identifier: METPO:1000665
label: photolithoautotrophic
definition: A trophic type in which an organism obtains energy from light and carbon
  from carbon dioxide using inorganic electron donors.
definition_source: DOI:10.3389/fmicb.2011.00165
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: photolithoautotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.3389/fmicb.2011.00165
  snippet: oxidize sulfide
  notes: Review supports sulfide oxidation coupled to phototrophic central carbon
    and energy metabolism.
- reference: DOI:10.3390/antiox10060829
  snippet: reduced sulfur compounds as an electron donor
  notes: Review supports reduced sulfur electron donors in photolithotrophic sulfur
    bacteria.
- reference: DOI:10.1128/AEM.02473-10
  snippet: autotrophic CO2 fixation
  notes: Review supports CO2 fixation as the autotrophic carbon-assimilation process.
canonical_examples:
- taxon_id: NCBITaxon:32046
  taxon_label: Synechococcus elongatus
  note: "water-splitting photolithoautotroph"
  reference: PMID:21226929
- taxon_id: NCBITaxon:1097
  taxon_label: Chlorobaculum tepidum
  note: "sulfide-using photolithoautotroph"
  reference: PMID:12093901
causal_graphs:
- graph_id: photolithoautotrophic_light_inorganic_donor_fixation
  title: Photolithoautotrophic light and inorganic-donor mechanism
  description: DOI-backed graph linking light, inorganic electron donors, photosynthetic
    electron transport, and autotrophic CO2 fixation.
  nodes:
  - node_id: photolithoautotrophic_trait
    label: photolithoautotrophic
    node_type: TRAIT
    grounding: METPO:1000665
    description: Trophic type using light, inorganic electron donors, and carbon dioxide.
  - node_id: light
    label: light
    node_type: ENVIRONMENTAL_FACTOR
    description: Energy source for photolithoautotrophic metabolism.
    grounding: PATO:0001717
  - node_id: photosynthetic_electron_transport
    label: photosynthetic electron transport
    node_type: PATHWAY
    description: Light-driven electron transport pathway.
    grounding: GO:0009767
  - node_id: inorganic_electron_donor
    label: inorganic electron donor
    node_type: CHEMICAL
    description: Reduced inorganic substrate supplying electrons.
    grounding: METPO:1007502
  - node_id: sulfide
    label: sulfide
    node_type: CHEMICAL
    description: Example inorganic electron donor for anoxygenic phototrophs.
    grounding: CHEBI:15138
  - node_id: sulfur_oxidation
    label: sulfur oxidation
    node_type: BIOLOGICAL_PROCESS
    description: Oxidation of reduced sulfur compounds during phototrophic metabolism.
    grounding: GO:0019417
  - node_id: reducing_power
    label: reducing power
    node_type: CAPACITY
    description: Reduced electron carriers used for biosynthesis.
    grounding: METPO:1007503
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Inorganic carbon source.
  - node_id: autotrophic_co2_fixation
    label: autotrophic CO2 fixation
    node_type: PATHWAY
    description: Carbon-assimilation pathway converting CO2 to cellular carbon.
    grounding: GO:0015977
  - node_id: biomass
    label: biomass
    node_type: CHEMICAL
    description: Cellular material formed from fixed carbon.
    grounding: METPO:1007501
  - node_id: nadph
    label: NADPH
    node_type: CHEMICAL
    description: Reduced electron carrier produced by photosynthetic electron transport.
    grounding: CHEBI:16474
  - node_id: carbonic_anhydrase
    label: carbonic anhydrase
    node_type: GENE_OR_PROTEIN
    description: Enzyme interconverting CO2 and bicarbonate for inorganic carbon supply.
    grounding: UniProtKB:A0A009PMS8
  - node_id: bicarbonate
    label: bicarbonate
    node_type: CHEMICAL
    description: Dissolved inorganic carbon species in equilibrium with CO2.
    grounding: CHEBI:17544
  - node_id: dic_transporter
    label: inorganic carbon transporter
    node_type: GENE_OR_PROTEIN
    description: Transporter importing dissolved inorganic carbon species into the
      cell.
  - node_id: rubisco
    label: RuBisCO
    node_type: GENE_OR_PROTEIN
    description: Ribulose-1,5-bisphosphate carboxylase/oxygenase, key autotrophic
      carboxylase.
    grounding: UniProtKB:A0A075WF79
  edges:
  - subject: photolithoautotrophic_trait
    predicate: uses energy source
    object: light
    description: Photolithoautotrophy depends on light as the energy source.
    evidence:
    - reference: DOI:10.3389/fmicb.2011.00165
      snippet: use light as the energy source
      notes: Supports light-powered metabolism in phototrophic bacteria.
    predicate_id: METPO:2000010
  - subject: light
    predicate: regulates
    object: photosynthetic_electron_transport
    description: Light drives photosynthetic electron transport.
