identifier: traitmech:000019
label: carbon fixation
definition: A metabolic process in which an organism assimilates inorganic carbon
  (CO2 or bicarbonate) into organic compounds (autotrophy). Six distinct natural autotrophic
  carbon-fixation pathways are currently recognized.
definition_source: DOI:10.1128/AEM.02473-10
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000060
synonyms:
- synonym_text: CO2 fixation
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1128/AEM.02473-10
- synonym_text: autotrophic carbon assimilation
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1146/annurev-marine-120709-142712
evidence:
- reference: DOI:10.1128/AEM.02473-10
  notes: Berg review of the distribution of autotrophic CO2-fixation pathways establishes
    that, besides the Calvin-Benson-Bassham cycle, five further autotrophic carbon-fixation
    pathways are known, parent of the six pathway sub-variants proposed here.
- reference: DOI:10.1146/annurev-marine-120709-142712
  notes: Hügler & Sievert, "Beyond the Calvin cycle", supports multiple autotrophic
    carbon-fixation pathways operating among ocean microorganisms.
canonical_examples:
- taxon_id: NCBITaxon:106590
  taxon_label: Cupriavidus necator
  note: "Model chemolithoautotroph fixing CO2 via the Calvin-Benson-Bassham cycle on H2+CO2 (strain H16)."
  reference: PMID:16964242
causal_graphs:
- graph_id: carbon_fixation_co2_assimilation
  title: Autotrophic carbon fixation assimilates CO2 into organic carbon
  description: Evidence-backed causal sketch linking inorganic CO2 to organic carbon
    via six recognized autotrophic carbon-fixation pathways.
  nodes:
  - node_id: carbon_fixation_trait
    label: carbon fixation
    node_type: TRAIT
    grounding: traitmech:000019
    description: Assimilation of inorganic carbon into organic compounds (autotrophy).
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Inorganic carbon substrate fixed into biomass.
  - node_id: carbon_fixation_process
    label: carbon fixation
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0015977
    description: Conversion of inorganic CO2/bicarbonate into organic compounds.
  - node_id: bicarbonate
    label: bicarbonate
    node_type: CHEMICAL
    description: Dissolved inorganic carbon species; substrate/intermediate in carbon
      fixation.
    grounding: CHEBI:17544
  - node_id: carbonic_anhydrase
    label: carbonic anhydrase
    node_type: GENE_OR_PROTEIN
    description: Enzyme accelerating interconversion of CO2 and bicarbonate.
    grounding: UniProtKB:A0A009PMS8
  - node_id: rubisco
    label: ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)
    node_type: GENE_OR_PROTEIN
    description: Carboxylating enzyme of the Calvin-Benson-Bassham cycle that fixes
      CO2.
  - node_id: cbb_cycle
    label: Calvin-Benson-Bassham cycle
    node_type: PATHWAY
    description: Canonical autotrophic carbon-fixation pathway.
  - node_id: rtca_cycle
    label: reverse (reductive) tricarboxylic acid cycle
    node_type: PATHWAY
    description: Reductive TCA autotrophic carbon-fixation pathway.
  - node_id: hp_hb_cycle
    label: 3-hydroxypropionate/4-hydroxybutyrate cycle
    node_type: PATHWAY
    description: Autotrophic carbon-fixation pathway in some archaea.
  - node_id: wood_ljungdahl_pathway
    label: Wood-Ljungdahl pathway
    node_type: PATHWAY
    description: Reductive acetyl-CoA autotrophic carbon-fixation pathway.
    grounding: GO:0030634
  - node_id: acetyl_coa
    label: acetyl-CoA
    node_type: CHEMICAL
    description: Product of CO2 fixation via the Wood-Ljungdahl pathway.
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    description: Energy cofactor consumed by carbon-fixation pathways.
  - node_id: nadph
    label: NADPH
    node_type: CHEMICAL
    description: Reducing-equivalent cofactor consumed by carbon-fixation pathways.
    grounding: CHEBI:16474
  - node_id: reduced_ferredoxin
    label: reduced ferredoxin
    node_type: CHEMICAL
    description: Low-potential electron carrier required by the reverse TCA cycle.
    grounding: CHEBI:17513
  - node_id: atp_citrate_lyase
    label: ATP citrate lyase (aclAB)
    node_type: GENE_OR_PROTEIN
    description: Key marker enzyme enabling the reverse TCA carbon-fixation cycle.
  edges:
  - subject: carbon_dioxide
    predicate: fixed by
    object: carbon_fixation_trait
    description: CO2 is the substrate fixed by autotrophic carbon-fixation pathways.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      notes: Berg reviews the distribution of autotrophic CO2-fixation pathways.
