identifier: METPO:1000612
label: facultative oxygen preference
definition: An oxygen preference that describes a microorganism that can grow with
  or without molecular oxygen.
definition_source: DOI:10.1111/cmi.13338
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000601
synonyms:
- synonym_text: Ox_facultative_aerobe_anaerobe
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1111/cmi.13338
  snippet: cope with changing oxygen levels
  notes: Supports facultative oxygen preference as growth across oxygen regimes.
- reference: DOI:10.1089/ars.2011.4051
  snippet: adaptation of respiratory metabolism to changing environments
  notes: Supports oxygen-responsive metabolic switching.
causal_graphs:
- graph_id: facultative_oxygen_preference_switching
  title: Facultative oxygen preference metabolic switching mechanism
  description: Evidence-backed causal sketch linking facultative oxygen preference
    to oxygen-responsive switching between aerobic and oxygen-independent growth.
  nodes:
  - node_id: facultative_oxygen_trait
    label: facultative oxygen preference
    node_type: TRAIT
    grounding: METPO:1000612
    description: Growth can occur with or without molecular oxygen.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Environmental oxygen availability.
  - node_id: aerobic_respiration
    label: aerobic respiration
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0009060
    description: Oxygen-dependent respiratory energy metabolism.
  - node_id: anaerobic_respiration_or_fermentation
    label: anaerobic respiration or fermentation
    node_type: BIOLOGICAL_PROCESS
    description: Oxygen-independent growth-supporting metabolism.
  - node_id: oxygen_sensing_regulation
    label: oxygen-sensing regulation
    node_type: GENE_OR_PROTEIN
    description: Regulatory systems such as FNR-type sensors that respond to oxygen.
  - node_id: aerobic_energy_pathways
    label: aerobic energy-generating pathways
    node_type: PATHWAY
    description: Aerobic respiratory energy-generation modules downregulated under
      anaerobiosis.
  - node_id: anaerobic_metabolism_genes
    label: anaerobic metabolism genes
    node_type: PATHWAY
    description: Genes encoding anaerobic metabolic functions induced when oxygen
      is low or absent.
  - node_id: nitrate_electron_acceptor
    label: nitrate
    node_type: CHEMICAL
    description: Alternative terminal electron acceptor supporting anaerobic respiration.
    grounding: CHEBI:17632
  - node_id: terminal_oxidase_cytochrome_bd
    label: cytochrome bd terminal oxidase
    node_type: GENE_OR_PROTEIN
    description: High-affinity terminal oxidase enabling oxygen respiration at low
      O2 tensions.
  edges:
  - subject: facultative_oxygen_trait
    predicate: responds to
    object: molecular_oxygen
    description: Facultative oxygen preference depends on coping with oxygen changes.
    evidence:
    - reference: DOI:10.1111/cmi.13338
      snippet: cope with changing oxygen levels
      notes: Supports oxygen flexibility as the trait-level mechanism.
  - subject: molecular_oxygen
    predicate: enables
    object: aerobic_respiration
    description: Oxygen availability permits aerobic respiratory growth.
    evidence:
    - reference: DOI:10.1016/j.celrep.2023.112444
      snippet: transfer electrons from the ETC to O2
      notes: Supports oxygen use by terminal oxidases during respiration.
    predicate_id: RO:0002327
  - subject: facultative_oxygen_trait
    predicate: has alternative process
    object: anaerobic_respiration_or_fermentation
    description: Growth without oxygen can use alternative electron acceptors or fermentation.
    evidence:
    - reference: DOI:10.1089/ars.2011.4051
      snippet: utilizing other substrates as final electron acceptors
      notes: Supports oxygen-independent respiratory alternatives under oxygen shortage.
  - subject: oxygen_sensing_regulation
    predicate: controls adaptation to
    object: molecular_oxygen
    description: Oxygen-sensing regulators mediate metabolic adaptation across oxygen
      regimes.
    evidence:
    - reference: DOI:10.1089/ars.2011.4051
      snippet: Fnr-type transcriptional regulators that directly sense O2
      notes: Supports regulatory oxygen sensing as a causal graph entity.
  - subject: oxygen_sensing_regulation
    predicate: represses
    object: aerobic_energy_pathways
    description: Oxygen-responsive regulators (FNR/ArcA) repress aerobic energy-generating
      pathways under anaerobiosis.
    evidence:
    - reference: DOI:10.1128/aem.01491-23
      notes: FNR and ArcA "repress aerobic energy-generating pathways" under anaerobiosis.
  - subject: oxygen_sensing_regulation
    predicate: induces
    object: anaerobic_metabolism_genes
    description: Oxygen-responsive regulators induce anaerobic metabolism genes enabling
      growth without O2.
    evidence:
    - reference: DOI:10.1128/aem.01491-23
      notes: FNR and ArcA "induce genes for anaerobic metabolism"; general regulatory
        edge for facultative bacteria.
  - subject: nitrate_electron_acceptor
    predicate: promotes
    object: anaerobic_respiration_or_fermentation
    description: Nitrate substitutes for O2 as terminal electron acceptor, supporting
      non-fermentative anaerobic respiration.
    evidence:
    - reference: DOI:10.1128/msphere.00774-23
      notes: '"addition of nitrate as a TEA promotes anaerobic respiration"; broadly
        relevant across facultative species with nitrate reductases.'
    predicate_id: RO:0002213
  - subject: molecular_oxygen
    predicate: enables
    object: terminal_oxidase_cytochrome_bd
    description: Trace/available oxygen lets cells use cytochrome bd as terminal oxidase;
      active terminal enzyme depends on which final electron acceptor (oxygen vs fumarate)
      is available.
    evidence:
    - reference: DOI:10.1128/jb.00389-22
      notes: '"which of these terminal enzymes is active in electron transfer depends
        on the availability of the final electron acceptor: fumarate or oxygen"; supports
        electron-acceptor-dependent branch switching.'
    predicate_id: RO:0002327
curation_history:
- timestamp: '2026-05-05T01:35:46.855860+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-10T00:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Reviewed facultative oxygen preference and added DOI-backed definition
    source, evidence, and causal graph for oxygen-responsive metabolic switching.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:29Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 4 evidence-backed generic edges (4 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:09Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×1, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:16Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:17632×1).
  llm_assisted: true