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chemoautotrophic

METPO:1000635 · CLASS · REVIEWED

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

Chemoautotrophic chemical-energy CO2 fixation

DOI-backed graph linking chemical electron donors, energy conservation, RuBisCO/Calvin-Benson carbon fixation, and biomass production.

Chemoautotrophic chemical-energy CO2 fixation Interactive directed graph showing evidence-backed causal relationships for chemoautotrophic.

Edge evidence

  • chemoautotrophic uses energy substrate reduced inorganic compound

    Chemoautotrophs derive energy from oxidizing reduced inorganic compounds.

    • DOI:10.1146/annurev.micro.52.1.191 physiology ... of chemoautotrophic bacteria Review supports chemoautotrophic metabolism based on chemical energy and CO2 fixation.
  • reduced inorganic compound enables respiratory energy conservation RO:0002327

    Oxidation of chemical substrates supports energy conservation.

    • DOI:10.1016/j.bbabio.2008.09.008 free energy of a redox reaction Supports energy conservation from redox reactions in respiratory systems.
  • respiratory energy conservation has output ATP RO:0002234

    Energy conservation produces ATP for biosynthesis.

    • DOI:10.1016/j.bbabio.2008.09.008 drives ATP synthesis Supports ATP synthesis from respiratory energy conservation.
  • respiratory energy conservation has output NADPH RO:0002234

    Chemoautotrophic electron flow supplies reducing equivalents.

    • DOI:10.1016/j.biortech.2021.125768 NADH, or ... NADPH Supports reduced redox cofactors in chemolithoautotrophic metabolism.
  • carbon dioxide fixed by Calvin-Benson cycle METPO:2007404

    CO2 can be fixed through the Calvin-Benson cycle.

    • DOI:10.1128/AEM.02473-10 Calvin-Benson reductive pentose phosphate cycle Supports Calvin-Benson as a microbial autotrophic CO2-fixation pathway.
  • RuBisCO catalyzes Calvin-Benson cycle biolink:catalyzes

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

    • DOI:10.1128/AEM.02473-10 form I RuBisCO Supports RuBisCO as a Calvin-Benson cycle enzyme.
  • ATP enables Calvin-Benson cycle RO:0002327

    ATP is required for chemoautotrophic CO2 fixation.

    • DOI:10.1128/AEM.02473-10 energy required for autotrophic CO2 fixation Supports ATP/energy requirement for carbon fixation.
  • NADPH enables Calvin-Benson cycle RO:0002327

    Reducing equivalents support reductive CO2 fixation.

    • DOI:10.1016/j.biortech.2021.125768 reduction of CO2 Supports NAD(P)H-like reductant use in carbon fixation.
  • Calvin-Benson cycle has output cellular biomass RO:0002234

    Fixed carbon is incorporated into cellular biomass.

    • DOI:10.1146/annurev.micro.52.1.191 physiology, ecology, and molecular biology Review scope supports chemoautotrophic bacterial growth from fixed carbon.
  • carboxysome encapsulates RuBisCO

    Carboxysomes encapsulate RuBisCO and carbonic anhydrase within a protein shell.

    • DOI:10.1128/AEM.01075-24 Carboxysomes encapsulate RubisCO and carbonic anhydrase (CA) within a protein shell.
  • carboxysome encapsulates carbonic anhydrase

    Carboxysomes encapsulate carbonic anhydrase alongside RuBisCO.

    • DOI:10.1128/AEM.01075-24 Carboxysomes encapsulate RubisCO and carbonic anhydrase (CA) within a protein shell.
  • carbonic anhydrase produces carbon dioxide METPO:2007800

    Carbonic anhydrase converts bicarbonate to CO2 inside the carboxysome for RuBisCO.

    • DOI:10.1128/AEM.01075-24 Inside carboxysomes, CA converts HCO3- to CO2, which RubisCO then fixes.
  • carbonic anhydrase uses substrate bicarbonate

    Carbonic anhydrase uses bicarbonate as substrate to generate CO2.

