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chemolithoautotrophic

METPO:1000637 · CLASS · REVIEWED

A trophic type in which an organism obtains energy from oxidation of inorganic compounds (lithotrophy) and carbon from carbon dioxide.

Chemolithoautotrophic energy and CO2 fixation

DOI-backed graph linking inorganic donor oxidation, respiratory energy conservation, reductant generation, and autotrophic CO2 fixation.

Chemolithoautotrophic energy and CO2 fixation Interactive directed graph showing evidence-backed causal relationships for chemolithoautotrophic.

Edge evidence

  • chemolithoautotrophic has electron donor inorganic electron donor METPO:2007701

    Inorganic electron donors supply the energy chemolithoautotrophs conserve.

    • DOI:10.1016/B978-0-12-378630-2.00219-X growth-supporting reductant and energy source Supports inorganic reductants as energy sources.
  • inorganic electron donor feeds electrons into electron transport chain METPO:2007402

    Donor oxidation supplies electrons to energy-conserving respiratory chains.

    • DOI:10.1016/j.bbabio.2008.09.008 membrane-bound electron transport chain Supports membrane-bound respiratory chains as redox energy-conserving systems.
  • electron transport chain generates proton motive force biolink:produces

    Respiratory chains generate an electrochemical ion gradient.

    • DOI:10.1016/j.bbabio.2008.09.008 generation of an electrochemical ion gradient Supports proton motive force generation.
  • proton motive force drives synthesis of ATP biolink:produces

    The ion gradient drives ATP synthesis.

    • DOI:10.1016/j.bbabio.2008.09.008 drives ATP synthesis Supports ATP synthesis from respiratory ion gradients.
  • inorganic electron donor supports generation of reducing power

    Electrons from inorganic donors provide reduced cofactors for biosynthesis.

    • DOI:10.1016/j.biortech.2021.125768 serve as reductive power Supports reduced cofactors generated from chemolithoautotrophic electron donors.
  • carbon dioxide fixed by CO2 fixation pathway METPO:2007404

    Chemolithoautotrophs use CO2 fixation pathways for carbon assimilation.

    • DOI:10.1146/annurev.micro.52.1.191 Carbon Dioxide Fixation in Chemoautotrophs Supports CO2 fixation in chemoautotrophic bacteria.
  • ATP enables CO2 fixation pathway RO:0002327

    ATP generated from donor oxidation supports autotrophic CO2 fixation.

    • DOI:10.1128/AEM.02473-10 energy required for autotrophic CO2 fixation Supports energy demand of autotrophic CO2 fixation.
  • reducing power enables CO2 fixation pathway RO:0002327

    Reducing power supports reductive CO2 assimilation.

    • DOI:10.1016/j.biortech.2021.125768 reduction of CO2 Supports reductant use in CO2 fixation.
  • CO2 fixation pathway has output biomass RO:0002234

    CO2 fixation generates cellular biomass.

    • DOI:10.1146/annurev.micro.52.1.191 physiology ... of chemoautotrophic bacteria Review scope supports chemoautotrophic growth from fixed carbon.
  • RuBisCO catalyzes CO2 fixation pathway biolink:catalyzes

    RuBisCO catalyzes the carboxylation step of the Calvin-Benson-Bassham CO2 fixation cycle.

    • DOI:10.1128/aem.01557-23 Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) drives CBB-cycle CO2 fixation.
  • carbonic anhydrase facilitates supply of dissolved inorganic carbon

    Carbonic anhydrase interconverts CO2 and bicarbonate to facilitate dissolved inorganic carbon fixation.

    • DOI:10.1128/aem.01557-23 carbonic anhydrase enzymes (CA) to facilitate DIC fixation.
  • dissolved inorganic carbon transporter increases availability of dissolved inorganic carbon

    DIC transporters bridge environmental inorganic carbon supply to autotrophic pathway demand.

    • DOI:10.1128/aem.01557-23 DIC transporters bridge supply from the environment to demand by the autotrophic pathway.
  • dissolved inorganic carbon supplies substrate to CO2 fixation pathway

    Dissolved inorganic carbon supplies the CO2/bicarbonate substrate for autotrophic fixation.

    • DOI:10.1128/aem.01557-23 DIC supply bridged to demand by the autotrophic pathway.
  • proton motive force drives reverse electron transport for reducing power

    PMF can reverse the electron transport chain to regenerate NADH/NADPH reducing power for fixation.

    • DOI:10.1038/s41467-023-43524-4 The proton motive force drives ATP synthesis and can reverse the electron transport chain to regenerate NADH/NADPH.

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1146/annurev.micro.52.1.191

Parent traits (1)

Synonyms (1)

  • chemolithoautotroph RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000637 [-1.631, -1.052, -4.107, +0.857, …]

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/chemolithoautotrophic-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: chemolithoautotrophic

**Trait:** chemolithoautotrophic  
**Identifier:** **METPO:1000637**  
**Category / kind / status:** PHYSIOLOGY / CLASS / REVIEWED  
**Parent:** METPO:1000631  
**Recommended interpretation:** a trophic phenotype in which oxidation of one or more inorganic electron donors supplies energy and reducing equivalents, while CO2/HCO3− supplies most or all assimilated carbon.

