chemotrophic
METPO:1000641 · CLASS · REVIEWED
A trophic type in which an organism obtains energy from chemical oxidation of either inorganic or organic compounds.
Chemotrophic chemical redox energy conservation
Edge evidence
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chemotrophic
has energy source
reduced chemical substrate
METPO:2007807Chemotrophy uses chemical substrates as energy sources.
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DOI:10.1016/B978-012373944-5.00083-3chemical energy
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inorganic compound
example of
reduced chemical substrate
rdfs:subClassOfInorganic substrates are chemical energy sources in lithotrophy.
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DOI:10.1016/B978-0-12-378630-2.00219-Xoxidize inorganic atoms or molecules
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organic compound
example of
reduced chemical substrate
rdfs:subClassOfOrganic substrates are chemical energy sources in organotrophy.
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DOI:10.1016/B978-012373944-5.00083-3reduced organic compound
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reduced chemical substrate
oxidized by
redox reaction
Chemical energy is released through oxidation-reduction chemistry.
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DOI:10.1016/j.bbabio.2008.09.008free energy of a redox reaction
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redox reaction
feeds electrons into
respiratory chain
METPO:2007402Redox reactions can feed electrons into membrane respiratory chains.
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DOI:10.1016/j.bbabio.2008.09.008membrane-bound electron transport chain
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respiratory chain
transfers electrons to
terminal electron acceptor
METPO:2007403Respiratory chains transfer electrons to terminal acceptors.
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DOI:10.1128/mmbr.61.4.533-616.1997terminal electron acceptor
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respiratory chain
generates
proton motive force
biolink:producesRespiratory electron transfer generates an ion gradient.
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DOI:10.1016/j.bbabio.2008.09.008generation of an electrochemical ion gradient
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proton motive force
drives production of
ATP
biolink:producesProton motive force drives ATP synthesis.
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DOI:10.1016/j.bbabio.2008.09.008drives ATP synthesis
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proton motive force
can be built by
quinone/quinol cycling
Proton motive force can be generated by quinone/quinol cycling.
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DOI:10.1016/j.bbabio.2008.09.008
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proton pumping
contributes to generation of
proton motive force
Active proton pumping contributes to building the proton motive force.
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DOI:10.1016/j.bbabio.2008.09.008
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redox loop
contributes to generation of
proton motive force
A redox loop contributes to building the proton motive force.
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DOI:10.1016/j.bbabio.2008.09.008
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redox loop
couples electron transport to
net proton transfer across membrane
A redox loop couples electron transport to net proton transfer across the membrane without proton pumping.
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DOI:10.1016/j.bbabio.2008.09.008
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Provenance
- Source
- METPO (2025-11-25)
- Definition source
- DOI:10.1016/B978-012373944-5.00083-3
Parent traits (1)
Synonyms (2)
- TT_chemotroph
- chemotroph
kg-microbe context
Matched 1 kg-microbe node via direct_metpo.
METPO:1000641[-1.746, -0.197, -4.063, +1.592, …]
Nearest neighbors in embedding space
- physiology organotrophic 0.838
- physiology lithotrophic 0.527
- physiology chemoorganotrophic 0.506
- environment NaCl delta low 0.426
- physiology trophic type 0.415
- morphology orange pigmented 0.410
- environment pH range mid2 0.408
- environment temperature delta mid2 0.407
Deep research
# Curation report: microbial chemotrophic trait ## 1. Scope summary **Target:** `METPO:1000641` — **chemotrophic**; category **PHYSIOLOGY**; term kind **CLASS**; mapping **REVIEWED**; parent `METPO:1000631`. **Operational definition.** Chemotrophy is the physiological capacity to obtain usable energy from oxidation–reduction reactions involving chemical compounds. A donor is oxidized, electrons pass to an acceptor, and the released free energy is conserved—commonly through a membrane electron-transfer chain, ion-motive force, and ATP synthesis. This agrees with the supplied definition: “A trophic type in which an organism obtains energy from chemical oxidation of either inorganic or organic compounds.” Modern reviews likewise describe chemotrophs as exploiting environmental electron donors and acceptors and respiratory complexes as generating proton-motive force for ATP synthase. (gupta2020extracellularelectronuptake pages 5-6) ### Important boundaries 1. **Chemotrophy is an energy-source classification, not a carbon-source classification.** Chemotrophs may be autotrophic, using CO₂, or heterotrophic, using organic carbon. Therefore, neither “autotrophic” nor “heterotrophic” should be made equivalent to `METPO:1000641`. 2. **Chemolithotrophy** is the subset using inorganic electron donors such as H₂, Fe(II), reduced sulfur compounds, ammonia, nitrite, or CO. **Chemoorganotrophy** uses organic donors. The parent chemotrophic graph should remain donor-agnostic, with these as branches. 