OceanWiki - User contributions [en]

Main Page

2026-02-25T05:07:26Z

Hagi BucknWise:

{{DISPLAYTITLE:Welcome to OceanWiki}}
'''While still under development, these are some of the exciting entries on models and measurements recently added by community members:'''<br>
[[Respiration from oxygen consumption: optodes]]<br>
[[Single Turnover Chlorophyll Fluorescence]]<br>
[[NifH amplicon sequence]]<br>
[[Net community production (NCP) - O₂/Ar]]<br>
[[PISCES]]<br>
[[Darwin]]<br>
[[CMIP]]<br>
[[Proteome Allocation Models]]

== Origin Story & Mission ==
Marine biogeochemistry needs a shared vocabulary between experimentalists and modelers for cross-disciplinary work to advance the field. Yet, to integrate disciplines successfully, researchers need to be vocal about discrepancy and uncertainty, and realize caveats of how values are determined. This community-driven collection of biogeochemical output began at the [https://biogeoscapes.org/ BioGeoScapes] modelling workshop and the following [https://www.primoscorwg.org PRiMO] session at Woods Hole Oceanographic Institution in September 2025. To highlight cross-discipline implications like ''What data was particularly helpful to inform a model?'' or ''How can a model help constrain experimental parameters?'', the idea arose to create a Wiki that provided a central repository for basic information related to interdisciplinary biogeochemistry science. This emerged as a way to address needs that have arisen in conversations specifically:
*defining key terms used across disciplines
*explain types of data generated by different methods, assumptions, and potential biases
*describe different types of models, required data inputs, computational demand, and limitations

== Content ==
'''OceanWiki''' is an encyclopedia of '''marine biogeochemistry''', and consists of three components:

=== [[:Category:Lexicon|Lexicon]] ===
A dictionary with definitions from both experimentalists, observationalists, and modelers.

=== [[Data Types]] ===
Types of data from experimental observations and how they are obtained, grouped by the process they investigate.
==== Primary Production ====
[[Photoautotrophy]] | [[Nitrogen Fixation]] | [[Phytoplankton C/N-Based Growth Rates]] | [[Chemoautotrophy]]
==== Secondary Production ====
[[Enzyme Activity]] | [[Growth Rate]] | [[Respiration]]
==== Nutrient Fluxes ====
[[Nitrogen]] | [[Phosphorous]] | [[Sulfur]] | [[Trace Metals]] | [[Biomineralization]]
==== Interactions ====
[[Grazing]] | [[Mixotrophy]] | [[Viruses]] | [[Allelopathy]] | [[Life cycles]]

=== [[Model Types]] ===
Types of models explained grouped by the scales they function at.
==== [[Cellular scale]] ====
[[Flux Balance Analysis]] | [[Proteome Allocation Models]] | [[Particle Simulation]] | [[Bio Particle Simulation]]
==== [[Biome scale]] ====
[[Community Flux Balance Analysis]] | [[GENOME]]
==== [[Global scale]] ====
[[CMIP]] | [[MARBL]] | [[Darwin]] | [[AWESOME-OCIM]] | [[PISCES]]

=== Teaching material ===

This was a suggestion from the BioGeoScapes leadership. If you are interested in leading the effort, please get in contact with one of us (see the bottom of [[How to contribute]]).

Main Page

2026-02-25T05:07:08Z

Hagi BucknWise:

{{DISPLAYTITLE:Welcome to OceanWiki}}
'''While still under development, these are some of the exciting entries on models and measurements recently added by community members:'''<br>
[[Respiration from oxygen consumption: optodes]]<br>
[[Single Turnover Chlorophyll Fluorescence]]<br>
[[NifH amplicon sequence]]<br>
[[Net community production (NCP) - O₂/Ar]]<br>
[[PISCES]]<br>
[[Darwin]]<br>
[[CMIP]]<br>
[[Proteome Allocation Models]]<br>

== Origin Story & Mission ==
Marine biogeochemistry needs a shared vocabulary between experimentalists and modelers for cross-disciplinary work to advance the field. Yet, to integrate disciplines successfully, researchers need to be vocal about discrepancy and uncertainty, and realize caveats of how values are determined. This community-driven collection of biogeochemical output began at the [https://biogeoscapes.org/ BioGeoScapes] modelling workshop and the following [https://www.primoscorwg.org PRiMO] session at Woods Hole Oceanographic Institution in September 2025. To highlight cross-discipline implications like ''What data was particularly helpful to inform a model?'' or ''How can a model help constrain experimental parameters?'', the idea arose to create a Wiki that provided a central repository for basic information related to interdisciplinary biogeochemistry science. This emerged as a way to address needs that have arisen in conversations specifically:
*defining key terms used across disciplines
*explain types of data generated by different methods, assumptions, and potential biases
*describe different types of models, required data inputs, computational demand, and limitations

== Content ==
'''OceanWiki''' is an encyclopedia of '''marine biogeochemistry''', and consists of three components:

=== [[:Category:Lexicon|Lexicon]] ===
A dictionary with definitions from both experimentalists, observationalists, and modelers.

