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photolithoautotrophic

METPO:1000665 · CLASS · REVIEWED

A trophic type in which an organism obtains energy from light and carbon from carbon dioxide using inorganic electron donors.

Trait evidence (3)

  • DOI:10.3389/fmicb.2011.00165
    oxidize sulfide

    Review supports sulfide oxidation coupled to phototrophic central carbon and energy metabolism.

  • DOI:10.3390/antiox10060829
    reduced sulfur compounds as an electron donor

    Review supports reduced sulfur electron donors in photolithotrophic sulfur bacteria.

  • DOI:10.1128/AEM.02473-10
    autotrophic CO2 fixation

    Review supports CO2 fixation as the autotrophic carbon-assimilation process.

Photolithoautotrophic light and inorganic-donor mechanism

DOI-backed graph linking light, inorganic electron donors, photosynthetic electron transport, and autotrophic CO2 fixation.

MECHANISTIC · This graph spans oxygenic and anoxygenic photolithoautotrophic modules and does not assert that water and sulfide are used by one organism. The S. elongatus PCC 7942 example anchors the CBB/RuBisCO branch.

Photolithoautotrophic light and inorganic-donor mechanism Interactive directed graph showing evidence-backed causal relationships for photolithoautotrophic.

Edge evidence

  • photolithoautotrophic has energy source light METPO:2007807

    Photolithoautotrophy depends on light as the energy source.

  • light regulates photosynthetic electron transport RO:0002211

    Light drives photosynthetic electron transport.

  • inorganic electron donor provides electrons to photosynthetic electron transport METPO:2007403

    Inorganic electron donors supply electrons for photolithotrophic metabolism.

    • DOI:10.3390/antiox10060829 reduced sulfur compounds as an electron donor Supports reduced inorganic sulfur compounds as electron donors for anoxygenic photolithotrophy.
  • sulfide participates in sulfur oxidation biolink:participates_in

    Sulfide is an example reduced inorganic donor oxidized by phototrophic bacteria.

  • photosynthetic electron transport has output reducing power RO:0002234

    Light-induced electron transport produces reductants.

  • carbon dioxide fixed by autotrophic CO2 fixation METPO:2007404

    CO2 is fixed during autotrophic carbon assimilation.

    • DOI:10.1128/AEM.02473-10 autotrophic CO2 fixation Supports CO2 fixation as the autotrophic carbon-assimilation process.
  • reducing power enables autotrophic CO2 fixation RO:0002327

    Reductants generated by light-driven electron transport support CO2 fixation.

    • DOI:10.3389/fmicb.2011.00165 reducing equivalent flow during photoautotrophic Supports reducing-equivalent flow in photoautotrophic growth.
  • autotrophic CO2 fixation has output biomass RO:0002234

    Autotrophic CO2 fixation produces cellular carbon.

  • photosynthetic electron transport generates NADPH biolink:produces

    Photosynthetic electron transport generates NADPH as terminal reductant.

  • carbonic anhydrase interconverts bicarbonate

    Carbonic anhydrase interconverts CO2 and bicarbonate, accelerating DIC equilibration.

    • DOI:10.1128/aem.01557-23 CA catalyzes CO2 <-> H2CO3 <-> HCO3- interconversion, accelerating DIC equilibration (general CCM mechanism).
  • inorganic carbon transporter imports bicarbonate METPO:2007805

    Inorganic carbon transporters import dissolved inorganic carbon species.

  • RuBisCO catalyzes autotrophic CO2 fixation biolink:catalyzes

    RuBisCO catalyzes the carboxylation step of autotrophic CO2 fixation.

  • reducing power has part NADPH

    NADPH is a concrete reductant constituting the reducing power for biosynthesis.

  • sulfide example of inorganic electron donor rdfs:subClassOf

    Sulfide is a reduced inorganic electron donor used by anoxygenic photolithoautotrophs.

    • DOI:10.3390/antiox10060829 These donors may be reduced sulfur compounds such as hydrogen sulfide Verified against the open Antioxidants article full text.
  • bicarbonate participates in autotrophic CO2 fixation biolink:participates_in

    Transported bicarbonate supplies inorganic carbon for photosynthetic autotrophic fixation.

    • DOI:10.1073/pnas.0405211101 cyanobacteria have evolved a very efficient mechanism for capturing CO2 and HCO3- for photosynthetic fixation into sugars Verified against the public PNAS article full text.

