identifier: METPO:1000647
label: lithoautotrophic
definition: A trophic type in which an organism obtains energy from inorganic electron
  donors and carbon from carbon dioxide.
definition_source: DOI:10.1128/AEM.02473-10
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: lithoautotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1016/B978-0-12-378630-2.00219-X
  snippet: inorganic atoms or molecules
  notes: Review supports inorganic compounds as reductants for lithotrophic growth.
- reference: DOI:10.1128/AEM.02473-10
  snippet: autotrophic CO2 fixation
  notes: Review supports CO2 fixation as the autotrophic carbon-assimilation process.
canonical_examples:
- taxon_id: NCBITaxon:915
  taxon_label: Nitrosomonas europaea
  note: "ammonia-oxidising lithoautotroph"
  reference: PMID:12700255
- taxon_id: NCBITaxon:106590
  taxon_label: Cupriavidus necator
  note: "H2-oxidising lithoautotroph"
  reference: PMID:36335362
causal_graphs:
- graph_id: lithoautotrophic_inorganic_donor_co2_fixation
  title: Lithoautotrophic inorganic-donor CO2 fixation
  description: DOI-backed graph linking inorganic electron donors to energy conservation,
    reducing power, and autotrophic CO2 fixation.
  nodes:
  - node_id: lithoautotrophic_trait
    label: lithoautotrophic
    node_type: TRAIT
    grounding: METPO:1000647
    description: Trophic type using inorganic electron donors and CO2 as carbon source.
  - node_id: inorganic_electron_donor
    label: inorganic electron donor
    node_type: CHEMICAL
    description: Reduced inorganic compound used for energy and reducing equivalents.
    grounding: METPO:1007502
  - node_id: respiratory_energy_conservation
    label: respiratory energy conservation
    node_type: BIOLOGICAL_PROCESS
    description: Conversion of redox energy into ion gradients and ATP.
  - node_id: reducing_power
    label: reducing power
    node_type: CAPACITY
    description: Reduced electron carriers used in biosynthesis.
    grounding: METPO:1007503
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Inorganic carbon source for autotrophy.
  - node_id: autotrophic_co2_fixation
    label: autotrophic CO2 fixation
    node_type: PATHWAY
    description: Pathways that assimilate CO2 into cellular carbon.
    grounding: GO:0015977
  - node_id: cellular_carbon
    label: cellular carbon
    node_type: BIOLOGICAL_PROCESS
    description: Organic cellular material derived from fixed CO2.
  - node_id: membrane_dehydrogenase
    label: membrane-bound (de)hydrogenase
    node_type: GENE_OR_PROTEIN
    description: Membrane-bound donor-oxidizing enzymes that reduce the quinone pool
      and drive the ETC.
  - node_id: electron_transport_chain
    label: electron transport chain
    node_type: BIOLOGICAL_PROCESS
    description: Membrane electron transfer coupling donor oxidation to proton translocation.
    grounding: GO:0022900
  - node_id: proton_motive_force
    label: proton motive force
    node_type: CAPACITY
    description: Transmembrane electrochemical proton gradient generated by the ETC.
  - node_id: atp_synthesis
    label: ATP synthesis
    node_type: BIOLOGICAL_PROCESS
    description: PMF-driven generation of ATP via ATP synthase.
    grounding: GO:0006754
  - node_id: reverse_electron_flow
    label: reverse electron flow
    node_type: BIOLOGICAL_PROCESS
    description: Endergonic uphill electron transfer that produces NAD(H) for biosynthesis.
  - node_id: nadh_reducing_equivalents
    label: NAD(H) reducing equivalents
    node_type: CHEMICAL
    description: Reduced nicotinamide cofactors used to drive CO2 fixation.
  - node_id: cytbc1_nadh_dehydrogenase
    label: cytochrome bc1 and NADH dehydrogenase
    node_type: GENE_OR_PROTEIN
    description: Respiratory complexes that mediate reverse electron transfer from
      the quinone pool to NAD+.