=== [[Data Types]] ===
Types of data from experimental observations and how they are obtained, grouped by the process they investigate.
==== Primary Production ====
[[Photoautotrophy]] | [[Nitrogen Fixation]] | [[Phytoplankton C/N-Based Growth Rates]] | [[Chemoautotrophy]]
==== Secondary Production ====
[[Enzyme Activity]] | [[Growth Rate]] | [[Respiration]]
==== Nutrient Fluxes ====
[[Nitrogen]] | [[Phosphorous]] | [[Sulfur]] | [[Trace Metals]] | [[Biomineralization]]
==== Interactions ====
[[Grazing]] | [[Mixotrophy]] | [[Viruses]] | [[Allelopathy]] | [[Life cycles]]

=== [[Model Types]] ===
Types of models explained grouped by the scales they function at.
==== [[Cellular scale]] ====
[[Flux Balance Analysis]] | [[Proteome Allocation Models]] | [[Particle Simulation]] | [[Bio Particle Simulation]]
==== [[Biome scale]] ====
[[Community Flux Balance Analysis]] | [[GENOME]]
==== [[Global scale]] ====
[[CMIP]] | [[MARBL]] | [[Darwin]] | [[AWESOME-OCIM]] | [[PISCES]]

=== Teaching material ===

This was a suggestion from the BioGeoScapes leadership. If you are interested in leading the effort, please get in contact with one of us (see the bottom of [[How to contribute]]).

Main Page

2026-02-25T05:06:35Z

Hagi BucknWise:

{{DISPLAYTITLE:Welcome to OceanWiki}}
'''While still under development, these are some of the exciting entries on models and measurements recently added by community members:'''<br>
[[Respiration from oxygen consumption: optodes]]<br>
[[Single Turnover Chlorophyll Fluorescence]]<br>
[[NifH amplicon sequence]]<br>
[[O2:Ar]]
[[PISCES]]<br>
[[Darwin]]<br>
[[CMIP]]<br>
[[Proteome Allocation Models]]<br>

== Origin Story & Mission ==
Marine biogeochemistry needs a shared vocabulary between experimentalists and modelers for cross-disciplinary work to advance the field. Yet, to integrate disciplines successfully, researchers need to be vocal about discrepancy and uncertainty, and realize caveats of how values are determined. This community-driven collection of biogeochemical output began at the [https://biogeoscapes.org/ BioGeoScapes] modelling workshop and the following [https://www.primoscorwg.org PRiMO] session at Woods Hole Oceanographic Institution in September 2025. To highlight cross-discipline implications like ''What data was particularly helpful to inform a model?'' or ''How can a model help constrain experimental parameters?'', the idea arose to create a Wiki that provided a central repository for basic information related to interdisciplinary biogeochemistry science. This emerged as a way to address needs that have arisen in conversations specifically:
*defining key terms used across disciplines
*explain types of data generated by different methods, assumptions, and potential biases
*describe different types of models, required data inputs, computational demand, and limitations

== Content ==
'''OceanWiki''' is an encyclopedia of '''marine biogeochemistry''', and consists of three components:

=== [[:Category:Lexicon|Lexicon]] ===
A dictionary with definitions from both experimentalists, observationalists, and modelers.

=== [[Data Types]] ===
Types of data from experimental observations and how they are obtained, grouped by the process they investigate.
==== Primary Production ====
[[Photoautotrophy]] | [[Nitrogen Fixation]] | [[Phytoplankton C/N-Based Growth Rates]] | [[Chemoautotrophy]]
==== Secondary Production ====
[[Enzyme Activity]] | [[Growth Rate]] | [[Respiration]]
==== Nutrient Fluxes ====
[[Nitrogen]] | [[Phosphorous]] | [[Sulfur]] | [[Trace Metals]] | [[Biomineralization]]
==== Interactions ====
[[Grazing]] | [[Mixotrophy]] | [[Viruses]] | [[Allelopathy]] | [[Life cycles]]

=== [[Model Types]] ===
Types of models explained grouped by the scales they function at.
==== [[Cellular scale]] ====
[[Flux Balance Analysis]] | [[Proteome Allocation Models]] | [[Particle Simulation]] | [[Bio Particle Simulation]]
==== [[Biome scale]] ====
[[Community Flux Balance Analysis]] | [[GENOME]]
==== [[Global scale]] ====
[[CMIP]] | [[MARBL]] | [[Darwin]] | [[AWESOME-OCIM]] | [[PISCES]]

=== Teaching material ===

This was a suggestion from the BioGeoScapes leadership. If you are interested in leading the effort, please get in contact with one of us (see the bottom of [[How to contribute]]).

Main Page

2026-02-25T04:59:52Z

Hagi BucknWise:

{{DISPLAYTITLE:Welcome to OceanWiki}}
'''While still under development, check out some of the exciting entries on models and measurements recently added by community members:'''<br>
[[Respiration from oxygen consumption: optodes]]
[[PISCES]]

== Origin Story & Mission ==
Marine biogeochemistry needs a shared vocabulary between experimentalists and modelers for cross-disciplinary work to advance the field. Yet, to integrate disciplines successfully, researchers need to be vocal about discrepancy and uncertainty, and realize caveats of how values are determined. This community-driven collection of biogeochemical output began at the [https://biogeoscapes.org/ BioGeoScapes] modelling workshop and the following [https://www.primoscorwg.org PRiMO] session at Woods Hole Oceanographic Institution in September 2025. To highlight cross-discipline implications like ''What data was particularly helpful to inform a model?'' or ''How can a model help constrain experimental parameters?'', the idea arose to create a Wiki that provided a central repository for basic information related to interdisciplinary biogeochemistry science. This emerged as a way to address needs that have arisen in conversations specifically:
*defining key terms used across disciplines
*explain types of data generated by different methods, assumptions, and potential biases
*describe different types of models, required data inputs, computational demand, and limitations

== Content ==
'''OceanWiki''' is an encyclopedia of '''marine biogeochemistry''', and consists of three components:

=== [[:Category:Lexicon|Lexicon]] ===
A dictionary with definitions from both experimentalists, observationalists, and modelers.

