identifier: METPO:1000638
label: chemolithoheterotrophic
definition: A trophic type characterized by the use of inorganic chemical compounds
  as electron donors for energy generation while utilizing organic compounds as the
  primary carbon source.
definition_source: DOI:10.1038/s41598-021-81412-3
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: chemolithoheterotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Anthea Guo
evidence:
- reference: DOI:10.1038/s41598-021-81412-3
  snippet: chemolithoheterotrophy
  notes: Experimental study supports chemolithoheterotrophy as Fe(II) oxidation for
    energy with glucose as carbon source.
- reference: DOI:10.1128/mBio.01112-19
  snippet: oxidize sulfur to fuel the uptake of organic compounds
  notes: Study supports sulfur oxidation coupled to organic compound uptake in a chemolithoheterotrophic
    symbiont context.
causal_graphs:
- graph_id: chemolithoheterotrophic_inorganic_energy_organic_carbon
  title: Chemolithoheterotrophic inorganic chemical energy and organic carbon use
  description: DOI-backed graph linking inorganic chemical electron donors, Fe(II)
    and reduced sulfur examples, respiratory energy conservation, organic carbon uptake,
    and biomass.
  nodes:
  - node_id: chemolithoheterotrophic_trait
    label: chemolithoheterotrophic
    node_type: TRAIT
    grounding: METPO:1000638
    description: Trophic type using inorganic chemical electron donors and organic
      carbon.
  - node_id: inorganic_chemical_donor
    label: inorganic chemical donor
    node_type: CHEMICAL
    description: Reduced inorganic chemical supplying electrons and energy.
  - node_id: ferrous_iron
    label: ferrous iron
    node_type: CHEMICAL
    description: Fe(II), an inorganic chemical energy source.
    grounding: CHEBI:29033
  - node_id: reduced_sulfur_compound
    label: reduced sulfur compound
    node_type: CHEMICAL
    description: Inorganic sulfur electron donor such as sulfide or thiosulfate.
  - node_id: organic_compound
    label: organic compound
    node_type: CHEMICAL
    description: Organic carbon source used for biosynthesis.
    grounding: CHEBI:50860
  - node_id: respiratory_chain
    label: respiratory chain
    node_type: PATHWAY
    description: Electron-transfer pathway conserving energy from donor oxidation.
    grounding: GO:0022904
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Electrochemical ion gradient generated by respiratory electron transport.
    grounding: METPO:1007500
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier produced from proton motive force.
  - node_id: nutrient_uptake
    label: organic nutrient uptake
    node_type: BIOLOGICAL_PROCESS
    description: Uptake of external organic compounds.
  - node_id: biomass
    label: biomass
    node_type: CHEMICAL
    description: Cell material formed from organic carbon.
    grounding: METPO:1007501
  - node_id: sox_pathway
    label: Sox sulfur-oxidation pathway
    node_type: PATHWAY
    description: soxCDYZAXB gene cluster mediating complete oxidation of thiosulfate
      to sulfate.
  - node_id: thiosulfate
    label: thiosulfate
    node_type: CHEMICAL
    description: Reduced inorganic sulfur electron donor oxidized to sulfate.
    grounding: CHEBI:16094
  - node_id: sulfate
    label: sulfate
    node_type: CHEMICAL
    description: Fully oxidized sulfur end product of sulfur-compound oxidation.
    grounding: CHEBI:16189
  - node_id: branched_thiosulfate_oxidation
    label: branched thiosulfate oxidation pathway
    node_type: PATHWAY
    description: Truncated Sox plus reverse Dsr/Apr/Sat oxidizing thiosulfate via
      an elemental sulfur intermediate.
  - node_id: elemental_sulfur
    label: elemental sulfur
    node_type: CHEMICAL
    description: S0 intermediate of branched sulfur-compound oxidation.
    grounding: CHEBI:26833
  - node_id: organic_carbon_importer
    label: organic carbon import system
    node_type: GENE_OR_PROTEIN
    description: Amino acid and carboxylic acid import systems mediating organic carbon
      uptake.
  edges:
  - subject: chemolithoheterotrophic_trait
    predicate: uses electron donor
    object: inorganic_chemical_donor
    description: Chemolithoheterotrophy uses inorganic chemical compounds as electron
      donors.
    evidence:
    - reference: DOI:10.1016/B978-0-12-378630-2.00219-X
      snippet: oxidize inorganic atoms or molecules
      notes: Supports inorganic chemical donors in chemolithotrophic metabolism.
