identifier: METPO:1000608
label: facultatively aerobic
definition: An oxygen preference in which growth can occur without oxygen but is capable
  of aerobic growth.
definition_source: PMID:21413255
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000601
synonyms:
- synonym_text: facultative
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: facultative aerobe
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: PMID:21413255
  snippet: preferentially utilize oxygen as a terminal electron acceptor
  notes: Supports facultative aerobic growth when oxygen is available.
- reference: PMID:16142505
  snippet: A facultative aerobic, moderately thermophilic, spore forming bacterium
  notes: 'Organism example: Anoxybacillus kamchatkensis strain JW/VK-KG4 is described
    as facultatively aerobic.'
causal_graphs:
- graph_id: facultative_aerobe_oxygen_flexible_growth
  title: Facultative aerobe oxygen-flexible growth mechanism
  description: Evidence-backed causal sketch linking facultative aerobic growth to
    oxygen-responsive respiratory switching.
  nodes:
  - node_id: facultative_aerobic_trait
    label: facultatively aerobic
    node_type: TRAIT
    grounding: METPO:1000608
    description: Growth can occur without oxygen but is capable of aerobic growth.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Dioxygen used when aerobic growth is possible.
  - node_id: aerobic_respiration
    label: aerobic respiration
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0009060
    description: Oxygen-dependent respiratory energy metabolism.
  - node_id: anaerobic_metabolism
    label: anaerobic metabolism
    node_type: BIOLOGICAL_PROCESS
    description: Growth-supporting metabolism when oxygen is unavailable.
  - node_id: fnr_type_regulation
    label: FNR-type oxygen-responsive regulation
    node_type: GENE_OR_PROTEIN
    description: Oxygen-sensing regulatory systems that tune respiratory metabolism.
  - node_id: terminal_acceptor_availability
    label: terminal electron acceptor availability
    node_type: ENVIRONMENTAL_FACTOR
    description: Availability of a final electron acceptor (e.g. oxygen vs fumarate)
      in the environment.
  - node_id: terminal_branch_choice
    label: terminal respiratory branch choice
    node_type: BIOLOGICAL_PROCESS
    description: Selection of which terminal respiratory enzyme/branch is active.
  - node_id: arcab_system
    label: ArcAB two-component system
    node_type: GENE_OR_PROTEIN
    description: Redox-responsive two-component regulatory system controlling aerobic
      respiration.
  - node_id: anaerobic_metabolism_genes
    label: anaerobic metabolism genes
    node_type: GENE_OR_PROTEIN
    description: Genes encoding anaerobic metabolic functions activated under anoxia.
  - node_id: aerobic_metabolism_genes
    label: aerobic metabolism genes
    node_type: GENE_OR_PROTEIN
    description: Genes encoding aerobic respiratory functions repressed under anoxia.
  - node_id: cytochrome_bd_oxidase
    label: cytochrome bd oxidase
    node_type: GENE_OR_PROTEIN
    description: High-affinity terminal oxidase that reduces oxygen at low O2 concentrations.
    grounding: UniProtKB:Q6L5L4
  edges:
  - subject: molecular_oxygen
    predicate: enables
    object: aerobic_respiration
    description: Facultatively aerobic organisms can use oxygen-dependent respiration
      when oxygen is available.
    evidence:
    - reference: DOI:10.1016/j.celrep.2023.112444
      snippet: terminal oxidases transfer electrons from the ETC to O2
      notes: Supports aerobic respiration through oxygen-reducing terminal oxidases.
    predicate_id: RO:0002327
  - subject: facultative_aerobic_trait
    predicate: has alternative process
    object: anaerobic_metabolism
    description: Facultative aerobic growth retains a growth mode when oxygen is absent.
    evidence:
    - reference: DOI:10.1089/ars.2011.4051
      snippet: utilizing other substrates as final electron acceptors
      notes: Review describes respiratory adaptation to oxygen shortage using alternative
        electron acceptors.
  - subject: molecular_oxygen
    predicate: regulates
    object: fnr_type_regulation
    description: Oxygen-responsive regulators tune metabolism across oxic and anoxic
      conditions.
    evidence:
    - reference: DOI:10.1089/ars.2011.4051
      snippet: Fnr-type transcriptional regulators that directly sense O2
      notes: Supports oxygen sensing by FNR-type regulators.
    predicate_id: RO:0002211
  - subject: fnr_type_regulation
    predicate: regulates switch between
    object: aerobic_respiration
    description: Oxygen-sensing regulation helps switch respiratory metabolism as
      oxygen availability changes.
    evidence:
    - reference: DOI:10.1089/ars.2011.4051
      snippet: adaptation of respiratory metabolism to changing environments
      notes: Supports regulatory switching between oxygen regimes.
  - subject: terminal_acceptor_availability
    predicate: determines
    object: terminal_branch_choice
    description: Which terminal respiratory enzyme is active depends on the available
      final electron acceptor.
    evidence:
    - reference: DOI:10.1128/jb.00389-22
      notes: 'which terminal enzyme is active depends on the availability of the final
        electron acceptor: fumarate or oxygen.'
  - subject: arcab_system
    predicate: represses
    object: aerobic_respiration
    description: ArcAB two-component regulatory system represses aerobic respiration
      under reducing conditions.
    evidence:
    - reference: DOI:10.1128/mbio.01448-23
      notes: ArcAB, a two-component regulatory system that represses aerobic respiration;
        conserved switch in Enterobacterales.
  - subject: molecular_oxygen
    predicate: inactivates
    object: fnr_type_regulation
    description: Oxygen directly inactivates FNR by oxidizing its iron-sulfur cluster,
      a core oxygen-sensing mechanism.
    evidence:
    - reference: DOI:10.1093/nar/gkad750
      notes: oxygen directly inactivates Fnr by oxidizing that iron-sulfur cluster;
        widely generalizable oxygen-sensing edge.
  - subject: fnr_type_regulation
    predicate: activates
    object: anaerobic_metabolism_genes
    description: When active under anoxia, FNR activates anaerobic metabolism genes.
    evidence:
    - reference: DOI:10.1093/nar/gkad750
      notes: when active, Fnr activates anaerobic metabolism genes and represses aerobic
        genes.
    predicate_id: RO:0002213
  - subject: fnr_type_regulation
    predicate: represses
    object: aerobic_metabolism_genes
    description: Active FNR represses aerobic metabolism genes under anoxic conditions.
    evidence:
    - reference: DOI:10.1093/nar/gkad750
      notes: Fnr activates anaerobic metabolism genes and represses aerobic genes.
  - subject: cytochrome_bd_oxidase
    predicate: has high affinity for
    object: molecular_oxygen
    description: Cytochrome bd is a high-affinity terminal oxidase enabling oxygen
      respiration at low O2.
    evidence:
    - reference: DOI:10.1128/aem.00378-23
      notes: cytochrome bd supports high O2 consumption and high-affinity oxygen reduction
        at the cell surface.
curation_history:
- timestamp: '2026-05-05T01:35:46.853277+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-05T01:09:05-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Added definition source and evidence for facultative oxygen use.
  llm_assisted: true
- timestamp: '2026-05-05T18:39:46-07:00'
  curator: codex
  action: ADDED_ORGANISM_EXAMPLE
  changes: Added Anoxybacillus kamchatkensis organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-10T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for facultative aerobic oxygen-responsive
    growth.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:29Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1, RO:0002211×1).
  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: '2026-06-24T17:21:09Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:17Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:Q6L5L4×1).
  llm_assisted: true