    evidence:
    - reference: DOI:10.3389/fmicb.2011.00165
      snippet: light-induced electron transport
      notes: Supports light-driven electron transport.
    predicate_id: RO:0002211
  - subject: inorganic_electron_donor
    predicate: provides electrons to
    object: photosynthetic_electron_transport
    description: Inorganic electron donors supply electrons for photolithotrophic
      metabolism.
    evidence:
    - reference: DOI:10.3390/antiox10060829
      snippet: reduced sulfur compounds as an electron donor
      notes: Supports reduced inorganic sulfur compounds as electron donors for anoxygenic
        photolithotrophy.
    predicate_id: METPO:2007403
  - subject: sulfide
    predicate: participates in
    object: sulfur_oxidation
    description: Sulfide is an example reduced inorganic donor oxidized by phototrophic
      bacteria.
    evidence:
    - reference: DOI:10.3390/antiox10060829
      snippet: oxidizes reduced sulfur compounds
      notes: Supports sulfur oxidation from reduced sulfur electron donors.
    predicate_id: biolink:participates_in
  - subject: photosynthetic_electron_transport
    predicate: produces
    object: reducing_power
    description: Light-induced electron transport produces reductants.
    evidence:
    - reference: DOI:10.3389/fmicb.2011.00165
      snippet: NAD(P)H and reduced ferredoxin
      notes: Supports generation of reducing equivalents.
    predicate_id: METPO:2000202
  - subject: carbon_dioxide
    predicate: fixed by
    object: autotrophic_co2_fixation
    description: CO2 is fixed during autotrophic carbon assimilation.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: autotrophic CO2 fixation
      notes: Supports CO2 fixation as the autotrophic carbon-assimilation process.
    predicate_id: METPO:2007404
  - subject: reducing_power
    predicate: enables
    object: autotrophic_co2_fixation
    description: Reductants generated by light-driven electron transport support CO2
      fixation.
    evidence:
    - reference: DOI:10.3389/fmicb.2011.00165
      snippet: reducing equivalent flow during photoautotrophic
      notes: Supports reducing-equivalent flow in photoautotrophic growth.
    predicate_id: RO:0002327
  - subject: autotrophic_co2_fixation
    predicate: produces
    object: biomass
    description: Autotrophic CO2 fixation produces cellular carbon.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: cellular carbon
      notes: Supports assimilation of CO2 into cellular carbon.
    predicate_id: METPO:2000202
  - subject: photosynthetic_electron_transport
    predicate: generates
    object: nadph
    description: Photosynthetic electron transport generates NADPH as terminal reductant.
    evidence:
    - reference: DOI:10.1038/s44222-023-00093-x
      notes: Ferredoxin and FNR yield NADPH as the terminal reductant of phototrophic
        electron transport.
    predicate_id: biolink:produces
  - subject: carbonic_anhydrase
    predicate: interconverts
    object: bicarbonate
    description: Carbonic anhydrase interconverts CO2 and bicarbonate, accelerating
      DIC equilibration.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: CA catalyzes CO2 <-> H2CO3 <-> HCO3- interconversion, accelerating DIC
        equilibration (general CCM mechanism).
  - subject: dic_transporter
    predicate: imports
    object: bicarbonate
    description: Inorganic carbon transporters import dissolved inorganic carbon species.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: HCO3- uptake systems bridge environmental DIC supply to fixation demand.
    predicate_id: METPO:2000208
  - subject: rubisco
    predicate: catalyzes
    object: autotrophic_co2_fixation
    description: RuBisCO catalyzes the carboxylation step of autotrophic CO2 fixation.
    evidence:
    - reference: DOI:10.1128/aem.01557-23
      notes: RuBisCO is the key CO2-specific carboxylase for autotrophic CO2 fixation
        (broadly accepted).
    predicate_id: biolink:catalyzes
  - subject: reducing_power
    predicate: has part
    object: nadph
    description: NADPH is a concrete reductant constituting the reducing power for
      biosynthesis.
    evidence:
    - reference: DOI:10.1038/s44222-023-00093-x
      notes: NADPH is the terminal reductant tabulated as reducing equivalent for
        phototrophic biosynthesis.
curation_history:
- timestamp: '2026-05-05T01:35:46.884349+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-driven electron transport, inorganic
    electron donors, sulfide oxidation, and autotrophic CO2 fixation.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  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:participates_in×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 2 causal-edge predicate label(s) to align with existing groundings:
    drives → regulates ×1; supports → enables ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:22Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:38:01Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (PATO:0001717×1, GO:0009767×1, CHEBI:15138×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:41:04Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007502×1, METPO:1007503×1, 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: '2026-05-26T02:30:14Z'
  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
    (GO:0019417×1).
  llm_assisted: true
- timestamp: '2026-06-14T07:26:20Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007403×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:15Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1, METPO:2000208×1, biolink:catalyzes×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
    (CHEBI:16474×1, UniProtKB:A0A075WF79×1).
  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:17544×1).
  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