organotrophic

METPO:1000655 · CLASS · REVIEWED

A trophic type in which an organism obtains energy from the oxidation of organic compounds.

Trait evidence (2)

DOI:10.1016/B978-012373944-5.00083-3
incorporation of a compound into biomass

Microbial metabolism reference supports assimilation and use of organic compounds in growth.
DOI:10.1016/j.bbabio.2008.09.008
membrane-bound electron transport chain

Review supports respiratory electron transport as an energy-conserving route.

Organotrophic organic compound oxidation

DOI-backed graph linking organic electron donors, catabolism, respiratory energy conservation, ATP production, and biomass precursors.

MECHANISTIC · This graph represents respiratory oxidation of organic substrates. The E. coli K-12 AtpD example anchors F-type ATP synthesis and is one beta component, not the complete rotary complex.

Edge evidence

organotrophic has electron donor organic compound METPO:2007701
Organic compounds serve as the electron donors for organotrophy.
- DOI:10.1016/B978-012373944-5.00083-3 incorporation of a compound into biomass Supports use and assimilation of organic compounds in microbial growth.
glucose example of organic compound rdfs:subClassOf
Glucose is a representative organic substrate.
- DOI:10.1021/acsomega.3c02205 glucose metabolism Supports glucose as a microbial organic substrate.
organic compound oxidized by catabolism
Organic substrates are oxidized through catabolic metabolism.
- DOI:10.1016/B978-012373944-5.00083-3 heterotrophic microorganisms Supports catabolism of organic compounds by heterotrophic microbial metabolism.
catabolism feeds electrons into respiratory chain METPO:2007402
Oxidative catabolism supplies electrons to energy-conserving respiration.
- DOI:10.1016/j.bbabio.2008.09.008 electron transfer process Supports electron transfer through respiratory chains.
respiratory chain generates proton motive force biolink:produces
Respiratory electron transfer generates an ion gradient.
- DOI:10.1016/j.bbabio.2008.09.008 generation of an electrochemical ion gradient Supports proton motive force generation by membrane electron transport.
proton motive force drives production of ATP biolink:produces
Proton motive force powers ATP synthesis.
- DOI:10.1016/j.bbabio.2008.09.008 drives ATP synthesis Supports ATP synthesis from respiratory energy conservation.
proton motive force drives ATP synthase RO:0002212
Proton motive force drives the F-type ATP synthase rotary mechanism.
- DOI:10.7554/eLife.21598 proton motive force drives rotation and conformational changes in the F1 catalytic sites The E. coli structural study directly supports the coupling mechanism of the beta-containing ATP synthase complex.
catabolism has output precursor metabolites RO:0002234
Organic-compound catabolism supplies biosynthetic precursors.
- DOI:10.1016/B978-012373944-5.00083-3 incorporation of a compound into biomass Supports use of compound-derived intermediates for biomass formation.
catabolism generates NADH and FADH2 biolink:produces
Oxidation of organic substrates by catabolic pathways generates reduced electron carriers.
- DOI:10.1186/s13213-024-01761-y Catabolic pathways (Krebs cycle and beta-oxidation) generate reduced carriers (NADH and FADH2).
NADH and FADH2 donates electrons to NADH dehydrogenase (Complex I) METPO:2007403
NADH donates electrons to NADH dehydrogenase (Complex I) to enter the respiratory chain.
- DOI:10.1186/s13213-024-01761-y NADH dehydrogenase (Complex I) extracts hydrogen/electrons from NADH; broad canonical ETC-entry edge.
NADH dehydrogenase (Complex I) feeds electrons into respiratory chain METPO:2007402
NADH dehydrogenase passes electrons into the membrane respiratory chain.
- DOI:10.1186/s13213-024-01761-y Reduced carriers feed electrons into membrane electron-transport systems via NADH dehydrogenase.
organic carbon availability increases abundance of organotrophic
Enriched organic carbon supports proliferation of organotrophs.
- DOI:10.1038/s41396-023-01437-6 Enriched organic C and dissolved organic C can support the rapid propagation of obligate organotrophic copiotrophs.

Protein and taxon examples

Graph node Protein Taxon UniProt status Role and evidence

ATP synthase

Graph node	Protein	Taxon	UniProt status	Role and evidence
ATP synthase	`UniProtKB:P0ABB4` ATP synthase subunit beta (atpD)	Escherichia coli K-12 `NCBITaxon:83333`	`REVIEWED` retrieved 2026-08-24 · entry v155 · sequence v2	Beta component of the E. coli F1 catalytic head; this accession is not presented as the complete F1Fo complex. `DOI:10.7554/eLife.21598` proton motive force drives rotation and conformational changes in the F1 catalytic sites The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head; UniProt verifies the reviewed K-12 AtpD entry.