  - node_id: dic_acquisition_toolkit
    label: carbonic anhydrase and DIC transporters
    node_type: GENE_OR_PROTEIN
    description: DIC transporters and carbonic anhydrase enzymes that supply inorganic
      carbon to fixation.
  edges:
  - subject: lithoautotrophic_trait
    predicate: uses electron donor
    object: inorganic_electron_donor
    description: Lithoautotrophy uses inorganic compounds as electron donors.
    evidence:
    - reference: DOI:10.1016/B978-0-12-378630-2.00219-X
      snippet: inorganic atoms or molecules as a growth-supporting reductant
      notes: Supports inorganic electron donors for lithotrophic growth.
    predicate_id: METPO:2000009
  - subject: inorganic_electron_donor
    predicate: enables
    object: respiratory_energy_conservation
    description: Oxidation of inorganic donors supplies redox energy.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: free energy of a redox reaction
      notes: Supports energy conservation from respiratory redox reactions.
    predicate_id: RO:0002327
  - subject: respiratory_energy_conservation
    predicate: generates
    object: reducing_power
    description: Lithoautotrophic energy metabolism supplies reducing equivalents
      for biosynthesis.
    evidence:
    - reference: DOI:10.1016/j.biortech.2021.125768
      snippet: NADH, or ... NADPH
      notes: Review discusses reduced redox cofactors generated from chemolithoautotrophic
        electron donors.
    predicate_id: biolink:produces
  - subject: carbon_dioxide
    predicate: fixed by
    object: autotrophic_co2_fixation
    description: CO2 is assimilated by autotrophic carbon fixation pathways.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: autotrophic CO2 fixation
      notes: Supports CO2 fixation as the autotrophic carbon-assimilation process.
    predicate_id: METPO:2007404
  - subject: reducing_power
    predicate: enables
    object: autotrophic_co2_fixation
    description: Reducing equivalents support conversion of CO2 into cell carbon.
    evidence:
    - reference: DOI:10.1016/j.biortech.2021.125768
      snippet: reduction of CO2 in the carbon fixation mechanisms
      notes: Supports reductant use for CO2 reduction.
    predicate_id: RO:0002327
  - subject: autotrophic_co2_fixation
    predicate: produces
    object: cellular_carbon
    description: Autotrophic CO2 fixation produces cellular organic carbon.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: CO2 ... into cellular carbon
      notes: Supports assimilation of CO2 into cellular carbon.
    predicate_id: METPO:2000202
  - subject: membrane_dehydrogenase
    predicate: drives
    object: electron_transport_chain
    description: Membrane-bound donor-oxidizing enzymes reduce the quinone pool and
      drive the electron transport chain.
    evidence:
    - reference: DOI:10.1128/aem.00748-24
      notes: Membrane-bound (de-)hydrogenases couple donor oxidation to quinone reduction
        which drives the ETC.
  - subject: electron_transport_chain
    predicate: builds
    object: proton_motive_force
    description: The electron transport chain builds up a proton motive force.
    evidence:
    - reference: DOI:10.1128/aem.00748-24
      notes: drives the electron transport chain (ETC) to build up a proton motive
        force.
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: drives
    object: atp_synthesis
    description: The proton motive force drives ATP synthesis.
    evidence:
    - reference: DOI:10.1007/s10295-020-02309-0
      notes: This process generates a proton motive force to drive ATP synthesis.
  - subject: reverse_electron_flow
    predicate: generates
    object: nadh_reducing_equivalents
    description: Endergonic reverse electron flow generates NAD(H) for carbon fixation.
    evidence:
    - reference: DOI:10.1007/s10295-020-02309-0
      notes: an uphill (endergonic) pathway to generate NAD(H) through reverse electron
        flow.
    predicate_id: biolink:produces
  - subject: cytbc1_nadh_dehydrogenase
    predicate: mediates
    object: reverse_electron_flow
    description: Cytochrome bc1 and NADH dehydrogenase mediate reverse electron transfer
      reducing NAD+ to NAD(H).
    evidence:
    - reference: DOI:10.1007/s10295-020-02309-0
      notes: mediated by cytochrome bc1 and NADH dehydrogenase which transfer electrons
        from the ubiquinone pool to reduce NAD+ to NAD(H).
  - subject: dic_acquisition_toolkit
    predicate: facilitates
    object: autotrophic_co2_fixation
    description: DIC transporters and carbonic anhydrase facilitate dissolved inorganic
      carbon fixation.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: Autotrophs make use of a toolkit of DIC transporters and carbonic anhydrase
        enzymes to facilitate DIC fixation; broad across autotrophs.
curation_history:
- timestamp: '2026-05-05T01:35:46.874845+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 inorganic electron donors, reducing power,
    and autotrophic CO2 fixation.
  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 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 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007404×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:13:19Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings:
    supports → enables ×2.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:22Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×2).
  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:1007503×1).
  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
    (GO:0015977×1).
  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: reducing power: CHEMICAL → CAPACITY ×1.'
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 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 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×2).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0022900×1, GO:0006754×1).
  llm_assisted: true