identifier: METPO:1000646
label: hydrogenotrophic
definition: A trophic type in which an organism uses molecular hydrogen as an electron
  donor for energy generation and carbon dioxide as the primary carbon source.
definition_source: DOI:10.21775/cimb.006.159
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
created_by: Luke Wang
evidence:
- reference: DOI:10.21775/cimb.006.159
  snippet: reversible oxidation of hydrogen gas
  notes: Review supports hydrogenase-catalyzed H2 oxidation and microbial energy metabolism.
- reference: DOI:10.1128/AEM.02473-10
  snippet: assimilation of CO2
  notes: Review supports CO2 assimilation into cellular carbon in autotrophic metabolism.
canonical_examples:
- taxon_id: NCBITaxon:106590
  taxon_label: Cupriavidus necator
  note: "aerobic H2 oxidiser (Knallgas)"
  reference: PMID:34723797
- taxon_id: NCBITaxon:2190
  taxon_label: Methanocaldococcus jannaschii
  note: "hydrogenotrophic methanogen"
  reference: PMID:31333590
causal_graphs:
- graph_id: hydrogenotrophic_hydrogen_oxidation_fixation
  title: Hydrogenotrophic H2 oxidation and CO2 fixation
  description: DOI-backed graph linking hydrogenase-catalyzed H2 oxidation, electron
    transport energy conservation, and autotrophic CO2 fixation.
  nodes:
  - node_id: hydrogenotrophic_trait
    label: hydrogenotrophic
    node_type: TRAIT
    grounding: METPO:1000646
    description: Trophic type using H2 as electron donor and CO2 as carbon source.
  - node_id: molecular_hydrogen
    label: molecular hydrogen
    node_type: CHEMICAL
    grounding: CHEBI:18276
    description: Electron donor oxidized by hydrogenotrophs.
  - node_id: hydrogenase
    label: hydrogenase
    node_type: GENE_OR_PROTEIN
    description: Metalloenzyme catalyzing H2 oxidation or production.
    grounding: UniProtKB:A0A059XQG3
  - node_id: protons_electrons
    label: protons and electrons
    node_type: CHEMICAL
    description: Products of hydrogen oxidation.
  - node_id: electron_transport_system
    label: electron transport system
    node_type: PATHWAY
    description: Membrane-linked electron-transfer route supporting energy conservation.
    grounding: GO:0022900
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Ion gradient used for energy conservation.
    grounding: METPO:1007500
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Inorganic carbon source.
  - node_id: autotrophic_co2_fixation
    label: autotrophic CO2 fixation
    node_type: PATHWAY
    description: Carbon fixation pathway converting inorganic carbon into cell carbon.
    grounding: GO:0015977
  - node_id: cellular_carbon
    label: cellular carbon
    node_type: BIOLOGICAL_PROCESS
    description: Reduced cell material produced from CO2.
  - node_id: oxygen
    label: oxygen
    node_type: CHEMICAL
    description: Terminal electron acceptor that can be reduced when coupled to H2
      oxidation.
  - node_id: nitrate
    label: nitrate
    node_type: CHEMICAL
    description: Inorganic electron acceptor reducible by H2 oxidation in anaerobic
      respiration.
    grounding: CHEBI:17632
  - node_id: sulfate
    label: sulfate
    node_type: CHEMICAL
    description: Inorganic electron acceptor reducible by H2 oxidation in anaerobic
      respiration.
    grounding: CHEBI:16189
  - node_id: h2_oxidation
    label: H2 oxidation
    node_type: BIOLOGICAL_PROCESS
    description: Hydrogenase-catalyzed oxidation of molecular hydrogen to protons
      and electrons.
  - node_id: o2_sensitivity
    label: oxygen sensitivity
    node_type: ENVIRONMENTAL_FACTOR
    description: Differential O2 sensitivity that constrains which hydrogenase classes
      are usable.
  edges:
  - subject: hydrogenotrophic_trait
    predicate: uses electron donor
    object: molecular_hydrogen
    description: Hydrogenotrophy uses molecular hydrogen as an electron donor.
    evidence:
    - reference: DOI:10.21775/cimb.006.159
      snippet: oxidation of hydrogen gas
      notes: Supports H2 oxidation as a microbial energy process.
    predicate_id: METPO:2000009
  - subject: hydrogenase
    predicate: oxidizes
    object: molecular_hydrogen
    description: Hydrogenases catalyze H2 oxidation.
    evidence:
    - reference: DOI:10.21775/cimb.006.159
      snippet: reversible oxidation of hydrogen gas
      notes: Supports hydrogenase-catalyzed H2 oxidation.
    predicate_id: METPO:2000016
  - subject: molecular_hydrogen
    predicate: oxidized to
    object: protons_electrons
    description: H2 oxidation yields protons and electrons.
    evidence:
    - reference: DOI:10.21775/cimb.006.159
      snippet: H2 <--> 2 H+ + 2 e-
      notes: Supports the H2 redox half reaction.