## 1. Scope and boundaries

Chemolithoautotrophy is best modeled as a **compound physiological capacity**, not as a single pathway. Its invariant causal architecture is:

**inorganic electron donor oxidation → electron transfer/ion-motive force → ATP and reducing equivalents → inorganic-carbon uptake and fixation → biomass.**

The interchangeable branches are the donor, terminal electron acceptor, respiratory components, and carbon-fixation pathway. Current examples include oxidation of H2, reduced sulfur compounds, Fe2+, ammonia, nitrite, and—in two unusual strict anaerobes—phosphite. Carbon assimilation may use the Calvin–Benson–Bassham (CBB), reductive TCA (rTCA), Wood–Ljungdahl (WL), 3-hydroxypropionate bicycle, 3-hydroxypropionate–4-hydroxybutyrate (3HP–4HB), or dicarboxylate–4-hydroxybutyrate pathway. DIC transport and carbonic-anhydrase systems bridge environmental CO2/HCO3− supply to these pathways. (scott2024widespreaddissolvedinorganic pages 10-13, scott2024widespreaddissolvedinorganic pages 2-4, prioretti2023carbonfixationin pages 1-2, mao2023anaerobicdissimilatoryphosphite pages 1-2)

### Boundary cases

- **Chemolithotrophy without autotrophy:** oxidation of inorganic donors is insufficient by itself; demonstrated incorporation of inorganic carbon into biomass is required.
- **Chemoorganoautotrophy:** chemical energy is retained, but an organic electron donor violates the lithotrophic component.
- **Photoautotrophy:** light, rather than oxidation of an inorganic chemical, is the principal energy source. The engineered rhodopsin/electrode system in *Cupriavidus necator* is therefore photoelectroautotrophic, not a clean natural instance of the target trait. (tu2023engineeringartificialphotosynthesis pages 1-2)
- **Electroautotrophy:** electrons supplied directly by an electrode constitute a distinct energy-input mode. *Acidithiobacillus ferrooxidans* can switch between Fe2+-dependent chemoautotrophy and electrode-dependent electroautotrophy; the latter showed slower growth and altered electron-uptake machinery. These modes should not be merged in the core trait graph. (wang2024characterizethegrowth pages 22-23)
- **Mixotrophy/facultative autotrophy:** organisms that simultaneously or alternatively assimilate organic carbon should receive the trait only when chemolithoautotrophic growth is experimentally demonstrated under the relevant condition.
- **Methane oxidation:** although CH4 is reduced and geochemically simple, it is conventionally an organic C1 substrate. Methanotrophy should not automatically be curated as lithotrophy.
- **Genomic potential:** marker genes alone establish potential, not the observed phenotype. Stable-isotope incorporation, growth with CO2 as carbon source, donor consumption, or pathway biochemistry provides stronger support.

## 2. Candidate nodes

Identifiers below are deliberately conservative. Stable identifiers are supplied only where confidence is high; otherwise a label-only node is preferable to an invented or over-specific CURIE.

### Trait and biological-process nodes

- **chemolithoautotrophic** — **METPO:1000637**
- chemolithotrophy — parent or related METPO term should be resolved against the local ontology release
- carbon fixation — **GO:0015977**
- aerobic respiration — **GO:0009060**
- proton transmembrane transport — **GO:1902600**
- ATP synthesis coupled proton transport — **GO:0015986**
- nitrification — label-only unless the project’s preferred process ontology is established
- sulfur oxidation, hydrogen oxidation, ferrous-iron oxidation, phosphite oxidation — label-only process nodes pending ontology verification

### Chemicals and environmental substrates

- carbon dioxide — **CHEBI:16526**
- hydrogencarbonate/bicarbonate — **CHEBI:17544**
- dihydrogen — **CHEBI:18276**
- dioxygen — **CHEBI:15379**
- ammonia — **CHEBI:16134**
- ammonium — **CHEBI:28938**
- nitrite — **CHEBI:16301**
- nitrate — **CHEBI:17632**
- sulfide — **CHEBI:26822**
- hydrogen sulfide — **CHEBI:16136**
- thiosulfate — **CHEBI:26977**
- iron(2+) — **CHEBI:29033**
- iron(3+) — **CHEBI:29034**
- phosphite, phosphate, elemental sulfur, sulfate, NADH, NADPH, ATP, proton motive force — retain as labels until CURIEs are checked against the project’s exact ChEBI release
- environmental parameters: oxygen concentration, pH, temperature, inorganic-donor concentration, CO2/HCO3− availability, salinity, heavy metals

### Enzymes, proteins, transporters, and complexes

Showing the first 60 of 257 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. · ADDED_CAUSAL_GRAPH · codex

    Added DOI-backed causal graph for inorganic donor oxidation, respiratory energy conservation, ATP/reductant generation, and CO2 fixation.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009×1, METPO:2000202×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

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

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402×1, METPO:2007404×1).

  6. · RENAME_PREDICATE_LABELS · claude

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

  7. · GROUND_CAUSAL_PREDICATES · claude

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

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502×1, METPO:1007500×1, METPO:1007503×1, METPO:1007501×1).

  9. · RETYPE_CAUSAL_NODES · claude

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

  10. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022900×1, GO:0015977×1).

  11. · RETYPE_CAUSAL_NODES · claude

    Re-typed 2 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1; reducing power: CHEMICAL → CAPACITY ×1.

  12. · GROUND_CAUSAL_PREDICATES · claude

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

  13. · ENRICH_CAUSAL_GRAPH · claude

    Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.

  14. · GROUND_CAUSAL_PREDICATES · claude

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

  15. · GROUND_CAUSAL_NODES · claude

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

  16. · GROUND_CAUSAL_NODES · claude

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

  17. · 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)

  18. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR033966×1, InterPro:IPR001765×1).

  19. · 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.

  20. · 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).

  21. · 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.

  22. · NORMALISE_NODE_TYPE · claude

    Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): electron_transport_chain is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes. Was 4 PATHWAY to 2 before this tranche.