., Twining, B. S., & Bruland, K. W. (2016). Using <sup>67</sup>Cu to study the biogeochemical cycling of copper in the northeast subarctic Pacific Ocean. ''Frontiers in Marine Science'', 3, 78. https://doi.org/10.3389/fmars.2016.00078</ref>.

Copper is both an essential micronutrient (for plastocyanin, cytochrome oxidase) and potentially toxic at elevated concentrations, making uptake rate measurements particularly relevant for understanding Cu nutrition and toxicity thresholds.

=== Scale of measurement ===

Sampling after 4–24 h incubation under trace-metal-clean conditions.

=== Data generated ===

Copper uptake rates (mol Cu L<sup>-1</sup> d<sup>-1</sup> or mol Cu biomass<sup>-1</sup> d<sup>-1</sup>). Combined with Cu quotas, cellular Cu:C ratios can be derived.

=== Units & currency ===

Units are (x)mol Cu biomass<sup>-1</sup> d<sup>-1</sup> or (x)mol Cu L<sup>-1</sup> d<sup>-1</sup>. The currency is Cu.

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

Isotopic fractionation between <sup>64/67</sup>Cu and ambient <sup>63/65</sup>Cu is minimal. The short half-life of <sup>64</sup>Cu limits its use to rapid lab experiments and requires proximity to a cyclotron or nuclear reactor for tracer production. Natural organic ligand complexation strongly controls Cu bioavailability; the equilibration step must achieve realistic speciation. Bottle effects and steady-state assumptions apply.

== Example Applications & Protocols ==

=== Classic examples ===
* Semeniuk et al. (2016) ''Using <sup>67</sup>Cu to study the biogeochemical cycling of copper in the northeast subarctic Pacific Ocean'' <ref name="Semeniuk2016" />

=== Recent applications ===
* González-Dávila et al. (2024) ''Cu transport and complexation by the marine diatom Phaeodactylum tricornutum'' <ref name="González2024">González-Dávila, M., Santana-Casiano, J. M., Laglera, L. M., & Millero, F. J. (2024). Cu transport and complexation by the marine diatom Phaeodactylum tricornutum: implications for trace metal complexation kinetics in the surface ocean. ''Science of The Total Environment'', 919, 170752. https://doi.org/10.1016/j.scitotenv.2024.170752</ref>

=== Common calculations/conversions ===
* Cu uptake rate = (cpm<sub>cells</sub> / cpm<sub>dissolved</sub>) × [Cu<sub>dissolved</sub>] / incubation time.

== References ==

[[Category:Main Pages|Model types]]

54-Manganese uptake

2026-05-13T00:10:40Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Manganese uptake (<sup>54</sup>Mn) |- | '''Approach:''' radiotracer (<sup>54</sup>Mn) incubation |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- | '''Temporal scale:''' 4..."

55-Iron uptake

2026-05-13T00:09:24Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Iron uptake (<sup>55</sup>Fe) |- | '''Approach:''' radiotracer (<sup>55</sup>Fe) incubation |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- | '''Temporal scale:''' 4–24..."

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* [[Page authors|Page authors]]: [[PRIMO]]
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----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Iron uptake (<sup>55</sup>Fe)
|-
| '''Approach:''' radiotracer (<sup>55</sup>Fe) incubation
|-
| '''Context:''' incubation, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' 4–24 h
|-
| '''Units:''' (x)mol Fe biomass<sup>-1</sup> d<sup>-1</sup>; (x)mol Fe L<sup>-1</sup> d<sup>-1</sup>
|-
| '''Community captured:''' all (usually > 0.2 or 0.7 µm)
|-
| '''Co-measurements:''' biomass (Chl, cells, POC, cell volume)
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Iron uptake rates are measured by adding <sup>55</sup>Fe (a low-energy gamma/X-ray emitter, half-life ~2.7 years) as a radiolabelled FeCl<sub>3</sub> tracer to seawater samples under trace-metal-clean conditions. The <sup>55</sup>Fe spike is added at concentrations comparable to ambient dissolved iron concentrations and allowed to equilibrate with the ambient iron-binding ligand pool before incubation. After a 4–24 h dark or light incubation, the particulate fraction is collected by filtration, washed with oxalate solution to remove adsorbed (extracellular) iron, and the filter radioactivity is measured by liquid scintillation counting. The uptake rate is calculated from the fraction of <sup>55</sup>Fe incorporated relative to the total dissolved <sup>55</sup>Fe in the incubation<ref name="Hudson1990">Hudson, R. J. M., & Morel, F. M. M. (1990). Iron transport in marine phytoplankton: kinetics of cellular and medium coordination reactions. ''Limnology and Oceanography'', 35(5), 1002–1020. https://doi.org/10.4319/lo.1990.35.5.1002</ref>.