    predicate_id: METPO:2007405
  - subject: hydrogenase
    predicate: interacts with
    object: electron_transport_system
    description: Hydrogenases can couple H2 metabolism to membrane electron transport
      systems.
    evidence:
    - reference: DOI:10.21775/cimb.006.159
      snippet: interact with membrane-bound electron transport systems
      notes: Supports coupling to electron transport.
    predicate_id: biolink:interacts_with
  - subject: electron_transport_system
    predicate: generates
    object: proton_motive_force
    description: Membrane-linked H2 metabolism can conserve energy as proton motive
      force.
    evidence:
    - reference: DOI:10.21775/cimb.006.159
      snippet: generation of a protonmotive force
      notes: Supports membrane-linked energy conservation.
    predicate_id: biolink:produces
  - subject: carbon_dioxide
    predicate: fixed by
    object: autotrophic_co2_fixation
    description: CO2 supplies carbon for autotrophic hydrogenotrophic growth.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: assimilation of CO2
      notes: Supports CO2 assimilation into cellular carbon.
    predicate_id: METPO:2007404
  - subject: autotrophic_co2_fixation
    predicate: produces
    object: cellular_carbon
    description: Carbon fixation converts CO2 into cell carbon.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: CO2 ... into cellular carbon
      notes: Supports the carbon-assimilation output.
    predicate_id: METPO:2000202
  - subject: h2_oxidation
    predicate: generates
    object: proton_motive_force
    description: Splitting H2 yields electrons and protons that can generate a proton
      gradient.
    evidence:
    - reference: DOI:10.2138/gselements.16.1.39
      notes: Splitting H2 yields electrons and protons that can generate proton gradients
        and ATP; general mechanistic process-level edge.
    predicate_id: biolink:produces
  - subject: h2_oxidation
    predicate: coupled to reduction of
    object: carbon_dioxide
    description: Hydrogen uptake can be coupled to reduction of CO2 in hydrogenotrophy.
    evidence:
    - reference: DOI:10.3390/microorganisms7020053
      notes: The hydrogenase reaction is involved in coupling hydrogen uptake to the
        reduction of electron acceptors (e.g., nitrate, sulfate, and carbon dioxide).
  - subject: h2_oxidation
    predicate: coupled to reduction of
    object: oxygen
    description: H2 oxidation can be coupled to reduction of O2 (aerobic hydrogen
      oxidation).
    evidence:
    - reference: DOI:10.2138/gselements.16.1.39
      notes: Hydrogen oxidation can be coupled to reduction of CO2/HCO3-, sulfate,
        nitrate, ferric iron and O2; high-confidence generic edge.
  - subject: h2_oxidation
    predicate: coupled to reduction of
    object: nitrate
    description: H2 oxidation can be coupled to reduction of nitrate in anaerobic
      respiration.
    evidence:
    - reference: DOI:10.2138/gselements.16.1.39
      notes: Hydrogen oxidation can be coupled to reduction of CO2/HCO3-, sulfate,
        nitrate, ferric iron and O2; generic respiratory coupling edge.
  - subject: h2_oxidation
    predicate: coupled to reduction of
    object: sulfate
    description: H2 oxidation can be coupled to reduction of sulfate in anaerobic
      respiration.
    evidence:
    - reference: DOI:10.2138/gselements.16.1.39
      notes: Hydrogen oxidation can be coupled to reduction of CO2/HCO3-, sulfate,
        nitrate, ferric iron and O2; generic respiratory coupling edge.
  - subject: h2_oxidation
    predicate: can support
    object: autotrophic_co2_fixation
    description: Coupling H2 oxidation to carbon fixation enables hydrogenotrophic
      chemosynthesis.
    evidence:
    - reference: DOI:10.1111/1751-7915.14300
      notes: By coupling hydrogen oxidation to carbon fixation, hydrogenotrophic chemosynthesis
        is a viable energy generation strategy; trait-level edge.
  - subject: o2_sensitivity
    predicate: constrains
    object: hydrogenase
    description: Differential O2 sensitivity across hydrogenase classes constrains
      their distribution and use.
    evidence:
    - reference: DOI:10.2138/gselements.16.1.39
      notes: Hydrogenase classes show different sensitivity to O2 and diverse H2 affinities;
        broad environmental constraint across classes.
curation_history:
- timestamp: '2026-05-05T01:35:46.874373+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 hydrogenase-mediated H2 oxidation, membrane-linked
    energy conservation, and CO2 fixation.
  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:2000016×1, METPO:2000202×1).
  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:interacts_with×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:2007405×1, METPO:2007404×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:41:04Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007500×1).
  llm_assisted: true
- timestamp: '2026-05-24T05:05:15Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A059XQG3×1).
  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 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.'
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 7 evidence-backed generic edges (5 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:produces×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:17632×1, CHEBI:16189×1).
  llm_assisted: true