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photolithotrophic

METPO:1000658 · CLASS · REVIEWED

A trophic type in which an organism uses light as the energy source and inorganic compounds as electron donors, typically with carbon dioxide as the primary carbon source.

Trait evidence (2)

  • DOI:10.3390/antiox10060829
    anoxygenic photosynthesis

    Review supports light-driven oxidation of reduced sulfur compounds by photolithotrophic sulfur bacteria.

  • DOI:10.3389/fmicb.2017.00323
    light as an energy source and reduced iron

    Review supports Fe(II) as an inorganic electron donor for photoferrotrophy.

Photolithotrophic inorganic electron donor photosynthesis

DOI-backed graph linking light capture, inorganic electron donors such as sulfide and Fe(II), anoxygenic photosynthetic electron transport, and CO2 assimilation.

MECHANISTIC · The retained graph specifically represents anoxygenic sulfur- and iron-oxidizing branches; the oxygenic Synechocystis example documents the broader trait but is not asserted to use this reaction center. The C. tepidum example anchors the Type I P840 branch.

Photolithotrophic inorganic electron donor photosynthesis Interactive directed graph showing evidence-backed causal relationships for photolithotrophic.

Edge evidence

  • photolithotrophic has energy source light METPO:2007807

    Photolithotrophic growth is powered by light.

  • photolithotrophic has electron donor inorganic electron donor METPO:2007701

    Inorganic electron donors supply the electrons lithotrophic phototrophs use.

  • hydrogen sulfide example of inorganic electron donor rdfs:subClassOf

    Hydrogen sulfide is a representative inorganic electron donor.

  • ferrous iron example of inorganic electron donor rdfs:subClassOf

    Fe(II) is a representative inorganic electron donor in photoferrotrophy.

    • DOI:10.3389/fmicb.2017.00323 reduced iron [Fe(II)] as an electron donor Supports Fe(II) as an inorganic electron donor for anoxygenic photosynthesis.
  • inorganic electron donor feeds electrons into anoxygenic photosynthesis METPO:2007402

    Inorganic donors supply electrons to anoxygenic photosynthetic metabolism.

  • light enables anoxygenic photosynthesis RO:0002327

    Light powers anoxygenic photosynthetic electron transport.

    • DOI:10.3390/antiox10060829 deriving energy from photosynthesis Supports photosynthetic energy capture in photolithotrophic sulfur bacteria.
  • carbon dioxide fixed during anoxygenic photosynthesis

    Many photolithotrophs reduce CO2 during photosynthetic growth.

  • anoxygenic photosynthesis has output biomass RO:0002234

    Fixed carbon supports biomass formation.

    • DOI:10.3389/fmicb.2017.00323 inorganic carbon is fixed into organic matter Supports organic matter formation from inorganic carbon in photoferrotrophy.
  • light provides energy to photosynthetic reaction center

    Light quanta excite the photosynthetic reaction center to drive electron transport.

  • hydrogen sulfide acts as electron donor for anoxygenic photosynthesis

    H2S is the main electron donor in sulfur-based anoxygenic photosynthesis.

  • hydrogen sulfide oxidation has output elemental sulfur RO:0002234

    Phototrophic oxidation of H2S yields elemental sulfur.

  • inorganic electron donor supports photosynthetic CO2 fixation

    Oxidation of reduced sulfur compounds supports photosynthetic CO2 fixation.

    • DOI:10.3390/life14050591 Oxidize sulfide, thiosulfate, and elemental sulfur for photosynthetic growth (anoxygenic photosynthetic CO2 fixation).
  • Fe(II) oxidation defines photoferrotrophy METPO:2007500

    Photoferrotrophy is the oxidation of reduced iron via anoxygenic photosynthesis.

    • DOI:10.1038/s41561-024-01560-9 Photoferrotrophy is the oxidation of reduced iron via anoxygenic photosynthesis; anoxygenic phototrophic Fe(II) oxidizers are photoferrotrophs.
  • hydrogen sulfide participates in hydrogen sulfide oxidation biolink:participates_in

    Hydrogen sulfide is the substrate oxidized to elemental sulfur in the sulfur-photolithotrophy branch.

    • DOI:10.3390/antiox10060829 The process of anoxygenic photosynthesis further involves the oxidation of hydrogen sulfide to atomic sulfur Verified against the open Antioxidants article full text.
  • ferrous iron participates in Fe(II) oxidation biolink:participates_in

    Ferrous iron is the electron-source substrate oxidized during photoferrotrophy.

