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trophic type

METPO:1000631 · CLASS · REVIEWED

A phenotype that is describing how an organism obtains carbon, energy, and electron donors for growth and metabolism.

Trophic type classification axes

DOI-backed graph linking the three classification axes (carbon source, energy source, electron donor) to the metabolic pathways an organism encodes, which jointly determine its trophic type.

Trophic type classification axes Interactive directed graph showing evidence-backed causal relationships for trophic type.

Edge evidence

  • carbon source utilization causes trophic type biolink:causes

    Carbon-source utilization defines the auto/heterotrophy axis of the trophic classification.

    • DOI:10.1146/annurev.micro.61.080706.093130 carbon source Supports carbon-source utilization as a primary trophic-type axis.
  • energy source utilization causes trophic type biolink:causes

    Energy-source utilization defines the photo/chemotrophy axis of the trophic classification.

    • DOI:10.1146/annurev.micro.61.080706.093130 energy source Supports energy-source utilization as a primary trophic-type axis.
  • electron donor utilization causes trophic type biolink:causes

    Electron-donor utilization defines the litho/organotrophy axis of the trophic classification.

    • DOI:10.1146/annurev.micro.61.080706.093130 electron donor Supports electron-donor utilization as a primary trophic-type axis.
  • encoded metabolic pathways realizes trophic type

    The genome-encoded set of carbon-fixation, energy-conserving, and electron-transfer pathways realizes the organism's trophic type.

    • DOI:10.1073/pnas.0903507106 molecular mechanisms of adaptation Supports genome-encoded pathway repertoires as the proximate determinant of trophic phenotypes.
  • autotrophic is a trophic type rdfs:subClassOf

    Autotrophy is a child phenotype of trophic type.

    • DOI:10.1146/annurev.micro.61.080706.093130 carbon source Supports autotrophy as one carbon-source-defined trophic phenotype.
  • heterotrophic is a trophic type rdfs:subClassOf

    Heterotrophy is a child phenotype of trophic type.

    • DOI:10.1146/annurev.micro.61.080706.093130 carbon source Supports heterotrophy as one carbon-source-defined trophic phenotype.
  • phototrophic is a trophic type rdfs:subClassOf

    Phototrophy is a child phenotype of trophic type.

    • DOI:10.1146/annurev.micro.61.080706.093130 energy source Supports phototrophy as one energy-source-defined trophic phenotype.
  • chemotrophic is a trophic type rdfs:subClassOf

    Chemotrophy is a child phenotype of trophic type.

    • DOI:10.1146/annurev.micro.61.080706.093130 energy source Supports chemotrophy as one energy-source-defined trophic phenotype.
  • Calvin-Benson-Bassham cycle (RuBisCO) enables CO2 fixation RO:0002327

    Form II RuBisCO and a full Calvin-Benson-Bassham cycle enable CO2 fixation, marking autotrophic carbon-assimilation potential.

    • DOI:10.1128/AEM.00599-24 All MAGs encode Form II RuBisCO (rbcL/cbbM) and a full CBB cycle, indicating CO2 fixation potential.
  • CO2 fixation causes carbon source utilization biolink:causes

    CO2 fixation establishes inorganic-carbon (autotrophic) use on the carbon-source axis of trophic type.

    • DOI:10.1128/AEM.00599-24 CBB-driven CO2 fixation defines autotrophic carbon assimilation on the carbon-source classification axis.
  • SOX sulfur/thiosulfate oxidation causes electron donor utilization biolink:causes

    SOX-mediated thiosulfate/sulfur oxidation supplies inorganic electron donors, defining lithotrophy on the electron-donor axis.

    • DOI:10.1128/AEM.00599-24 Presence of soxABXYZ (and soxCD) is tied to thiosulfate oxidation, enabling use of sulfur species as electron donors.
  • sugar/polysaccharide uptake and CAZyme catabolism causes carbon source utilization biolink:causes

    Sugar transporters and CAZyme catabolism enable heterotrophic/organotrophic use of organic carbon on the carbon-source axis.

    • DOI:10.1128/AEM.00599-24 Sugar transporters (gtsABC, frcABC), maltodextrin import/degradation and CAZy enzymes indicate capacity for heterotrophic use of sugars and polysaccharides.
  • [NiFe]-hydrogenase H2 oxidation causes electron donor utilization biolink:causes

    [NiFe]-hydrogenase H2 oxidation supplies an inorganic electron donor, contributing hydrogen lithotrophy to the electron-donor axis.

    • DOI:10.1128/mSystems.00148-24 Hydrogenase genes link hydrogen-based lithotrophy to chemoautotrophic metabolism.

Provenance

Source
METPO (2025-11-25)
Author
Luke Wang
Definition source
DOI:10.1146/annurev.micro.61.080706.093130

Parent traits (1)

Children (28)

Synonyms (3)

  • Physiology and metabolism.nutrition type.type RELATED_SYNONYM · metpo.owl
  • nutritional type RELATED_SYNONYM · metpo.owl
  • pathways RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000631 [-1.491, -2.608, -4.371, +0.721, …]

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/trophic_type-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: microbial trophic type

**Target trait:** `METPO:1000631` — **trophic type**  
**Category / kind / status:** PHYSIOLOGY / CLASS / REVIEWED  
**Parent:** `METPO:1000059`

## 1. Scope summary

Trophic type is a **composite physiological classification** describing how an organism obtains (i) energy, (ii) electrons/reducing power, and (iii) carbon for growth. The conventional axes are:

- **Energy:** light → *phototroph*; chemical reactions → *chemotroph*.
- **Electron donor:** inorganic donor → *lithotroph*; organic donor → *organotroph*.
- **Carbon:** inorganic carbon, principally CO₂/DIC → *autotroph*; preformed organic carbon → *heterotroph*.

