Nitrogen Cycle Module

Overview

The biological nitrogen cycle is the set of microbially driven redox
transformations that interconvert the major inorganic nitrogen species —
dinitrogen gas (N₂), ammonia/ammonium (NH₃/NH₄⁺), hydroxylamine (NH₂OH),
nitrite (NO₂⁻), nitrate (NO₃⁻), nitric oxide (NO), nitrous oxide (N₂O), and (in
anammox) hydrazine (N₂H₄). Unlike the carbon cycle, essentially all of the
key dissimilatory steps are catalysed by prokaryotes (bacteria and archaea),
which makes this an explicitly multi-organism, microbial module rather than a
single model-species project.

This module collects the canonical, well-characterised marker enzymes for each
arm of the cycle so their GO annotations can be reviewed against a coherent,
mechanistically-organised picture. It is deliberately scoped to dissimilatory
and assimilatory inorganic-nitrogen metabolism; downstream amino-acid and
nucleotide biosynthesis are out of scope except for the ammonia-assimilation
entry point (GS/GOGAT).

Companion project. NITROGEN_CYCLE_OBSOLETION.md
tracks the proposed do_not_annotate flag on the ecosystem-level grouping
term GO:0071941 nitrogen cycle metabolic process and the obsoletion of its
three regulation children. That project documents over-annotation of
mammalian genes onto the parent term; this module documents the legitimate
microbial machinery and the specific descendant pathway terms that
mis-annotated entries should be re-routed to. Read the two together.

Core transformations

Candidate genes for review

All accessions below are reviewed (Swiss-Prot) entries verified against the
UniProt REST API on 2026-06-20. Organisms are the canonical biochemical/genetic
models for each enzyme; where the cycle is studied across several models, the
best-characterised reviewed entry is listed and alternates are noted.

1. Nitrogen fixation — nitrogenase

Notes: K. pneumoniae is the classical nif genetic model; A. vinelandii
is the structural model (MoFe-protein crystal structures). Alternative
nitrogenases (V-dependent vnfH, Fe-only anfH) are out of the initial seed.

2. Nitrification — ammonia & nitrite oxidation

3. Denitrification

Notes: nirS (cytochrome cd₁) and nirK (Cu-type) are mutually exclusive,
convergent solutions to the same NO₂⁻→NO step — reviewing both makes the
"either/or" distribution across denitrifiers explicit.

4. DNRA (dissimilatory nitrate reduction to ammonium)

5. Anammox (anaerobic ammonium oxidation)

6. Assimilatory nitrate/nitrite reduction & ammonia assimilation

7. Ammonification (organic-N mineralization)

Relevant GO descendant terms

When re-routing annotations off the grouping term GO:0071941, the specific
pathway children below are the targets (see the obsoletion project for the
annotation-by-annotation plan):

• GO:0009399 nitrogen fixation
• GO:0019333 denitrification pathway
• GO:0019331 anaerobic respiration, nitrate to nitrite (and related)
• nitrification / nitrite-oxidation children
• GO:0019676 ammonia assimilation cycle (GS/GOGAT)

GO IDs above are provided as routing guidance; verify each label/definition in
OLS or QuickGO before using it in a review, per repo policy on not trusting
unverified IDs.

Scope & approach

1. Microbial, multi-species by nature. None of these genes live in the
   model-organism directories (human, mouse, …); each will need
   just fetch-gene <CODE> <gene> with the appropriate UniProt species code
   (e.g. NITEU for Nitrosomonas europaea, PARDE for Paracoccus
   denitrificans, KUEST for Kuenenia stuttgartiensis). Confirm the species
   subdirectory exists or create it before fetching.
2. Seed with marker enzymes, not whole operons. The lists above are the
   catalytic/diagnostic subunits. Accessory and regulatory genes (nifEN,
   nirSEFCJ maturation, nosDFYL, two-component narXL/ntrBC, etc.) are
   intentionally deferred to keep the first review pass focused.
3. Use the cycle as a consistency check. Because each step has a defined
   substrate→product redox couple, reviewing a gene against the diagram surfaces
   over-annotations (e.g. a nitrite reductase annotated to the broad parent
   GO:0071941 should move to its denitrification or DNRA child).
4. Coordinate with the obsoletion project. Any annotation found on
   GO:0071941 during these reviews should be logged in
   NITROGEN_CYCLE_OBSOLETION.md.

Status

• 2026-06-20 — Module created. Compiled the canonical marker-gene set for the
  six core nitrogen-cycle arms plus assimilation and ammonification. All listed
  accessions are reviewed Swiss-Prot entries verified via the UniProt REST API
  on this date. The one unresolved marker is NOB nitrite oxidoreductase
  (nxrA), which has no reviewed entry and is flagged for accession resolution.
  No gene reviews started yet.