identifier: traitmech:000038 label: photosynthesis definition: A phototrophic metabolism that uses light energy and chlorophyll- or bacteriochlorophyll-based photochemical reaction centers to drive electron flow, fixing CO2 and/or generating reducing power. Subdivided into oxygenic and anoxygenic photosynthesis. definition_source: DOI:10.1016/j.tim.2006.09.001 trait_category: METABOLISM term_kind: CLASS mapping_status: REVIEWED parent_traits: - traitmech:000037 evidence: - reference: DOI:10.1016/j.tim.2006.09.001 notes: Bryant & Frigaard treat prokaryotic photosynthesis (reaction-center based) as encompassing both oxygenic and anoxygenic forms across five phyla. - reference: DOI:10.1146/annurev-earth-060313-054810 notes: Fischer et al., "Evolution of Oxygenic Photosynthesis", supports reaction-center photosynthesis as the chlorophyll-based, CO2-fixing branch of phototrophy distinct from rhodopsin-based light capture. canonical_examples: - taxon_id: NCBITaxon:1148 taxon_label: Synechocystis sp. PCC 6803 note: "oxygenic photosynthesis" reference: PMID:16228363 - taxon_id: NCBITaxon:1063 taxon_label: Cereibacter sphaeroides note: "anoxygenic photosynthesis" reference: PMID:21777427 causal_graphs: - graph_id: photosynthesis_chlorophyll_reaction_center title: Chlorophyll-based photosynthesis drives electron flow and CO2 fixation description: Evidence-backed causal sketch linking chlorophyll-based reaction centers to electron flow that powers CO2 fixation. nodes: - node_id: photosynthesis_trait label: photosynthesis node_type: TRAIT grounding: traitmech:000038 description: Chlorophyll/bacteriochlorophyll-based reaction-center metabolism. - node_id: photosynthesis_process label: photosynthesis node_type: BIOLOGICAL_PROCESS grounding: GO:0015979 description: Conversion of light energy to chemical energy via reaction centers. - node_id: carbon_fixation label: carbon fixation node_type: BIOLOGICAL_PROCESS grounding: GO:0015977 description: Assimilation of inorganic CO2 into organic carbon. - node_id: light_energy label: light energy node_type: ENVIRONMENTAL_FACTOR description: Photon energy absorbed and channeled by photosynthetic pigments. - node_id: light_harvesting label: light harvesting / excitation transfer node_type: BIOLOGICAL_PROCESS description: Absorption and transfer of excitation energy by antenna pigments to reaction centers. - node_id: charge_separation label: reaction-center charge separation node_type: BIOLOGICAL_PROCESS description: Light-driven primary charge separation in chlorophyll/bacteriochlorophyll reaction centers. - node_id: electron_transport label: photosynthetic electron transport node_type: BIOLOGICAL_PROCESS description: Light-driven electron flow through the photosynthetic electron transport chain (linear or cyclic). - node_id: proton_gradient label: transmembrane electrochemical proton gradient node_type: STATE description: Proton motive force generated across the membrane by photosynthetic electron transport. - node_id: atp_synthesis label: ATP synthesis node_type: BIOLOGICAL_PROCESS description: Chemiosmotic ATP generation coupled to the proton motive force. grounding: GO:0006754 - node_id: reducing_power label: reducing power (NAD(P)H) node_type: CHEMICAL description: NADPH/NAD(P)H reducing equivalents produced by the light reactions. edges: - subject: photosynthesis_process predicate: enables object: photosynthesis_trait description: Reaction-center photochemistry underlies the photosynthetic trait. evidence: - reference: DOI:10.1016/j.tim.2006.09.001 notes: Bryant & Frigaard treat reaction-center photosynthesis as encompassing both oxygenic and anoxygenic forms. predicate_id: RO:0002327 - subject: photosynthesis_trait predicate: contributes to object: carbon_fixation description: Photosynthetic electron flow powers autotrophic CO2 fixation. evidence: - reference: DOI:10.1146/annurev-earth-060313-054810 notes: Fischer et al. frame reaction-center photosynthesis as the chlorophyll-based, CO2-fixing branch of phototrophy. predicate_id: RO:0002326 - subject: light_energy predicate: enables object: light_harvesting description: Light energy drives pigment absorption and excitation transfer to reaction-center antennae. evidence: - reference: DOI:10.1111/1751-7915.14519 notes: Chlorophyll/antenna pigments absorb and transfer light energy to the photosystems (light harvesting). predicate_id: RO:0002327 - subject: light_harvesting predicate: initiates object: charge_separation description: Transferred excitation energy drives primary charge separation at the reaction-center special pair. evidence: - reference: DOI:10.3390/biom14030311 notes: Light-driven charge separation in reaction-center photosystems initiates downstream electron flow (generic to Type I/II RCs). - subject: charge_separation predicate: powers object: electron_transport description: Reaction-center charge separation drives photosynthetic electron transport (linear or cyclic). evidence: - reference: DOI:10.3390/biom14030311 notes: Light-driven charge separation powers electron transfer pathways; generalization for reaction-center photosystems. - subject: electron_transport predicate: generates object: proton_gradient description: Photosynthetic electron transport establishes a transmembrane electrochemical proton gradient. evidence: - reference: DOI:10.3390/biom14030311 notes: Electron transfer creates a transmembrane electrochemical proton gradient (energy-conservation edge). predicate_id: biolink:produces - subject: proton_gradient predicate: drives object: atp_synthesis description: The proton motive force is used to drive chemiosmotic ATP synthesis. evidence: - reference: DOI:10.3390/biom14030311 notes: The electrochemical proton gradient drives ATP synthesis; canonical bioenergetic edge. - subject: photosynthesis_process predicate: produces object: reducing_power description: Light-dependent reactions generate ATP and NAD(P)H reducing power. evidence: - reference: DOI:10.5287/ora-8jgz2nrvd notes: Light-dependent reactions generate ATP and NAD(P)H; broad linkage across chlorophyll-based photosynthetic systems. predicate_id: METPO:2000202 - subject: reducing_power predicate: used in object: carbon_fixation description: NADPH reducing power supplies electrons for autotrophic CO2 fixation. evidence: - reference: DOI:10.1111/1751-7915.14519 notes: NADPH from the light reactions is used in biosynthesis, including carbon fixation. curation_history: - timestamp: '2026-05-31T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Minted intermediate axis class (photosynthesis) under phototrophy to parent the oxygenic- and anoxygenic-photosynthesis traits. llm_assisted: true - timestamp: '2026-06-10T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (reaction-center photosynthesis / CO2 fixation) with GO node groundings and RO 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 (7 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:12Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1, biolink:produces×1, METPO:2000202×1). llm_assisted: true - timestamp: '2026-06-24T17:23:33Z' 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