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
RuBisCO UniProtKB:Q31NB3
Ribulose bisphosphate carboxylase large chain (rbcL) 		Synechococcus elongatus PCC 7942
NCBITaxon:1140 		REVIEWED
retrieved 2026-08-24 · entry v112 · sequence v1

Large-chain component of the hexadecameric RbcL/RbcS RuBisCO that fixes CO2 through the CBB cycle; this accession does not denote the complete enzyme.

  • DOI:10.1093/plphys/kiac065 Rubisco is a hexadecameric protein complex of large (RbcL) and small (RbcS) subunits that catalyzes the carbon fixation step of the Calvin-Benson-Bassham cycle The primary PCC 7942 carbon-status study identifies the RuBisCO subunit architecture and function; UniProtKB Q31NB3 is the reviewed rbcL entry for that strain.

Provenance

Identifier source
METPO (2026-06-12)
Definition source
DOI:10.3389/fmicb.2011.00165

Parent traits (1)

Synonyms (1)

  • photolithoautotroph RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000665 [-2.042, -2.782, -5.220, +0.946, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/physiology/photolithoautotrophic-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation report: photolithoautotrophic

## Target record

- **Trait:** photolithoautotrophic
- **Identifier:** **METPO:1000665**
- **Category / kind / status:** PHYSIOLOGY / CLASS / REVIEWED
- **Parent:** METPO:1000631
- **Recommended operational definition:** an organism can use **light as its energy source**, an **inorganic compound as electron donor**, and **CO2 or bicarbonate as the principal carbon source for biomass production**. This three-part conjunction—not any component alone—is the phenotype to represent. An authoritative review uses essentially this formulation and explains that chlorophyll-based photochemistry generates proton-motive force, ATP, and reductant for CO2 fixation. (thiel2018diversityofchlorophototrophic pages 2-3)

## 1. Scope and boundaries

The trait is a physiological capacity, usually demonstrated by growth or inorganic-carbon assimilation under illumination with an inorganic electron donor. It includes both:

1. **Oxygenic photolithoautotrophy**, principally cyanobacteria: water supplies electrons through photosystems II and I, oxygen is evolved, and carbon is generally assimilated through the Calvin–Benson–Bassham (CBB) cycle.
2. **Anoxygenic photolithoautotrophy**, including green and purple sulfur bacteria and some purple nonsulfur bacteria: donors can include H2S/HS−, S0, thiosulfate, H2, or Fe2+; oxygen is not produced; and CBB, reverse TCA, or other lineage-specific fixation pathways may operate. Reviews document at least H2S, S0, thiosulfate, H2, Fe2+, and H2O across photolithoautotrophic lineages, and CBB, reverse TCA, and 3-hydroxypropionate-bicycle-type carbon fixation. (martin2018aphysiologicalperspective pages 2-3)

### Exclusions and boundary cases

- **Photoorganoheterotrophy:** light supplies energy, but organic compounds supply electrons and usually carbon. This does not satisfy the trait.
- **Chemolithoautotrophy:** inorganic donors and CO2 are used, but energy is not derived from light. It should not be included merely because sulfur-oxidation or carbon-fixation genes are present.
- **Generic photoautotrophy:** may not identify whether the electron donor is inorganic; evidence must establish the lithotrophic component.
- **Mixotrophy:** simultaneous organic-carbon assimilation does not negate photolithoautotrophic capacity, but a mixotrophic growth observation alone does not demonstrate strict photolithoautotrophy.
- **Aerobic anoxygenic phototrophs:** many are obligate photoheterotrophs and therefore should not be assigned this trait without inorganic-carbon assimilation and inorganic-donor evidence.
- **Phototrophy inferred from pigment or reaction-center genes:** genomic potential alone is insufficient to establish growth phenotype.
- **Donor-specific phenotypes:** photoferrotrophy and photothiotrophy are subtypes or contextual realizations, not synonyms for the full class.
- **Anoxia:** appropriate for many sulfur-based anoxygenic assays, but not a universal requirement because oxygenic photolithoautotrophs produce and tolerate O2.