=== [[Data Types]] ===
Types of data from experimental observations and how they are obtained, grouped by the process they investigate.
==== Primary Production ====
[[Photoautotrophy]] | [[Nitrogen Fixation]] | [[Phytoplankton C/N-Based Growth Rates]] | [[Chemoautotrophy]]
==== Secondary Production ====
[[Enzyme Activity]] | [[Growth Rate]] | [[Respiration]]
==== Nutrient Fluxes ====
[[Nitrogen]] | [[Phosphorous]] | [[Sulfur]] | [[Trace Metals]] | [[Biomineralization]]
==== Interactions ====
[[Grazing]] | [[Mixotrophy]] | [[Viruses]] | [[Allelopathy]] | [[Life cycles]]

=== [[Model Types]] ===
Types of models explained grouped by the scales they function at.
==== [[Cellular scale]] ====
[[Flux Balance Analysis]] | [[Proteome Allocation Models]] | [[Particle Simulation]] | [[Bio Particle Simulation]]
==== [[Biome scale]] ====
[[Community Flux Balance Analysis]] | [[GENOME]]
==== [[Global scale]] ====
[[CMIP]] | [[MARBL]] | [[Darwin]] | [[AWESOME-OCIM]] | [[PISCES]]

=== Teaching material ===

This was a suggestion from the BioGeoScapes leadership. If you are interested in leading the effort, please get in contact with one of us (see the bottom of [[How to contribute]]).

User:Hagi BucknWise

2026-02-18T20:13:10Z

Hagi BucknWise:

Please feel free to email me if you have any questions regarding how to contribute to the OceanWiki!
buckwies@usc.edu
[[File:P7273857.JPG|400px]]

User:Hagi BucknWise

2026-02-18T20:12:36Z

Hagi BucknWise:

Please feel free to email me if you have any questions regarding how to contribute to the OceanWiki!
buckwies@usc.edu
[[File:P7273857.JPG]]

File:P7273857.JPG

2026-02-18T20:11:25Z

Hagi BucknWise:

User:Hagi BucknWise

2026-02-18T20:00:11Z

Hagi BucknWise: Created page with "Please feel free to email me if you have any questions regarding how to contribute to the OceanWiki! buckwies@usc.edu"

Please feel free to email me if you have any questions regarding how to contribute to the OceanWiki!
buckwies@usc.edu

Main Page

2026-02-12T01:07:10Z

Hagi BucknWise:

{{DISPLAYTITLE:Welcome to OceanWiki}}
== Origin Story & Mission ==
Marine biogeochemistry needs a shared vocabulary between experimentalists and modelers for cross-disciplinary work to advance the field. Yet, to integrate disciplines successfully, researchers need to be vocal about discrepancy and uncertainty, and realize caveats of how values are determined. This community-driven collection of biogeochemical output began at the [https://biogeoscapes.org/ BioGeoScapes] modelling workshop and the following [https://www.primoscorwg.org PRiMO] session at Woods Hole Oceanographic Institution in September 2025. To highlight cross-discipline implications like ''What data was particularly helpful to inform a model?'' or ''How can a model help constrain experimental parameters?'', the idea arose to create a Wiki that provided a central repository for basic information related to interdisciplinary biogeochemistry science. This emerged as a way to address needs that have arisen in conversations specifically:
*defining key terms used across disciplines
*explain types of data generated by different methods, assumptions, and potential biases
*describe different types of models, required data inputs, computational demand, and limitations

== Content ==
'''OceanWiki''' is an encyclopedia of '''marine biogeochemistry''', and consists of three components:

=== [[:Category:Lexicon|Lexicon]] ===
A dictionary with definitions from both experimentalists, observationalists, and modelers.

=== [[Data Types]] ===
Types of data from experimental observations and how they are obtained, grouped by the process they investigate.
==== Primary Production ====
[[Photoautotrophy]] | [[Nitrogen Fixation]] | [[Phytoplankton C/N-Based Growth Rates]] | [[Chemoautotrophy]]
==== Secondary Production ====
[[Enzyme Activity]] | [[Growth Rate]] | [[Respiration]]
==== Nutrient Fluxes ====
[[Nitrogen]] | [[Phosphorous]] | [[Sulfur]] | [[Trace Metals]] | [[Biomineralization]]
==== Interactions ====
[[Grazing]] | [[Mixotrophy]] | [[Viruses]] | [[Allelopathy]] | [[Life cycles]]

=== [[Model Types]] ===
Types of models explained grouped by the scales they function at.
==== [[Cellular scale]] ====
[[Flux Balance Analysis]] | [[Proteome Allocation Models]] | [[Particle Simulation]] | [[Bio Particle Simulation]]
==== [[Biome scale]] ====
[[Community Flux Balance Analysis]] | [[GENOME]]
==== [[Global scale]] ====
[[CMIP]] | [[MARBL]] | [[Darwin]] | [[AWESOME-OCIM]]

These pages contain definitions, limitations, context, and references.<br>
They are populated by researchers, naming responsible authors for context and credit.

=== Teaching material ===

This was a suggestion from the BioGeoScapes leadership and we are working on incorporating it.