=== Scale of measurement ===

Sampling after 4–24 h incubation. Trace-metal-clean sampling and handling are essential throughout to avoid iron contamination.

=== Data generated ===

Iron uptake rates normalized to biomass (mol Fe cell<sup>-1</sup> d<sup>-1</sup>, mol Fe mol C<sup>-1</sup> d<sup>-1</sup>) or expressed as volumetric rates (mol Fe L<sup>-1</sup> d<sup>-1</sup>). When combined with iron quotas (cellular Fe content), growth-rate-specific iron requirements (K<sub>Fe</sub>) can be derived.

=== Units & currency ===

Units are (x)mol Fe biomass<sup>-1</sup> d<sup>-1</sup> or (x)mol Fe L<sup>-1</sup> d<sup>-1</sup>. The currency is Fe.

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

The method assumes minimal isotopic fractionation between <sup>55</sup>Fe and ambient <sup>56/54</sup>Fe. In field incubations, bottle effects can alter iron speciation and uptake rates relative to ''in situ'' conditions. The distribution of iron between the organic-ligand-bound and inorganic forms (bioavailability) must equilibrate before incubation; inadequate equilibration leads to inaccurate estimates. Radiotracer recycling (released iron taken up again) can overestimate rates in longer incubations.

== Example Applications & Protocols ==

=== Classic examples ===
* Hudson & Morel (1990) ''Iron transport in marine phytoplankton: kinetics of cellular and medium coordination reactions'' <ref name="Hudson1990" />

=== Recent applications ===
*

=== Common calculations/conversions ===
* Fe uptake rate (mol Fe L<sup>-1</sup> d<sup>-1</sup>) = (cpm<sub>cells</sub> / cpm<sub>total dissolved</sub>) × [Fe<sub>dissolved</sub>] / incubation time.
* Biomass-specific rate = volumetric rate / [biomass]; requires cell counts or POC measurements.

== References ==

[[Category:Main Pages|Model types]]

Rates of DMS and DMSP oxidation to DMSO

2026-05-13T00:07:22Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! DMS and DMSP oxidation rates |- | '''Approach:''' deuterium-labelled DMS/DMSP tracers; D<sub>3</sub>-DMSO and D<sub>6</sub>-DMSO formation by GC-MS |- | '''Context:''' ''in situ'' incubations, lab |-..."

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* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! DMS and DMSP oxidation rates
|-
| '''Approach:''' deuterium-labelled DMS/DMSP tracers; D<sub>3</sub>-DMSO and D<sub>6</sub>-DMSO formation by GC-MS
|-
| '''Context:''' ''in situ'' incubations, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' 4–12 h
|-
| '''Units:''' nM d<sup>-1</sup>; rate constants h<sup>-1</sup> or d<sup>-1</sup>
|-
| '''Community captured:''' all
|-
| '''Co-measurements:''' (none specified in inventory)
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

