identifier: traitmech:000044 label: nitrogen-fixing symbiosis definition: A mutualistic symbiosis in which a diazotrophic bacterium fixes atmospheric N2 for a host plant — classically rhizobia in legume root nodules — in exchange for photosynthate. definition_source: DOI:10.1038/nrmicro.2017.171 trait_category: ECOLOGY term_kind: CLASS mapping_status: REVIEWED parent_traits: - traitmech:000041 synonyms: - synonym_text: nitrogen-fixing symbiont synonym_type: RELATED_SYNONYM source: DOI:10.1038/nrmicro.2017.171 - synonym_text: root-nodule symbiosis synonym_type: RELATED_SYNONYM source: DOI:10.1038/nrmicro2990 evidence: - reference: DOI:10.1038/nrmicro.2017.171 notes: Poole et al. describe the free-living-to-endosymbiont transition of rhizobia that forms N2-fixing legume root nodules. - reference: DOI:10.1038/nrmicro2990 notes: Oldroyd, "Speak, friend, and enter", supports the symbiotic signalling that establishes beneficial nitrogen-fixing plant-microbe associations. canonical_examples: - taxon_id: NCBITaxon:382 taxon_label: Sinorhizobium meliloti note: "Model rhizobium-legume symbiont (alfalfa / Medicago); strain 1021 (NCBITaxon:266834) is the most-studied reference." reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC3164228/ causal_graphs: - graph_id: rhizobia_legume_n2_fixation title: Rhizobia–legume root-nodule N2-fixing mutualism description: Evidence-backed causal sketch linking symbiotic signalling and root-nodule colonization to N2 fixation in exchange for plant photosynthate. nodes: - node_id: n2_fix_symbiosis_trait label: nitrogen-fixing symbiosis node_type: TRAIT grounding: traitmech:000044 description: Mutualistic N2 fixation in plant-microbe associations. - node_id: symbiotic_signalling label: nodulation signalling node_type: BIOLOGICAL_PROCESS description: Nod-factor signalling establishing the rhizobium-legume partnership. - node_id: nitrogen_fixation label: nitrogen fixation node_type: BIOLOGICAL_PROCESS grounding: GO:0009399 description: Reduction of atmospheric N2 to ammonia by nitrogenase. - node_id: flavonoids label: flavonoids node_type: CHEMICAL description: Host-root exudate signalling compounds secreted by legumes. - node_id: nod_factor label: Nod factor (lipochitooligosaccharide) node_type: CHEMICAL description: Rhizobial lipochitooligosaccharide signal triggering symbiosis. - node_id: leghemoglobin label: leghemoglobin node_type: GENE_OR_PROTEIN description: Nodule oxygen-binding protein buffering O2 around bacteroids. - node_id: nodule_oxygen_diffusion_barrier label: nodule oxygen diffusion barrier node_type: CELLULAR_LOCALIZATION description: Tightly packed cortical cell layer limiting O2 flux into the nodule interior. - node_id: microaerobic_environment label: microaerobic environment node_type: ENVIRONMENTAL_FACTOR description: Low-oxygen condition inside the nodule required for nitrogenase. - node_id: nitrogenase_complex label: nitrogenase complex node_type: GENE_OR_PROTEIN description: Bacterial enzyme complex catalyzing reduction of N2 to NH3. - node_id: organic_acids label: organic acids node_type: CHEMICAL description: Reductant/carbon source the plant transfers to intracellular bacteroids. grounding: CHEBI:64709 - node_id: iron_availability label: iron availability node_type: ENVIRONMENTAL_FACTOR description: Availability of iron, a cofactor for nitrogenase and leghemoglobin. edges: - subject: symbiotic_signalling predicate: enables object: n2_fix_symbiosis_trait description: Nod-factor signalling between rhizobia and legume hosts establishes the symbiosis. evidence: - reference: DOI:10.1038/nrmicro2990 notes: Oldroyd reviews symbiotic signalling establishing nitrogen-fixing plant-microbe associations. predicate_id: RO:0002327 - subject: n2_fix_symbiosis_trait predicate: enables object: nitrogen_fixation description: The symbiosis houses bacteroids that fix N2 inside root nodules. evidence: - reference: DOI:10.1038/nrmicro.2017.171 notes: Poole et al. describe the free-living-to-endosymbiont transition of rhizobia forming N2-fixing legume root nodules. predicate_id: RO:0002327 - subject: flavonoids predicate: induces production of object: nod_factor description: Legume flavonoid exudates induce rhizobia to produce Nod factors. evidence: - reference: DOI:10.3389/fpls.2023.1284720 notes: Legumes secrete flavonoids that induce rhizobia to produce Nod factors. - subject: nod_factor predicate: enables object: symbiotic_signalling description: Perceived Nod factors initiate the nodulation signalling cascade. evidence: - reference: DOI:10.3389/fpls.2023.1284720 notes: Nod factors are perceived by Nod-factor receptors, triggering symbiotic signalling. predicate_id: RO:0002327 - subject: leghemoglobin predicate: buffers object: microaerobic_environment description: Leghemoglobin buffers oxygen concentration within nodules. evidence: - reference: DOI:10.3389/fpls.2023.1284720 notes: Leghemoglobins buffer the oxygen concentration within the nodules. - subject: nodule_oxygen_diffusion_barrier predicate: maintains object: microaerobic_environment description: A tightly packed cortical diffusion barrier limits oxygen flux into the nodule interior. evidence: - reference: DOI:10.1038/s41564-024-01762-2 notes: A diffusion barrier of tightly packed cells limits oxygen flux; the multilayered cortex functions as an adaptable oxygen diffusion barrier. - subject: microaerobic_environment predicate: enables object: nitrogen_fixation description: A low-oxygen environment is required for proper nitrogenase activity. evidence: - reference: DOI:10.3389/fpls.2023.1284720 notes: Symbiotic nitrogen fixation requires a low-oxygen environment for proper activity of nitrogenase. predicate_id: RO:0002327 - subject: nitrogenase_complex predicate: enables object: nitrogen_fixation description: The nitrogenase complex reduces N2 to NH3 (16 ATP per N2). evidence: - reference: DOI:10.1017/S1062798724000309 notes: The nitrogenase reaction consumes 16 ATP in the reduction of N2 to NH3. predicate_id: RO:0002327 - subject: organic_acids predicate: enables object: nitrogen_fixation description: The plant supplies organic acids as reductant to intracellular bacteroids fueling fixation. evidence: - reference: DOI:10.1038/s41564-024-01762-2 notes: The plant transfers reductant, typically organic acids, from plant cells to intracellular rhizobia. predicate_id: RO:0002327 - subject: iron_availability predicate: is required for object: nitrogenase_complex description: Iron is an essential cofactor for nitrogenase assembly and leghemoglobin function. evidence: - reference: DOI:10.1093/pcp/pcae128 notes: Fe is essential as a cofactor for leghemoglobin and for assembling the nitrogenase complex. curation_history: - timestamp: '2026-06-02T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate ECOLOGY trait (nitrogen-fixing symbiosis); sub-variant of mutualism. llm_assisted: true - timestamp: '2026-06-09T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (rhizobia-legume N2 fixation) with GO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:09Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×4). llm_assisted: true - timestamp: '2026-06-24T17:23:29Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:64709×1). llm_assisted: true