identifier: METPO:1000632
label: autotrophic
definition: A trophic type in which an organism produces organic compounds from inorganic
  carbon sources (primarily carbon dioxide or bicarbonate) using energy from light
  (photoautotrophy) or from the oxidation of inorganic compounds (chemoautotrophy).
definition_source: DOI:10.1038/nrmicro.2016.130
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: TT_autotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: autotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: autotrophy
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Jed Dongjin Kim-Ozaeta
evidence:
- reference: DOI:10.1038/nrmicro.2016.130
  snippet: require only CO2 as a carbon source
  notes: Review defines autotrophic organisms by CO2 use as carbon source for growth.
- reference: DOI:10.1128/AEM.02473-10
  snippet: autotrophic CO2 fixation
  notes: Minireview supports Calvin-Benson and other microbial CO2-fixation pathways.
- reference: PMID:8590279
  snippet: Synechocystis sp. strain PCC6803
  notes: 'Organism example: Synechocystis sp. PCC 6803 is a model autotrophic cyanobacterium
    that fixes CO2 via the Calvin-Benson cycle (Kaneko et al. 1996, DNA Res, full
    genome).'
canonical_examples:
- taxon_id: NCBITaxon:106590
  taxon_label: Cupriavidus necator
  note: "H2/CO2 chemolithoautotroph"
  reference: PMID:16964242
- taxon_id: NCBITaxon:915
  taxon_label: Nitrosomonas europaea
  note: "ammonia-oxidising chemoautotroph"
  reference: PMID:12700255
- taxon_id: NCBITaxon:32046
  taxon_label: Synechococcus elongatus
  note: "photoautotrophic cyanobacterium"
  reference: PMID:25633131
causal_graphs:
- graph_id: autotrophic_inorganic_carbon_fixation
  title: Autotrophic inorganic carbon fixation
  description: DOI-backed graph linking inorganic carbon, energy and reductant supply,
    CO2-fixation pathways, carboxylating enzymes, precursor metabolites, and biomass.
  nodes:
  - node_id: autotrophic_trait
    label: autotrophic
    node_type: TRAIT
    grounding: METPO:1000632
    description: Trophic type producing organic compounds from inorganic carbon.
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Inorganic carbon source fixed by autotrophs.
  - node_id: bicarbonate
    label: bicarbonate
    node_type: CHEMICAL
    grounding: CHEBI:17544
    description: Dissolved inorganic carbon species used by many microbes.
  - node_id: energy_and_reductant
    label: energy and reductant
    node_type: CHEMICAL
    description: ATP and reducing equivalents required for carbon fixation.
  - node_id: co2_fixation_pathway
    label: CO2-fixation pathway
    node_type: PATHWAY
    description: Autotrophic pathway converting inorganic carbon into cellular carbon.
    grounding: GO:0015977
  - node_id: calvin_benson_cycle
    label: Calvin-Benson cycle
    node_type: PATHWAY
    description: Common autotrophic CO2-fixation pathway using RuBisCO.
    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: precursor_metabolites
    label: precursor metabolites
    node_type: CHEMICAL
    description: Fixed-carbon intermediates feeding biosynthesis.
  - node_id: biomass
    label: biomass
    node_type: CHEMICAL
    description: Cellular material produced from fixed inorganic carbon.
    grounding: METPO:1007501
  - node_id: environmental_ph
    label: environmental pH
    node_type: ENVIRONMENTAL_FACTOR
    description: Ambient pH that controls the speciation of dissolved inorganic carbon.
  - node_id: dissolved_inorganic_carbon
    label: dissolved inorganic carbon
    node_type: CHEMICAL
    description: Pool of CO2, bicarbonate, and carbonate available to autotrophs.
  - node_id: carbon_concentrating_mechanism
    label: carbon-concentrating mechanism
    node_type: BIOLOGICAL_PROCESS
    description: System that elevates intracellular CO2 around RuBisCO to favor carboxylation.
