identifier: METPO:1000635
label: chemoautotrophic
definition: A trophic type in which an organism obtains energy from oxidation of inorganic
  compounds 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: chemoautotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1146/annurev.micro.52.1.191
  snippet: Carbon Dioxide Fixation in Chemoautotrophs
  notes: Review supports CO2 fixation as central to chemoautotrophic bacteria.
- reference: DOI:10.1128/AEM.02473-10
  snippet: Calvin-Benson reductive pentose phosphate cycle
  notes: Review supports Calvin-Benson and other microbial autotrophic CO2-fixation
    pathways.
canonical_examples:
- taxon_id: NCBITaxon:915
  taxon_label: Nitrosomonas europaea
  note: "ammonia-oxidising chemoautotroph"
  reference: PMID:12700255
- taxon_id: NCBITaxon:36861
  taxon_label: Thiobacillus denitrificans
  note: "sulfur-oxidising chemoautotroph"
  reference: PMID:16452431
causal_graphs:
- graph_id: chemoautotrophic_chemical_energy_co2_fixation
  title: Chemoautotrophic chemical-energy CO2 fixation
  description: DOI-backed graph linking chemical electron donors, energy conservation,
    RuBisCO/Calvin-Benson carbon fixation, and biomass production.
  nodes:
  - node_id: chemoautotrophic_trait
    label: chemoautotrophic
    node_type: TRAIT
    grounding: METPO:1000635
    description: Trophic type using chemical energy and CO2 as carbon source.
  - node_id: reduced_inorganic_compound
    label: reduced inorganic compound
    node_type: CHEMICAL
    description: Chemical energy substrate oxidized by chemoautotrophs.
  - node_id: respiratory_energy_conservation
    label: respiratory energy conservation
    node_type: BIOLOGICAL_PROCESS
    description: Energy conservation from redox reactions.
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier used in carbon fixation.
  - node_id: nadph
    label: NADPH
    node_type: CHEMICAL
    description: Reducing equivalent used in reductive biosynthesis.
    grounding: CHEBI:16474
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Inorganic carbon source.
  - node_id: calvin_benson_cycle
    label: Calvin-Benson cycle
    node_type: PATHWAY
    description: Common microbial CO2-fixation pathway.
    grounding: GO:0019253
  - node_id: rubisco
    label: RuBisCO
    node_type: GENE_OR_PROTEIN
    description: Carboxylating enzyme of the Calvin-Benson cycle.
    grounding: UniProtKB:A0A075WF79
  - node_id: cellular_biomass
    label: cellular biomass
    node_type: BIOLOGICAL_PROCESS
    description: Cellular material produced from fixed carbon.
  - node_id: carboxysome
    label: carboxysome
    node_type: ORGANELLE
    description: Bacterial microcompartment that encapsulates RuBisCO and carbonic
      anhydrase to concentrate CO2.
    grounding: GO:0031470
  - node_id: carbonic_anhydrase
    label: carbonic anhydrase
    node_type: GENE_OR_PROTEIN
    description: Enzyme converting bicarbonate to CO2 inside the carboxysome to feed
      RuBisCO.
    grounding: UniProtKB:A0A009PMS8
  - node_id: bicarbonate
    label: bicarbonate
    node_type: CHEMICAL
    description: Dissolved inorganic carbon species imported and converted to CO2
      for fixation.
    grounding: CHEBI:17544
  - node_id: dic_transporter
    label: dissolved inorganic carbon transporter
    node_type: GENE_OR_PROTEIN
    description: CO2/HCO3- transporters that supply inorganic carbon to the carbon-concentrating
      mechanism.
  - node_id: carbon_concentrating_mechanism
    label: carbon-concentrating mechanism
    node_type: BIOLOGICAL_PROCESS
    description: System of DIC transporters and carboxysomes that elevates CO2 around
      RuBisCO.
  - node_id: inorganic_carbon_assimilation
    label: inorganic carbon assimilation
    node_type: BIOLOGICAL_PROCESS
    description: Incorporation of inorganic carbon into cellular metabolites.
  - node_id: hp_hb_cycle
    label: 3-hydroxypropionate/4-hydroxybutyrate cycle
    node_type: PATHWAY
    description: Energy-efficient aerobic autotrophic CO2-fixation pathway.
  edges:
  - subject: chemoautotrophic_trait
    predicate: uses energy substrate
    object: reduced_inorganic_compound
    description: Chemoautotrophs derive energy from oxidizing reduced inorganic compounds.
    evidence:
    - reference: DOI:10.1146/annurev.micro.52.1.191
      snippet: physiology ... of chemoautotrophic bacteria
      notes: Review supports chemoautotrophic metabolism based on chemical energy
        and CO2 fixation.
  - subject: reduced_inorganic_compound
    predicate: enables
    object: respiratory_energy_conservation
    description: Oxidation of chemical substrates supports energy conservation.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: free energy of a redox reaction
      notes: Supports energy conservation from redox reactions in respiratory systems.
    predicate_id: RO:0002327
  - subject: respiratory_energy_conservation
    predicate: produces
    object: atp
    description: Energy conservation produces ATP for biosynthesis.
