identifier: traitmech:000037 label: phototrophy definition: A metabolism in which an organism captures light as its energy source. It encompasses chlorophyll-based photosynthesis (with photochemical reaction centers) and retinal-based (rhodopsin) light-driven ion pumping. definition_source: DOI:10.1016/j.tim.2006.09.001 trait_category: METABOLISM term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000060 synonyms: - synonym_text: phototrophic metabolism synonym_type: RELATED_SYNONYM source: DOI:10.1016/j.tim.2006.09.001 evidence: - reference: DOI:10.1016/j.tim.2006.09.001 notes: Bryant & Frigaard, "Prokaryotic photosynthesis and phototrophy illuminated", frames phototrophy as the broad use of light for energy, spanning chlorophyll- and rhodopsin-based mechanisms; parent of the photosynthesis and proteorhodopsin phototrophy sub-variants. - reference: DOI:10.1126/science.289.5486.1902 notes: Béjà et al. established retinal-based proteorhodopsin phototrophy as a light-energy capture mechanism distinct from chlorophyll-based photosynthesis. canonical_examples: - taxon_id: NCBITaxon:1148 taxon_label: Synechocystis sp. PCC 6803 note: "photolithotroph" reference: PMID:23945601 - taxon_id: NCBITaxon:1085 taxon_label: Rhodospirillum rubrum note: "photoorganotroph" reference: PMID:21886856 causal_graphs: - graph_id: phototrophy_light_energy_capture title: Phototrophy captures light as cellular energy description: Evidence-backed causal sketch linking light input to ATP/PMF generation across chlorophyll- and retinal-based phototrophic mechanisms. nodes: - node_id: phototrophy_trait label: phototrophy node_type: TRAIT grounding: traitmech:000037 description: Use of light as cellular energy source. - node_id: light label: light node_type: ENVIRONMENTAL_FACTOR grounding: PATO:0001717 description: Radiant energy captured for cellular use. - node_id: proton_motive_force label: proton motive force node_type: STATE grounding: METPO:1007500 description: Bioenergetic gradient driving ATP synthesis. - node_id: microbial_rhodopsin label: microbial rhodopsin node_type: GENE_OR_PROTEIN description: Retinal-binding light-activated membrane protein driving the photocycle. - node_id: rhodopsin_photocycle label: rhodopsin photocycle node_type: BIOLOGICAL_PROCESS description: Light-driven cyclic conformational/photochemical cycle of microbial rhodopsins. - node_id: atp_synthesis label: ATP synthesis node_type: BIOLOGICAL_PROCESS description: Synthesis of ATP driven by the transmembrane proton gradient. grounding: GO:0006754 - node_id: photosystem_ii label: photosystem II node_type: GENE_OR_PROTEIN description: Light-driven water-oxidizing complex initiating photosynthetic electron transport. - node_id: photosynthetic_electron_transport label: photosynthetic electron transport chain node_type: BIOLOGICAL_PROCESS description: Electron flow from water through PSII, cytochrome b6f and PSI. grounding: GO:0009767 - node_id: nadph label: NADPH node_type: CHEMICAL description: Reducing power produced by photosynthetic electron transport. grounding: CHEBI:16474 - node_id: atp label: ATP node_type: CHEMICAL description: Cellular energy currency produced from the photosynthetic proton gradient. - node_id: high_light label: high light intensity node_type: ENVIRONMENTAL_FACTOR description: Excess photon flux causing photodamage. edges: - subject: light predicate: causes object: phototrophy_trait description: Light availability is the input the phototrophic trait realizes. evidence: - reference: DOI:10.1016/j.tim.2006.09.001 notes: Bryant & Frigaard frame phototrophy as the broad use of light for energy. predicate_id: biolink:causes - subject: phototrophy_trait predicate: enables object: proton_motive_force description: Chlorophyll- and retinal-based phototrophy generate proton motive force from absorbed light. evidence: - reference: DOI:10.1126/science.289.5486.1902 notes: Béjà et al. established retinal-based proteorhodopsin phototrophy as a light-driven proton pump, complementing chlorophyll-based photosynthesis. predicate_id: RO:0002327 - subject: light predicate: activates object: rhodopsin_photocycle description: Visible light activates the microbial rhodopsin photocycle across taxa. evidence: - reference: DOI:10.1093/ismejo/wrae175 notes: '"All rhodopsins are activated by visible light and return to their original state through a photocycle"; broad rhodopsin mechanism, not limited to one taxon.' predicate_id: RO:0002213 - subject: microbial_rhodopsin predicate: enables object: rhodopsin_photocycle description: During the photocycle, microbial rhodopsins exhibit ion-transport function. evidence: - reference: DOI:10.1093/ismejo/wrae175 notes: '"During the photocycle, they exhibit their cognate protein functions such as ion transport"; general mechanistic edge for rhodopsin phototrophy.' predicate_id: RO:0002327 - subject: proton_motive_force predicate: drives object: atp_synthesis description: The proton gradient drives ATP synthesis, conserving light-derived energy. evidence: - reference: DOI:10.1128/spectrum.02177-23 notes: '"creating a proton gradient to drive the synthesis of ATP"; direct support for rhodopsin-based energy conservation.' - subject: photosystem_ii predicate: supplies electrons to object: photosynthetic_electron_transport description: PSII water oxidation supplies electrons to the photosynthetic electron transport chain. evidence: - reference: DOI:10.1111/1751-7915.14519 notes: '"electrons from the photo-oxidation of water in PSII are transferred through plastoquinone to cytochrome b6f"; canonical oxygenic phototrophy edge.' - subject: photosynthetic_electron_transport predicate: produces object: nadph description: Electron flow through cytochrome b6f and PSI reduces ferredoxin/NADP+ to NADPH. evidence: - reference: DOI:10.1111/1751-7915.14519 notes: '"These electrons are eventually transferred to ferredoxin and NADP+ to form NADPH"; canonical oxygenic phototrophy edge.' predicate_id: METPO:2000202 - subject: photosynthetic_electron_transport predicate: produces object: atp description: Photosynthetic electron transfer establishes a proton gradient that produces ATP. evidence: - reference: DOI:10.1111/1751-7915.14519 notes: '"NADPH and ATP are produced from a proton gradient"; canonical oxygenic phototrophy edge.' predicate_id: METPO:2000202 - subject: high_light predicate: damages object: photosystem_ii description: High light intensity and resulting free radicals damage PSII (photoinhibition). evidence: - reference: DOI:10.1111/1751-7915.14519 notes: '"High-energy photons and the generation of free radicals damage PSII"; strong environmental inhibitor edge.' curation_history: - timestamp: '2026-05-31T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Minted intermediate axis class (phototrophy) to parent the photosynthesis and proteorhodopsin-phototrophy traits, replacing their direct attachment to METPO:1000060 (metabolism). llm_assisted: true - timestamp: '2026-06-10T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (phototrophy / light → PMF) with PATO/METPO node groundings and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report. 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 (METPO:2000202×2, RO:0002213×1, RO:0002327×1). llm_assisted: true - timestamp: '2026-06-24T17:21:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16474×1). llm_assisted: true - timestamp: '2026-06-24T17:23:33Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006754×1, GO:0009767×1). llm_assisted: true