identifier: METPO:1000660
label: phototrophic
definition: A trophic type characterized by the use of light as the primary energy
  source for metabolic processes, regardless of carbon source.
definition_source: DOI:10.3389/fmicb.2011.00165
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: TT_phototroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: aerobic_anoxygenic_phototrophy
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: phototroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Anthea Guo
evidence:
- reference: DOI:10.3389/fmicb.2011.00165
  snippet: use light as the energy source
  notes: Review supports light-driven ATP and reductant generation by phototrophic
    bacteria.
- reference: DOI:10.1093/femsre/fuv032
  snippet: bacteriochlorophyll-containing reaction centers
  notes: Review supports bacteriochlorophyll reaction centers in aerobic anoxygenic
    phototrophs.
canonical_examples:
- taxon_id: NCBITaxon:1148
  taxon_label: Synechocystis sp. PCC 6803
  note: "oxygenic phototroph"
  reference: PMID:23945601
- taxon_id: NCBITaxon:1085
  taxon_label: Rhodospirillum rubrum
  note: "anoxygenic phototroph"
  reference: PMID:21886856
causal_graphs:
- graph_id: phototrophic_light_energy_capture
  title: Phototrophic light-energy capture mechanism
  description: DOI-backed graph for bacterial light capture, photosynthetic electron
    transport, ATP generation, and reductant formation.
  nodes:
  - node_id: phototrophic_trait
    label: phototrophic
    node_type: TRAIT
    grounding: METPO:1000660
    description: Trophic type using light as an energy source.
  - node_id: light
    label: light
    node_type: ENVIRONMENTAL_FACTOR
    description: Electromagnetic energy harvested by phototrophic cells.
    grounding: PATO:0001717
  - node_id: photosynthetic_reaction_center
    label: photosynthetic reaction center
    node_type: GENE_OR_PROTEIN
    description: Pigment-protein complex that initiates photochemical charge separation.
  - node_id: bacteriochlorophyll
    label: bacteriochlorophyll
    node_type: CHEMICAL
    description: Light-harvesting pigment in many anoxygenic phototrophic bacteria.
    grounding: CHEBI:38201
  - node_id: photosynthetic_electron_transport
    label: photosynthetic electron transport
    node_type: PATHWAY
    description: Light-induced electron-transfer route producing ATP and reductants.
    grounding: GO:0009767
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier generated by phototrophic electron transport.
  - node_id: reducing_power
    label: reducing power
    node_type: CAPACITY
    description: NAD(P)H or reduced ferredoxin generated by photosynthetic electron
      transport.
    grounding: METPO:1007503
  - node_id: carotenoid
    label: carotenoid
    node_type: CHEMICAL
    description: Auxiliary light-harvesting pigment in phototrophic bacteria.
    grounding: CHEBI:23044
  - node_id: blue_green_light
    label: blue-green light
    node_type: ENVIRONMENTAL_FACTOR
    description: Blue-green region of the spectrum absorbed by carotenoid antennas.
  - node_id: proton_motive_force
    label: proton motive force
    node_type: CAPACITY
    description: Transmembrane electrochemical proton gradient generated by photosynthetic
      electron transport.
  - node_id: atp_synthase
    label: ATP synthase complex
    node_type: GENE_OR_PROTEIN
    description: Membrane enzyme complex that synthesizes ATP driven by proton motive
      force.
  - node_id: rhodopsin
    label: rhodopsin
    node_type: GENE_OR_PROTEIN
    description: Retinal-based light-driven ion-pumping membrane protein used in retinalophototrophy.
    grounding: UniProtKB:A0A059ZUX4
  - node_id: ion_transport
    label: ion transport across membrane
    node_type: BIOLOGICAL_PROCESS
    description: Light-driven transmembrane ion pumping that establishes a gradient
      for energy conservation.
  edges:
  - subject: phototrophic_trait
    predicate: uses energy source
    object: light
    description: Phototrophic growth uses light as the energy input.
    evidence:
    - reference: DOI:10.3389/fmicb.2011.00165
      snippet: use light as the energy source
      notes: Supports light as the defining energy source for phototrophic bacteria.
    predicate_id: METPO:2000010
  - subject: bacteriochlorophyll
    predicate: part of
    object: photosynthetic_reaction_center
    description: Bacteriochlorophyll-containing complexes harvest light in many bacterial
      phototrophs.
    evidence:
    - reference: DOI:10.1093/femsre/fuv032
      snippet: bacteriochlorophyll-containing reaction centers
      notes: Supports pigment-reaction-center coupling in aerobic anoxygenic phototrophs.
    predicate_id: biolink:part_of
  - subject: light
    predicate: captured by
    object: photosynthetic_reaction_center
    description: Reaction centers convert absorbed light into charge separation.
    evidence:
    - reference: DOI:10.1093/femsre/fuv032
      snippet: harvest light energy
      notes: Supports light harvesting by reaction centers.