The oxidation of DMS and DMSP to DMSO is measured using deuterium-labelled tracers. D<sub>3</sub>-DMS is added to measure DMS oxidation (D<sub>3</sub>-DMSO formation), and D<sub>6</sub>-DMSP is added to measure DMSP oxidation to DMSO (D<sub>6</sub>-DMSO formation). These reactions are catalyzed by bacterial mono-oxygenases and represent a significant biological sink for DMS in marine surface waters. The rate of labelled DMSO accumulation, detected by GC-MS and corrected for the fractional enrichment of the substrate pool, gives the gross oxidation rate for each pathway<ref name="McCulloch2023">McCulloch, J. E., & Tortell, P. D. (2023). The determination of dimethyl sulfoxide in natural waters using electrochemical reduction. ''Limnology and Oceanography: Methods'', 21(9), 529–541. https://doi.org/10.1002/lom3.10562</ref>.

=== Scale of measurement ===

Point samples from sealed serum vials for 4–12 h incubations.

=== Data generated ===

Gross DMS oxidation rate and DMSP oxidation rate (nM d<sup>-1</sup>), each measured simultaneously in the same incubation. Together with DMSO reduction rates, the net DMS and DMSO budget can be assembled.

=== Units & currency ===

Units are nM d<sup>-1</sup> or h<sup>-1</sup>/d<sup>-1</sup> (rate constants). The currency is sulfur metabolite (DMSO).

=== Sample size ===

Typical samples are < 200 mL in volume.

=== Repositories & databases ===

== Limitations ==

Deuterium-labelled DMS and DMSP must rapidly equilibrate with the endogenous pools. DMSP may be cleaved to DMS before being oxidized, potentially complicating the DMSP → DMSO pathway measurement. Bottle effects and steady-state assumptions apply as for other DMS/P/O turnover measurements.

== Example Applications & Protocols ==

=== Classic examples ===
* McCulloch & Tortell (2023) ''The determination of dimethyl sulfoxide in natural waters using electrochemical reduction'' <ref name="McCulloch2023" />

=== Recent applications ===
* McNabb & Tortell (2025) ''A potential photo-protective, antioxidant function for DMSO in marine phytoplankton'' <ref name="McNabb2025">McNabb, M. L., & Tortell, P. D. (2025). A potential photo-protective, antioxidant function for DMSO in marine phytoplankton. ''PLOS ONE'', 20(2), e0317951. https://doi.org/10.1371/journal.pone.0317951</ref>

=== Common calculations/conversions ===
* DMS oxidation rate = d[D<sub>3</sub>-DMSO]/dt × ([DMS]<sub>total</sub> / [D<sub>3</sub>-DMS]<sub>added</sub>).
* DMSP oxidation rate = d[D<sub>6</sub>-DMSO]/dt × ([DMSP]<sub>total</sub> / [D<sub>6</sub>-DMSP]<sub>added</sub>).

== References ==

[[Category:Main Pages|Model types]]

Rates of DMSO reduction to DMS

2026-05-13T00:05:52Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! DMSO reduction rate |- | '''Approach:''' deuterium-labelled DMSO tracer; D<sub>6</sub>-DMS formation measured by GC-MS |- | '''Context:''' ''in situ'' incubations, lab |- | '''Spatial scale:''' point..."

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* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! DMSO reduction rate
|-
| '''Approach:''' deuterium-labelled DMSO tracer; D<sub>6</sub>-DMS formation measured by GC-MS
|-
| '''Context:''' ''in situ'' incubations, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' 4–12 h
|-
| '''Units:''' nM d<sup>-1</sup>; rate constants h<sup>-1</sup> or d<sup>-1</sup>
|-
| '''Community captured:''' all
|-
| '''Co-measurements:''' (none specified in inventory)
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

The reduction of dimethylsulfoxide (DMSO) to dimethylsulfide (DMS) is measured by adding fully deuterium-labelled D<sub>6</sub>,<sup>13</sup>C<sub>2</sub>-DMSO (or D<sub>6</sub>-DMSO) to seawater samples. Bacteria possessing DMSO reductase enzymes reduce the deuterated DMSO to D<sub>6</sub>-DMS, which is distinguishable from natural DMS (mass 62 vs. 62+6=68) by GC-MS analysis. The rate of D<sub>6</sub>-DMS accumulation, corrected for the fractional labelling of the DMSO pool, gives the gross DMSO reduction rate<ref name="McNabb2025">McNabb, M. L., & Tortell, P. D. (2025). A potential photo-protective, antioxidant function for DMSO in marine phytoplankton. ''PLOS ONE'', 20(2), e0317951. https://doi.org/10.1371/journal.pone.0317951</ref>. DMSO reduction is a significant biological DMS production pathway that is often overlooked relative to DMSP cleavage.