Phytoplankton

2026-02-11T19:54:05Z

Hagi BucknWise:

Phytoplankton are microscopic plant-like organisms that dominate photosynthetic primary production in the ocean<ref>Falkowski, P. Ocean Science: The power of plankton. Nature 483, S17–S20 (2012). https://doi.org/10.1038/483S17a</ref>. Phylogenetically, phytoplankton comprises both bacterial groups such as the cyanobacteria [[Synechococcus]] and [[Prochlorococcus]], and unicellular eukaryotic groups<ref name="Liu & Levine 2021">Liu, X., Levine, N. M. Ecosystem implications of fine-scale frontal disturbances in the oligotrophic ocean – An idealized modeling approach. Progress in Oceanography 192 (2021) https://doi.org/10.1016/j.pocean.2021.102519</ref>. Operationally, modelers differentiate between [[picophytoplankton]], which dominates [[oligotrophic]] regions, and [[microphytoplankton]], which is more abundant in nutrient-rich areas like [[upwelling]] regions and the [[polar oceans]]<ref name="Liu & Levine 2021"/>.

=== References ===

[[Category:Lexicon]]

Model Types

2026-02-11T19:49:18Z

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

== References ==
<references />

NifH amplicon sequence

2026-02-11T19:45:57Z

Hagi BucknWise:

{{BreadcrumbsNFixation}}

* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Chreaa|Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' Sequencing
|-
| '''Context:''' ''Environmental'', incubation
|-
| '''Spatial scale:''' stations, across oceans
|-
| '''Temporal scale:''' days, seasons
|-
| '''Units:'''
|-
| '''Community captured:''' all, can be size-fractionated
|-
| '''Co-measurements:'''

|}
</div>
<div style="clear:both"></div>

== Method Overview ==
nifH amplicon sequencing targets the nifH gene, which encodes the iron protein subunit of nitrogenase and is widely used as a functional marker for biological nitrogen fixation. Environmental DNA is extracted, the nifH gene is amplified a nested PCR approach with degenerate primers (outer primers: NifH3 and NifH4 and inner primers: NifH1 and NifH2), and amplicons are sequenced (typically via high-throughput sequencing). Resulting sequences are used to assess the diversity, composition, and relative abundance of diazotrophic microorganisms across environments.

== Output ==
* nifH amplicon sequence variants (ASVs) or operational taxonomic units (OTUs)
* Taxonomic or phylogenetic assignment of diazotrophs
* Relative abundance profiles of nifH variants

=== Scale of measurement ===
* Molecular / gene-level
* Semi-quantitative (relative abundance, not absolute gene copy number unless combined with qPCR)
* Community-level inference of functional potential

=== Data generated ===
* DNA sequence reads (FASTQ files)
* ASV or OTU tables
* Phylogenetic trees (commonly used for nifH)
* Metadata-linked abundance matrices

=== Units & currency ===
* Sequence counts or relative abundance (%)
* Reads per sample

=== Sample size ===
* Varies by study design
* Commonly:
o 10–100 environmental samples
o Thousands to millions of reads per sequencing run
* Replication often includes biological and technical replicates

=== Repositories & databases ===
* nFixDB – curated nifH sequences and annotations
* NCBI GenBank – raw nifH sequences
* ENA / SRA – raw sequencing reads
* IMG/M – integrated microbial genomes and marker genes

e.g. [https://github.com/raw-lab/NFixDB nFixDB]

== Limitations ==
* Primer bias due to high nifH sequence diversity
* Degenerate primers can amplify non-target genes
* Does not directly measure nitrogen fixation activity
* Limited taxonomic resolution for some diazotroph groups
* Horizontal gene transfer complicates phylogenetic interpretation

== Example Applications & Protocols ==

=== Classic examples ===
* Zehr & McReynolds (1989) – First use of nifH as a molecular marker for diazotrophs <ref>Zehr, J. P., & McReynolds, L. A. (1989). Use of degenerate oligonucleotides for amplification of the nifH gene. Applied and Environmental Microbiology.</ref>
* Zehr et al. (2003) – nifH diversity in marine environments <ref>Zehr, J. P., et al. (2003). Global distribution and diversity of nitrogen-fixing microorganisms. Nature.</ref>
* Gaby & Buckley (2012) – Evaluation of nifH primers and phylogeny <ref>Gaby, J. C., & Buckley, D. H. (2012). A comprehensive evaluation of PCR primers to amplify the nifH gene. PLOS ONE.</ref>

=== Common calculations/conversions ===
* Relative abundance = (reads per nifH ASV) / (total nifH reads per sample)
* Rarefaction to standardize sequencing depth
* Conversion of read counts to proportions (%)
* Phylogenetic clustering (e.g., nifH clusters I–IV)

== References ==

NifH amplicon sequence

2026-02-11T19:45:00Z

Hagi BucknWise:

{{BreadcrumbsNFixation}}

* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Chreaa|Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' Sequencing
|-
| '''Context:''' ''Environmental'', incubation
|-
| '''Spatial scale:''' stations, across oceans
|-
| '''Temporal scale:''' days, seasons
|-
| '''Units:'''
|-
| '''Community captured:''' all, can be size-fractionated
|-
| '''Co-measurements:'''

|}
</div>
<div style="clear:both"></div>

== Method Overview ==
nifH amplicon sequencing targets the nifH gene, which encodes the iron protein subunit of nitrogenase and is widely used as a functional marker for biological nitrogen fixation. Environmental DNA is extracted, the nifH gene is amplified a nested PCR approach with degenerate primers (outer primers: NifH3 and NifH4 and inner primers: NifH1 and NifH2), and amplicons are sequenced (typically via high-throughput sequencing). Resulting sequences are used to assess the diversity, composition, and relative abundance of diazotrophic microorganisms across environments.

