identifier: METPO:1000652
label: mixotrophic
definition: A trophic type in which an organism can use both organic and inorganic
  carbon sources for growth.
definition_source: DOI:10.1128/AEM.01559-06
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: mixotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1128/AEM.01559-06
  snippet: Evidence for the ubiquity of mixotrophic bacteria
  notes: Review supports bacterial mixotrophy as combined metabolic modes in marine
    systems.
- reference: DOI:10.1073/pnas.1305998110
  snippet: combination of modes by which an organism can obtain its energy and carbon
  notes: Perspective supports mixotrophy as combined energy and carbon acquisition
    modes.
canonical_examples:
- taxon_id: NCBITaxon:1021
  taxon_label: Beggiatoa
  note: "chemolitho/organo mixotroph"
  reference: PMID:32575621
- taxon_id: NCBITaxon:266
  taxon_label: Paracoccus denitrificans
  note: "facultative mixotroph"
  reference: PMID:29946833
causal_graphs:
- graph_id: mixotrophic_dual_carbon_energy_use
  title: Mixotrophic dual carbon and energy use
  description: DOI-backed graph linking organic carbon uptake, inorganic carbon fixation,
    light or chemical energy capture, and biomass production.
  nodes:
  - node_id: mixotrophic_trait
    label: mixotrophic
    node_type: TRAIT
    grounding: METPO:1000652
    description: Trophic type combining organic and inorganic carbon-use modes.
  - node_id: organic_carbon
    label: organic carbon
    node_type: CHEMICAL
    description: Organic compounds assimilated or catabolized by mixotrophs.
    grounding: CHEBI:50860
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Inorganic carbon source fixed by autotrophic modules.
  - node_id: dissolved_organic_matter
    label: dissolved organic matter
    node_type: CHEMICAL
    description: Environmental organic substrate pool available to aquatic microbes.
  - node_id: phototrophic_energy_capture
    label: phototrophic energy capture
    node_type: PATHWAY
    description: Light-driven energy capture, including rhodopsin or photosynthetic
      systems.
  - node_id: co2_fixation_pathway
    label: CO2-fixation pathway
    node_type: PATHWAY
    description: Autotrophic carbon assimilation route.
    grounding: GO:0015977
  - node_id: biomass
    label: biomass
    node_type: CHEMICAL
    description: Cell material formed from combined carbon acquisition.
    grounding: METPO:1007501
  - node_id: electron_transport_chain
    label: electron transport chain
    node_type: PATHWAY
    description: Membrane redox chain transferring electrons to terminal acceptors.
    grounding: GO:0022900
  - node_id: atp_synthesis
    label: ATP synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Formation of ATP coupling energy metabolism to cellular work.
    grounding: GO:0006754
  - node_id: proton_motive_force
    label: proton motive force
    node_type: BIOLOGICAL_PROCESS
    description: Transmembrane proton gradient driving ATP synthase.
  - node_id: rubisco
    label: RuBisCO
    node_type: GENE_OR_PROTEIN
    description: Ribulose-1,5-bisphosphate carboxylase/oxygenase, key CBB enzyme.
    grounding: UniProtKB:A0A075WF79
  - node_id: cbb_cycle
    label: Calvin-Benson-Bassham cycle
    node_type: PATHWAY
    description: Reductive pentose phosphate cycle fixing CO2 into organic carbon.
  - node_id: organic_matter_limitation
    label: organic matter limitation
    node_type: ENVIRONMENTAL_FACTOR
    description: Low availability of organic substrates in the environment.
  - node_id: light_limitation
    label: light limitation
    node_type: ENVIRONMENTAL_FACTOR
    description: Low light availability limiting phototrophic energy capture.
  edges:
  - subject: mixotrophic_trait
    predicate: uses carbon source
    object: organic_carbon
    description: Mixotrophs can use organic carbon as a carbon source.
    evidence:
    - reference: DOI:10.1073/pnas.1305998110
      snippet: organic carbon (C) for their C needs
      notes: Supports organic carbon use as part of mixotrophic metabolism.
    predicate_id: METPO:2000006
  - subject: mixotrophic_trait
    predicate: uses carbon source
    object: carbon_dioxide
    description: Mixotrophy can include inorganic carbon acquisition by CO2 fixation.
    evidence:
    - reference: DOI:10.1073/pnas.1305998110
      snippet: obtain its energy and carbon
      notes: Supports combining autotrophic and heterotrophic carbon-acquisition modes.
    predicate_id: METPO:2000006
  - subject: dissolved_organic_matter
    predicate: supplies
    object: organic_carbon
    description: Dissolved organic matter provides organic substrates in aquatic mixotrophy.
    evidence:
    - reference: DOI:10.1128/AEM.01559-06
      snippet: DOM, dissolved organic matter
      notes: Figure legend identifies dissolved organic matter as a substrate pool
        in bacterial metabolic modes.