=== Scale of measurement ===

Point samples from sealed serum vials to prevent DMS volatilization during the 4–12 h incubation.

=== Data generated ===

Gross DMSO reduction rate (nM d<sup>-1</sup>) and first-order rate constant (d<sup>-1</sup>). Relative to total DMS production, this reveals the contribution of DMSO reduction vs. DMSP cleavage.

=== Units & currency ===

Units are nM d<sup>-1</sup> or h<sup>-1</sup>/d<sup>-1</sup> (rate constants). The currency is sulfur metabolite (DMS).

=== Sample size ===

Typical samples are < 200 mL in volume.

=== Repositories & databases ===

== Limitations ==

Steady-state intracellular and dissolved DMSO pool dynamics are assumed. Bottle artifacts can alter community composition and DMSO availability. The labelled DMSO must equilibrate rapidly with the endogenous DMSO pool for accurate rate estimation.

== Example Applications & Protocols ==

=== Classic examples ===
* McNabb & Tortell (2025) ''A potential photo-protective, antioxidant function for DMSO in marine phytoplankton'' <ref name="McNabb2025" />

=== Recent applications ===
* Herr et al. (2020) ''Potential roles of dimethylsulfoxide in regional sulfur cycling in the NE subarctic Pacific'' <ref name="Herr2020">Herr, A. E., Bass, M., Granger, J., & Tortell, P. D. (2020). Potential roles of dimethylsulfoxide in regional sulfur cycling and phytoplankton physiological ecology in the NE subarctic Pacific. ''Limnology and Oceanography'', 66(1), 76–94. https://doi.org/10.1002/lno.11589</ref>

=== Common calculations/conversions ===
* DMSO reduction rate = d[D<sub>6</sub>-DMS]/dt × ([DMSO]<sub>total</sub> / [D<sub>6</sub>-DMSO]<sub>added</sub>).

== References ==

[[Category:Main Pages|Model types]]

DMS/P/O cycling

2026-05-13T00:03:38Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! DMS/DMSP/DMSO cycling rates |- | '''Approach:''' isotope dilution with deuterated DMS/DMSP/DMSO standards; GC-MS detection |- | '''Context:''' ''in situ'' |- | '''Spatial scale:''' point sample |- | '..."

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----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! DMS/DMSP/DMSO cycling rates
|-
| '''Approach:''' isotope dilution with deuterated DMS/DMSP/DMSO standards; GC-MS detection
|-
| '''Context:''' ''in situ''
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' 4–12 h
|-
| '''Units:''' nM d<sup>-1</sup>; rate constants h<sup>-1</sup> or d<sup>-1</sup>
|-
| '''Community captured:''' all
|-
| '''Co-measurements:''' (none specified in inventory)
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Turnover rates among dimethylsulfoniopropionate (DMSP), dimethylsulfide (DMS), and dimethylsulfoxide (DMSO) are measured by isotope dilution. Deuterium-labelled standards (e.g., D<sub>3</sub>-DMSO, D<sub>6</sub>-DMSP) are added to seawater samples, and the rate of label appearance in product pools (e.g., D<sub>3</sub>-DMS from DMSO reduction) is tracked by GC-MS over a time course. Because the biological transformations process both labelled and unlabelled substrate simultaneously, the rate of label dilution (or appearance in the product pool) provides a direct measure of gross transformation rates. Both production and consumption of each compound can be quantified by combining multiple tracer experiments<ref name="Asher2016">Asher, E. C., Dacey, J. W. H., Ianson, D., Peña, A., & Tortell, P. D. (2016). Processes driving seasonal variability in DMS, DMSP, and DMSO concentrations and turnover in coastal Antarctic waters. ''Limnology and Oceanography'', 62(1), 104–124. https://doi.org/10.1002/lno.10379</ref>.

