identifier: METPO:1000648
label: lithoheterotrophic
definition: A trophic type in which an organism obtains energy from the oxidation
  of inorganic compounds while using organic compounds as the primary carbon source
  for biosynthesis.
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: lithoheterotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Jed Dongjin Kim-Ozaeta
evidence:
- reference: DOI:10.1038/s41598-021-81412-3
  snippet: engineered lithoheterotrophic strain
  notes: Experimental study supports Fe(II)-dependent lithoheterotrophic growth with
    glucose as carbon source.
- reference: DOI:10.1016/B978-0-12-378630-2.00219-X
  snippet: oxidize inorganic atoms or molecules
  notes: Review supports inorganic compound oxidation as lithotrophic energy metabolism.
causal_graphs:
- graph_id: lithoheterotrophic_inorganic_energy_organic_carbon
  title: Lithoheterotrophic inorganic energy and organic carbon use
  description: DOI-backed graph linking inorganic electron donors, Fe(II) oxidation,
    respiratory energy conservation, organic carbon uptake, precursor metabolites,
    and biomass.
  nodes:
  - node_id: lithoheterotrophic_trait
    label: lithoheterotrophic
    node_type: TRAIT
    grounding: METPO:1000648
    description: Trophic type using inorganic donors for energy and organic compounds
      for carbon.
  - node_id: inorganic_electron_donor
    label: inorganic electron donor
    node_type: CHEMICAL
    description: Reduced inorganic substrate oxidized for energy.
    grounding: METPO:1007502
  - node_id: ferrous_iron
    label: ferrous iron
    node_type: CHEMICAL
    description: Fe(II), an inorganic electron donor in lithoheterotrophic iron oxidation.
    grounding: CHEBI:29033
  - node_id: organic_carbon
    label: organic carbon
    node_type: CHEMICAL
    description: Organic compound used as the cellular carbon source.
    grounding: CHEBI:50860
  - node_id: glucose
    label: glucose
    node_type: CHEMICAL
    grounding: CHEBI:17234
    description: Experimental organic carbon source in engineered lithoheterotrophy.
  - node_id: respiratory_chain
    label: respiratory chain
    node_type: PATHWAY
    description: Electron-transport route conserving energy from inorganic donor oxidation.
    grounding: GO:0022904
  - node_id: oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Electron acceptor for aerobic Fe(II)-oxidizing growth.
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier generated by respiratory energy conservation.
  - node_id: precursor_metabolites
    label: precursor metabolites
    node_type: CHEMICAL
    description: Organic-carbon intermediates used for biosynthesis.
  - node_id: biomass
    label: biomass
    node_type: CHEMICAL
    description: Cell material formed from organic carbon.
    grounding: METPO:1007501
  - node_id: microaerobic_conditions
    label: microaerobic conditions
    node_type: ENVIRONMENTAL_FACTOR
    description: Low-oxygen conditions that permit biological Fe(II) oxidation by
      limiting abiotic Fe(II) oxidation.
  - node_id: ferrous_iron_oxidation
    label: Fe(II) oxidation
    node_type: BIOLOGICAL_PROCESS
    description: Oxidation of ferrous iron serving as the energy-yielding lithotrophic
      process.
  - node_id: sulfide
    label: sulfide
    node_type: CHEMICAL
    description: Reduced inorganic sulfur electron donor oxidized for lithotrophic
      energy.
    grounding: CHEBI:15138
  - node_id: sqr
    label: sulfide:quinone oxidoreductase (SQR)
    node_type: GENE_OR_PROTEIN
    description: Key enzyme catalyzing oxidation/detoxification of sulfide in lithotrophic
      sulfur oxidizers.
  - node_id: thiosulfate
    label: thiosulfate
    node_type: CHEMICAL
    description: Inorganic sulfur electron donor oxidized via the Sox system.
    grounding: CHEBI:16094
  - node_id: sox_system
    label: periplasmic Sox system
    node_type: GENE_OR_PROTEIN
    description: Periplasmic sox gene cluster encoding thiosulfate oxidation.
  - node_id: conductive_pili_cytochromes
    label: conductive pili and c-type cytochromes
    node_type: GENE_OR_PROTEIN
    description: Surface structures mediating extracellular/direct interspecies electron
      transfer.
  - node_id: diet
    label: direct interspecies electron transfer
    node_type: BIOLOGICAL_PROCESS
    description: Cell-to-cell electron conduction via conductive pili and c-type cytochromes.
  edges:
  - subject: lithoheterotrophic_trait
    predicate: uses electron donor
    object: inorganic_electron_donor
    description: Lithoheterotrophy uses inorganic compounds as energy-generating electron
      donors.
    evidence:
    - reference: DOI:10.1016/B978-0-12-378630-2.00219-X
      snippet: oxidize inorganic atoms or molecules
      notes: Supports inorganic chemical oxidation as lithotrophic energy metabolism.
    predicate_id: METPO:2000009
  - subject: ferrous_iron
    predicate: example of
    object: inorganic_electron_donor
    description: Fe(II) is an example inorganic electron donor for lithotrophic growth.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      snippet: Fe(II) as the energy source
      notes: Supports Fe(II) oxidation as the energy source in engineered lithoheterotrophy.
    predicate_id: rdfs:subClassOf
  - subject: inorganic_electron_donor
    predicate: feeds electrons into
    object: respiratory_chain
    description: Oxidation of inorganic donors feeds respiratory electron transport.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: membrane-bound electron transport chain
      notes: Supports respiratory chains as energy-conserving redox systems.