3. **Phototrophy** differs because light is the primary energy input. A facultative organism can express both modes under different conditions, but phototrophic growth alone is not evidence for chemotrophy. 4. **Aerobic versus anaerobic respiration** concerns the terminal acceptor, not whether an organism is chemotrophic. Oxygen, nitrate, sulfate, sulfur species, metals, and other compounds can serve as acceptors in different taxa. Sulfur oxidizers, for example, couple reduced-sulfur oxidation to oxygen or nitrate reduction. (gupta2020extracellularelectronuptake pages 8-9) 5. **Fermentation is a boundary case.** It is chemical energy metabolism, but it lacks an external terminal electron acceptor and often conserves energy by substrate-level phosphorylation. Curating fermentation under this broad METPO definition may be defensible, but a respiratory-chain mechanism must not be asserted for every fermentative chemotroph. 6. **Electroautotrophy/electrolithotrophy is another boundary case.** Electrode-derived electrons can support metabolism and CO₂ fixation, but an electrode is not conventionally a molecular compound. It should be represented as an assay-specific extension or sibling mode rather than silently generalized to all chemotrophy. (wang2024characterizethegrowth pages 22-23, llorente2024novelelectrochemicalstrategies pages 1-2) 7. **Genes alone do not establish the trait.** Detection of `sox`, hydrogenase, or carbon-fixation genes supports metabolic potential, but physiological evidence requires donor-dependent growth, substrate turnover, energy conservation, or comparable functional measurements. ## 2. Recommended graph architecture The existing 13-node/12-edge graph appears appropriately sized for a **minimal core**, but it should separate universal bioenergetics from taxon-specific examples: **chemical electron donor → donor oxidation/redox reaction → electron transfer → energy-conserving membrane complex → ion-motive force → ATP synthase → ATP → growth/maintenance** Add conditional branches for: - terminal electron acceptor reduction; - reverse electron transport and reducing-equivalent generation; - carbon fixation only for chemoautotrophs; - substrate-level phosphorylation for fermentative chemoorganotrophs; - donor-specific modules such as Fe(II)/Cyc2/Rus or thiosulfate/Sox. The literature supports outer-membrane cytochromes, periplasmic carriers, and inner-membrane respiratory complexes as an electron-transfer route that generates proton-motive force, which ATP synthase uses to make ATP. Reverse electron flow can generate NADH for CO₂ fixation. (gupta2020extracellularelectronuptake pages 5-6) ## 3. Candidate nodes grouped by type Ontology identifiers below are limited to high-confidence mappings. Labels without CURIEs should undergo ontology lookup before YAML insertion. ### Trait and taxon/context nodes - chemotrophic — `METPO:1000641` - chemolithotrophy — label-only pending METPO verification - chemoorganotrophy — label-only pending METPO verification - chemoautotrophy — label-only pending METPO verification - *Acidithiobacillus ferrooxidans* — NCBITaxon identifier should be verified at curation time - *Hydrogenovibrio* strain 104 / hydrothermal-vent *Hydrogenovibrio* isolates — strain-specific label - sulfate-reducing bacteria — taxonomic/functional group; not one NCBITaxon node - autotrophic electroactive microbial enrichment — assay-community node ### Chemicals and environmental substrates - chemical electron donor — role node; label-only - chemical electron acceptor — role node; label-only - dioxygen — `CHEBI:15379` - carbon dioxide — `CHEBI:16526` - proton — `CHEBI:15378` - ATP — `CHEBI:30616` - Fe(II), Fe(III), molecular hydrogen, sulfide, elemental sulfur, thiosulfate, nitrate, sulfate, water, NADH, acetate, formate, propionate — use ChEBI after identifier validation - reduced inorganic sulfur compounds — collection/class node rather than a single molecule - polarized carbon electrode — experimental-factor/material node
Curation history
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SEEDED_FROM_METPO · seed_from_metpo
imported from data/raw/metpo.owl (CLASS)
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ADDED_CAUSAL_GRAPH · codex
Added DOI-backed causal graph for chemical substrate oxidation, respiratory electron transfer, proton motive force, and ATP synthesis.
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GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000010×1).
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GROUND_CAUSAL_PREDICATES · claude
Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×2, biolink:produces×1).
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GROUND_CAUSAL_PREDICATES · claude
Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402×1, METPO:2007403×1).
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GROUND_CAUSAL_NODES · claude
Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016491×1, GO:0022904×1).
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GROUND_CAUSAL_NODES · claude
Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007504×1, METPO:1007500×1).
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GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50860×1).
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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.
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GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1).
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ENRICH_CAUSAL_GRAPH · claude
Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.
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MIGRATE_MICROBE_DOMAIN_EDGES · claude
Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has energy source), 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.