identifier: traitmech:000103 label: nitrogen fixation definition: A metabolism in which an organism reduces atmospheric dinitrogen (N2) to ammonia using the nitrogenase enzyme complex, making fixed nitrogen biologically available (diazotrophy). definition_source: DOI:10.1038/nrmicro.2018.9 trait_category: METABOLISM term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000060 synonyms: - synonym_text: diazotrophy synonym_type: RELATED_SYNONYM source: DOI:10.1038/nrmicro954 evidence: - reference: DOI:10.1038/nrmicro.2018.9 notes: Kuypers, Marchant & Kartal place nitrogen fixation as the reductive entry point of the microbial nitrogen-cycling network. - reference: DOI:10.1038/nrmicro954 notes: Dixon & Kahn review the genetic regulation of biological nitrogen fixation and nitrogenase. canonical_examples: - taxon_id: NCBITaxon:354 taxon_label: Azotobacter vinelandii note: "Preferred model free-living aerobic diazotroph; fixes N2 at high O2 via respiratory protection." reference: DOI:10.1128/mbio.02593-21 causal_graphs: - graph_id: nitrogen_fixation_nitrogenase title: Nitrogenase-catalyzed dinitrogen reduction description: Evidence-backed causal sketch linking the nitrogenase complex to reduction of atmospheric dinitrogen to ammonia. nodes: - node_id: nitrogen_fixation_trait label: nitrogen fixation node_type: TRAIT grounding: traitmech:000103 description: Capacity to reduce N2 to ammonia. - node_id: nitrogenase label: nitrogenase node_type: GENE_OR_PROTEIN description: Oxygen-sensitive enzyme complex that reduces dinitrogen. grounding: UniProtKB:A0A089HR75 - node_id: nitrogen_fixation_process label: nitrogen fixation node_type: BIOLOGICAL_PROCESS grounding: GO:0009399 description: Reduction of dinitrogen to ammonia. - node_id: dinitrogen label: dinitrogen node_type: CHEMICAL grounding: CHEBI:17997 description: Atmospheric N2 substrate. - node_id: ammonia label: ammonia node_type: CHEMICAL grounding: CHEBI:16134 description: Fixed-nitrogen product. - node_id: ferredoxin_flavodoxin label: ferredoxin/flavodoxin node_type: GENE_OR_PROTEIN description: Low-potential electron carriers that donate electrons to the nitrogenase Fe-protein (NifH). grounding: UniProtKB:A0A7Y9D8L6 - node_id: nifh_fe_protein label: NifH (Fe-protein) node_type: GENE_OR_PROTEIN description: Nitrogenase iron protein; ATP-dependent electron donor to the MoFe protein. - node_id: p_cluster label: P-cluster node_type: GENE_OR_PROTEIN description: '[8Fe-7S] metallocluster in NifDK that relays electrons to the FeMo-cofactor.' - node_id: femo_cofactor label: FeMo-cofactor (M-cluster) node_type: GENE_OR_PROTEIN description: '[7Fe-9S-Mo-C-homocitrate] active-site cofactor that binds and reduces N2.' - node_id: atp label: ATP node_type: CHEMICAL grounding: CHEBI:30616 description: Mg-ATP hydrolyzed by NifH to drive electron transfer to the MoFe protein. - node_id: oxygen label: molecular oxygen node_type: CHEMICAL grounding: CHEBI:15379 description: O2, which irreversibly inactivates oxygen-sensitive nitrogenase. edges: - subject: nitrogenase predicate: enables object: nitrogen_fixation_process description: The nitrogenase complex carries out biological nitrogen fixation. evidence: - reference: DOI:10.1038/nrmicro954 notes: Dixon & Kahn review nitrogenase as the catalyst of biological nitrogen fixation. predicate_id: RO:0002327 - subject: nitrogen_fixation_process predicate: consumes object: dinitrogen description: Nitrogen fixation consumes atmospheric dinitrogen. evidence: - reference: DOI:10.1038/nrmicro.2018.9 notes: Kuypers et al. place N2 reduction as the reductive entry to the nitrogen cycle. predicate_id: biolink:consumes - subject: nitrogen_fixation_process predicate: produces object: ammonia description: Nitrogen fixation produces ammonia. evidence: - reference: DOI:10.1038/nrmicro954 notes: Supports ammonia as the product of nitrogenase-catalyzed N2 reduction. predicate_id: METPO:2000202 - subject: nitrogen_fixation_trait predicate: depends on object: nitrogenase description: The nitrogen-fixation trait depends on the nitrogenase complex. evidence: - reference: DOI:10.1038/nrmicro954 notes: Supports nitrogenase as required for the trait. predicate_id: RO:0002502 - subject: ferredoxin_flavodoxin predicate: transfers electron to object: nifh_fe_protein description: Reduced ferredoxin/flavodoxin donate electrons to the [4Fe-4S] cluster of the NifH homodimer. evidence: - reference: DOI:10.1128/aem.00378-23 notes: Reduced electron carriers donate electrons to the [4Fe-4S] cluster at the interface of the NifH homodimer; core Mo-nitrogenase mechanism. - subject: nifh_fe_protein predicate: transfers electron to object: p_cluster description: The Fe-protein accepts electrons from Fd/Fld and reduces the P-cluster in the MoFe protein in an ATP-dependent step. evidence: - reference: DOI:10.1128/aem.00378-23 notes: The Fe-protein FeS cluster accepts electrons from Fd or Fld and reduces the P-cluster in the MoFe protein in an ATP-dependent electron transfer. - subject: p_cluster predicate: transfers electron to object: femo_cofactor description: The P-cluster relays electrons to the FeMo-cofactor for N2 reduction. evidence: - reference: DOI:10.1128/aem.00378-23 notes: The P-cluster delivers electrons to the MoFe cofactor allowing electrons to be loaded for the reduction of N2; core electron relay. - subject: femo_cofactor predicate: enables object: nitrogen_fixation_process description: The FeMo-cofactor binds and reduces N2 to ammonia. evidence: - reference: DOI:10.34133/bdr.0005 notes: FeMo-co binds and reduces N2 to form NH3 and H2 in the canonical Mo-dependent nitrogenase. predicate_id: RO:0002327 - subject: nifh_fe_protein predicate: requires object: atp description: NifH hydrolyzes Mg-ATP during each electron transfer to the MoFe protein. evidence: - reference: DOI:10.34133/bdr.0005 notes: NifH transiently binds and dissociates from NifDK, hydrolyzing 2 Mg-ATP per electron transfer; supports per-electron ATP cost. - subject: oxygen predicate: inhibits object: nitrogenase description: Molecular oxygen inactivates the oxygen-sensitive nitrogenase complex. evidence: - reference: DOI:10.1128/aem.00378-23 notes: Nitrogenase is an O2-sensitive enzyme; broad, well-supported claim across diazotrophs. predicate_id: RO:0002212 curation_history: - timestamp: '2026-06-08T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate METABOLISM trait (nitrogen fixation / diazotrophy); round 2, nitrogen-cycle gap. llm_assisted: true - timestamp: '2026-06-08T12:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (nitrogenase-catalyzed N2 reduction) with CHEBI/GO node groundings and RO/METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-14T06:38:15Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A089HR75×1). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:12Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1, RO:0002212×1). llm_assisted: true - timestamp: '2026-06-26T07:15:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A7Y9D8L6×1). llm_assisted: true