    predicate_id: METPO:2007402
  - subject: respiratory_chain
    predicate: transfers electrons to
    object: oxygen
    description: Aerobic Fe(II)-oxidizing lithotrophy can reduce oxygen.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      snippet: oxidation of Fe(II) coupled to the reduction of oxygen
      notes: Supports oxygen reduction coupled to Fe(II) oxidation.
    predicate_id: METPO:2007403
  - subject: respiratory_chain
    predicate: produces
    object: atp
    description: Respiratory electron transport supports 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: METPO:2000202
  - subject: lithoheterotrophic_trait
    predicate: uses carbon source
    object: organic_carbon
    description: Lithoheterotrophy uses organic compounds as carbon sources.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      snippet: glucose as the sole carbon source
      notes: Supports organic carbon use under Fe(II)-oxidizing lithoheterotrophic
        conditions.
    predicate_id: METPO:2000006
  - subject: glucose
    predicate: example of
    object: organic_carbon
    description: Glucose is an experimentally supported organic carbon source.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      snippet: glucose as the sole carbon source
      notes: Supports glucose as the organic carbon source in the engineered strain.
    predicate_id: rdfs:subClassOf
  - subject: organic_carbon
    predicate: converted to
    object: precursor_metabolites
    description: Organic carbon supplies biosynthetic precursors.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      snippet: biomass precursors provided by glucose
      notes: Supports glucose-derived carbon as a source of biomass precursors.
  - subject: precursor_metabolites
    predicate: incorporated into
    object: biomass
    description: Organic-carbon precursors are incorporated into cellular material.
    evidence:
    - reference: DOI:10.1016/B978-012373944-5.00083-3
      snippet: incorporation of a compound into biomass
      notes: Supports assimilation of compounds into biomass.
    predicate_id: biolink:part_of
  - subject: microaerobic_conditions
    predicate: supports
    object: ferrous_iron_oxidation
    description: Microaerobic conditions support Fe(II)-oxidizing growth by limiting
      abiotic Fe(II) oxidation.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      notes: requiring microaerobic conditions because atmospheric O2 abiotically
        oxidizes Fe(II)
  - subject: ferrous_iron
    predicate: oxidized in
    object: ferrous_iron_oxidation
    description: Ferrous iron is the substrate oxidized in the energy-yielding Fe(II)
      oxidation process.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      notes: the oxidation of Fe(II) coupled to the reduction of oxygen
  - subject: ferrous_iron_oxidation
    predicate: feeds electrons into
    object: respiratory_chain
    description: Fe(II) oxidation provides electrons for respiratory energy conservation.
    evidence:
    - reference: DOI:10.1038/s41598-021-81412-3
      notes: Fe(II) oxidation provides energy while organic carbon serves primarily
        as the carbon source
    predicate_id: METPO:2007402
  - subject: sulfide
    predicate: example of
    object: inorganic_electron_donor
    description: Sulfide is an inorganic electron donor for lithotrophic sulfur oxidation.
    evidence:
    - reference: DOI:10.1038/s41467-025-56588-1
      notes: sulfide oxidation as lithotrophic energy metabolism in nitrate-reducing
        chemolithotrophs/heterotrophs
    predicate_id: rdfs:subClassOf
  - subject: sqr
    predicate: oxidizes
    object: sulfide
    description: SQR catalyzes oxidation/detoxification of sulfide as a sulfide-oxidation
      module.
    evidence:
    - reference: DOI:10.1038/s41467-025-56588-1
      notes: a key enzyme that can catalyze sulfide detoxification in nitrate-reducing
        chemolithoautotrophs
    predicate_id: METPO:2000016
  - subject: thiosulfate
    predicate: example of
    object: inorganic_electron_donor
    description: Thiosulfate is an inorganic sulfur electron donor for lithotrophic
      oxidation.
    evidence:
    - reference: DOI:10.1038/s41467-025-56588-1
      notes: periplasmic sox gene clusters encoding for thiosulfate oxidation
    predicate_id: rdfs:subClassOf
  - subject: sox_system
    predicate: oxidizes
    object: thiosulfate
    description: The periplasmic Sox system encodes oxidation of thiosulfate.
    evidence:
    - reference: DOI:10.1038/s41467-025-56588-1
      notes: periplasmic sox gene clusters encoding for thiosulfate oxidation
    predicate_id: METPO:2000016
  - subject: conductive_pili_cytochromes
    predicate: enables
    object: diet
    description: Conductive pili and outer-surface c-type cytochromes enable direct
      interspecies electron transfer.
    evidence:
    - reference: DOI:10.3390/life14050591
      notes: direct interspecies electron transfer (DIET) via conductive pili and
        outer-surface c-type cytochromes
    predicate_id: RO:0002327
curation_history:
- timestamp: '2026-05-05T01:35:46.875356+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 electron donor oxidation, Fe(II),
    respiratory energy conservation, organic carbon use, and biomass formation.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000009×1, METPO:2000202×1, METPO:2000006×1).
  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×2).
  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 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:29033×1, CHEBI:50860×1, 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:1007502×1, METPO:1007501×1).
  llm_assisted: true
- timestamp: '2026-05-24T07:34:59Z'
  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: '2026-06-13T21:03:27Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:part_of×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 8 evidence-backed generic edges (8 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×2, METPO:2000016×2, METPO:2007402×1, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:15138×1, CHEBI:16094×1).
  llm_assisted: true