UniProtKB:P0ABB4
ATP synthase subunit beta (atpD)

Escherichia coli K-12
NCBITaxon:83333

REVIEWED
retrieved 2026-08-24 · entry v155 · sequence v2

Beta component of the E. coli F1 catalytic head; this accession is not presented as the complete F1Fo complex.

DOI:10.7554/eLife.21598 proton motive force drives rotation and conformational changes in the F1 catalytic sites The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head; UniProt verifies the reviewed K-12 AtpD entry.

Provenance

Identifier source: METPO (2026-06-12)
Definition source: DOI:10.1016/B978-012373944-5.00083-3

Parent traits (1)

trophic type METPO:1000631

Synonyms (2)

TT_organotroph RELATED_SYNONYM · metpo.owl
organotroph RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

METPO:1000655 [+0.165, -1.239, -2.986, +1.908, …]

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).

physiology chemotrophic 0.838
physiology chemoorganotrophic 0.531
morphology orange pigmented 0.408
physiology chemoorganoheterotrophic 0.406
physiology trophic type 0.400
morphology red pigmented 0.400
morphology cell length 0.392
morphology cell width 0.383

Deep research

Generated by just research-trait; source: research/traits/physiology/organotrophic-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: organotrophic

## Trait record and scope

- **Trait:** organotrophic
- **Identifier:** **METPO:1000655**
- **Category / kind / status:** PHYSIOLOGY / CLASS / REVIEWED
- **Parent:** METPO:1000631
- **Definition supplied:** “A trophic type in which an organism obtains energy from the oxidation of organic compounds.”
- **Synonyms:** *TT_organotroph*, *organotroph*

### Recommended interpretation

Organotrophy is fundamentally an **electron-donor/energy-source classification**. An organism is organotrophic when an organic compound participates as the reduced substrate in an energy-conserving redox process. An authoritative formulation is “energy conservation from redox reactions involving at least one organic substrate”; examples include glucose oxidation with O₂ and isopropanol oxidation coupled to CO₂ reduction. This is broader than aerobic heterotrophic respiration and includes anaerobic respiration and fermentation. (schonheit2016ontheorigin pages 2-4)

The trait should not be treated as synonymous with **heterotrophy**. Heterotrophy concerns the source of biomass carbon, whereas organotrophy concerns the source of electrons/chemical energy. The two commonly coincide as chemoorganoheterotrophy, but organic compounds can supply electrons while carbon is obtained partly or principally by CO₂ fixation, and phototrophs may use organic electron donors. A 2024 review explicitly contrasts organotrophy—organic electron donors—with lithotrophy—inorganic electron donors—and separately distinguishes heterotrophic reduced-organic carbon from autotrophic oxidized carbon sources. (fukala2024naturalpolyhydroxyalkanoates—anoverview pages 6-8)

Likewise, organotrophy is distinct from:

- **Lithotrophy:** energy/electrons are obtained from inorganic donors. An organism able to switch between organic and inorganic donors is metabolically versatile, not exclusively organotrophic.
- **Phototrophy:** light supplies energy. A photoheterotroph may assimilate organic carbon, but organotrophy additionally requires evidence that an organic compound acts in energy-yielding electron transfer.
- **Respiration:** one possible organotrophic energy-conservation mode, using an environmental terminal electron acceptor.
- **Fermentation:** another organotrophic mode. Here the substrate supplies both electron-donor and acceptor equivalents, and ATP can be conserved by substrate-level phosphorylation or ion-gradient mechanisms. (muller2012biochemistryandevolution pages 5-6, buckel2021energyconservationin pages 1-2)
- **Assimilation/growth on an organic compound:** supportive but not sufficient by itself. Incorporation into biomass demonstrates carbon use; it does not necessarily establish that oxidation of that compound supplies energy.

**Recommended graph scope:** represent a generic mechanistic core with explicit alternative branches for respiration and fermentation. Do not require O₂, a complete TCA cycle, a membrane electron-transport chain, or any single transporter/gene as universal defining features.

## Candidate nodes

Ontology grounding below is intentionally conservative. Broad or taxon-dependent entities are left label-only rather than assigned speculative identifiers.

