== How to help ==

Oceancyclopedia is built by scientists, undergrad to emeritus, like you, and there are tons of ways to help!

If you're interested in getting involved but not sure where to start, we'd recommend joining our email list by filling out our interest form: [[OceanWiki Interest Form]]. We'll keep you updated with emails, high priority orphaned pages, wiki 'hackathons', sections in need of curators, or whatever else comes up. Emails will be infrequent!

__TOC__

== Contribute to a page ==

Each page was written by a human expert on the topic. If there's a topic you feel qualified to speak on, or have been interested in recently, contribute to it! You can edit existing pages or start a new one. There are currently tons of blank pages, which we hope will help prompt content. Any red link is an uncreated page waiting for someone to take it on, and if you're interested in it, that person could be you.

If you need to upload an image or some sort of media, use [[Special:Upload|Upload a file]], then reference it in your text as [[imageName.png|thumb|caption]].

=== Hierarchy of contribution ===

Generally, the content on each page was written by the [[#Page authors| Page authors]]. Each page was curated by the [[#Responsible curator|Responsible curator]], who may have also reached out to authors to ask for their contributions. If you are interested in being a curator, please contact the section curator or one of the main website admins for assistance and more information. If you're interested in authoring a page, go for it! If you would like support, please feel free to add tags next to your name as page author (e.g., 'Need coauthor', 'Undergrad', 'Junior author'), or reach out to the section curator.

==== Page authors ====

==== Responsible curator ====

==== Making your user page ====

When adding yourself as an author or curator, it would be great to also create your own user page (so that your name shows up as blue instead of red). If you have an ORCiD ID, please include that information on your user page so that readers can learn more about the author's background.

=== Lexicon ===

Contribute a definition! These, ideally, are a paragraph or less, and could include graphics. It is totally fine, and even good, to contribute a definition that (kindly) conflicts with a pre-existing one and to highlight disagreements or inconsistent usage of terminology.

=== Data wiki ===

See [[Data wiki template]] for a blank template to use for new page generation.

=== Model wiki ===

See [[Model wiki template]] for a blank template to use for new page generation.

=== Organization ===

When making a new category for the Breadcrumbs extension, you must create the new Template page and enter the navigation information, as shown in [[Template:BreadcrumbsPhotoautotrophy]] or [[Template:BreadcrumbsCellular]]. If you need to make a new Breadcrumbs category, start by making the actual page of interest using one of the templates above. You'll notice that the first line for both data and model wiki pages is something like <nowiki>{{BreadcrumbsPhotoautotrophy}}</nowiki>. Replace 'Photoautotrophy' with whatever category you are trying to generate. If it does not already exist, it will appear as a red link when you go to 'Read' the page. If you click that link, it will take you to a new page that you can create using the template examples at [[Template:BreadcrumbsPhotoautotrophy]] or [[Template:BreadcrumbsCellular]].

== MediaWiki editing quick reference ==

{| class="wikitable sortable"
|+ '''MediaWiki Editing Reference'''
! Feature !! Syntax !! Example Output / Notes

|-
| Link to another page
| <nowiki>[[Page Name]]</nowiki>
| Links to *Page Name*

|-
| Link with custom label
| <nowiki>[[Page Name|Visible Text]]</nowiki>
| Shows as → **Visible Text**

|-
| External link (implicit)
| <nowiki>https://example.com</nowiki>
| Auto-links as URL

|-
| External link (labeled)
| <nowiki>[https://example.com My link text]</nowiki>
| Shows as → **My link text**

|-
| Link to a user page
| <nowiki>[[User:Username|]]</nowiki>
| Goes to that user’s profile

|-
| User link with label
| <nowiki>[[User:Username||Name]]</nowiki>
| Shows as **Name**, links to profile

|-
| Upload files (images, PDFs, etc.)
| Go to: <nowiki>Special:Upload</nowiki>
| Or click **Upload file** in right sidebar

|-
| Insert an image
| <nowiki>[[File:Image.png]]</nowiki>
| Display at default size

|-
| Image with formatting
| <nowiki>[[File:Image.png|thumb|300px|Caption text]]</nowiki>
| Thumbnail + caption + size control

|-
| Edit page title
| <nowiki>{{DISPLAYTITLE:New title with formatting}}</nowiki>
| Edit page's title and (sometimes) links to it

|-
| Bold text
| <nowiki>'''text'''</nowiki>
| '''text'''

|-
| Italic text
| <nowiki>''text''</nowiki>
| ''text''

|-
| Superscript
| <nowiki><sup>14</sup>C</nowiki>
| <sup>14</sup>C

|-
| Subscript
| <nowiki>H<sub>2</sub>O</nowiki>
| H<sub>2</sub>O

|-
| Headings
| <nowiki>== Heading 2 ==</nowiki><br><nowiki>=== Heading 3 ===</nowiki>
| Used for structure + automatic TOC

|-
| Bullet list
| <nowiki>* Item</nowiki>
| • Item

|-
| Numbered list
| <nowiki># Step</nowiki>
| 1. Step

|-
| Code/monospace
| <nowiki><code>text</code></nowiki> or <nowiki>nowiki</nowiki> tags
| <code>text</code>

|-
| Template call
| <nowiki>{{TemplateName|param=value}}</nowiki>
| Inserts reusable content

|-
| Math
| <nowiki><math>E=mc^2</math></nowiki>
| <math>E=mc^2</math>

|-
| References
| <nowiki><ref>citation</ref> ... <references/></nowiki>
| <ref>citation</ref> ... <references/>

|}

== Contact information for the main folks on this project ==

Web maintenance, Oceancyclopedia co-creator: [[User:Kate Evans|Kate Evans]] (USC), evansk@usc.edu