    • DOI:10.3389/fmicb.2014.00713 photoferrotrophic bacteria use light as energy and Fe(II) as an electron source for carbon fixation and biomass formation Verified against the open Frontiers primary article.

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
photosynthetic reaction center UniProtKB:Q8KEP5
P840 reaction center 17 kDa protein (pscD) 		Chlorobaculum tepidum TLS
NCBITaxon:194439 		REVIEWED
retrieved 2026-08-24 · entry v84 · sequence v1

Peripheral PscD component of the C. tepidum P840 Type I reaction center; this accession is not presented as the complete 12-subunit FMO-RC apparatus.

  • DOI:10.1073/pnas.2216734120 two peripheral subunits (PscB and PscD) and six FMO proteins (FMO-1 to 6) are arranged as two FMO trimers The primary cryo-EM study resolves PscD in the C. tepidum TLS whole reaction-center apparatus; UniProtKB Q8KEP5 is the reviewed strain-level PscD entry.

Provenance

Identifier source
METPO (2026-06-12)
Author
Luke Wang
Definition source
DOI:10.3390/antiox10060829

Parent traits (1)

Synonyms (1)

  • photolithotroph RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000658 [-1.986, -2.827, -4.047, -0.222, …]

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/photolithotrophic-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: photolithotrophic

## Record and recommendation

- **Trait:** photolithotrophic
- **Identifier:** **`METPO:1000658`**
- **Category / kind / status:** PHYSIOLOGY / CLASS / REVIEWED
- **Parent:** `METPO:1000631`
- **Recommended graph design:** retain the trait as a high-level physiological capacity, then represent alternative, taxon-scoped mechanistic branches for sulfur photolithotrophy, photoferrotrophy, hydrogen-based photolithotrophy, and oxygenic water oxidation. The strongest evidence retrieved here supports the sulfur and Fe(II) branches.

## 1. Scope and boundaries

### Operational definition

Photolithotrophy is the capacity to use **light as the energy source** and a **reduced inorganic compound as the electron donor**. In the best-characterized microbial examples, electron transfer supports generation of ATP and reductant, while inorganic carbon is assimilated into biomass. Green sulfur bacteria (GSB) use H₂S as a principal donor, oxidize it initially to elemental sulfur, and fix CO₂ through the reductive—or reverse—TCA cycle. Photoferrotrophy uses light, Fe(II), and inorganic carbon. (kushkevych2024anoxygenicphotosynthesiswith pages 1-2, gupta2020extracellularelectronuptake pages 7-8)

The submitted definition says CO₂ is “typically” the primary carbon source. That qualification is important: **photolithotrophy describes energy and electron sources, whereas autotrophy describes carbon source**. Thus, `photolithotrophic` should not be made logically equivalent to `photolithoautotrophic`. A separate edge such as `photolithotrophic organism — may_fix — CO2` is safer than making CO₂ fixation universally necessary.

### Boundary cases

1. **Photoorganoheterotrophy:** light is used, but electrons and/or carbon are obtained from organic compounds. This is not photolithotrophy.
2. **Chemolithotrophy:** the donor is inorganic, but energy is obtained from chemical oxidation without light. This is not photolithotrophy.
3. **Oxygenic photolithotrophy:** cyanobacteria use water as the donor and produce O₂. It belongs within the broad trait definition, but not within an anoxygenic-sulfur-specific mechanism.
4. **Anoxygenic photolithotrophy:** H₂S, thiosulfate, H₂, or Fe(II) can replace water as donor; oxygen is not evolved. The retrieved 2024 review explicitly lists H₂S, H₂, and ferrous iron as alternative donors. (kushkevych2024anoxygenicphotosynthesiswith pages 16-17)
5. **Mixotrophy:** some GSB can assimilate acetate while retaining light-driven lithotrophic metabolism. Conversely, inability to grow heterotrophically on glucose was reported for the reviewed GSB models. Carbon-substrate utilization therefore must not be inferred solely from the photolithotrophic label. (kushkevych2024anoxygenicphotosynthesiswith pages 13-14)
6. **Genotype-only assignments:** presence of `sqr`, `cyc2`, `pioABC`, `sox`, or photosynthesis genes is mechanistic evidence, but not by itself a demonstrated trait. For example, SQR homologues occur even in *Chlorobium ferrooxidans*, which cannot use sulfur as its sole donor. (kushkevych2021anoxygenicphotosynthesisin pages 3-5)