  - node_id: carboxysome
    label: carboxysome
    node_type: ORGANELLE
    description: Protein-shell microcompartment encapsulating RuBisCO and carbonic
      anhydrase.
    grounding: GO:0031470
  - node_id: carbonic_anhydrase
    label: carbonic anhydrase
    node_type: GENE_OR_PROTEIN
    description: Enzyme interconverting bicarbonate and CO2, supplying CO2 to RuBisCO.
    grounding: UniProtKB:A0A009PMS8
  - node_id: wood_ljungdahl_pathway
    label: Wood-Ljungdahl pathway
    node_type: PATHWAY
    description: Reductive acetyl-CoA pathway fixing two CO2 into acetyl-CoA.
    grounding: GO:0030634
  - node_id: acetyl_coa
    label: acetyl-CoA
    node_type: CHEMICAL
    grounding: CHEBI:15351
    description: Central metabolite product of Wood-Ljungdahl CO2 fixation.
  - node_id: codh_acs
    label: CO dehydrogenase/acetyl-CoA synthase (CODH/ACS)
    node_type: GENE_OR_PROTEIN
    description: Enzyme complex catalyzing the terminal acetyl-CoA-forming step of
      the Wood-Ljungdahl pathway.
  - node_id: molecular_hydrogen
    label: molecular hydrogen
    node_type: CHEMICAL
    grounding: CHEBI:18276
    description: Electron donor supplying reducing equivalents for CO2 reduction.
  edges:
  - subject: autotrophic_trait
    predicate: uses carbon source
    object: carbon_dioxide
    description: Autotrophs use CO2 as an inorganic carbon source.
    evidence:
    - reference: DOI:10.1038/nrmicro.2016.130
      snippet: require only CO2 as a carbon source
      notes: Supports CO2 as the defining autotrophic carbon source.
    predicate_id: METPO:2000006
  - subject: bicarbonate
    predicate: alternative inorganic carbon source for
    object: autotrophic_trait
    description: Bicarbonate is another inorganic carbon species available for autotrophic
      fixation.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: autotrophic carbon dioxide assimilation pathway
      notes: Supports inorganic carbon assimilation by autotrophic pathways.
  - subject: energy_and_reductant
    predicate: regulates
    object: co2_fixation_pathway
    description: Autotrophic carbon fixation requires energy and reducing power.
    evidence:
    - reference: DOI:10.1038/nrmicro2365
      snippet: energy demand of the autotrophic pathways
      notes: Supports energy requirements of autotrophic carbon fixation pathways.
    predicate_id: RO:0002211
  - subject: carbon_dioxide
    predicate: fixed by
    object: co2_fixation_pathway
    description: CO2 is converted into organic carbon by autotrophic fixation pathways.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: autotrophic CO2 fixation
      notes: Supports CO2 fixation as the core autotrophic biosynthetic process.
    predicate_id: METPO:2007404
  - subject: calvin_benson_cycle
    predicate: example of
    object: co2_fixation_pathway
    description: The Calvin-Benson cycle is a major autotrophic CO2-fixation pathway.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: Calvin-Benson reductive pentose phosphate cycle
      notes: Supports the Calvin-Benson cycle as a microbial autotrophic pathway.
    predicate_id: rdfs:subClassOf
  - subject: rubisco
    predicate: catalyzes
    object: calvin_benson_cycle
    description: RuBisCO is the key carboxylating enzyme of the Calvin-Benson cycle.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: ribulose-1,5-bisphosphate carboxylase
      notes: Supports RuBisCO as the marker enzyme for Calvin-Benson autotrophy.
    predicate_id: biolink:catalyzes
  - subject: co2_fixation_pathway
    predicate: produces
    object: precursor_metabolites
    description: Fixed carbon is converted into central biosynthetic precursors.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: converted to other central intermediates
      notes: Supports conversion of fixed carbon into central metabolites.
    predicate_id: METPO:2000202
  - subject: precursor_metabolites
    predicate: incorporated into
    object: biomass
    description: Fixed-carbon precursors are incorporated into cellular biomass.
    evidence:
    - reference: DOI:10.1038/nrmicro.2016.130
      snippet: microbial autotrophic production
      notes: Supports production of biomass and products from autotrophic CO2 fixation.
    predicate_id: biolink:part_of
  - subject: environmental_ph
    predicate: determines speciation of
    object: dissolved_inorganic_carbon
    description: pH sets the relative abundance of CO2, bicarbonate, and carbonate
      available for fixation.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: CO2 predominates below ~pH 6.4, HCO3- at circumneutral pH, and CO32-
        above ~pH 10.3; DIC form availability constrains the fixation route.