== Output ==
* nifH amplicon sequence variants (ASVs) or operational taxonomic units (OTUs)
* Taxonomic or phylogenetic assignment of diazotrophs
* Relative abundance profiles of nifH variants

=== Scale of measurement ===
* Molecular / gene-level
* Semi-quantitative (relative abundance, not absolute gene copy number unless combined with qPCR)
* Community-level inference of functional potential

=== Data generated ===
* DNA sequence reads (FASTQ files)
* ASV or OTU tables
* Phylogenetic trees (commonly used for nifH)
* Metadata-linked abundance matrices

=== Units & currency ===
* Sequence counts or relative abundance (%)
* Reads per sample

=== Sample size ===
* Varies by study design
* Commonly:
o 10–100 environmental samples<br>
o Thousands to millions of reads per sequencing run<br>
* Replication often includes biological and technical replicates

=== Repositories & databases ===
* nFixDB – curated nifH sequences and annotations
* NCBI GenBank – raw nifH sequences
* ENA / SRA – raw sequencing reads
* IMG/M – integrated microbial genomes and marker genes

e.g. [https://github.com/raw-lab/NFixDB nFixDB]

== Limitations ==
* Primer bias due to high nifH sequence diversity
* Degenerate primers can amplify non-target genes
* Does not directly measure nitrogen fixation activity
* Limited taxonomic resolution for some diazotroph groups
* Horizontal gene transfer complicates phylogenetic interpretation

== Example Applications & Protocols ==

=== Classic examples ===
* Zehr & McReynolds (1989) – First use of nifH as a molecular marker for diazotrophs <ref>Zehr, J. P., & McReynolds, L. A. (1989). Use of degenerate oligonucleotides for amplification of the nifH gene. Applied and Environmental Microbiology.</ref>
* Zehr et al. (2003) – nifH diversity in marine environments <ref>Zehr, J. P., et al. (2003). Global distribution and diversity of nitrogen-fixing microorganisms. Nature.</ref>
* Gaby & Buckley (2012) – Evaluation of nifH primers and phylogeny <ref>Gaby, J. C., & Buckley, D. H. (2012). A comprehensive evaluation of PCR primers to amplify the nifH gene. PLOS ONE.</ref>

=== Common calculations/conversions ===
* Relative abundance = (reads per nifH ASV) / (total nifH reads per sample)
* Rarefaction to standardize sequencing depth
* Conversion of read counts to proportions (%)
* Phylogenetic clustering (e.g., nifH clusters I–IV)

== References ==

NifH amplicon sequence

2026-02-11T19:42:23Z

Hagi BucknWise:

{{BreadcrumbsNFixation}}

* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Chreaa|Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' Sequencing
|-
| '''Context:''' ''Environmental'', incubation
|-
| '''Spatial scale:''' stations, across oceans
|-
| '''Temporal scale:''' days, seasons
|-
| '''Units:'''
|-
| '''Community captured:''' all, can be size-fractionated
|-
| '''Co-measurements:'''

|}
</div>
<div style="clear:both"></div>

== Method Overview ==
nifH amplicon sequencing targets the nifH gene, which encodes the iron protein subunit of nitrogenase and is widely used as a functional marker for biological nitrogen fixation. Environmental DNA is extracted, the nifH gene is amplified a nested PCR approach with degenerate primers (outer primers: NifH3 and NifH4 and inner primers: NifH1 and NifH2), and amplicons are sequenced (typically via high-throughput sequencing). Resulting sequences are used to assess the diversity, composition, and relative abundance of diazotrophic microorganisms across environments.

== Output ==
* nifH amplicon sequence variants (ASVs) or operational taxonomic units (OTUs)
* Taxonomic or phylogenetic assignment of diazotrophs
* Relative abundance profiles of nifH variants

=== Scale of measurement ===
• Molecular / gene-level
• Semi-quantitative (relative abundance, not absolute gene copy number unless combined with qPCR)
• Community-level inference of functional potential

=== Data generated ===
• DNA sequence reads (FASTQ files)
• ASV or OTU tables
• Phylogenetic trees (commonly used for nifH)
• Metadata-linked abundance matrices

=== Units & currency ===
• Sequence counts or relative abundance (%)
• Reads per sample

=== Sample size ===
• Varies by study design
• Commonly:
o 10–100 environmental samples
o Thousands to millions of reads per sequencing run
• Replication often includes biological and technical replicates

=== Repositories & databases ===
• nFixDB – curated nifH sequences and annotations
• NCBI GenBank – raw nifH sequences
• ENA / SRA – raw sequencing reads
• IMG/M – integrated microbial genomes and marker genes

e.g. [https://github.com/raw-lab/NFixDB nFixDB]

== Limitations ==
• Primer bias due to high nifH sequence diversity
• Degenerate primers can amplify non-target genes
• Does not directly measure nitrogen fixation activity
• Limited taxonomic resolution for some diazotroph groups
• Horizontal gene transfer complicates phylogenetic interpretation

== Example Applications & Protocols ==

=== Classic examples ===
* Zehr & McReynolds (1989) – First use of nifH as a molecular marker for diazotrophs <ref>Zehr, J. P., & McReynolds, L. A. (1989). Use of degenerate oligonucleotides for amplification of the nifH gene. Applied and Environmental Microbiology.</ref>
* Zehr et al. (2003) – nifH diversity in marine environments <ref>Zehr, J. P., et al. (2003). Global distribution and diversity of nitrogen-fixing microorganisms. Nature.</ref>
* Gaby & Buckley (2012) – Evaluation of nifH primers and phylogeny <ref>Gaby, J. C., & Buckley, D. H. (2012). A comprehensive evaluation of PCR primers to amplify the nifH gene. PLOS ONE.</ref>

