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chemolithotrophic

METPO:1000639 · CLASS · REVIEWED

A trophic type characterized by the use of inorganic chemical compounds as electron donors and carbon dioxide as the primary carbon source for energy generation and biosynthesis.

Chemolithotrophic inorganic chemical oxidation

DOI-backed graph for inorganic chemical electron donors, representative ammonia and sulfur oxidation, and respiratory energy conservation.

Chemolithotrophic inorganic chemical oxidation Interactive directed graph showing evidence-backed causal relationships for chemolithotrophic.

Edge evidence

  • chemolithotrophic has electron donor inorganic chemical electron donor METPO:2007701

    Inorganic chemicals serve as the electron donors for chemolithotrophy.

    • DOI:10.1016/B978-0-12-378630-2.00219-X oxidize inorganic atoms or molecules Supports inorganic chemical oxidation as chemolithotrophy.
  • ammonia monooxygenase oxidizes ammonia METPO:2007803

    Ammonia monooxygenase initiates ammonia oxidation.

    • DOI:10.1146/annurev.micro.55.1.485 ammonia-oxidizing bacteria Supports ammonia oxidation as a chemolithoautotrophic process.
  • ammonia oxidized to hydroxylamine METPO:2007405

    Ammonia oxidation proceeds through hydroxylamine.

    • DOI:10.1007/s00775-020-01820-0 convert ammonia to hydroxylamine Supports AMO-catalyzed ammonia-to-hydroxylamine conversion.
  • hydroxylamine oxidized to nitrite METPO:2007405

    Hydroxylamine oxidation yields nitrite in ammonia oxidizers.

    • DOI:10.3389/fmicb.2012.00210 oxidation of hydroxylamine to nitrite Supports hydroxylamine oxidation as the next nitrification step.
  • Sox enzyme system oxidizes thiosulfate METPO:2007803

    Sox proteins mediate oxidation of reduced sulfur compounds such as thiosulfate.

    • DOI:10.1111/j.1574-6976.2009.00187.x oxidation of thiosulfate Supports the Sox multienzyme system in lithotrophic sulfur oxidation.
  • inorganic chemical electron donor feeds electrons into respiratory chain METPO:2007402

    Oxidation of inorganic donors feeds electrons into respiratory chains.

    • DOI:10.1016/j.bbabio.2008.09.008 membrane-bound electron transport chain Supports respiratory chains as energy-conserving redox systems.
  • respiratory chain has output ATP RO:0002234

    Respiratory energy conservation produces ATP.

    • DOI:10.1016/j.bbabio.2008.09.008 drives ATP synthesis Supports ATP synthesis from the respiratory ion gradient.
  • Calvin-Benson-Bassham cycle mediates fixation of carbon dioxide

    Chemolithoautotrophs fix CO2 via the Calvin-Benson-Bassham cycle.

    • DOI:10.3390/microorganisms12030590 fixes atmospheric CO2 via the Calvin-Benson-Bassham (CBB) cycle
  • acidification decreases nitrification rate RO:0002212

    Environmental acidification reduces nitrification rates.

    • DOI:10.1038/s41467-023-37104-9 a 5.8-18.1% drop and ~11.1-34.1% decline when pCO2 was doubled
  • acidification stimulates generation of nitrous oxide

    Acidification stimulates N2O byproduct generation during nitrification.

    • DOI:10.1038/s41467-023-37104-9 Acidification also stimulate[s] generation of byproduct nitrous oxide (N2O)

Provenance

Source
METPO (2025-11-25)
Author
Anthea Guo
Definition source
DOI:10.1016/B978-0-12-378630-2.00219-X

Parent traits (1)

Synonyms (1)

  • chemolithotroph RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000639 [-0.145, -1.567, -3.045, -0.245, …]

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/chemolithotrophic-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: chemolithotrophic

## 1. Executive scope

**Trait:** chemolithotrophic  
**Identifier:** `METPO:1000639`  
**Category:** PHYSIOLOGY; **term kind:** CLASS; **mapping:** REVIEWED  
**Parent:** `METPO:1000631`  
**Synonym:** chemolithotroph

For this term, the defensible scope is **chemolithoautotrophy**: a cell oxidizes one or more inorganic chemical electron donors, conserves the released energy as ATP and reducing power, and uses CO2/dissolved inorganic carbon as its primary biomass-carbon source. The phenotype therefore requires both an **energy module** and an **autotrophic carbon-assimilation module**. Oxidation of an inorganic compound alone is insufficient.

This interpretation agrees with contemporary descriptions of chemolithoautotrophs as organisms that use energy released by oxidation of reduced compounds to drive inorganic-carbon fixation. It also matches the supplied definition more narrowly than the broader usage of “chemolithotroph,” which can include organisms using inorganic donors but organic carbon. (laufermeiser2024oxidationofsulfur pages 1-2, bayer2024contributionofammonia pages 1-4)

### Recommended inclusion criteria

Curate the trait when evidence establishes:

1. Growth or energy conservation supported by an inorganic donor such as NH3, NO2−, H2, Fe2+, H2S/HS−, S0, thiosulfate, CO, or another reduced inorganic compound.
2. CO2/HCO3−/DIC as the primary carbon source, preferably demonstrated by growth in mineral medium, isotope incorporation, or a complete and expressed fixation pathway.
3. A compatible electron acceptor and respiratory or energy-conserving mechanism.
4. Biomass production or sustained growth—not merely oxidation, detoxification, or transient maintenance.