  - subject: carbon_concentrating_mechanism
    predicate: supplies substrate to
    object: co2_fixation_pathway
    description: CCMs elevate intracellular CO2 to enhance autotrophic carbon fixation.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: Transporters and CO2-active systems generate elevated intracellular HCO3-
        delivered for carboxysomal CO2 fixation.
  - subject: carboxysome
    predicate: contains
    object: rubisco
    description: Carboxysomes encapsulate RuBisCO to concentrate CO2 around the carboxylating
      enzyme.
    evidence:
    - reference: DOI:10.1111/ppl.14140
      notes: Carboxysomes are protein shell encapsulated ribulose-1,5-bisphosphate
        carboxylase/oxygenase (RuBisCO).
  - subject: carboxysome
    predicate: contains
    object: carbonic_anhydrase
    description: Carboxysomes house carbonic anhydrase alongside RuBisCO.
    evidence:
    - reference: DOI:10.1128/aem.01075-24
      notes: 'Carboxysomes contain two key enzymes: carbonic anhydrase and RuBisCO.'
  - subject: carbonic_anhydrase
    predicate: converts
    object: carbon_dioxide
    description: Carbonic anhydrase converts bicarbonate to CO2 for RuBisCO fixation.
    evidence:
    - reference: DOI:10.1128/aem.01075-24
      notes: When cytoplasmic HCO3- enters carboxysomes, CA converts it to CO2, which
        is fixed by RuBisCO.
  - subject: wood_ljungdahl_pathway
    predicate: example of
    object: co2_fixation_pathway
    description: The Wood-Ljungdahl pathway is an autotrophic CO2-fixation pathway
      producing acetyl-CoA.
    evidence:
    - reference: DOI:10.1039/D4CB00099D
      notes: Two CO2 molecules are fixed to acetyl-CoA via the WLP, requiring one
        ATP and eight electrons.
    predicate_id: rdfs:subClassOf
  - subject: wood_ljungdahl_pathway
    predicate: produces
    object: acetyl_coa
    description: The Wood-Ljungdahl pathway yields acetyl-CoA from fixed CO2.
    evidence:
    - reference: DOI:10.1039/D4CB00099D
      notes: Two CO2 molecules to acetyl-CoA via the WLP.
    predicate_id: METPO:2000202
  - subject: codh_acs
    predicate: catalyzes
    object: wood_ljungdahl_pathway
    description: CODH/ACS catalyzes the terminal acetyl-CoA-forming step of the Wood-Ljungdahl
      pathway.
    evidence:
    - reference: DOI:10.1039/D4CB00099D
      notes: CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) produces acetyl-CoA in
        the WLP.
    predicate_id: biolink:catalyzes
  - subject: molecular_hydrogen
    predicate: provides reductant for
    object: wood_ljungdahl_pathway
    description: H2 supplies reducing equivalents driving CO2 reduction in the Wood-Ljungdahl
      pathway.
    evidence:
    - reference: DOI:10.1039/D4CB00099D
      notes: H2 or CO must be utilized as an energy source to provide reducing equivalents
        for full CO2 reduction.
curation_history:
- timestamp: '2026-05-05T01:35:46.867544+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-09T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for inorganic carbon fixation, Calvin-Benson
    cycle, RuBisCO, precursor metabolites, and biomass formation.
  llm_assisted: true
- timestamp: '2026-05-16T05:00:00-07:00'
  curator: claude
  action: ADDED_ORGANISM_EXAMPLE
  changes: Added Synechocystis sp. PCC 6803 organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000006×1, 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:catalyzes×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
    (rdfs:subClassOf×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 1 causal-edge predicate label(s) to align with existing groundings:
    drives → regulates ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:22Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1).
  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: '2026-05-24T04:41:04Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007501×1).
  llm_assisted: true
- timestamp: '2026-05-24T07:34:58Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: biomass: BIOLOGICAL_PROCESS → CHEMICAL ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T08:14:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0015977×1).
  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: '2026-06-13T21:03:27Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:part_of×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 9 evidence-backed generic edges (9 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×1, METPO:2000202×1, biolink:catalyzes×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0030634×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0031470×1).
  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