## 2. Mechanistic model

The minimal taxon-neutral mechanism is:

**light → pigment/antenna excitation → reaction-center charge separation → photosynthetic electron transport → proton-motive force → ATP synthesis**, while **inorganic-donor oxidation → electron supply/reductant generation**, and **ATP + reductant + CO2/HCO3− → autotrophic carbon fixation → biomass**. Chlorophototrophs can use radiation over approximately **350–1,100 nm**, reflecting substantial pigment and antenna diversity rather than a single universal wavelength response. (thiel2018diversityofchlorophototrophic pages 2-3)

This core should be separated from alternative donor-oxidation and fixation modules. In sulfur phototrophs, flavocytochrome c/FccAB can relay sulfide-derived electrons through cytochrome c to reaction centers, whereas membrane-bound SQR transfers them into the quinone pool. In *Rhodovulum sulfidophilum*, Sox enzymes oxidize thiosulfate to sulfate. These are documented mechanisms but are not universal across all photolithoautotrophs. (kushkevych2021anoxygenicphotosynthesisin pages 3-5)

## 3. Candidate nodes

### Trait and process nodes

- photolithoautotrophic — **METPO:1000665**
- photosynthesis — candidate **GO:0015979**
- light reaction / photosynthetic electron transport — candidate GO term; verify exact child term during implementation
- carbon fixation — candidate **GO:0015977**
- ATP synthesis coupled to proton transport — candidate GO term; verify exact term for the intended granularity
- anoxygenic photosynthesis — label-only unless a verified ontology term is selected
- oxygenic photosynthesis — candidate GO term
- photoferrotrophy — label-only candidate
- phototrophic sulfur oxidation — label-only candidate
- autotrophic growth / biomass production — label-only process or METPO phenotype node

### Environmental and experimental factors

- light / electromagnetic radiation — use an ENVO or radiation ontology term only after identifier verification
- illuminated condition; darkness control
- anoxic condition — relevant to many sulfur-bacterium assays, not universal
- inorganic-carbon medium
- absence of organic carbon — assay condition supporting strict autotrophy
- near-infrared illumination: *R. sulfidophilum* experiments used approximately **850 nm**, anoxic artificial seawater, and 30°C. (gupta2021photoferrotrophyandphototrophic pages 1-2)

Showing the first 60 of 248 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (2)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · ADDED_CAUSAL_GRAPH · codex

    Added DOI-backed causal graph for light-driven electron transport, inorganic electron donors, sulfide oxidation, and autotrophic CO2 fixation.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×2, METPO:2000010×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in×1).

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007404×1).

  6. · RENAME_PREDICATE_LABELS · claude

    Renamed 2 causal-edge predicate label(s) to align with existing groundings: drives → regulates ×1; supports → enables ×1.

  7. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1, RO:0002327×1).

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001717×1, GO:0009767×1, CHEBI:15138×1).

  9. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502×1, METPO:1007503×1, METPO:1007501×1).

  10. · RETYPE_CAUSAL_NODES · claude

    Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS → CHEMICAL ×1.

  11. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0015977×1).

  12. · RETYPE_CAUSAL_NODES · claude

    Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: reducing power: CHEMICAL → CAPACITY ×1.

  13. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019417×1).

  14. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403×1).

  15. · ENRICH_CAUSAL_GRAPH · claude

    Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.

  16. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1, METPO:2000208×1, biolink:catalyzes×1).

  17. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16474×1, UniProtKB:A0A075WF79×1).

  18. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17544×1).

  19. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8×1).

  20. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  21. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR001765×1, InterPro:IPR006007×1, InterPro:IPR033966×1).

  22. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (1 to has energy source, 2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.

  23. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to imports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.

  24. · NORMALISE_NODE_TYPE · claude

    Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): photosynthetic_electron_transport is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route in every record that carries it, though NOT THE SAME ROUTE, which is why no single step list belongs in this rationale. metabolism/phototrophy.yaml enumerates the oxygenic form ('Electron flow from water through PSII, cytochrome b6f and PSI'); photoheterotrophic.yaml and photoorganoheterotrophic.yaml cover ANOXYGENIC phototrophy -- one reaction centre, cyclic flow, no water oxidation -- and say the neutral thing on purpose. Quoting the oxygenic steps at them would assert biology they specifically do not claim (#400 review). Both forms are named routes whose steps a curator could list, which is the test. Was 5 PATHWAY to 1 before this tranche.

  25. · REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON · codex

    Marked the graph mechanistic, documented its alternative donor and photosystem scope, upgraded canonical taxa to strain-level DOI citations, and added the reviewed S. elongatus PCC 7942 RbcL component example.

  26. · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex

    Resolved issue #183 graph fragmentation (3 components to 1) with 2 public-source, verbatim-snippet-backed connector(s). No paid research service was called.