identifier: METPO:1000663
label: chemoorganotrophic
definition: A trophic type in which an organism obtains energy through chemical oxidation
  of organic compounds that also serve as the carbon source for biosynthesis.
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: chemoorganotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Jed Dongjin Kim-Ozaeta
evidence:
- reference: DOI:10.1016/B978-012373944-5.00083-3
  snippet: chemical energy
  notes: Encyclopedia chapter classifies chemotrophy by chemical rather than light
    energy sources.
- reference: DOI:10.1016/j.bbabio.2008.09.008
  snippet: membrane-bound electron transport chain
  notes: Review supports respiratory-chain energy conservation from redox reactions.
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "organic compounds as energy and carbon"
  reference: DOI:10.5772/intechopen.105508
- taxon_id: NCBITaxon:303
  taxon_label: Pseudomonas putida
  note: "versatile chemoorganotroph"
  reference: PMID:12534463
causal_graphs:
- graph_id: chemoorganotrophic_organic_oxidation_energy
  title: Chemoorganotrophic organic chemical oxidation
  description: DOI-backed graph for chemical oxidation of organic compounds, electron
    transfer to respiratory chains, proton motive force, ATP synthesis, and organic
    carbon assimilation.
  nodes:
  - node_id: chemoorganotrophic_trait
    label: chemoorganotrophic
    node_type: TRAIT
    grounding: METPO:1000663
    description: Trophic type obtaining energy from chemical oxidation of organic
      compounds.
  - node_id: organic_compound
    label: organic compound
    node_type: CHEMICAL
    description: Reduced organic substrate serving as chemical energy source.
    grounding: CHEBI:50860
  - node_id: substrate_oxidation
    label: organic substrate oxidation
    node_type: BIOLOGICAL_PROCESS
    description: Oxidation of organic compounds releasing electrons and energy.
  - node_id: respiratory_chain
    label: respiratory chain
    node_type: PATHWAY
    description: Energy-conserving membrane electron-transfer system.
    grounding: GO:0022904
  - node_id: terminal_electron_acceptor
    label: terminal electron acceptor
    node_type: CHEMICAL
    description: Oxidized compound accepting electrons at the end of respiration.
    grounding: METPO:1007504
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Ion gradient generated by respiratory electron transport.
    grounding: METPO:1007500
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier formed by ATP synthase.
  - node_id: biomass
    label: biomass
    node_type: CHEMICAL
    description: Cell material built from organic carbon.
    grounding: METPO:1007501
  - node_id: reduced_cofactor
    label: reduced redox cofactor (NADH)
    node_type: CHEMICAL
    description: Reduced electron-carrying cofactor (e.g. NADH) formed during organic
      substrate oxidation.
  - node_id: quinone_pool
    label: quinone pool
    node_type: CHEMICAL
    description: Membrane ubiquinone/menaquinone pool that shuttles electrons within
      the respiratory chain.
  - node_id: aerobic_respiration
    label: aerobic respiration
    node_type: BIOLOGICAL_PROCESS
    description: Respiratory metabolism using oxygen as terminal electron acceptor.
    grounding: GO:0009060
  - node_id: anaerobic_respiration
    label: anaerobic respiration
    node_type: BIOLOGICAL_PROCESS
    description: Respiratory metabolism using inorganic acceptors such as nitrate
      or nitrite.
    grounding: GO:0009061
  - node_id: oxygen
    label: oxygen
    node_type: ENVIRONMENTAL_FACTOR
    description: Molecular oxygen acting as terminal electron acceptor when present.
    grounding: ENVO:01001495
  - node_id: nitrate_nitrite
    label: nitrate/nitrite
    node_type: ENVIRONMENTAL_FACTOR
    description: Inorganic alternative electron acceptors enabling anaerobic respiration.
  - node_id: acceptor_absence
    label: absence of external electron acceptor
    node_type: ENVIRONMENTAL_FACTOR
    description: Condition in which no external terminal electron acceptor is available.
  - node_id: fermentation
    label: fermentation
    node_type: BIOLOGICAL_PROCESS
    description: Energy metabolism with electrons relocated onto an organic catabolic
      product.
    grounding: GO:0006113
  - node_id: substrate_level_phosphorylation
    label: substrate-level phosphorylation
    node_type: BIOLOGICAL_PROCESS
    description: ATP generation by direct phosphate transfer from a phosphorylated
      intermediate.
  edges:
  - subject: chemoorganotrophic_trait
    predicate: uses chemical energy source
    object: organic_compound
    description: Chemoorganotrophic metabolism derives energy from organic chemicals.
    evidence:
    - reference: DOI:10.1016/B978-012373944-5.00083-3
      snippet: reduced organic compound
      notes: Supports reduced organic compounds as the source for chemoorganotrophic
        growth.
  - subject: organic_compound
    predicate: oxidized during
    object: substrate_oxidation
    description: Organic substrates are oxidized to release reducing equivalents.
    evidence:
    - reference: DOI:10.1016/B978-012373944-5.00083-3
      snippet: oxidation of a reduced ... organic compound
      notes: Supports dissimilatory oxidation of reduced organic compounds.