    • DOI:10.1128/AEM.01075-24 Inside carboxysomes, CA converts HCO3- to CO2, which RubisCO then fixes.
  • dissolved inorganic carbon transporter enables carbon-concentrating mechanism RO:0002327

    DIC (CO2/HCO3-) transporters supply substrate for the carbon-concentrating mechanism.

    • DOI:10.1128/AEM.01075-24 CCMs consist of CO2 and HCO3- transporters and carboxysomes.
  • carbon-concentrating mechanism enables Calvin-Benson cycle RO:0002327

    The carbon-concentrating mechanism elevates CO2 around RuBisCO to support Calvin-Benson fixation.

    • DOI:10.1128/AEM.01075-24 CCMs consisting of transporters and carboxysomes concentrate CO2 for RubisCO-mediated fixation.
  • Calvin-Benson cycle enables inorganic carbon assimilation RO:0002327

    The Calvin-Benson-Bassham cycle drives inorganic carbon assimilation in chemolithoautotrophs.

    • DOI:10.1101/2024.08.01.606197 The CBB cycle accounts for >99% of global autotrophy and is used in chemolithoautotrophs.
  • carbon dioxide fixed by 3-hydroxypropionate/4-hydroxybutyrate cycle METPO:2007404

    The 3HP/4HB cycle is an energy-efficient aerobic CO2-fixation pathway used by chemoautotrophs.

    • DOI:10.1038/s42003-024-06432-x Currently considered the most energy-efficient aerobic carbon fixation pathway.

Provenance

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

Parent traits (1)

Synonyms (1)

  • chemoautotroph RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000635 [-0.624, -3.507, -4.293, +0.160, …]

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/chemoautotrophic-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: chemoautotrophic

**Target:** `METPO:1000635`  
**Category:** PHYSIOLOGY · **Kind:** CLASS · **Status:** REVIEWED  
**Parent:** `METPO:1000631`

## 1. Scope and current understanding

The trait denotes a trophic phenotype in which an organism obtains energy by oxidizing inorganic compounds and obtains cellular carbon primarily by fixing CO₂ or bicarbonate. The graph should therefore require two connected capacities: **(i) inorganic electron-donor oxidation coupled to energy conservation and (ii) autotrophic inorganic-carbon assimilation**. Classical donors include H₂, H₂S, thiosulfate, NH₄⁺/NH₃, NO₂⁻, and Fe²⁺; common terminal acceptors include O₂ and nitrate. Facultative chemoautotrophs may also grow heterotrophically or mixotrophically. (shively1998somethingfromalmost pages 3-5)

“Chemoautotrophic” is often used nearly interchangeably with **chemolithoautotrophic**, but the latter makes the inorganic nature of the electron donor explicit. Neither **chemolithotrophy alone** nor possession of an inorganic-substrate oxidation module is sufficient: gamma-methanotrophs examined in 2023 possessed putative thiosulfate-oxidation genes but lacked autotrophic fixation and showed no corresponding growth benefit. Conversely, an organism fixing CO₂ using light energy is photoautotrophic rather than chemoautotrophic. Methanotrophy and methylotrophy use reduced one-carbon compounds containing carbon and therefore are not automatically chemoautotrophic. (marc2023physiologicalandgenetic pages 98-103)

### Boundary rules recommended for TraitMech

- **Include:** demonstrated growth or biomass synthesis from inorganic carbon, energized predominantly by oxidation of an inorganic donor.
- **Include with qualifier:** facultative organisms when the chemoautotrophic growth mode is directly demonstrated.
- **Do not infer from donor oxidation genes alone.** Require a complete carbon-fixation module or preferably physiological/isotope evidence.
- **Do not treat mixotrophic CO₂ incorporation as equivalent to strict chemoautotrophic growth** unless inorganic energy supply and net biomass production are established.
- **Do not require the Calvin–Benson–Bassham cycle universally.** Modern environmental genomes also support rTCA and Wood–Ljungdahl implementations. In 2024 groundwater data, 60% of reconstructed MAGs encoded autotrophic pathways, dominated by CBB but including rTCA and Wood–Ljungdahl pathways. (atencio2024metabolicadaptationsunderpin pages 6-8)

