identifier: METPO:1000637
label: chemolithoautotrophic
definition: A trophic type in which an organism obtains energy from oxidation of inorganic
  compounds (lithotrophy) and carbon from carbon dioxide.
definition_source: DOI:10.1146/annurev.micro.52.1.191
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: chemolithoautotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1146/annurev.micro.52.1.191
  snippet: physiology ... of chemoautotrophic bacteria
  notes: Review supports chemoautotrophic bacterial CO2 fixation.
- reference: DOI:10.1016/B978-0-12-378630-2.00219-X
  snippet: growth-supporting reductant and energy source
  notes: Review supports inorganic reductants as energy sources for chemolithotrophic
    growth.
canonical_examples:
- taxon_id: NCBITaxon:920
  taxon_label: Acidithiobacillus ferrooxidans
  note: "Archetypal iron/sulfur chemolithoautotroph; bioleaching model organism."
  reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC2754497/
causal_graphs:
- graph_id: chemolithoautotrophic_energy_and_fixation
  title: Chemolithoautotrophic energy and CO2 fixation
  description: DOI-backed graph linking inorganic donor oxidation, respiratory energy
    conservation, reductant generation, and autotrophic CO2 fixation.
  nodes:
  - node_id: chemolithoautotrophic_trait
    label: chemolithoautotrophic
    node_type: TRAIT
    grounding: METPO:1000637
    description: Trophic type using inorganic donor oxidation and CO2 fixation.
  - node_id: inorganic_electron_donor
    label: inorganic electron donor
    node_type: CHEMICAL
    description: Reduced inorganic compound oxidized for energy.
    grounding: METPO:1007502
  - node_id: electron_transport_chain
    label: electron transport chain
    node_type: PATHWAY
    description: Membrane redox chain conserving energy from donor oxidation.
    grounding: GO:0022900
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Electrochemical gradient generated by energy-conserving electron
      transfer.
    grounding: METPO:1007500
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier supporting biosynthesis.
  - node_id: reducing_power
    label: reducing power
    node_type: CAPACITY
    description: NAD(P)H or related reductants supporting CO2 reduction.
    grounding: METPO:1007503
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Primary carbon source.
  - node_id: co2_fixation_pathway
    label: CO2 fixation pathway
    node_type: PATHWAY
    description: Autotrophic pathway reducing CO2 into cell carbon.
    grounding: GO:0015977
  - node_id: biomass
    label: biomass
    node_type: CHEMICAL
    description: Cellular material generated from fixed carbon.
    grounding: METPO:1007501
  - node_id: rubisco
    label: RuBisCO
    node_type: GENE_OR_PROTEIN
    description: Ribulose-1,5-bisphosphate carboxylase/oxygenase, the carboxylating
      enzyme of the CBB cycle.
    grounding: UniProtKB:A0A075WF79
  - node_id: carbonic_anhydrase
    label: carbonic anhydrase
    node_type: GENE_OR_PROTEIN
    description: Enzyme interconverting CO2 and bicarbonate to facilitate dissolved
      inorganic carbon fixation.
    grounding: UniProtKB:A0A009PMS8
  - node_id: dic_transporter
    label: dissolved inorganic carbon transporter
    node_type: GENE_OR_PROTEIN
    description: Membrane transporter that increases intracellular availability of
      dissolved inorganic carbon.
  - node_id: dissolved_inorganic_carbon
    label: dissolved inorganic carbon
    node_type: CHEMICAL
    description: Pool of CO2 and bicarbonate supplied to autotrophic carbon-fixation
      pathways.
  edges:
  - subject: chemolithoautotrophic_trait
    predicate: uses electron donor
    object: inorganic_electron_donor
    description: Chemolithoautotrophs obtain energy from inorganic electron donors.
    evidence:
    - reference: DOI:10.1016/B978-0-12-378630-2.00219-X
      snippet: growth-supporting reductant and energy source
      notes: Supports inorganic reductants as energy sources.
    predicate_id: METPO:2000009
  - subject: inorganic_electron_donor
    predicate: feeds electrons into
    object: electron_transport_chain
    description: Donor oxidation supplies electrons to energy-conserving respiratory
      chains.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: membrane-bound electron transport chain
      notes: Supports membrane-bound respiratory chains as redox energy-conserving
        systems.
    predicate_id: METPO:2007402
  - subject: electron_transport_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.