    predicate_id: METPO:2000009
  - subject: ferrous_iron
    predicate: example of
    object: inorganic_chemical_donor
    description: Fe(II) is an experimentally supported inorganic donor for chemolithoheterotrophy.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      snippet: Fe(II) oxidation provides energy
      notes: Supports Fe(II) as energy source in engineered chemolithoheterotrophy.
    predicate_id: rdfs:subClassOf
  - subject: reduced_sulfur_compound
    predicate: example of
    object: inorganic_chemical_donor
    description: Reduced sulfur compounds can fuel chemolithoheterotrophic metabolism.
    evidence:
    - reference: DOI:10.1128/mBio.01112-19
      snippet: oxidize sulfur to fuel
      notes: Supports sulfur oxidation as an energy source coupled to organic compound
        uptake.
    predicate_id: rdfs:subClassOf
  - subject: inorganic_chemical_donor
    predicate: feeds electrons into
    object: respiratory_chain
    description: Oxidized inorganic donors feed electrons into respiratory energy
      conservation.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: electron transfer process
      notes: Supports electron transfer in energy-conserving 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 production from respiratory energy conservation.
    predicate_id: biolink:produces
  - subject: chemolithoheterotrophic_trait
    predicate: uses carbon source
    object: organic_compound
    description: Organic compounds provide carbon for chemolithoheterotrophic growth.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      snippet: glucose as the sole carbon source
      notes: Supports organic carbon use under inorganic donor oxidizing conditions.
    predicate_id: METPO:2000006
  - subject: organic_compound
    predicate: imported by
    object: nutrient_uptake
    description: Organic compounds are taken up for heterotrophic carbon assimilation.
    evidence:
    - reference: DOI:10.1128/mBio.01112-19
      snippet: uptake of organic compounds
      notes: Supports organic compound uptake fueled by sulfur oxidation.
  - subject: nutrient_uptake
    predicate: supports formation of
    object: biomass
    description: Uptaken organic carbon supports cell-material production.
    evidence:
    - reference: DOI:10.1016/B978-012373944-5.00083-3
      snippet: incorporation of a compound into biomass
      notes: Supports assimilation of organic compounds into biomass.
  - subject: sox_pathway
    predicate: enables
    object: sulfate
    description: The conserved soxCDYZAXB gene cluster enables complete oxidation
      of thiosulfate to sulfate without free intermediates.
    evidence:
    - reference: DOI:10.1038/s41396-021-01163-x
      notes: Gene clusters of the conserved soxCDYZAXB gene order facilitate the complete
        oxidation of thiosulfate to sulfate, without free intermediates.
    predicate_id: RO:0002327
  - subject: thiosulfate
    predicate: oxidized by
    object: sox_pathway
    description: Thiosulfate, a reduced inorganic sulfur donor, is oxidized by the
      Sox pathway.
    evidence:
    - reference: DOI:10.1038/s41396-021-01163-x
      notes: Sox system mediates complete oxidation of thiosulfate to sulfate.
  - subject: branched_thiosulfate_oxidation
    predicate: produces intermediate
    object: elemental_sulfur
    description: Truncated soxXYZAB with reverse Dsr/Apr/Sat oxidizes thiosulfate
      via an elemental sulfur intermediate.
    evidence:
    - reference: DOI:10.1038/s41396-021-01163-x
      notes: Branched thiosulfate oxidation pathway in which Dsr operating in reverse
        oxidizes sulfane-derived sulfur to sulfite, with elemental sulfur as intermediate.
  - subject: organic_carbon_importer
    predicate: supports
    object: nutrient_uptake
    description: Amino acid and carboxylic acid import systems support organic carbon
      uptake in heterotrophs and mixotrophs.
    evidence:
    - reference: DOI:10.1038/s41396-021-01163-x
      notes: Import systems for amino acids and carboxylic acids were overly abundant
        in mixotrophs and heterotrophs, supporting the organic-carbon dependency of
        the trait.
curation_history:
- timestamp: '2026-05-05T01:35:46.870986+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: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for inorganic chemical donors, Fe(II), reduced
    sulfur, respiratory energy conservation, organic nutrient uptake, and biomass.
  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:2000006×1).
  llm_assisted: true
- timestamp: '2026-05-23T08:21:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×2, 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 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:29033×1, GO:0022904×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:41:04Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (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 4 evidence-backed generic edges (6 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  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: '2026-06-24T17:21:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:16094×1, CHEBI:16189×1, CHEBI:26833×1).
  llm_assisted: true