  - subject: mixotrophic_trait
    predicate: can use energy capture route
    object: phototrophic_energy_capture
    description: Some microbial mixotrophs supplement organic carbon use with light-harvesting
      energy systems.
    evidence:
    - reference: DOI:10.1128/AEM.01559-06
      snippet: rhodopsin and other pigment
      notes: Review discusses pigment/rhodopsin-associated bacterial metabolic modes.
  - subject: carbon_dioxide
    predicate: fixed by
    object: co2_fixation_pathway
    description: Inorganic carbon assimilation converts CO2 into cellular carbon.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: autotrophic CO2 fixation
      notes: Supports CO2 fixation as the inorganic-carbon assimilation process.
    predicate_id: METPO:2007404
  - subject: organic_carbon
    predicate: incorporated into
    object: biomass
    description: Organic carbon contributes to cell material in mixotrophic growth.
    evidence:
    - reference: DOI:10.1016/B978-012373944-5.00083-3
      snippet: incorporation of a compound into biomass
      notes: Supports assimilatory conversion of organic compounds into biomass.
    predicate_id: biolink:part_of
  - subject: electron_transport_chain
    predicate: drives
    object: atp_synthesis
    description: Electron transport chain activity drives ATP synthesis.
    evidence:
    - reference: DOI:10.1128/aem.00599-24
      notes: Complete ETC complexes and F-type ATPase support ETC-driven ATP synthesis.
  - subject: proton_motive_force
    predicate: drives
    object: atp_synthesis
    description: Proton gradient drives ATP synthesis via ATP synthase.
    evidence:
    - reference: DOI:10.1128/spectrum.02177-23
      notes: A proton gradient drives ATP synthesis (canonical bioenergetic edge).
  - subject: phototrophic_energy_capture
    predicate: generates
    object: proton_motive_force
    description: Proton-pump rhodopsin photosystems generate a proton gradient.
    evidence:
    - reference: DOI:10.1128/spectrum.02177-23
      notes: Proton-pump rhodopsin acts as a photosystem-independent proton pump creating
        a proton gradient.
    predicate_id: biolink:produces
  - subject: rubisco
    predicate: enables
    object: cbb_cycle
    description: RuBisCO enables the Calvin-Benson-Bassham cycle.
    evidence:
    - reference: DOI:10.1128/aem.00599-24
      notes: MAGs encode Form II RuBisCO (rbcL/cbbM) and a full CBB cycle.
    predicate_id: RO:0002327
  - subject: cbb_cycle
    predicate: fixes
    object: carbon_dioxide
    description: The Calvin-Benson-Bassham cycle fixes CO2 into organic carbon.
    evidence:
    - reference: DOI:10.1128/aem.00599-24
      notes: A full CBB cycle is consistent with CO2 fixation potential.
  - subject: organic_matter_limitation
    predicate: promotes switching to
    object: phototrophic_energy_capture
    description: When organic matter is limiting, mixotrophs switch to light-based
      energy and inorganic carbon use.
    evidence:
    - reference: DOI:10.1128/AEM.01559-06
      notes: If organic matter is limiting, a mixotroph can switch to using light
        as an energy source and inorganic carbon as a carbon source.
  - subject: light_limitation
    predicate: promotes switching to
    object: organic_carbon
    description: When light is limiting, mixotrophs switch back to degradation of
      organic substances.
    evidence:
    - reference: DOI:10.1128/AEM.01559-06
      notes: As light gets limiting, the organism can switch back to degradation of
        organic substances.
curation_history:
- timestamp: '2026-05-05T01:35:46.877636+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: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed mixotrophy graph for dual organic/inorganic carbon use
    and light-associated energy capture.
  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:2000006×2).
  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: '2026-05-24T04:38:01Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:50860×1).
  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: '2026-05-24T07:34:59Z'
  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: '2026-06-13T21:03:27Z'
  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 7 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1, RO:0002327×1).
  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
    (GO:0022900×1, UniProtKB:A0A075WF79×1).
  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:0006754×1).
  llm_assisted: true