  - subject: photosynthetic_reaction_center
    predicate: initiates
    object: photosynthetic_electron_transport
    description: Photochemical reaction centers initiate electron transport.
    evidence:
    - reference: DOI:10.3389/fmicb.2011.00165
      snippet: light-induced electron transport
      notes: Supports reaction-center-driven photosynthetic electron transport.
  - subject: photosynthetic_electron_transport
    predicate: produces
    object: atp
    description: Photosynthetic electron transport produces ATP.
    evidence:
    - reference: DOI:10.3389/fmicb.2011.00165
      snippet: produce phosphate bond energy (ATP)
      notes: Supports ATP as a product of phototrophic electron transport.
    predicate_id: METPO:2000202
  - subject: photosynthetic_electron_transport
    predicate: produces
    object: reducing_power
    description: Photosynthetic electron transport generates reducing equivalents.
    evidence:
    - reference: DOI:10.3389/fmicb.2011.00165
      snippet: reductants [e.g., NAD(P)H and reduced ferredoxin]
      notes: Supports reductant production by photosynthetic electron transport.
    predicate_id: METPO:2000202
  - subject: carotenoid
    predicate: transfers excitation energy to
    object: bacteriochlorophyll
    description: Excitation energy captured by carotenoids is transferred to BChl
      a.
    evidence:
    - reference: DOI:10.1093/femsre/fuv032
      notes: The excitation energy captured by the carotenoids is transferred within
        picoseconds to the BChl a molecules.
  - subject: carotenoid
    predicate: extends light absorption into
    object: blue_green_light
    description: Carotenoids serve as auxiliary pigments extending absorption to the
      blue-green spectrum.
    evidence:
    - reference: DOI:10.1093/femsre/fuv032
      notes: Carotenoids serve as auxiliary pigments which extend absorption to the
        blue-green part of the spectrum.
  - subject: photosynthetic_electron_transport
    predicate: forms
    object: proton_motive_force
    description: Photosynthetic electron transport generates a proton motive force.
    evidence:
    - reference: DOI:10.1128/aem.00863-24
      notes: Along with electron transport, proton motive force (PMF) is formed.
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: powers
    object: atp_synthase
    description: Proton motive force drives ATP synthase complexes.
    evidence:
    - reference: DOI:10.1128/aem.00863-24
      notes: and powers ATP synthase complexes.
  - subject: atp_synthase
    predicate: produces
    object: atp
    description: ATP synthase complexes generate ATP from the proton motive force.
    evidence:
    - reference: DOI:10.1128/aem.00863-24
      notes: PMF powers ATP synthase complexes that synthesize ATP, the cellular energy
        carrier.
    predicate_id: METPO:2000202
  - subject: rhodopsin
    predicate: pumps
    object: ion_transport
    description: Rhodopsins use light to pump ions across the membrane (retinalophototrophy).
    evidence:
    - reference: DOI:10.1038/s43705-023-00334-5
      notes: retinalophototrophy, which uses rhodopsins to pump ions through the membrane.
curation_history:
- timestamp: '2026-05-05T01:35:46.882505+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-08T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for light capture, reaction centers, photosynthetic
    electron transport, ATP, and reductant generation.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:32Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×2, METPO:2000010×1).
  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:part_of×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:38:01Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (PATO:0001717×1, GO:0009767×1).
  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:1007503×1).
  llm_assisted: true
- timestamp: '2026-05-26T02:30:14Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: reducing power: CHEMICAL → CAPACITY ×1.'
  llm_assisted: true
- timestamp: '2026-06-14T05:51:47Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:38201×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (6 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:15Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1, METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:35Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:23044×1).
  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:A0A059ZUX4×1).
  llm_assisted: true