Oceancyclopedia co-creator: Hagen aka. [[User:Hagi BucknWise|HagiBucknWise]] Buck-Wiese (USC), buckwies@usc.edu

OceanWiki Interest Form

2026-02-12T22:23:08Z

Kate Evans:

2026-02-12T15:58:10Z

Kate Evans: Created page with "<div class="breadcrumbs"> Model types <span class="sep">›</span> Global scale <span class="sep">›</span> {{PAGENAME}} </div>"

<div class="breadcrumbs">
[[Model Types|Model types]]
<span class="sep">›</span>
[[Model types/Global scale|Global scale]]
<span class="sep">›</span>
{{PAGENAME}}
</div>

Talk:PICES

2026-02-12T15:57:02Z

Kate Evans:

Chemoautotrophy

2026-02-11T23:35:39Z

Kate Evans:

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

Nano SIP

2026-02-11T23:33:47Z

Kate Evans: Created page with " * Page authors: Kate Evans, Grommet the Cat, PRIMO * Responsible curator: Kate Evans ---- __TOC__ <div class="model-box"> {| class="model-ib" ! What is being measured in 1 - 3 words |- | '''Approach:''' tracer quantification, remote sensing, sequencing, etc. |- | '''Context:''' ''in situ'', incubation |- | '''Spatial scale:''' mL, km<sup>2</sup> |- | '''Temporal scale:''' seconds, days, seasons |..."

* [[Page authors|Page authors]]: [[Kate Evans]], [[Grommet the Cat]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Kate Evans|Kate Evans]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' tracer quantification, remote sensing, sequencing, etc.
|-
| '''Context:''' ''in situ'', incubation
|-
| '''Spatial scale:''' mL, km<sup>2</sup>
|-
| '''Temporal scale:''' seconds, days, seasons
|-
| '''Units:'''
|-
| '''Community captured:''' all, 0.7 - 3 µm, target species
|-
| '''Co-measurements:''' Other measurements required for interpretation of results e.g., temperature, salinity, wind speed history
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

== Output ==

=== Scale of measurement ===

=== Data generated ===

=== Units & currency ===

=== Sample size ===

=== Repositories & databases ===

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

== Limitations ==

== Example Applications & Protocols ==

=== Classic examples ===
* Classic/original papers

=== Recent applications ===
* New papers + protocol links (e.g. word doc used in lab) if applicable

=== Common calculations/conversions ===
* E.g. conversion to standard units

== References ==

[[Category:Main Pages|Model types]]

Other diazotroph marker genes: nifD, nifK

2026-02-11T19:35:12Z

Kate Evans:

{{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 ==
nifD and nifK amplicon sequencing targets genes encoding the α- and β-subunits of the molybdenum–iron (MoFe) protein of nitrogenase, respectively. These genes can be complementary to nifH sequencing and provide additional phylogenetic and functional resolution of diazotrophic communities. Environmental DNA is extracted, followed by PCR amplification of nifD and/or nifK using gene-specific primers. Amplicons are sequenced using high-throughput platforms, and resulting sequences are used to assess diazotroph diversity, composition, and relative abundance across environments.

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

=== Scale of measurement ===
* Molecular / gene-level
* Semi-quantitative (relative abundance; absolute abundance requires complementary quantification)
* Community-level inference of nitrogen fixation potential

=== Data generated ===
* DNA sequence reads (FASTQ files)
* ASV or OTU tables
* Phylogenetic trees (often higher resolution than nifH)
* Metadata-linked abundance matrices

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

=== Sample size ===
* Varies by study design
* Biological and technical replication recommended

=== Repositories & databases ===
* nifDdada2, github – focused on nifD
* NCBI GenBank – nifD and nifK reference sequences
* ENA / SRA – raw sequencing reads
* IMG/M – integrated microbial genomes and functional genes

== Limitations ==
* Lower primer coverage and fewer validated primer sets compared to nifH
* Larger gene size can complicate amplification and sequencing
* Lower reference database coverage relative to nifH
* Does not directly measure nitrogen fixation activity
* Horizontal gene transfer complicates evolutionary interpretation

== Example Applications & Protocols ==
* PCR amplification protocols adapted from specific primers
* Custom laboratory SOPs due to limited standardized protocols

=== Classic examples ===

=== Common calculations/conversions ===
* Relative abundance = (reads per nifD or nifK ASV) / (total nifD/nifK reads per sample)
* Rarefaction to standardize sequencing depth
* Phylogenetic clustering based on nifD/nifK sequences
* Comparative analyses with nifH-derived community profiles

== References ==