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: drives synthesis of
    object: atp
    description: The ion gradient drives ATP synthesis.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: drives ATP synthesis
      notes: Supports ATP synthesis from respiratory ion gradients.
    predicate_id: biolink:produces
  - subject: inorganic_electron_donor
    predicate: supports generation of
    object: reducing_power
    description: Electrons from inorganic donors provide reduced cofactors for biosynthesis.
    evidence:
    - reference: DOI:10.1016/j.biortech.2021.125768
      snippet: serve as reductive power
      notes: Supports reduced cofactors generated from chemolithoautotrophic electron
        donors.
  - subject: carbon_dioxide
    predicate: fixed by
    object: co2_fixation_pathway
    description: Chemolithoautotrophs use CO2 fixation pathways for carbon assimilation.
    evidence:
    - reference: DOI:10.1146/annurev.micro.52.1.191
      snippet: Carbon Dioxide Fixation in Chemoautotrophs
      notes: Supports CO2 fixation in chemoautotrophic bacteria.
    predicate_id: METPO:2007404
  - subject: atp
    predicate: enables
    object: co2_fixation_pathway
    description: ATP generated from donor oxidation supports autotrophic CO2 fixation.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: energy required for autotrophic CO2 fixation
      notes: Supports energy demand of autotrophic CO2 fixation.
    predicate_id: RO:0002327
  - subject: reducing_power
    predicate: enables
    object: co2_fixation_pathway
    description: Reducing power supports reductive CO2 assimilation.
    evidence:
    - reference: DOI:10.1016/j.biortech.2021.125768
      snippet: reduction of CO2
      notes: Supports reductant use in CO2 fixation.
    predicate_id: RO:0002327
  - subject: co2_fixation_pathway
    predicate: produces
    object: biomass
    description: CO2 fixation generates cellular biomass.
    evidence:
    - reference: DOI:10.1146/annurev.micro.52.1.191
      snippet: physiology ... of chemoautotrophic bacteria
      notes: Review scope supports chemoautotrophic growth from fixed carbon.
    predicate_id: METPO:2000202
  - subject: rubisco
    predicate: catalyzes
    object: co2_fixation_pathway
    description: RuBisCO catalyzes the carboxylation step of the Calvin-Benson-Bassham
      CO2 fixation cycle.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) drives CBB-cycle
        CO2 fixation.
    predicate_id: biolink:catalyzes
  - subject: carbonic_anhydrase
    predicate: facilitates supply of
    object: dissolved_inorganic_carbon
    description: Carbonic anhydrase interconverts CO2 and bicarbonate to facilitate
      dissolved inorganic carbon fixation.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: carbonic anhydrase enzymes (CA) to facilitate DIC fixation.
  - subject: dic_transporter
    predicate: increases availability of
    object: dissolved_inorganic_carbon
    description: DIC transporters bridge environmental inorganic carbon supply to
      autotrophic pathway demand.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: DIC transporters bridge supply from the environment to demand by the
        autotrophic pathway.
  - subject: dissolved_inorganic_carbon
    predicate: supplies substrate to
    object: co2_fixation_pathway
    description: Dissolved inorganic carbon supplies the CO2/bicarbonate substrate
      for autotrophic fixation.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: DIC supply bridged to demand by the autotrophic pathway.
  - subject: proton_motive_force
    predicate: drives reverse electron transport for
    object: reducing_power
    description: PMF can reverse the electron transport chain to regenerate NADH/NADPH
      reducing power for fixation.
    evidence:
    - reference: DOI:10.1038/s41467-023-43524-4
      notes: The proton motive force drives ATP synthesis and can reverse the electron
        transport chain to regenerate NADH/NADPH.
curation_history:
- timestamp: '2026-05-05T01:35:46.870482+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 donor oxidation, respiratory
    energy conservation, ATP/reductant generation, and 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 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007402×1, 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 4 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007502×1, METPO:1007500×1, METPO:1007503×1, 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 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0022900×1, GO:0015977×1).
  llm_assisted: true
- timestamp: '2026-05-26T02:30:13Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 2 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1; reducing power:
    CHEMICAL → CAPACITY ×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 5 evidence-backed generic edges (4 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
    (biolink:catalyzes×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A075WF79×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A009PMS8×1).
  llm_assisted: true