### Trait and biological-process nodes

| Candidate node | Suggested grounding | Curation comment |
|---|---|---|
| organotrophic | **METPO:1000655** | Target trait; quote CURIE verbatim in YAML. |
| organic-compound oxidation | GO:0016054, *organic acid catabolic process*, only for organic-acid-specific instances | No single GO term safely covers oxidation of every organic donor; retain a label-only generic node if necessary. |
| glycolytic process | GO:0006096 | Common carbohydrate-catabolism module, not universal. |
| tricarboxylic-acid cycle | GO:0006099 | Respiratory/catabolic module; incomplete or absent in some organotrophs. |
| cellular respiration | GO:0045333 | Parent process for respiratory branches. |
| aerobic respiration | GO:0009060 | Conditional branch requiring O₂. |
| anaerobic respiration | GO:0009061 | Conditional branch requiring a non-O₂ environmental acceptor. |
| fermentation | GO:0006113 | Alternative energy-conservation branch. |
| oxidative phosphorylation | GO:0006119 | Conditional on respiratory or other chemiosmotic machinery. |
| ATP synthesis coupled proton transport | GO:0015986 | Proton-driven ATP-synthase branch. |
| substrate-level phosphorylation | label-only candidate | Confirm a suitable ontology term before release. |
| organic-substrate transport | label-only parent | Instantiate substrate/transporter-specific children where evidence exists. |
| biomass assimilation | label-only candidate | Keep downstream of uptake and precursor generation, not as the defining energy edge. |

### Chemicals and energetic entities

| Candidate node | Suggested grounding | Role |
|---|---|---|
| organic compound / organic electron donor | label-only class, or substrate-specific CHEBI term | Defining input; examples include glucose, organic acids, amino acids, alcohols, hydrocarbons and methane. |
| glucose | CHEBI:17234 | Model organic donor for respiratory and fermentative examples. |
| pyruvate | CHEBI:15361 | Central catabolic intermediate and fermentation acceptor. |
| acetyl-CoA | CHEBI:15351 | Links substrate oxidation to TCA, biosynthesis and storage polymers. |
| NAD⁺ | CHEBI:15846 | Oxidized soluble redox carrier. |
| NADH | CHEBI:16908 | Reduced carrier generated by many catabolic pathways. |
| ATP | CHEBI:15422 | Conserved chemical-energy currency. |

Showing the first 60 of 209 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 (3)

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

Escherichia coli NCBITaxon:562 PMID:9278503 organic electron-donor organotroph
Bacillus subtilis NCBITaxon:1423 PMID:9384377 soil organotroph
Escherichia coli K-12 NCBITaxon:83333 DOI:10.7554/eLife.21598 Strain-level organotrophic model paired to the reviewed AtpD beta component of its F-type ATP synthase.

Curation history

2026-05-05T01:35:46.879073+00:00 · SEEDED_FROM_METPO · seed_from_metpo
imported from data/raw/metpo.owl (CLASS)
2026-05-09T00:00:00-07:00 · CURATED_CAUSAL_GRAPH · Codex
Added DOI-backed organotrophy graph for organic substrate oxidation, respiratory energy conservation, ATP, and biosynthetic precursors.
2026-05-20T03:35:31Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009×1, METPO:2000202×1).
2026-05-23T08:21:50Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×1, biolink:produces×1).
2026-05-23T21:30:07Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402×1).
2026-05-24T04:38:01Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904×1).
2026-05-24T04:41:04Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500×1).
2026-05-24T08:14:33Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50860×1).
2026-05-26T02:30:14Z · RETYPE_CAUSAL_NODES · claude
Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.
2026-06-13T21:03:27Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1).
2026-06-23T00:00:00Z · ENRICH_CAUSAL_GRAPH · claude
Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report.
2026-06-24T17:21:15Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1, METPO:2007403×1, METPO:2007402×1).
2026-08-05T12:00:00Z · 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.
2026-08-06T00:00:00Z · 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).
2026-08-06T01:00:00Z · MIGRATE_MICROBE_DOMAIN_EDGES · claude
Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 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.
2026-08-26T03:23:00Z · CURATE_PROTEIN_TAXON_EXAMPLE · claude
Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope organotrophic_organic_compound_oxidation=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:P0ABB4 on atp_synthase (NCBITaxon:83333); regrounded 1 node(s) (nadh_dehydrogenase: none->GO:0030964); added 1 node(s) and 1 edge(s) (atp_synthase); added canonical example(s) NCBITaxon:83333.