### Boundary cases

- **Chemolithoheterotrophy:** inorganic donor oxidation with organic carbon as the biomass source is outside this term. *Arcobacter peruensis* oxidizes sulfide and reduces nitrate but assimilates acetate and does not substantially fix CO2; it is therefore a strong negative-control example. (callbeck2019arcobacterperuensissp. pages 1-2)
- **Mixotrophy:** simultaneous CO2 fixation and organic-carbon uptake should be represented separately or qualified as facultative/mixotrophic. In sulfur-stimulated groundwater microcosms, mixotrophs rather than strict autotrophs dominated and balanced CO2 fixation with organic-carbon uptake. (taubert2022bolsteringfitnessvia pages 1-2)
- **Electroautotrophy:** direct uptake of electrode-derived electrons can support CO2 fixation, but it is mechanistically distinct because the energy input is an electrode rather than oxidation of an inorganic chemical donor. *Acidithiobacillus ferrooxidans* changes pilin, porin, EPS, and electron-transfer expression under electrode growth. (wang2024characterizethegrowth pages 22-23)
- **Photolithoautotrophy:** light, rather than chemical oxidation, is the principal energy source and should be excluded.
- **Methanotrophy/methylotrophy:** methane and reduced one-carbon organics are generally treated as organic substrates, not lithotrophic donors. H2-supported growth by a methanotroph may represent mixotrophic flexibility rather than the defining trait.
- **Sulfur detoxification:** possession or activity of Sqr alone does not establish energy-conserving sulfur chemolithotrophy. Donor disappearance must be linked to respiration, ATP/reductant formation, CO2 fixation, and growth.
- **Genomic potential alone:** donor-oxidation genes plus carbon-fixation genes are suggestive but do not prove that the modules are simultaneously functional.

## 2. Candidate nodes

Only identifiers that can be used with high confidence are given below. Nodes whose exact database accession depends on protonation state, species, enzyme family, or taxonomic context should remain **label-only pending ontology lookup** rather than receive a guessed CURIE.

### Trait and biological-process nodes

- chemolithotrophic — `METPO:1000639`
- Calvin–Benson–Bassham cycle — `GO:0019253`
- proton transmembrane transport — `GO:0015992`
- ATP synthesis coupled to proton transport — use the appropriate GO child after confirming cellular context
- reductive TCA cycle — label only pending exact pathway grounding
- 3-hydroxypropionate/4-hydroxybutyrate cycle — label only pending exact pathway grounding
- Wood–Ljungdahl pathway, 3-hydroxypropionate bicycle, dicarboxylate/4-hydroxybutyrate cycle — optional taxon-specific alternatives; do not imply that every chemolithotroph uses the CBB cycle
- phosphoglycolate salvage; glycerate pathway; malate cycle — label-only maintenance modules

### Chemicals and environmental factors

**Electron donors:** ammonia, nitrite, molecular hydrogen, ferrous iron, hydrogen sulfide/sulfide, elemental sulfur, thiosulfate, carbon monoxide, and potentially other reduced inorganic species. Preserve chemical state explicitly—for example, NH3 rather than NH4+ for AMO substrate and Fe2+ rather than generic “iron.” The 2023 AOA review states that NH3, not NH4+, is the AMO substrate. (wright2023nitrificationandbeyond pages 1-2)

**Carbon source:** carbon dioxide — `CHEBI:16526`; bicarbonate/DIC may be included as experimentally supplied inorganic-carbon forms.

**Electron acceptors:** oxygen, nitrate, and—in taxon-specific anaerobic systems—Fe3+. Hydrogen-grown *A. ferrooxidans* can transfer electrons to O2 aerobically or Fe3+ anaerobically. (kucera2020amodelof pages 1-2, kucera2020amodelof pages 4-8)

**Energy/redox products:** ATP — `CHEBI:15422`; NADH — `CHEBI:57540`; NADPH; proton motive force; quinone/quinol pools.

**Environmental nodes:** oxic, microoxic, and anoxic conditions; low pH; hydrothermal vent mixing zone; aphotic/dark ocean; groundwater; sulfide–nitrate redoxcline; bioleaching reactor; donor concentration; CO2 availability; temperature and salinity.

Showing the first 60 of 293 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 chemical electron donors, ammonia oxidation, sulfur oxidation, respiratory energy conservation, and ATP synthesis.

  3. · ADDED_ORGANISM_EXAMPLE · claude

    Added Nitrosomonas europaea organism example with PMID-backed evidence.

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000016×2, METPO:2000009×1, METPO:2000202×1).

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405×2, METPO:2007402×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904×1).

  7. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A059V4Z9×1).

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:33542×1).

  9. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15429×1).

  10. · FIX_NODE_GROUNDING_CURIE · claude

    Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).

  11. · ENRICH_CAUSAL_GRAPH · claude

    Added 3 evidence-backed generic edges (5 new nodes) from the deep-research report.

  12. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212×1).

  13. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17045×1).

  14. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  15. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0018597×1).

  16. · 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.

  17. · 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).

  18. · 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.

  19. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to oxidizes), issue 301 part 2. 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. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.