=== Scale of measurement ===

Point samples from 4–12 h incubations in sealed serum vials to prevent DMS outgassing during the experiment.

=== Data generated ===

First-order turnover rate constants (h<sup>-1</sup> or d<sup>-1</sup>) and gross production/consumption rates (nM d<sup>-1</sup>) for DMS, DMSP, and DMSO. These constrain the sulfur mass balance and the contribution of biological processes to sea-to-air DMS flux.

=== Units & currency ===

Units are nM d<sup>-1</sup> (rates) or h<sup>-1</sup> / d<sup>-1</sup> (rate constants). The currency is sulfur metabolite (DMS, DMSP, or DMSO).

=== Sample size ===

Typical samples are < 200 mL in volume.

=== Repositories & databases ===

== Limitations ==

The method assumes that intracellular and dissolved pools are at steady state during the incubation, and that the added deuterated standard equilibrates rapidly with the endogenous substrate pool. Bottle and incubation artifacts can alter the biological activity and DMS outgassing relative to ''in situ'' conditions. For field studies, it is currently uncertain whether measured rates are representative of the whole community or only specific taxa active under the incubation conditions.

== Example Applications & Protocols ==

=== Classic examples ===
* Asher et al. (2016) ''Processes driving seasonal variability in DMS, DMSP, and DMSO concentrations and turnover in coastal Antarctic waters'' <ref name="Asher2016" />

=== Recent applications ===
*

=== Common calculations/conversions ===
* Gross production rate = (dP<sub>labelled</sub>/dt) / f<sub>labelled</sub>; where P<sub>labelled</sub> is the concentration of labelled product and f<sub>labelled</sub> is the labelled fraction of the precursor pool.

== References ==

[[Category:Main Pages|Model types]]

32-P incorporation

2026-05-13T00:01:59Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Phosphate uptake (<sup>32</sup>P) |- | '''Approach:''' radiotracer (<sup>32</sup>P-phosphate) incubation |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- | '''Temporal sca..."

Reduction of phosphite to phosphate for growth (ptxABCD)

2026-05-12T23:59:39Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Phosphite utilization (ptxABCD) |- | '''Approach:''' culture growth assay with phosphite as sole P source |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' culture flask (point) |- | '''Te..."

Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity

2026-05-12T23:57:55Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! 5'-nucleotidase activity (5'NT) |- | '''Approach:''' radiolabelled ATP substrate assay |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- | '''Temporal scale:''' hours to da..."

Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)

2026-05-12T23:56:02Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! C-P lyase activity (CLA) |- | '''Approach:''' dansyl-labelled phosphonate substrate + HPLC fluorescence detection |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- | '''Tem..."

Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)

2026-05-12T23:54:30Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Phosphodiesterase activity (PDE) |- | '''Approach:''' fluorescent bis-MUF-phosphate substrate assay |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- | '''Temporal scale:''..."

Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)

2026-05-12T23:52:39Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Alkaline phosphatase activity (APA) |- | '''Approach:''' fluorescent MUF-phosphate substrate assay |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- | '''Temporal scale:'''..."