## 2. Candidate nodes

### Trait-defining processes

- `METPO:1000635` — chemoautotrophic.
- Carbon fixation — `GO:0015977`.
- Generation of precursor metabolites and energy — `GO:0006091`.
- Aerobic electron-transport chain — `GO:0019646`.
- Inorganic electron-donor oxidation; chemiosmotic energy conservation; proton-motive force; ATP synthesis; NAD(P)H generation — retain as label-only candidates until exact GO terms are verified.

### Carbon sources and electron donors/acceptors

- Carbon dioxide — `CHEBI:16526`.
- H₂/bicarbonate, H₂S, sulfide, thiosulfate, NH₃/NH₄⁺, nitrite, Fe²⁺, O₂, nitrate, sulfate and elemental sulfur — ground only after identifier validation against the target ontology release.
- O₂ and nitrate are alternative acceptors in different taxa and conditions; they should not be represented as universally required. (shively1998somethingfromalmost pages 3-5)

### Carbon-fixation pathways and enzymes

- Calvin–Benson–Bassham cycle.
- RuBisCO — `EC:4.1.1.39`.
- Phosphoribulokinase — `EC:2.7.1.19`.
- Sedoheptulose-bisphosphatase.
- Reverse/reductive TCA cycle.
- Wood–Ljungdahl/reductive acetyl-CoA pathway.
- 3-hydroxypropionate-related fixation module, relevant to engineering rather than a universal core.
- Carbonic anhydrase and inorganic-carbon concentrating mechanisms.

The foundational review identifies RuBisCO, phosphoribulokinase and sedoheptulose-bisphosphatase as characteristic CBB activities and notes that some bacteria concentrate RuBisCO in carboxysomes. It also describes regulation of clustered `cbb` genes by CbbR in response to carbon and reduced-substrate availability. These are strong **CBB-branch** nodes, not universal chemoautotrophy requirements. (shively1998somethingfromalmost pages 3-5)

### Complexes, locations, and regulators

- Cytoplasmic membrane electron-transport chain.
- Proton-translocating respiratory complexes, terminal oxidases and ATP synthase.
- Carboxysome.
- CbbR and `cbb` operons.
- Sox sulfur-oxidation system; hydrogenases; ammonia monooxygenase and nitrite oxidoreductase as taxon-specific donor modules.
- Cytochrome bd and high-affinity terminal oxidases for low-oxygen or stress-adapted branches.
- MtrCAB and Gloeobacter rhodopsin only in an explicitly **engineered-system** branch.

### Environments, taxa, and assays

Showing the first 60 of 170 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 chemical energy conservation, ATP/reductant generation, Calvin-Benson CO2 fixation, and biomass production.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×3).

  4. · GROUND_CAUSAL_PREDICATES · claude

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

  5. · GROUND_CAUSAL_PREDICATES · claude

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

  6. · RENAME_PREDICATE_LABELS · claude

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

  7. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×3).

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019253×1).

  9. · GROUND_CAUSAL_NODES · claude

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

  10. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16474×1).

  11. · ENRICH_CAUSAL_GRAPH · claude

    Added 8 evidence-backed generic edges (7 new nodes) from the deep-research report.

  12. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×3, METPO:2000202×1, METPO:2007404×1).

  13. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031470×1, CHEBI:17544×1).

  14. · GROUND_CAUSAL_NODES · claude

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

  15. · 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)

  16. · GROUND_CAUSAL_NODES · claude

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

  17. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (3 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.

  18. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), 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.