## 2. Current mechanistic understanding

### Sulfur-based branch

In GSB, chlorosomes collect light and transfer excitation through the Fenna–Matthews–Olson complex to a type-I reaction center. Chlorosomes are exceptionally effective under low irradiance: the 2024 review reports operation below **4 µEinstein m⁻² s⁻¹** and describes assemblies containing hundreds of thousands of bacteriochlorophyll molecules. (kushkevych2024anoxygenicphotosynthesiswith pages 4-6)

H₂S oxidation is initiated by membrane-associated sulfide:quinone oxidoreductase (SQR). SQR oxidizes sulfide while reducing menaquinone to menaquinol; flavocytochrome-c sulfide dehydrogenase can provide an alternative route. Reaction-center electron transfer proceeds through chlorophyll *a*, phylloquinone, and Fe–S centers to ferredoxin. Reduced ferredoxin and ferredoxin:NAD⁺ oxidoreductase systems provide reducing power for biosynthesis. (kushkevych2024anoxygenicphotosynthesiswith pages 9-10)

Thiosulfate use is lineage-dependent. The Sox system supports thiosulfate oxidation in organisms such as *Rhodovulum sulfidophilum*, while some GSB can oxidize thiosulfate and tetrathionate. Stored elemental sulfur and its subsequent oxidation involve additional systems, including reverse/dissimilatory sulfite-reductase machinery, but these modules are not universal among all photolithotrophs. (kushkevych2024anoxygenicphotosynthesiswith pages 9-10, kushkevych2024anoxygenicphotosynthesiswith pages 18-18, kushkevych2021anoxygenicphotosynthesisin pages 3-5)

### Photoferrotrophic branch

Photoferrotrophs couple light energy to oxidation of soluble Fe(II) or reduced iron minerals. In *Rhodopseudomonas palustris* TIE-1, PioA is a periplasmic decaheme cytochrome, PioB an outer-membrane β-barrel, and PioC a periplasmic high-potential Fe–S protein. The reviewed model transfers electrons from Fe(II) through PioAB and PioC toward the photosynthetic reaction center. PioAB-mediated uptake from solid extracellular substrates has direct support in TIE-1. (gupta2020extracellularelectronuptake pages 7-8, gupta2020extracellularelectronuptake pages 8-9)

Cyc2 homologues occur in some *Chlorobium* genomes and are candidates for extracellular Fe(II) oxidation, but the review stresses that molecular mechanisms remain incompletely resolved. Cyc2 presence should therefore be curated as a **candidate mechanism**, not as proof of photoferrotrophy. (gupta2020extracellularelectronuptake pages 7-8, gupta2020extracellularelectronuptake pages 4-5, gupta2020extracellularelectronuptake pages 8-9)

## 3. Candidate nodes

### Trait and biological-process nodes

- `METPO:1000658` — photolithotrophic
- `GO:0015979` — photosynthesis
- `GO:0015977` — carbon fixation
- Anoxygenic photosynthesis — verify the current GO identifier before YAML insertion
- Photoferrotrophy — label-only candidate
- Sulfide-dependent photolithotrophy — label-only candidate
- Thiosulfate-dependent photolithotrophy — label-only candidate
- Reverse/reductive TCA cycle — pathway node; verify pathway CURIE against the target ontology release
- Calvin–Benson–Bassham cycle — pathway node; applies to selected photoferrotrophs and oxygenic phototrophs, not GSB generally

### Chemicals and physical factors

- `CHEBI:16136` — hydrogen sulfide

Showing the first 60 of 214 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 anoxygenic photosynthesis with sulfide and Fe(II) as inorganic electron donors.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000010×1, METPO:2000009×1, METPO:2000202×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×2).

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001717×1, CHEBI:29033×1).

  7. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502×1, METPO:1007501×1).

  8. · RETYPE_CAUSAL_NODES · claude

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

  9. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: powers → enables ×1.

  10. · GROUND_CAUSAL_PREDICATES · claude

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

  11. · ENRICH_CAUSAL_GRAPH · claude

    Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.

  12. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, METPO:2007500×1).

  13. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:26833×1).

  14. · REVERSE_CAUSAL_EDGE_DIRECTION · claude

    Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.

  15. · MIGRATE_ENABLES_TRAIT_EDGES · claude

    Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).

  16. · 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.

  17. · REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON · codex

    Marked the graph mechanistic with explicit anoxygenic scope, reviewed the generic reaction center as label-only, upgraded canonical taxa to strain-level DOI citations, and added the reviewed C. tepidum PscD component example.

  18. · 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.

  19. · GROUND_CAUSAL_NODE · codex

    Grounded the photoferrotrophy causal node to traitmech:000193 after minting the same-scope phototrophic Fe(II) oxidation TraitRecord.