  - subject: substrate_oxidation
    predicate: feeds electrons into
    object: respiratory_chain
    description: Organic substrate oxidation supplies electrons to respiration.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: electron transfer process
      notes: Supports electron flow through respiratory chains.
    predicate_id: METPO:2007402
  - subject: respiratory_chain
    predicate: transfers electrons to
    object: terminal_electron_acceptor
    description: Respiration moves electrons to terminal electron acceptors.
    evidence:
    - reference: DOI:10.1128/mmbr.61.4.533-616.1997
      snippet: terminal electron acceptor
      notes: Supports terminal electron acceptors in respiratory metabolism.
    predicate_id: METPO:2007403
  - subject: respiratory_chain
    predicate: generates
    object: proton_motive_force
    description: Respiratory chains generate an electrochemical 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 from electron transport.
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: drives production of
    object: atp
    description: Proton motive force drives ATP synthesis.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: drives ATP synthesis
      notes: Supports ATP production from respiratory energy conservation.
    predicate_id: biolink:produces
  - subject: organic_compound
    predicate: assimilated into
    object: biomass
    description: Organic compounds also supply carbon for biosynthesis.
    evidence:
    - reference: DOI:10.1016/B978-012373944-5.00083-3
      snippet: carbon source
      notes: Supports organic compounds as carbon sources for biosynthesis.
  - subject: substrate_oxidation
    predicate: produces reduced cofactor
    object: reduced_cofactor
    description: Organic substrate oxidation reduces redox cofactors such as NAD to
      NADH.
    evidence:
    - reference: DOI:10.1093/femsre/fuae016
      notes: Redox cofactors (NAD and ferredoxin) accept electrons and become reduced
        during organic oxidation.
  - subject: reduced_cofactor
    predicate: feeds electrons into
    object: quinone_pool
    description: Reduced cofactors donate electrons to the membrane quinone pool via
      dehydrogenases.
    evidence:
    - reference: DOI:10.1186/s13213-024-01761-y
      notes: Some dehydrogenases inject electrons into the quinone pool of the respiratory
        chain.
    predicate_id: METPO:2007402
  - subject: quinone_pool
    predicate: transfers electrons to
    object: terminal_electron_acceptor
    description: The quinone pool passes electrons to terminal oxidases reducing the
      terminal acceptor.
    evidence:
    - reference: DOI:10.1186/s13213-024-01761-y
      notes: Quinol oxidases pass electrons from ubiquinols/menaquinones to oxygen.
    predicate_id: METPO:2007403
  - subject: oxygen
    predicate: enables
    object: aerobic_respiration
    description: Presence of oxygen enables aerobic respiratory chemoorganotrophy.
    evidence:
    - reference: DOI:10.2166/9781789062304_0009
      notes: Electron acceptors range from O2 in aerobic respiration.
    predicate_id: RO:0002327
  - subject: nitrate_nitrite
    predicate: enables
    object: anaerobic_respiration
    description: Inorganic acceptors such as nitrate/nitrite enable anaerobic respiratory
      chemoorganotrophy.
    evidence:
    - reference: DOI:10.2166/9781789062304_0009
      notes: Organisms catabolize an organic e-donor by respiration with an inorganic
        e-acceptor such as nitrite or nitrate.
    predicate_id: RO:0002327
  - subject: acceptor_absence
    predicate: leads to
    object: fermentation
    description: Absence of an external terminal electron acceptor leads to fermentation.
    evidence:
    - reference: DOI:10.2166/9781789062304_0009
      notes: In fermentation, no terminal e-acceptor is available; electrons are relocated
        onto an organic catabolic product.
  - subject: fermentation
    predicate: generates ATP via
    object: substrate_level_phosphorylation
    description: Fermentation generates ATP primarily by substrate-level phosphorylation.
    evidence:
    - reference: DOI:10.1093/femsre/fuae016
      notes: In fermentation, ATP is generated primarily by substrate-level phosphorylation.
  - subject: substrate_level_phosphorylation
    predicate: produces
    object: atp
    description: Substrate-level phosphorylation directly produces ATP.
    evidence:
    - reference: DOI:10.1093/femsre/fuae016
      notes: Fermentative ATP is produced by substrate-level phosphorylation.
    predicate_id: METPO:2000202
curation_history:
- timestamp: '2026-05-05T01:35:46.883201+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-08T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for organic chemical oxidation, respiratory
    electron transport, ATP synthesis, and biomass formation.
  llm_assisted: true
- timestamp: '2026-05-23T08:21:50Z'
  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: '2026-05-23T21:30:07Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007402×1, METPO:2007403×1).
  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 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007504×1, METPO:1007500×1, METPO:1007501×1).
  llm_assisted: true
- timestamp: '2026-05-24T07:34:58Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: biomass: BIOLOGICAL_PROCESS → CHEMICAL ×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: '2026-05-26T02:30:13Z'
  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 8 evidence-backed generic edges (9 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×2, METPO:2007402×1, METPO:2007403×1, METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0009060×1, GO:0009061×1, GO:0006113×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (ENVO:01001495×1).
  llm_assisted: true