    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: respiratory_energy_conservation
    predicate: produces
    object: nadph
    description: Chemoautotrophic electron flow supplies reducing equivalents.
    evidence:
    - reference: DOI:10.1016/j.biortech.2021.125768
      snippet: NADH, or ... NADPH
      notes: Supports reduced redox cofactors in chemolithoautotrophic metabolism.
    predicate_id: METPO:2000202
  - subject: carbon_dioxide
    predicate: fixed by
    object: calvin_benson_cycle
    description: CO2 can be fixed through the Calvin-Benson cycle.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: Calvin-Benson reductive pentose phosphate cycle
      notes: Supports Calvin-Benson as a microbial autotrophic CO2-fixation pathway.
    predicate_id: METPO:2007404
  - subject: rubisco
    predicate: catalyzes
    object: calvin_benson_cycle
    description: RuBisCO catalyzes the carboxylation step of Calvin-Benson CO2 fixation.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: form I RuBisCO
      notes: Supports RuBisCO as a Calvin-Benson cycle enzyme.
    predicate_id: biolink:catalyzes
  - subject: atp
    predicate: enables
    object: calvin_benson_cycle
    description: ATP is required for chemoautotrophic CO2 fixation.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: energy required for autotrophic CO2 fixation
      notes: Supports ATP/energy requirement for carbon fixation.
    predicate_id: RO:0002327
  - subject: nadph
    predicate: enables
    object: calvin_benson_cycle
    description: Reducing equivalents support reductive CO2 fixation.
    evidence:
    - reference: DOI:10.1016/j.biortech.2021.125768
      snippet: reduction of CO2
      notes: Supports NAD(P)H-like reductant use in carbon fixation.
    predicate_id: RO:0002327
  - subject: calvin_benson_cycle
    predicate: produces
    object: cellular_biomass
    description: Fixed carbon is incorporated into cellular biomass.
    evidence:
    - reference: DOI:10.1146/annurev.micro.52.1.191
      snippet: physiology, ecology, and molecular biology
      notes: Review scope supports chemoautotrophic bacterial growth from fixed carbon.
    predicate_id: METPO:2000202
  - subject: carboxysome
    predicate: encapsulates
    object: rubisco
    description: Carboxysomes encapsulate RuBisCO and carbonic anhydrase within a
      protein shell.
    evidence:
    - reference: DOI:10.1128/AEM.01075-24
      notes: Carboxysomes encapsulate RubisCO and carbonic anhydrase (CA) within a
        protein shell.
  - subject: carboxysome
    predicate: encapsulates
    object: carbonic_anhydrase
    description: Carboxysomes encapsulate carbonic anhydrase alongside RuBisCO.
    evidence:
    - reference: DOI:10.1128/AEM.01075-24
      notes: Carboxysomes encapsulate RubisCO and carbonic anhydrase (CA) within a
        protein shell.
  - subject: carbonic_anhydrase
    predicate: produces
    object: carbon_dioxide
    description: Carbonic anhydrase converts bicarbonate to CO2 inside the carboxysome
      for RuBisCO.
    evidence:
    - reference: DOI:10.1128/AEM.01075-24
      notes: Inside carboxysomes, CA converts HCO3- to CO2, which RubisCO then fixes.
    predicate_id: METPO:2000202
  - subject: carbonic_anhydrase
    predicate: uses substrate
    object: bicarbonate
    description: Carbonic anhydrase uses bicarbonate as substrate to generate CO2.
    evidence:
    - reference: DOI:10.1128/AEM.01075-24
      notes: Inside carboxysomes, CA converts HCO3- to CO2, which RubisCO then fixes.
  - subject: dic_transporter
    predicate: enables
    object: carbon_concentrating_mechanism
    description: DIC (CO2/HCO3-) transporters supply substrate for the carbon-concentrating
      mechanism.
    evidence:
    - reference: DOI:10.1128/AEM.01075-24
      notes: CCMs consist of CO2 and HCO3- transporters and carboxysomes.
    predicate_id: RO:0002327
  - subject: carbon_concentrating_mechanism
    predicate: enables
    object: calvin_benson_cycle
    description: The carbon-concentrating mechanism elevates CO2 around RuBisCO to
      support Calvin-Benson fixation.
    evidence:
    - reference: DOI:10.1128/AEM.01075-24
      notes: CCMs consisting of transporters and carboxysomes concentrate CO2 for
        RubisCO-mediated fixation.
    predicate_id: RO:0002327
  - subject: calvin_benson_cycle
    predicate: enables
    object: inorganic_carbon_assimilation
    description: The Calvin-Benson-Bassham cycle drives inorganic carbon assimilation
      in chemolithoautotrophs.
    evidence:
    - reference: DOI:10.1101/2024.08.01.606197
      notes: The CBB cycle accounts for >99% of global autotrophy and is used in chemolithoautotrophs.
    predicate_id: RO:0002327
  - subject: carbon_dioxide
    predicate: fixed by
    object: hp_hb_cycle
    description: The 3HP/4HB cycle is an energy-efficient aerobic CO2-fixation pathway
      used by chemoautotrophs.
    evidence:
    - reference: DOI:10.1038/s42003-024-06432-x
      notes: Currently considered the most energy-efficient aerobic carbon fixation
        pathway.
    predicate_id: METPO:2007404
curation_history:
- timestamp: '2026-05-05T01:35:46.869416+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 chemical energy conservation, ATP/reductant
    generation, Calvin-Benson CO2 fixation, and biomass production.
  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:2000202×3).
  llm_assisted: true
- timestamp: '2026-05-20T05:49:25Z'
  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: '2026-05-23T21:30:07Z'
  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 3 causal-edge predicate label(s) to align with existing groundings:
    supports → enables ×3.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:22Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×3).
  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:0019253×1).
  llm_assisted: true
- timestamp: '2026-05-26T02:27:52Z'
  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: '2026-06-14T05:51:46Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:16474×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 8 evidence-backed generic edges (7 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:0002327×3, METPO:2000202×1, METPO:2007404×1).
  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:0031470×1, CHEBI:17544×1).
  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