{{BreadcrumbsNutrients}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
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__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Alkaline phosphatase activity (APA)
|-
| '''Approach:''' fluorescent MUF-phosphate substrate assay
|-
| '''Context:''' incubation, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' mol fluorescent tag L<sup>-1</sup> h<sup>-1</sup>
|-
| '''Community captured:''' heterotrophs, microalgae
|-
| '''Co-measurements:''' cell abundance
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Alkaline phosphatase (AP) is an ectoenzyme that cleaves phosphate monoesters from dissolved organic phosphorus (DOP) compounds, releasing inorganic phosphate and making it available for uptake. APA is measured using 4-methylumbelliferyl phosphate (MUF-P) as a fluorogenic substrate: AP cleaves the phosphate group, releasing 4-methylumbelliferone (MUF), which fluoresces strongly (excitation ~365 nm, emission ~450 nm). The rate of MUF release over a time course is measured fluorimetrically in a flow-through fluorimeter or plate reader, and calibrated against a MUF standard curve to yield APA at saturating substrate concentration (V<sub>max</sub>). APA is a widely used indicator of phosphorus stress in marine phytoplankton and heterotrophic bacteria, as AP expression is strongly induced under inorganic phosphate (Pi) limitation.

The assay is commonly applied in both bulk mode (measuring community APA) or can reach single-cell resolution by flow cytometry using fluorescent MUF substrates added directly to seawater samples.

=== Scale of measurement ===

Sampling incubations after hours to days at ''in situ'' or controlled temperature.

=== Data generated ===

Potential APA rate at V<sub>max</sub> (mol MUF L<sup>-1</sup> h<sup>-1</sup>), reflecting the maximum enzymatic capacity for phosphate monoester hydrolysis. High APA is indicative of phosphorus stress.

=== Units & currency ===

Units are mol fluorescent tag L<sup>-1</sup> h<sup>-1</sup>. The currency is phosphorus.

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

Rates represent V<sub>max</sub> at saturating substrate and may substantially exceed ''in situ'' rates under sub-saturating ambient DOP concentrations. MUF-P is a proxy substrate for the full range of phosphate monoesters in natural waters. The assay does not distinguish between AP expressed by bacteria, phytoplankton, or released as dissolved extracellular enzymes.

== Example Applications & Protocols ==

=== Classic examples ===
* Hoppe (1983) ''Significance of exoenzymatic activities in the ecology of brackish water: measurements by means of methylumbelliferyl-substrates'' <ref name="Hoppe1983">Hoppe, H.-G. (1983). Significance of exoenzymatic activities in the ecology of brackish water: measurements by means of methylumbelliferyl-substrates. ''Marine Ecology Progress Series'', 11, 299–308.</ref>

=== Recent applications ===
* Su et al. (2023) ''A dataset of global ocean alkaline phosphatase activity'' <ref name="Su2023">Su, B., Song, X., Duhamel, S., Mahaffey, C., Davis, C., Ivančić, I., & Liu, J. (2023). A dataset of global ocean alkaline phosphatase activity. ''Scientific Data'', 10, 205. https://doi.org/10.1038/s41597-023-02081-7</ref>
* Thomson et al. (2020) ''Relative importance of phosphodiesterase vs. phosphomonoesterase activities for DOP hydrolysis in epi- and mesopelagic waters'' <ref name="Thomson2020">Thomson, B., Wenley, J., Lockwood, S., Twigg, I., Currie, K., Herndl, G. J., Hepburn, C. D., & Baltar, F. (2020). Relative importance of phosphodiesterase vs. phosphomonoesterase (alkaline phosphatase) activities for dissolved organic phosphorus hydrolysis in epi- and mesopelagic waters. ''Frontiers in Earth Science'', 8, 560893. https://doi.org/10.3389/feart.2020.560893</ref>

=== Common calculations/conversions ===
* APA (nmol MUF L<sup>-1</sup> h<sup>-1</sup>) = ΔRFU / incubation time / calibration slope; where calibration slope is from an MUF standard curve.

== References ==

[[Category:Main Pages|Model types]]

Degradation of dissolved organic nitrogen: Endopeptidase activity

2026-05-12T23:49:53Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Endopeptidase activity |- | '''Approach:''' fluorescent substrate assay (MCA-oligopeptide) |- | '''Context:''' lab incubation |- | '''Spatial scale:''' point sample |- | '''Temporal scale:''' hours to..."

Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity

2026-05-12T23:47:57Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Leucine-aminopeptidase activity |- | '''Approach:''' fluorescent substrate assay (MCA-Leu) |- | '''Context:''' lab incubation |- | '''Spatial scale:''' point sample |- | '''Temporal scale:''' hours to..."

{{BreadcrumbsNutrients}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Leucine-aminopeptidase activity
|-
| '''Approach:''' fluorescent substrate assay (MCA-Leu)
|-
| '''Context:''' lab incubation
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' nmol L<sup>-1</sup> h<sup>-1</sup>
|-
| '''Community captured:''' heterotrophic bacteria
|-
| '''Co-measurements:''' temperature, DOC, bacterial abundance
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Leucine-aminopeptidase (LAP) activity is measured using the fluorogenic substrate L-leucine-7-amido-4-methylcoumarin (MCA-Leu). When the substrate is cleaved by exopeptidase enzymes at the cell surface or in solution, it releases the fluorescent product 7-amino-4-methylcoumarin (MCA), which is measured fluorimetrically (excitation ~380 nm, emission ~440 nm) over a time course. The linear rate of fluorescence increase, calibrated against an MCA standard curve, yields the LAP hydrolysis rate at saturating substrate concentration (V<sub>max</sub>). LAP is a broadly distributed bacterial ectoenzyme that degrades peptide bonds in dissolved organic nitrogen compounds, releasing amino acids that can be directly assimilated.

=== Scale of measurement ===

Point sample using incubations of hours to days in the dark at ''in situ'' or controlled temperature.

=== Data generated ===

Potential LAP hydrolysis rate at V<sub>max</sub> (nmol MCA released L<sup>-1</sup> h<sup>-1</sup>). This reflects the maximum enzymatic capacity for leucyl-peptide bond cleavage in the community and is used as a proxy for the community's capacity to degrade proteinaceous dissolved organic nitrogen.

=== Units & currency ===

Units are nmol L<sup>-1</sup> h<sup>-1</sup>. The currency is carbon (nitrogen hydrolysis products contribute to the dissolved organic carbon and nitrogen pools).

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

Rates measured represent V<sub>max</sub> at saturating substrate, which may substantially overestimate ''in situ'' rates if ambient peptide concentrations are sub-saturating. Bottle effects can alter community composition during incubation. The synthetic MCA-Leu substrate is a proxy for natural peptides and may not be representative of the full range of substrates cleaved by LAP in situ.

== Example Applications & Protocols ==

=== Classic examples ===
* Hoppe (1983) ''Significance of exoenzymatic activities in the ecology of brackish water: measurements by means of methylumbelliferyl-substrates'' <ref name="Hoppe1983">Hoppe, H.-G. (1983). Significance of exoenzymatic activities in the ecology of brackish water: measurements by means of methylumbelliferyl-substrates. ''Marine Ecology Progress Series'', 11, 299–308.</ref>

=== Recent applications ===
* Thomson et al. (2020) ''Relative importance of phosphodiesterase vs. phosphomonoesterase activities for dissolved organic phosphorus hydrolysis in epi- and mesopelagic waters'' <ref name="Thomson2020">Thomson, B., Wenley, J., Lockwood, S., Twigg, I., Currie, K., Herndl, G. J., Hepburn, C. D., & Baltar, F. (2020). Relative importance of phosphodiesterase vs. phosphomonoesterase (alkaline phosphatase) activities for dissolved organic phosphorus hydrolysis in epi- and mesopelagic waters. ''Frontiers in Earth Science'', 8, 560893. https://doi.org/10.3389/feart.2020.560893</ref>

=== Common calculations/conversions ===
* LAP rate (nmol N L<sup>-1</sup> h<sup>-1</sup>) = Δ[MCA] / incubation time; calibrated from MCA standard curve.

