Data Types
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[1]. 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[2].
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[1].
This literature review, initiated by 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.
We have divided the inventory into four sections: Primary Production, Secondary Production, Nutrient Fluxes, and Interactions.
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Data Type Sections
Expand a section below to browse methods by type.
- 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
- Global optics-based
- Omics-based
- Nitrogen Uptake
- (15N-ρNO3-) uptake New Production
- Size-fractionated (15N-ρNO3-) uptake New Production
- 15N-ρNO3/chl a (N assimilation rate)
- Size-fractionated 15N-ρNO3/chl a (N assimilation rate)
- (15N-ρNH4+) uptake Regenerated Production
- Size-fractionated (15N-ρNH4+) uptake Regenerated Production
- (15N-ρurea) uptake Regenerated Production
- Size-fractionated (15N-ρurea) uptake Regenerated Production
- Nitrogen Assimilation
- [[Eukaryotic Assimilatory nitrate reductase, NAD(P)H dependent, Nitrate -> Nitrite, Nitrate (NR)]]
- Nitrification
- DIN inventory with inhibitors
- Inhibitors with 14 or 13CO2 uptake
- Nitrite oxidation (Nxr)
- amoA gene or transcript abundance
- Natural abundance of N and O isotopes in nitrate, nitrite and ammonium
- 15N tracers
- Denitrification
- Acetylene-block proxy for denitrifcation enzyme activity
- 15N tracer-based method
- N2:Ar ratio quantification
- Mass Balance
- Stoichiometric approach
- Natural Abundances of 15N and 18O
- Other Processes (DNRA, Anammox, DON)
- Isotopic measurements of 15NH4+ accumulation (DNRA)
- 15N tracers for anaerobic ammonium oxidation
- Functional gene quantification (hzs, hzo)
- FISH staining of anammox bacteria
- 13C- and 15N-labeled algal exudates with nanoSIMS
- Leucine-aminopeptidase activity measurement
- Endopeptidase activity measurement
- Degradation of dissolved organic phosphorus
- Alkaline phosphatase activity (APA)
- Phosphodiesterase activity (PDE)
- C-P lyase activity (CLA)
- 5'NT/5PN activity
- P nutrition
- 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
References
- ↑ 1.0 1.1 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
- ↑ 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