identifier: traitmech:000107 label: iron oxidation definition: A metabolism in which an organism oxidizes ferrous iron (Fe2+) to ferric iron (Fe3+) to conserve energy, at acidic or circumneutral pH and under aerobic or anaerobic conditions. definition_source: DOI:10.1146/annurev.micro.112408.134208 trait_category: METABOLISM term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000060 synonyms: - synonym_text: ferrous iron oxidation synonym_type: RELATED_SYNONYM source: DOI:10.1146/annurev.micro.112408.134208 evidence: - reference: DOI:10.1146/annurev.micro.112408.134208 notes: Emerson, Fleming & McBeth review iron-oxidizing bacteria from an environmental and genomic perspective. - reference: DOI:10.1099/mic.0.045344-0 notes: Hedrich, Schlomann & Johnson review the iron-oxidizing proteobacteria and their energy metabolism. canonical_examples: - taxon_id: NCBITaxon:180 taxon_label: Leptospirillum ferrooxidans note: "Acidophilic Fe(II) oxidiser (bioleaching/AMD). Gallionella ferruginea is the neutrophilic stalk-forming Fe oxidiser." reference: PMID:22815442 causal_graphs: - graph_id: iron_oxidation_ferrous_to_ferric title: Ferrous iron oxidation for energy description: Evidence-backed causal sketch linking the iron-oxidation trait to oxidation of ferrous iron to ferric iron for energy conservation. nodes: - node_id: iron_oxidation_trait label: iron oxidation node_type: TRAIT grounding: traitmech:000107 description: Capacity to oxidize Fe(II) to Fe(III) for energy. - node_id: ferrous_iron label: ferrous iron node_type: CHEMICAL grounding: CHEBI:29033 description: Fe(2+) electron-donor substrate. - node_id: ferric_iron label: ferric iron node_type: CHEMICAL grounding: CHEBI:29034 description: Fe(3+) oxidized product. - node_id: cyc2 label: Cyc2 node_type: GENE_OR_PROTEIN description: Outer-membrane cytochrome c that extracts electrons from extracellular Fe(II); the central iron oxidase across many FeOB. - node_id: cbb3_oxidase label: cbb3-type terminal oxidase node_type: GENE_OR_PROTEIN description: High-oxygen-affinity terminal oxidase used by FeOB. - node_id: bd_oxidase label: cytochrome bd-type terminal oxidase node_type: GENE_OR_PROTEIN description: High-oxygen-affinity terminal oxidase used by FeOB. - node_id: microaerobic_conditions label: microaerobic conditions node_type: ENVIRONMENTAL_FACTOR description: Low-oxygen environmental niche favored by FeOB. - node_id: low_oxygen_organic_rich label: low-oxygen organic-rich niche node_type: ENVIRONMENTAL_FACTOR description: Low-O2, organic-rich environmental niche. - node_id: nitrite_no label: nitrite and nitric oxide node_type: CHEMICAL description: Reactive nitrogen species that bind hemes and abiotically oxidize Fe(II). - node_id: enzymatic_iron_oxidation label: enzymatic iron oxidation node_type: BIOLOGICAL_PROCESS description: Biological Fe(II) oxidation catalyzed by cytochromes. - node_id: multiheme_cytochromes label: multiheme c-type cytochromes node_type: GENE_OR_PROTEIN description: FeOB-enriched multiheme cytochromes conducting electrons across long distances and wide redox-potential ranges. - node_id: extracellular_electron_transfer label: extracellular electron transfer node_type: BIOLOGICAL_PROCESS description: Electron transfer across minerals and long distances, expanding usable iron substrates. edges: - subject: iron_oxidation_trait predicate: oxidizes object: ferrous_iron description: Iron oxidizers oxidize ferrous iron as an electron donor. evidence: - reference: DOI:10.1146/annurev.micro.112408.134208 notes: Emerson et al. review iron-oxidizing bacteria that use Fe(II) for energy. predicate_id: METPO:2000016 - subject: iron_oxidation_trait predicate: produces object: ferric_iron description: Ferrous-iron oxidation yields ferric iron. evidence: - reference: DOI:10.1099/mic.0.045344-0 notes: Hedrich et al. describe Fe(II) to Fe(III) oxidation by iron-oxidizing proteobacteria. predicate_id: METPO:2000202 - subject: cyc2 predicate: oxidizes object: ferrous_iron description: The outer-membrane cytochrome Cyc2 extracts electrons from extracellular Fe(II). evidence: - reference: DOI:10.1128/mSystems.00720-23 notes: '"electrons are initially extracted from extracellular Fe(II) by the outer membrane cytochrome c Cyc2"; Cyc2 also validated in neutrophiles.' predicate_id: METPO:2000016 - subject: cbb3_oxidase predicate: supports growth in object: microaerobic_conditions description: High-O2-affinity cbb3 oxidase enables FeOB growth under microaerobic conditions. evidence: - reference: DOI:10.1128/AEM.00599-24 notes: '"These terminal oxidases have high affinity for oxygen and therefore are widely understood to be used under microaerobic conditions"; consistent with FeOB ecology.' - subject: bd_oxidase predicate: supports growth in object: low_oxygen_organic_rich description: High-O2-affinity cytochrome bd oxidase supports FeOB growth in low-oxygen, organic-rich niches. evidence: - reference: DOI:10.1128/mSystems.00038-23 notes: '"cytochrome bd-type oxidases have a high affinity for oxygen ... can be more highly expressed ... under low-oxygen, organic-rich conditions".' - subject: nitrite_no predicate: negatively regulates object: enzymatic_iron_oxidation description: Nitrite and NO bind hemes inhibiting cytochromes and abiotically oxidize Fe(II), competing with enzymatic iron oxidation. evidence: - reference: DOI:10.1128/mSystems.00038-23 notes: '"they bind to hemes, inhibiting the activity of cytochromes, and also directly oxidize Fe(II), thus competing with enzymatic iron oxidation".' - subject: multiheme_cytochromes predicate: enables object: extracellular_electron_transfer description: FeOB multiheme cytochromes conduct electrons across long distances and broad redox potentials, enabling extracellular electron transfer. evidence: - reference: DOI:10.1128/mSystems.00038-23 notes: '"MHCs efficiently conduct electrons across longer distances and function across a wide range of redox potentials ... which can expand the range of usable iron substrates".' predicate_id: RO:0002327 curation_history: - timestamp: '2026-06-08T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate METABOLISM trait (iron oxidation); round 2, metal-cycle gap. Complements round-1 dissimilatory iron reduction. llm_assisted: true - timestamp: '2026-06-08T12:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (Fe(II) to Fe(III) oxidation) with CHEBI node groundings and METPO predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 5 evidence-backed generic edges (9 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 (METPO:2000016×1, RO:0002327×1). llm_assisted: true