identifier: METPO:1000655
label: organotrophic
definition: A trophic type in which an organism obtains energy from the oxidation
  of organic compounds.
definition_source: DOI:10.1016/B978-012373944-5.00083-3
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: TT_organotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: organotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1016/B978-012373944-5.00083-3
  snippet: incorporation of a compound into biomass
  notes: Microbial metabolism reference supports assimilation and use of organic compounds
    in growth.
- reference: DOI:10.1016/j.bbabio.2008.09.008
  snippet: membrane-bound electron transport chain
  notes: Review supports respiratory electron transport as an energy-conserving route.
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "organic electron-donor organotroph"
  reference: PMID:9278503
- taxon_id: NCBITaxon:1423
  taxon_label: Bacillus subtilis
  note: "soil organotroph"
  reference: PMID:9384377
causal_graphs:
- graph_id: organotrophic_organic_compound_oxidation
  title: Organotrophic organic compound oxidation
  description: DOI-backed graph linking organic electron donors, catabolism, respiratory
    energy conservation, ATP production, and biomass precursors.
  nodes:
  - node_id: organotrophic_trait
    label: organotrophic
    node_type: TRAIT
    grounding: METPO:1000655
    description: Trophic type using organic compounds as electron donors for energy.
  - node_id: organic_compound
    label: organic compound
    node_type: CHEMICAL
    description: Reduced organic substrate serving as electron donor.
    grounding: CHEBI:50860
  - node_id: glucose
    label: glucose
    node_type: CHEMICAL
    grounding: CHEBI:17234
    description: Representative organic substrate.
  - node_id: catabolism
    label: catabolism
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0009056
    description: Oxidative breakdown of organic compounds.
  - node_id: respiratory_chain
    label: respiratory chain
    node_type: PATHWAY
    description: Electron-transfer pathway conserving energy.
    grounding: GO:0022904
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Electrochemical ion gradient generated by respiration.
    grounding: METPO:1007500
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Cellular energy carrier.
  - node_id: precursor_metabolites
    label: precursor metabolites
    node_type: CHEMICAL
    description: Catabolic intermediates used for biosynthesis.
  - node_id: reduced_electron_carriers
    label: NADH and FADH2
    node_type: CHEMICAL
    description: Reduced electron carriers (NADH/FADH2) generated by catabolic oxidation.
  - node_id: nadh_dehydrogenase
    label: NADH dehydrogenase (Complex I)
    node_type: GENE_OR_PROTEIN
    description: Respiratory enzyme complex extracting electrons from NADH.
  - node_id: organic_carbon_availability
    label: organic carbon availability
    node_type: ENVIRONMENTAL_FACTOR
    description: Availability of organic carbon substrates in the environment.
  edges:
  - subject: organotrophic_trait
    predicate: uses electron donor
    object: organic_compound
    description: Organotrophy uses organic compounds as electron donors.
    evidence:
    - reference: DOI:10.1016/B978-012373944-5.00083-3
      snippet: incorporation of a compound into biomass
      notes: Supports use and assimilation of organic compounds in microbial growth.
    predicate_id: METPO:2000009
  - subject: glucose
    predicate: example of
    object: organic_compound
    description: Glucose is a representative organic substrate.
    evidence:
    - reference: DOI:10.1021/acsomega.3c02205
      snippet: glucose metabolism
      notes: Supports glucose as a microbial organic substrate.
    predicate_id: rdfs:subClassOf
  - subject: organic_compound
    predicate: oxidized by
    object: catabolism
    description: Organic substrates are oxidized through catabolic metabolism.
    evidence:
    - reference: DOI:10.1016/B978-012373944-5.00083-3
      snippet: heterotrophic microorganisms
      notes: Supports catabolism of organic compounds by heterotrophic microbial metabolism.
  - subject: catabolism
    predicate: feeds electrons into
    object: respiratory_chain
    description: Oxidative catabolism supplies electrons to energy-conserving respiration.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: electron transfer process
      notes: Supports electron transfer through respiratory chains.
    predicate_id: METPO:2007402
  - subject: respiratory_chain
    predicate: generates
    object: proton_motive_force
    description: Respiratory electron transfer generates an ion gradient.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: generation of an electrochemical ion gradient
      notes: Supports proton motive force generation by membrane electron transport.
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: drives production of
    object: atp
    description: Proton motive force powers ATP synthesis.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: drives ATP synthesis
      notes: Supports ATP synthesis from respiratory energy conservation.
    predicate_id: biolink:produces
  - subject: catabolism
    predicate: produces
    object: precursor_metabolites
    description: Organic-compound catabolism supplies biosynthetic precursors.
    evidence:
    - reference: DOI:10.1016/B978-012373944-5.00083-3
      snippet: incorporation of a compound into biomass
      notes: Supports use of compound-derived intermediates for biomass formation.
    predicate_id: METPO:2000202
  - subject: catabolism
    predicate: generates
    object: reduced_electron_carriers
    description: Oxidation of organic substrates by catabolic pathways generates reduced
      electron carriers.
    evidence:
    - reference: DOI:10.1186/s13213-024-01761-y
      notes: Catabolic pathways (Krebs cycle and beta-oxidation) generate reduced
        carriers (NADH and FADH2).
    predicate_id: biolink:produces
  - subject: reduced_electron_carriers
    predicate: donates electrons to
    object: nadh_dehydrogenase
    description: NADH donates electrons to NADH dehydrogenase (Complex I) to enter
      the respiratory chain.
    evidence:
    - reference: DOI:10.1186/s13213-024-01761-y
      notes: NADH dehydrogenase (Complex I) extracts hydrogen/electrons from NADH;
        broad canonical ETC-entry edge.
    predicate_id: METPO:2007403
  - subject: nadh_dehydrogenase
    predicate: feeds electrons into
    object: respiratory_chain
    description: NADH dehydrogenase passes electrons into the membrane respiratory
      chain.
    evidence:
    - reference: DOI:10.1186/s13213-024-01761-y
      notes: Reduced carriers feed electrons into membrane electron-transport systems
        via NADH dehydrogenase.
    predicate_id: METPO:2007402
  - subject: organic_carbon_availability
    predicate: increases abundance of
    object: organotrophic_trait
    description: Enriched organic carbon supports proliferation of organotrophs.
    evidence:
    - reference: DOI:10.1038/s41396-023-01437-6
      notes: Enriched organic C and dissolved organic C can support the rapid propagation
        of obligate organotrophic copiotrophs.
curation_history:
- timestamp: '2026-05-05T01:35:46.879073+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-09T00:00:00-07:00'
  curator: Codex
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed organotrophy graph for organic substrate oxidation, respiratory
    energy conservation, ATP, and biosynthetic precursors.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000009×1, METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-05-23T08:21:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×1, biolink:produces×1).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:07Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007402×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:38:01Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0022904×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:41:04Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007500×1).
  llm_assisted: true
- timestamp: '2026-05-24T08:14:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:50860×1).
  llm_assisted: true
- timestamp: '2026-05-26T02:30:14Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.'
  llm_assisted: true
- timestamp: '2026-06-13T21:03:27Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 4 evidence-backed generic edges (3 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:15Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1, METPO:2007403×1, METPO:2007402×1).
  llm_assisted: true