    predicate_id: METPO:2007404
  - subject: carbon_fixation_process
    predicate: enables
    object: carbon_fixation_trait
    description: The autotrophic carbon-fixation process realizes the trait.
    evidence:
    - reference: DOI:10.1146/annurev-marine-120709-142712
      notes: Hügler & Sievert support multiple autotrophic carbon-fixation pathways
        operating among ocean microorganisms.
    predicate_id: RO:0002327
  - subject: carbonic_anhydrase
    predicate: accelerates interconversion of
    object: carbon_dioxide
    description: Carbonic anhydrase speeds interconversion of CO2 and bicarbonate,
      bridging DIC supply to demand.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: 'Scott 2024: CA activity speeds the interconversion of CO2 and HCO3-.'
  - subject: rubisco
    predicate: uses substrate
    object: carbon_dioxide
    description: RubisCO fixes CO2 as its carboxylation substrate in CBB-associated
      fixation.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: 'Scott 2024: RubisCO substrate is CO2; applies broadly to CBB-associated
        fixation.'
  - subject: cbb_cycle
    predicate: consumes
    object: atp
    description: CBB carbon fixation consumes ATP (nine ATP per three CO2 fixed to
      one GAP).
    evidence:
    - reference: DOI:10.1186/s40643-023-00705-9
      notes: 'Bahrle 2023: three CO2 to one GAP at the cost of nine ATP and six NADPH.'
    predicate_id: biolink:consumes
  - subject: cbb_cycle
    predicate: consumes
    object: nadph
    description: CBB carbon fixation consumes NADPH (six NADPH per three CO2 fixed).
    evidence:
    - reference: DOI:10.1186/s40643-023-00705-9
      notes: 'Bahrle 2023: three CO2 to one GAP at the cost of nine ATP and six NADPH.'
    predicate_id: biolink:consumes
  - subject: rtca_cycle
    predicate: requires
    object: reduced_ferredoxin
    description: The reverse TCA carbon-fixation cycle requires reduced ferredoxin
      as a cofactor.
    evidence:
    - reference: DOI:10.4014/jmb.2306.06005
      notes: 'Kang 2023: rTCA cycle cofactors include NAD(P)H, ATP, Fdred, FADH.'
  - subject: hp_hb_cycle
    predicate: requires
    object: nadph
    description: The 3HP/4HB carbon-fixation cycle requires NADPH and ATP.
    evidence:
    - reference: DOI:10.4014/jmb.2306.06005
      notes: 'Kang 2023: 3-HP/4-HB cycle NADPH and ATP required.'
  - subject: wood_ljungdahl_pathway
    predicate: fixes CO2 to produce
    object: acetyl_coa
    description: The Wood-Ljungdahl pathway fixes CO2 to produce acetyl-CoA.
    evidence:
    - reference: DOI:10.3390/bioengineering10121357
      notes: 'Kurt 2023: WLP is employed for CO2 fixation and acetyl-CoA production.'
  - subject: atp_citrate_lyase
    predicate: enables
    object: rtca_cycle
    description: ATP citrate lyase (aclAB) is a key enzyme enabling the reverse TCA
      carbon-fixation cycle.
    evidence:
    - reference: DOI:10.1038/s41564-024-01704-y
      notes: 'Mitchell 2024: aclAB ATP citrate lyase is one of four key enzymes to
        run the TCA cycle in reverse.'
    predicate_id: RO:0002327
  - subject: carbonic_anhydrase
    predicate: produces
    object: bicarbonate
    description: Carbonic anhydrase interconverts CO2 and bicarbonate, supplying inorganic
      carbon to fixation.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      notes: Connecting edge wiring the enrichment node into the graph.
    predicate_id: METPO:2000202
curation_history:
- timestamp: '2026-05-30T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate METABOLISM trait (autotrophic carbon fixation) from
    literature research to fill the carbon-fixation-pathway coverage gap. Parent of
    the six pathway-specific sub-variants.
  llm_assisted: true
- timestamp: '2026-06-10T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (CO2 assimilation axis) with CHEBI/GO
    node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 8 evidence-backed generic edges (12 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: FIX_ORPHAN_NODE
  changes: Connected orphaned node 'bicarbonate' via carbonic_anhydrase -[produces]->
    bicarbonate.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:12Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:consumes×2, RO:0002327×1, METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:18Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0030634×1, CHEBI:16474×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:32Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:17544×1, CHEBI:17513×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:18Z'
  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