The nitrogen cycle

Scoping a multi-organism review of the microbial nitrogen-cycle enzymes

AI Gene Review · projects/NITROGEN_CYCLE · scoping

Bottom line

  • Scoped, no gene reviews started. The cycle's dissimilatory steps are almost all bacterial or archaeal.
  • We chose 27 reviewed Swiss-Prot marker enzymes across seven arms, plus nxrA, which has no reviewed entry.
  • A taxon-neutral module (modules/nitrogen_cycle.yaml, DRAFT) is built; it gives the specific pathway terms that annotations on GO:0071941 should move to.

The cycle and its markers

Candidate genes by arm

Arm Markers Model organisms
Fixation nifH, nifD, nifK K. pneumoniae, A. vinelandii
Nitrification amoA/B/C, hao, cycA; nxrA (no Swiss-Prot) N. europaea
Denitrification narG, napA, nirS, nirK, norB, norC, nosZ E. coli, P. aeruginosa, P. denitrificans ...
DNRA nrfA E. coli
Anammox hzsA, hzsB, hzsG, hdh K. stuttgartiensis
Assimilation narB, nasA, nirA, nirB, glnA, gltB S. elongatus, E. coli, K. oxytoca
Ammonification ureC K. aerogenes

nirS and nirK are convergent solutions to the same NO₂⁻ → NO step; reviewing both makes the either/or distribution explicit.

The draft module

pages/modules/nitrogen_cycle.html: one part per arm, variant sets for convergent enzymes, Swiss-Prot exemplars as grounding.

Status and next steps

  • ✅ Marker set chosen and accessions verified (2026-06-20); module drafted.
  • ⬜ Resolve an accession for NOB nitrite oxidoreductase (nxrA).
  • ⬜ just fetch-gene each marker under its species code (e.g. NITEU, PARDE, KUEST) and review.
  • ⬜ Log any GO:0071941 rows found to the companion obsoletion project.

Read more: projects/NITROGEN_CYCLE.md · modules/nitrogen_cycle.yaml · projects/NITROGEN_CYCLE_OBSOLETION.md