identifier: traitmech:000109
label: fermentative hydrogen production
definition: A fermentation in which an organism disposes of excess reducing equivalents
  by producing molecular hydrogen (H2), typically via hydrogenases acting on reduced
  ferredoxin or formate.
definition_source: DOI:10.3389/fmicb.2021.703525
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1002005
synonyms:
- synonym_text: biohydrogen production
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1016/S0360-3199(02)00131-3
evidence:
- reference: DOI:10.3389/fmicb.2021.703525
  notes: Review of fermentative energy conservation supports H2 production as a redox-balancing
    fermentation output via hydrogenases.
- reference: DOI:10.1016/S0360-3199(02)00131-3
  notes: Hallenbeck & Benemann review biological hydrogen production, including dark
    fermentative H2 generation.
canonical_examples:
- taxon_id: NCBITaxon:2336
  taxon_label: Thermotoga maritima
  note: "Model dark-fermentative hydrogen producer (near-theoretical 4 H2 per glucose); hyperthermophilic anaerobe."
  reference: PMID:19411328
causal_graphs:
- graph_id: fermentative_h2_production
  title: Fermentative H2 production disposes of excess reducing equivalents
  description: Evidence-backed causal sketch linking hydrogenase activity on reduced
    ferredoxin or formate to molecular hydrogen production as a redox-balancing fermentation
    output.
  nodes:
  - node_id: fermentative_h2_trait
    label: fermentative hydrogen production
    node_type: TRAIT
    grounding: traitmech:000109
    description: Fermentation that yields H2 to dispose of excess electrons.
  - node_id: fermentation_process
    label: fermentation
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0006113
    description: ATP-yielding catabolism with organic terminal acceptors.
  - node_id: molecular_hydrogen
    label: molecular hydrogen
    node_type: CHEMICAL
    grounding: CHEBI:18276
    description: H2 produced by hydrogenases.
  - node_id: fefe_hydrogenase
    label: '[FeFe] hydrogenase'
    node_type: GENE_OR_PROTEIN
    description: Hydrogenase enzyme that catalyzes reduction of protons to molecular
      hydrogen in dark fermentation.
  - node_id: low_h2_partial_pressure
    label: low H2 partial pressure
    node_type: ENVIRONMENTAL_FACTOR
    description: Low ambient hydrogen partial pressure in the environment.
  - node_id: high_h2_partial_pressure
    label: high H2 partial pressure
    node_type: ENVIRONMENTAL_FACTOR
    description: High ambient hydrogen partial pressure in the environment.
  - node_id: environmental_ph
    label: pH
    node_type: ENVIRONMENTAL_FACTOR
    description: Environmental pH affecting hydrogenase activity and fermentative
      H2 yield.
    grounding: PATO:0001842
  edges:
  - subject: fermentative_h2_trait
    predicate: participates in
    object: fermentation_process
    description: Fermentative H2 production is a class of fermentation metabolism.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.703525
      notes: Energy-conservation review supports H2 production as a redox-balancing
        fermentation output via hydrogenases.
    predicate_id: biolink:participates_in
  - subject: fermentative_h2_trait
    predicate: produces
    object: molecular_hydrogen
    description: Hydrogenases produce H2 to regenerate oxidized cofactors.
    evidence:
    - reference: DOI:10.1016/S0360-3199(02)00131-3
      notes: Hallenbeck & Benemann review biological hydrogen production, including
        dark fermentative H2 generation.
    predicate_id: METPO:2000202
  - subject: fefe_hydrogenase
    predicate: produces
    object: molecular_hydrogen
    description: '[FeFe]-hydrogenases are producers of H2 in dark fermentation.'
    evidence:
    - reference: DOI:10.3390/en16083321
      notes: '[FeFe]-hydrogenases explicitly noted as producers of H2 in dark fermentation.'
    predicate_id: METPO:2000202
  - subject: low_h2_partial_pressure
    predicate: stimulates
    object: fermentative_h2_trait
    description: Low ambient H2 partial pressure stimulates H2 formation.
    evidence:
    - reference: DOI:10.1128/aem.00634-23
      notes: Low ambient H2 stimulated hydrogen (H2) formation; likely broadly relevant
        across fermenters.
  - subject: high_h2_partial_pressure
    predicate: inhibits
    object: fermentative_h2_trait
    description: High ambient H2 partial pressure inhibits H2 formation (product feedback).
    evidence:
    - reference: DOI:10.1128/aem.00634-23
      notes: High H2 inhibited H2 formation.
    predicate_id: RO:0002212
  - subject: environmental_ph
    predicate: affects
    object: fermentative_h2_trait
    description: pH affects the activity of hydrogenase enzymes and thus dark fermentative
      H2 yield.
    evidence:
    - reference: DOI:10.3390/en16083321
      notes: pH affects the activity of hydrogenase enzymes and dark fermentative
        H2 yield.
curation_history:
- timestamp: '2026-06-08T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate METABOLISM trait (fermentative hydrogen production);
    round 2, sub-variant of the existing Fermentation class (METPO:1002005).
  llm_assisted: true
- timestamp: '2026-06-10T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (fermentative H2 production) with GO/CHEBI
    node groundings and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 4 evidence-backed generic edges (4 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:12Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×1, RO:0002212×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:32Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (PATO:0001842×1).
  llm_assisted: true