=== Common calculations/conversions ===
• Relative abundance = (reads per nifH ASV) / (total nifH reads per sample)
• Rarefaction to standardize sequencing depth
• Conversion of read counts to proportions (%)
• Phylogenetic clustering (e.g., nifH clusters I–IV)

== References ==

NifH amplicon sequence

2026-02-11T19:41:09Z

Hagi BucknWise:

{{BreadcrumbsNFixation}}

* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Chreaa|Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' Sequencing
|-
| '''Context:''' ''Environmental'', incubation
|-
| '''Spatial scale:''' stations, across oceans
|-
| '''Temporal scale:''' days, seasons
|-
| '''Units:'''
|-
| '''Community captured:''' all, can be size-fractionated
|-
| '''Co-measurements:'''

|}
</div>
<div style="clear:both"></div>

== Method Overview ==
nifH amplicon sequencing targets the nifH gene, which encodes the iron protein subunit of nitrogenase and is widely used as a functional marker for biological nitrogen fixation. Environmental DNA is extracted, the nifH gene is amplified a nested PCR approach with degenerate primers (outer primers: NifH3 and NifH4 and inner primers: NifH1 and NifH2), and amplicons are sequenced (typically via high-throughput sequencing). Resulting sequences are used to assess the diversity, composition, and relative abundance of diazotrophic microorganisms across environments.

== Output ==
• nifH amplicon sequence variants (ASVs) or operational taxonomic units (OTUs)
• Taxonomic or phylogenetic assignment of diazotrophs
• Relative abundance profiles of nifH variants

=== Scale of measurement ===
• Molecular / gene-level
• Semi-quantitative (relative abundance, not absolute gene copy number unless combined with qPCR)
• Community-level inference of functional potential

=== Data generated ===
• DNA sequence reads (FASTQ files)
• ASV or OTU tables
• Phylogenetic trees (commonly used for nifH)
• Metadata-linked abundance matrices

=== Units & currency ===
• Sequence counts or relative abundance (%)
• Reads per sample

=== Sample size ===
• Varies by study design
• Commonly:
o 10–100 environmental samples
o Thousands to millions of reads per sequencing run
• Replication often includes biological and technical replicates

=== Repositories & databases ===
• nFixDB – curated nifH sequences and annotations
• NCBI GenBank – raw nifH sequences
• ENA / SRA – raw sequencing reads
• IMG/M – integrated microbial genomes and marker genes

e.g. [https://github.com/raw-lab/NFixDB nFixDB]

== Limitations ==
• Primer bias due to high nifH sequence diversity
• Degenerate primers can amplify non-target genes
• Does not directly measure nitrogen fixation activity
• Limited taxonomic resolution for some diazotroph groups
• Horizontal gene transfer complicates phylogenetic interpretation

== Example Applications & Protocols ==

=== Classic examples ===
• Zehr & McReynolds (1989) – First use of nifH as a molecular marker for diazotrophs <ref>Zehr, J. P., & McReynolds, L. A. (1989). Use of degenerate oligonucleotides for amplification of the nifH gene. Applied and Environmental Microbiology.</ref>
• Zehr et al. (2003) – nifH diversity in marine environments <ref>Zehr, J. P., et al. (2003). Global distribution and diversity of nitrogen-fixing microorganisms. Nature.</ref>
• Gaby & Buckley (2012) – Evaluation of nifH primers and phylogeny <ref>Gaby, J. C., & Buckley, D. H. (2012). A comprehensive evaluation of PCR primers to amplify the nifH gene. PLOS ONE.</ref>

=== Common calculations/conversions ===
• Relative abundance = (reads per nifH ASV) / (total nifH reads per sample)
• Rarefaction to standardize sequencing depth
• Conversion of read counts to proportions (%)
• Phylogenetic clustering (e.g., nifH clusters I–IV)

== References ==

NifH amplicon sequence

2026-02-11T19:40:31Z

Hagi BucknWise:

{{BreadcrumbsNFixation}}

* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Chreaa|Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' Sequencing
|-
| '''Context:''' ''Environmental'', incubation
|-
| '''Spatial scale:''' stations, across oceans
|-
| '''Temporal scale:''' days, seasons
|-
| '''Units:'''
|-
| '''Community captured:''' all, can be size-fractionated
|-
| '''Co-measurements:'''

|}
</div>
<div style="clear:both"></div>

== Method Overview ==
nifH amplicon sequencing targets the nifH gene, which encodes the iron protein subunit of nitrogenase and is widely used as a functional marker for biological nitrogen fixation. Environmental DNA is extracted, the nifH gene is amplified a nested PCR approach with degenerate primers (outer primers: NifH3 and NifH4 and inner primers: NifH1 and NifH2), and amplicons are sequenced (typically via high-throughput sequencing). Resulting sequences are used to assess the diversity, composition, and relative abundance of diazotrophic microorganisms across environments.