These axes combine into labels such as *photolithoautotroph*, *photoorganoheterotroph*, *chemolithoautotroph*, and *chemoorganoheterotroph*. For example, nitrifiers are classically chemolithoautotrophic, while purple sulfur bacteria can be anoxygenic photolithoautotrophs using light, H₂S, and CO₂. Purple nonsulfur bacteria often exhibit photoorganoheterotrophy and considerable trophic flexibility. (weissbrodt2023basicmicrobiologyand pages 19-22)

**Recommended interpretation for TraitMech:** the phenotype should represent an organism’s **demonstrated or condition-qualified trophic mode**, not merely the presence of one pathway marker. The causal graph should therefore connect environmental resources through uptake and energy-conservation modules to carbon assimilation and growth.

### Boundaries and nearby traits

1. **Respiration type is related but distinct.** O₂, nitrate, sulfate, and other terminal acceptors determine respiratory mode and energetic feasibility, but they do not replace the three primary trophic naming axes. They should enter the graph as environmental/chemical determinants of a condition-specific trophic phenotype. Redox zones create niches for different trophic guilds. (weissbrodt2023basicmicrobiologyand pages 19-22)
2. **Substrate utilization is narrower.** Growth on acetate or H₂ is evidence for a trophic component, but a complete classification also requires carbon-source and energy-source interpretation.
3. **Carbon fixation is not sufficient evidence of obligate autotrophy.** Organisms may express carbon-fixation pathways while also assimilating organics; *Leptothrix ochracea* and marine Arcobacteraceae illustrate this mixotrophic boundary. (tothero2024leptothrixochraceagenomes pages 1-2, li2024arcobacteraceaeareubiquitous pages 1-2)
4. **Mixotrophy is not one uniform mechanism.** It can mean simultaneous or condition-dependent combination of autotrophic and heterotrophic nutrition. In protists, constitutive mixotrophs possess photosystems, whereas non-constitutive mixotrophs acquire photosynthetic capacity from prey through kleptoplasty. (schenone2024mixotrophicprotistsand pages 2-3)
5. **Genetic potential is not the same as phenotype.** MAG pathway completeness, transcription, isotope incorporation, and growth assays provide progressively different evidence. Even transcript abundance is normally a proxy for potential activity rather than direct flux. (li2024insitucommunity pages 1-2)
6. **Ecological “trophic level” or food-web position is out of scope.** `METPO:1000631` concerns nutritional physiology, not predator–prey rank.

## 2. Candidate causal-graph nodes

Identifiers below are limited to stable CURIEs that can be assigned confidently. Candidate labels without a CURIE should remain label-only until ontology validation.

### A. Trait and trophic-state nodes

- `METPO:1000631` — trophic type
- phototrophy; chemotrophy
- lithotrophy; organotrophy
- autotrophy; heterotrophy; mixotrophy
- photolithoautotrophy; photoorganoheterotrophy
- chemolithoautotrophy; chemoorganoheterotrophy
- photoferrotrophy; photohydrogenotrophy; photoelectrotrophy
- condition-dependent trophic switching

### B. Environmental and experimental nodes

- light availability
- oxic, hypoxic, anoxic, and dark conditions
- organic-carbon availability
- electron-donor availability
- hypersaline sediment; deep groundwater; marine water column; wetland iron mat
- growth medium with H₂/CO₂/O₂, formate, succinate, fructose, Fe(II), sulfide, thiosulfate, or butyrate
- RB-TnSeq/barcoded transposon fitness assay
- stable-isotope carbon incorporation
- metagenomics, metatranscriptomics, and metabolic modeling

Deep aquifers exemplify environmental control: nine wells reached depths up to 1.5 km and contained hypoxic-to-anoxic water; measured chemosynthetic productivity was **0.55 ± 0.06 to 0.82 ± 0.07 μg C L⁻¹ d⁻¹**, and **60% of recovered MAGs** encoded autotrophic pathways, principally CBB and Wood–Ljungdahl modules. (atencio2024metabolicadaptationsunderpin pages 1-2)

### C. Pathways and biological processes

- Calvin–Benson–Bassham cycle (CBB); **GO:0015977** carbon fixation
- Wood–Ljungdahl/reductive acetyl-CoA pathway

Showing the first 60 of 266 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

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

  2. · CURATED_CAUSAL_GRAPH · claude

    Added DOI-backed causal graph framing trophic type by its three classification axes (carbon source, energy source, electron donor) and child phenotypes (autotroph, heterotroph, phototroph, chemotroph).

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×4).

  4. · RENAME_PREDICATE_LABELS · claude

    Renamed 3 causal-edge predicate label(s) to align with existing groundings: determines → causes ×3.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes×3).

  6. · ENRICH_CAUSAL_GRAPH · claude

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

  7. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes×4, RO:0002327×1).