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TraitMech › METABOLISM

carbon fixation

traitmech:000019 · CLASS · REVIEWED

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.

Autotrophic carbon fixation assimilates CO2 into organic carbon

Evidence-backed causal sketch linking inorganic CO2 to organic carbon via six recognized autotrophic carbon-fixation pathways.

Autotrophic carbon fixation assimilates CO2 into organic carbon Interactive directed graph showing evidence-backed causal relationships for carbon fixation.

Edge evidence

  • carbon dioxide fixed by carbon fixation METPO:2007404

    CO2 is the substrate fixed by autotrophic carbon-fixation pathways.

    • DOI:10.1128/AEM.02473-10 Berg reviews the distribution of autotrophic CO2-fixation pathways.
  • carbon fixation enables carbon fixation RO:0002327

    The autotrophic carbon-fixation process realizes the trait.

    • DOI:10.1146/annurev-marine-120709-142712 Hügler & Sievert support multiple autotrophic carbon-fixation pathways operating among ocean microorganisms.
  • carbonic anhydrase accelerates interconversion of carbon dioxide

    Carbonic anhydrase speeds interconversion of CO2 and bicarbonate, bridging DIC supply to demand.

    • DOI:10.1128/aem.01557-23 Scott 2024: CA activity speeds the interconversion of CO2 and HCO3-.
  • ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) uses substrate carbon dioxide

    RubisCO fixes CO2 as its carboxylation substrate in CBB-associated fixation.

    • DOI:10.1128/aem.01557-23 Scott 2024: RubisCO substrate is CO2; applies broadly to CBB-associated fixation.
  • Calvin-Benson-Bassham cycle consumes ATP biolink:consumes

    CBB carbon fixation consumes ATP (nine ATP per three CO2 fixed to one GAP).

    • DOI:10.1186/s40643-023-00705-9 Bahrle 2023: three CO2 to one GAP at the cost of nine ATP and six NADPH.
  • Calvin-Benson-Bassham cycle consumes NADPH biolink:consumes

    CBB carbon fixation consumes NADPH (six NADPH per three CO2 fixed).

    • DOI:10.1186/s40643-023-00705-9 Bahrle 2023: three CO2 to one GAP at the cost of nine ATP and six NADPH.
  • reverse (reductive) tricarboxylic acid cycle requires reduced ferredoxin

    The reverse TCA carbon-fixation cycle requires reduced ferredoxin as a cofactor.

    • DOI:10.4014/jmb.2306.06005 Kang 2023: rTCA cycle cofactors include NAD(P)H, ATP, Fdred, FADH.
  • 3-hydroxypropionate/4-hydroxybutyrate cycle requires NADPH

    The 3HP/4HB carbon-fixation cycle requires NADPH and ATP.

    • DOI:10.4014/jmb.2306.06005 Kang 2023: 3-HP/4-HB cycle NADPH and ATP required.
  • Wood-Ljungdahl pathway fixes CO2 to produce acetyl-CoA

    The Wood-Ljungdahl pathway fixes CO2 to produce acetyl-CoA.

    • DOI:10.3390/bioengineering10121357 Kurt 2023: WLP is employed for CO2 fixation and acetyl-CoA production.
  • ATP citrate lyase (aclAB) enables reverse (reductive) tricarboxylic acid cycle RO:0002327

    ATP citrate lyase (aclAB) is a key enzyme enabling the reverse TCA carbon-fixation cycle.

    • DOI:10.1038/s41564-024-01704-y Mitchell 2024: aclAB ATP citrate lyase is one of four key enzymes to run the TCA cycle in reverse.
  • carbonic anhydrase produces bicarbonate METPO:2000202

    Carbonic anhydrase interconverts CO2 and bicarbonate, supplying inorganic carbon to fixation.

    • DOI:10.1128/AEM.02473-10 Connecting edge wiring the enrichment node into the graph.

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1128/AEM.02473-10

Parent traits (1)

Children (6)

Synonyms (2)

  • CO2 fixation RELATED_SYNONYM · DOI:10.1128/AEM.02473-10
  • autotrophic carbon assimilation RELATED_SYNONYM · DOI:10.1146/annurev-marine-120709-142712

kg-microbe context

Matched 1 kg-microbe node via parent_proxy.

  • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Curation history

  1. · PROPOSED_FROM_RESEARCH · claude

    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.

  2. · CURATED_CAUSAL_GRAPH · claude

    Added evidence-backed causal graph (CO2 assimilation axis) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.

  3. · ENRICH_CAUSAL_GRAPH · claude

    Added 8 evidence-backed generic edges (12 new nodes) from the deep-research report.

  4. · FIX_ORPHAN_NODE · claude

    Connected orphaned node 'bicarbonate' via carbonic_anhydrase -[produces]-> bicarbonate.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:consumes×2, RO:0002327×1, METPO:2000202×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030634×1, CHEBI:16474×1).

  7. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17544×1, CHEBI:17513×1).

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8×1).