== Output ==
• nifH amplicon sequence variants (ASVs) or operational taxonomic units (OTUs)
• Taxonomic or phylogenetic assignment of diazotrophs
• Relative abundance profiles of nifH variants

=== Scale of measurement ===
• Molecular / gene-level
• Semi-quantitative (relative abundance, not absolute gene copy number unless combined with qPCR)
• Community-level inference of functional potential

=== Data generated ===
• DNA sequence reads (FASTQ files)
• ASV or OTU tables
• Phylogenetic trees (commonly used for nifH)
• Metadata-linked abundance matrices

=== Units & currency ===
• Sequence counts or relative abundance (%)
• Reads per sample

=== Sample size ===
• Varies by study design
• Commonly:
o 10–100 environmental samples
o Thousands to millions of reads per sequencing run
• Replication often includes biological and technical replicates

=== Repositories & databases ===
• nFixDB – curated nifH sequences and annotations
• NCBI GenBank – raw nifH sequences
• ENA / SRA – raw sequencing reads
• IMG/M – integrated microbial genomes and marker genes

e.g. [https://github.com/raw-lab/NFixDB nFixDB]

== Limitations ==
• Primer bias due to high nifH sequence diversity
• Degenerate primers can amplify non-target genes
• Does not directly measure nitrogen fixation activity
• Limited taxonomic resolution for some diazotroph groups
• Horizontal gene transfer complicates phylogenetic interpretation

== Example Applications & Protocols ==

=== Classic examples ===
• Zehr & McReynolds (1989) – First use of nifH as a molecular marker for diazotrophs <ref>Zehr, J. P., & McReynolds, L. A. (1989). Use of degenerate oligonucleotides for amplification of the nifH gene. Applied and Environmental Microbiology.</ref>
• Zehr et al. (2003) – nifH diversity in marine environments <ref>Zehr, J. P., et al. (2003). Global distribution and diversity of nitrogen-fixing microorganisms. Nature.</ref>
• Gaby & Buckley (2012) – Evaluation of nifH primers and phylogeny <ref>Gaby, J. C., & Buckley, D. H. (2012). A comprehensive evaluation of PCR primers to amplify the nifH gene. PLOS ONE.</ref>

=== Common calculations/conversions ===
• Relative abundance = (reads per nifH ASV) / (total nifH reads per sample)
• Rarefaction to standardize sequencing depth
• Conversion of read counts to proportions (%)
• Phylogenetic clustering (e.g., nifH clusters I–IV)

== References ==

• Zehr, J. P., & McReynolds, L. A. (1989). Use of degenerate oligonucleotides for amplification of the nifH gene. Applied and Environmental Microbiology.
• Zehr, J. P., et al. (2003). Global distribution and diversity of nitrogen-fixing microorganisms. Nature.
• Gaby, J. C., & Buckley, D. H. (2012). A comprehensive evaluation of PCR primers to amplify the nifH gene. PLOS ONE.

Model wiki template

2026-02-03T12:55:38Z

Hagi BucknWise:

{{BreadcrumbsCellular}}

* [[Page authors|Page authors]]: [[User:]]
* [[Responsible curator|Responsible curator]]: [[User:]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! Model type
|-
| '''Approach:''' Statistical, Mechanistic optimized, or Mechanistic time-dependent
|-
| '''Computational demand:''' Local or HPC
|-
| '''Typical physical scales:''' grid: e.g. μm, L, ocean basin

domain:
|-
| '''Appropriate timescales:''' time step: e.g. s, h, day, steady-state

output:
|}
</div>
<div style="clear:both"></div>

== Model overview ==

== Scales of interest ==

== Data inputs ==

== Example Studies & Code ==

=== Classic examples ===

=== Recent applications ===

== Limitations ==

== References ==

[[Category:Main Pages|Model types]]

14-Carbon uptake (NPP)

2026-02-02T21:51:45Z

Hagi BucknWise: Created page with "{{DISPLAYTITLE:<sup>14</sup>C-carbon uptake (NPP)}}"

Life cycles

2026-02-02T21:50:06Z

Hagi BucknWise: Created page with "*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)"

*[[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)]]

Allelopathy

2026-02-02T21:49:25Z

Hagi BucknWise: Created page with "*Filtrate cross-culturing *Size-fractionated extract spiking"

*[[Filtrate cross-culturing]]
*[[Size-fractionated extract spiking]]

Viruses

2026-02-02T21:48:52Z

Hagi BucknWise: Created page with "*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)"

*[[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)]]

Mixotrophy

2026-02-02T21:47:32Z

Hagi BucknWise: Created page with "*LysoTracker Green Incorporation *15N/13C-labelled DOM/cells *Bead consumption rates by cells with chloroplasts *BrdU-labeled prey incorporation into things with chloroplasts"

*[[LysoTracker Green Incorporation]]
*[[15N/13C-labelled DOM/cells]]
*[[Bead consumption rates by cells with chloroplasts]]
*[[BrdU-labeled prey incorporation into things with chloroplasts]]

Grazing

2026-02-02T21:46:25Z

Hagi BucknWise: Created page with "===Microzooplankton on phyto loss process=== *Incubation dilution experiments *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"

===Microzooplankton on phyto loss process===
*[[Incubation dilution experiments]]
*[[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]]

Biomineralization

2026-02-02T21:36:52Z

Hagi BucknWise: Created page with "===Silicon=== *Silicon uptake *Kinetics of silicon uptake *Silica production *Silica production - PDMPO *Biogenic silica accumulation ===Calcification (coccolithophore and other calcifiers)=== *Calcification (13-Carbon uptake)"

===Silicon===
*[[Silicon uptake]]
*[[Kinetics of silicon uptake]]
*[[Silica production]]
*[[Silica production - PDMPO]]
*[[Biogenic silica accumulation]]

===Calcification (coccolithophore and other calcifiers)===
*[[Calcification (13-Carbon uptake)]]

Trace Metals

2026-02-02T21:33:57Z

Hagi BucknWise:

*[[55-Iron uptake]]
*[[54-Manganese uptake]]
*[[67-Copper (half-life 62 h; incubation) & 64-Cu (half-life 12.7 h; lab) uptake]]
*[[Cobalamin uptake with 57Cobalt-B12]]

Sulfur

2026-02-02T21:32:20Z

Hagi BucknWise:

*[[DMS/P/O cycling]]
*[[Rates of DMSO reduction to DMS]]
*[[Rates of DMS and DMSP oxidation to DMSO]]

Phosphorus

2026-02-02T21:30:44Z

Hagi BucknWise:

===Degradation of dissolved organic phosphorous===
*[[Degradation of dissolved organic phosphorus (P-monoesters): Alkaline phosphatase activity (APA)]]
*[[Degradation of dissolved organic phosphorus (P-diesters): Phosphodiesterase activity (PDE)]]
*[[Degradation of dissolved organic phosphorus (phosphonates): C-P lyase activity (CLA)]]
*[[Cleavage of phosphate from 5'-nucleotides: 5'NT/5PN activity]]

===P nutrition===
*[[Reduction of phosphite to phosphate for growth (ptxABCD)]]
*[[32-P incorporation]]

Nitrogen

2026-02-02T21:27:39Z

Hagi BucknWise:

===Nitrogen Uptake===
*[[(15N-ρNO3-) uptake New Production]]
*[[(15N-ρNO3-) uptake New Production]]
*[[15N-ρNO3/chl a (N assimilation rate)]]
*[[15N-ρNO3/chl a (N assimilation rate)]]
*[[(15N-ρNH4+) uptake Regenerated Production]]
*[[(15N-ρNH4+) uptake Regenerated Production]]
*[[(15N-ρurea) uptake Regenerated Production]]
*[[(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]]

===Dissimilatory Nitrate Reduction to Ammonium===
*[[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation]]

===Anaerobic Ammonium Oxidation===
*[[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)]]
*[[Functional gene quantification (hzs, hzo)]]
*[[FISH staining of anammox bacteria]]

===Bacterial Assimilation & Remineralization===
*[[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)]]
*[[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity]]
*[[Degradation of dissolved organic nitrogen: Endopeptidase activity ]]

Nitrogen

2026-02-02T21:26:43Z

Hagi BucknWise:

===Nitrogen Uptake===
*[[(15N-ρNO3-) uptake New Production]]
*[[(15N-ρNO3-) uptake New Production]]
*[[15N-ρNO3/chl a (N assimilation rate)]]
*[[15N-ρNO3/chl a (N assimilation rate)]]
*[[(15N-ρNH4+) uptake Regenerated Production]]
*[[(15N-ρNH4+) uptake Regenerated Production]]
*[[(15N-ρurea) uptake Regenerated Production]]
*[[(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]]

===Dissimilatory Nitrate Reduction to Ammonium===
*[[Isotopic measurements---15N-labeled ammonium (15NH4+) accumulation rate in 15NO3- added incubation]]

===Anaerobic Ammonium Oxidation===
*[[15N tracers (15N labeled gases upon addition of 15NO3, 15NO2, or 15NH4)]]
*[[Functional gene quantification (hzs, hzo)]]
*[[FISH staining of anammox bacteria]]

===Bacterial Assimilation & Remineralization===
*[[13C- and 15N-labeled algal exudates (isotope tracing & nanoSIMS)]]
*[[Degradation of dissolved organic nitrogen: Leucine-aminopeptidase activity]]
*[[Degradation of dissolved organic nitrogen: Endopeptidase activity ]]

Dark 14C-bicarbonate fixation

2026-02-02T21:18:23Z

Hagi BucknWise: Created page with "{{DISPLAYTITLE:Dark <sup>14</sup>C-bicarbonate fixation}}"

Chemoautotrophy

2026-02-02T21:17:34Z

Hagi BucknWise:

*[[mass balance approach]]
*[[Dark 14C-bicarbonate fixation]]
*[[nano SIP]]

Phytoplankton C/N-Based Growth Rates

2026-02-02T21:16:37Z

Hagi BucknWise:

*[[Carbon content]]
*[[Nitrogen content]]

H2 supersaturation

2026-02-02T21:15:20Z

Hagi BucknWise:

H2 supersaturation

2026-02-02T21:14:11Z

Hagi BucknWise: Created page with "{DISPLAYTITLE:H<sub>2</sub> supersaturation}"

{DISPLAYTITLE:H<sub>2</sub> supersaturation}

Nitrogen Fixation

2026-02-02T21:13:24Z

Hagi BucknWise:

*[[Bulk uptake 15N2]]
*[[Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)]]
*[[Acetylene Reduction Assays (ARA)]]
*[[nifH detection/quantification (qPCR, RT-qPCR; nifH database)]]
*[[nifH amplicon sequence]]
*[[H2 supersaturation]]
*[[Nitrogenase quantification]]
*[[Other diazotroph marker genes: nifD, nifK]]

Respiration

2026-02-02T21:09:33Z

Hagi BucknWise:

*[[Respiration from BGC-Argo floats and AOU]]
*[[Respiration from oxygen consumption]]
*[[Respiration from activity of respiratory chain: enzymatic assays]]
*[[Respiration from activity of respiratory chain: redoxsensor green]]
*[[Respiration from oxygen consumption]]

Growth Rate

2026-02-02T21:08:04Z

Hagi BucknWise:

*[[Growth rate from biomass observation]]
*[[Radiolabeled tracer method]]

Enzyme Activity

2026-02-02T21:06:26Z

Hagi BucknWise:

*[[Enzyme assay with fluoresceinamine labeled biopolymers]]
*[[Enzyme assay with RBB labeled polysaccharides]]
*[[Enzyme assay with DNS]]
*[[Enzyme assay/alkaline phosphatase with fluorescently labeled substrate]]

Trace Metals

2026-02-02T20:59:04Z