== References ==

[[Category:Main Pages|Model types]]

13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)

2026-05-12T23:42:41Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Bacterial DOM assimilation (algal exudate tracing, nanoSIMS) |- | '''Approach:''' <sup>13</sup>C/<sup>15</sup>N-labelled algal exudates + nanoSIMS single-cell analysis |- | '''Context:''' lab incubati..."

{{BreadcrumbsNutrients}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Bacterial DOM assimilation (algal exudate tracing, nanoSIMS)
|-
| '''Approach:''' <sup>13</sup>C/<sup>15</sup>N-labelled algal exudates + nanoSIMS single-cell analysis
|-
| '''Context:''' lab incubations
|-
| '''Spatial scale:''' single cell
|-
| '''Temporal scale:''' hours to days
|-
| '''Units:''' µmol C or N L<sup>-1</sup> d<sup>-1</sup>; fmol cell<sup>-1</sup> d<sup>-1</sup> (single cell)
|-
| '''Community captured:''' heterotrophic bacteria
|-
| '''Co-measurements:''' temperature, DOC, bacterial abundance
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

Phytoplankton are labelled with <sup>13</sup>C-bicarbonate and <sup>15</sup>N-ammonium or -nitrate, and allowed to exude isotopically enriched dissolved organic matter (DOM) into the medium. This labelled algal exudate is then added to seawater containing heterotrophic bacteria, and the incorporation of <sup>13</sup>C and <sup>15</sup>N from algal-derived DOM into bacterial biomass is tracked over time. At the single-cell level, nanoSIMS measures the <sup>13</sup>C:<sup>12</sup>C and <sup>15</sup>N:<sup>14</sup>N ratios in individual bacterial cells, revealing which bacteria in the community are actively assimilating algal exudates and at what rate<ref name="Mayali2023">Mayali, X., Weber, P. K., Brodie, E. L., Mabery, S., Hoeprich, P. D., & Pett-Ridge, J. (2023). Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum. ''Nature Communications'', 14, 3516. https://doi.org/10.1038/s41467-023-41179-9</ref>. This approach links bacterial metabolic activity directly to algal DOM production at the single-cell level.

=== Scale of measurement ===

Single-cell resolution on incubations of hours to days. Lab-based method that requires controlled co-cultures or mesocosm incubations.

=== Data generated ===

Per-cell carbon and nitrogen assimilation rates from algal exudates (fmol cell<sup>-1</sup> d<sup>-1</sup>). The community-level transfer rate is obtained by multiplying per-cell rates by bacterial abundance. Identifies functional guilds of bacteria specialized in algal DOM assimilation.

=== Units & currency ===

Units are µmol L<sup>-1</sup> d<sup>-1</sup> (community) or fmol cell<sup>-1</sup> d<sup>-1</sup> (single cell). The currency is carbon and nitrogen.

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

The labelled exudate pool is a proxy for ''in situ'' algal DOM but may differ in composition from natural exudates. Low throughput of nanoSIMS analysis limits the number of cells measured. Isotope dilution from unlabelled background DOM reduces sensitivity, particularly over longer incubations.

== Example Applications & Protocols ==

=== Classic examples ===
* Mayali et al. (2023) ''Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum'' <ref name="Mayali2023" />

=== Recent applications ===
*

=== Common calculations/conversions ===
* Per-cell C assimilation rate = [(<sup>13</sup>C/<sup>12</sup>C)<sub>cell</sub> − (<sup>13</sup>C/<sup>12</sup>C)<sub>natural</sub>] / [(<sup>13</sup>C/<sup>12</sup>C)<sub>exudate</sub> − (<sup>13</sup>C/<sup>12</sup>C)<sub>natural</sub>] × C<sub>cell</sub> / incubation time.

== References ==

[[Category:Main Pages|Model types]]

FISH staining of anammox bacteria

2026-05-12T23:18:41Z

Hagi BucknWise: Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Anammox cell abundance (CARD-FISH) |- | '''Approach:''' catalyzed reporter deposition – fluorescence in situ hybridization (CARD-FISH) |- | '''Context:''' lab |- | '''Spatial scale:''' point sample..."