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hydrogenotrophic

METPO:1000646 · CLASS · REVIEWED

A trophic type in which an organism uses molecular hydrogen as an electron donor for energy generation and carbon dioxide as the primary carbon source.

Hydrogenotrophic H2 oxidation and CO2 fixation

DOI-backed graph linking hydrogenase-catalyzed H2 oxidation, electron transport energy conservation, and autotrophic CO2 fixation.

Hydrogenotrophic H2 oxidation and CO2 fixation Interactive directed graph showing evidence-backed causal relationships for hydrogenotrophic.

Edge evidence

  • hydrogenotrophic has electron donor molecular hydrogen METPO:2007701

    Molecular hydrogen serves as the electron donor for hydrogenotrophy.

    • DOI:10.21775/cimb.006.159 oxidation of hydrogen gas Supports H2 oxidation as a microbial energy process.
  • hydrogenase oxidizes molecular hydrogen METPO:2007803

    Hydrogenases catalyze H2 oxidation.

    • DOI:10.21775/cimb.006.159 reversible oxidation of hydrogen gas Supports hydrogenase-catalyzed H2 oxidation.
  • molecular hydrogen oxidized to protons and electrons METPO:2007405

    H2 oxidation yields protons and electrons.

    • DOI:10.21775/cimb.006.159 H2 <--> 2 H+ + 2 e- Supports the H2 redox half reaction.
  • hydrogenase interacts with electron transport system biolink:interacts_with

    Hydrogenases can couple H2 metabolism to membrane electron transport systems.

    • DOI:10.21775/cimb.006.159 interact with membrane-bound electron transport systems Supports coupling to electron transport.
  • electron transport system generates proton motive force biolink:produces

    Membrane-linked H2 metabolism can conserve energy as proton motive force.

    • DOI:10.21775/cimb.006.159 generation of a protonmotive force Supports membrane-linked energy conservation.
  • carbon dioxide fixed by autotrophic CO2 fixation METPO:2007404

    CO2 supplies carbon for autotrophic hydrogenotrophic growth.

    • DOI:10.1128/AEM.02473-10 assimilation of CO2 Supports CO2 assimilation into cellular carbon.
  • autotrophic CO2 fixation has output cellular carbon RO:0002234

    Carbon fixation converts CO2 into cell carbon.

    • DOI:10.1128/AEM.02473-10 CO2 ... into cellular carbon Supports the carbon-assimilation output.
  • H2 oxidation generates proton motive force biolink:produces

    Splitting H2 yields electrons and protons that can generate a proton gradient.

    • DOI:10.2138/gselements.16.1.39 Splitting H2 yields electrons and protons that can generate proton gradients and ATP; general mechanistic process-level edge.
  • H2 oxidation coupled to reduction of carbon dioxide

    Hydrogen uptake can be coupled to reduction of CO2 in hydrogenotrophy.

    • DOI:10.3390/microorganisms7020053 The hydrogenase reaction is involved in coupling hydrogen uptake to the reduction of electron acceptors (e.g., nitrate, sulfate, and carbon dioxide).
  • H2 oxidation coupled to reduction of oxygen

    H2 oxidation can be coupled to reduction of O2 (aerobic hydrogen oxidation).

    • DOI:10.2138/gselements.16.1.39 Hydrogen oxidation can be coupled to reduction of CO2/HCO3-, sulfate, nitrate, ferric iron and O2; high-confidence generic edge.
  • H2 oxidation coupled to reduction of nitrate

    H2 oxidation can be coupled to reduction of nitrate in anaerobic respiration.

    • DOI:10.2138/gselements.16.1.39 Hydrogen oxidation can be coupled to reduction of CO2/HCO3-, sulfate, nitrate, ferric iron and O2; generic respiratory coupling edge.
  • H2 oxidation coupled to reduction of sulfate

    H2 oxidation can be coupled to reduction of sulfate in anaerobic respiration.

    • DOI:10.2138/gselements.16.1.39 Hydrogen oxidation can be coupled to reduction of CO2/HCO3-, sulfate, nitrate, ferric iron and O2; generic respiratory coupling edge.
  • H2 oxidation can support autotrophic CO2 fixation

    Coupling H2 oxidation to carbon fixation enables hydrogenotrophic chemosynthesis.

    • DOI:10.1111/1751-7915.14300 By coupling hydrogen oxidation to carbon fixation, hydrogenotrophic chemosynthesis is a viable energy generation strategy; trait-level edge.
  • oxygen sensitivity constrains hydrogenase

    Differential O2 sensitivity across hydrogenase classes constrains their distribution and use.

    • DOI:10.2138/gselements.16.1.39 Hydrogenase classes show different sensitivity to O2 and diverse H2 affinities; broad environmental constraint across classes.

Provenance

Source
METPO (2025-11-25)
Author
Luke Wang
Definition source
DOI:10.21775/cimb.006.159

Parent traits (1)

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000646 [-2.114, -2.957, -5.142, +0.724, …]

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/hydrogenotrophic-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: hydrogenotrophic microbial physiology

## Executive scope

**Target:** `METPO:1000646` (“hydrogenotrophic”), category **PHYSIOLOGY**, term kind **CLASS**, mapping **REVIEWED**. The supplied definition—use of molecular hydrogen as electron donor for energy generation and CO2 as the primary carbon source—is appropriately **stricter than “H2 oxidizing.”** A defensible TraitMech graph should therefore require two linked capacities:

1. **H2 oxidation/electron transfer**, and
2. **predominantly inorganic-carbon assimilation**, usually through the Calvin–Benson–Bassham (CBB) cycle or reductive Wood–Ljungdahl pathway (WLP).

Hydrogenotrophy is not one pathway. It is a trophic architecture realized in aerobic Knallgas bacteria, anaerobic acetogens, hydrogenotrophic methanogens, and some nitrate- or sulfate-reducing autotrophs. Uptake hydrogenases oxidize H2 and route electrons to respiratory chains or soluble carriers; the resulting reducing power and chemiosmotic energy support CO2 fixation and growth. Hydrogenotrophic methanogens and acetogens additionally use CO2 as a catabolic electron acceptor, producing methane or acetate, respectively (culp2023crossfeedinginthe pages 7-9, pichechoquette2019molecularhydrogena pages 8-9, pichechoquette2019molecularhydrogena pages 6-8).

## 1. Trait boundaries

### Include

* Demonstrated growth with **H2 as principal electron donor** and **CO2/bicarbonate as principal carbon source**.
* Facultative organisms, such as *Cupriavidus necator*, when assayed specifically under H2–CO2 autotrophic conditions. *C. necator* uses H2 and CO2 as sole energy and carbon sources and encodes soluble and membrane-bound uptake hydrogenases plus a branched respiratory chain (cramm2009genomicviewof pages 1-2).
* Obligately or facultatively autotrophic acetogens growing by H2-dependent WLP activity. The 2023 description of *Aceticella autotrophica* reports obligate autotrophic acetogenic growth and the reaction `4 H2 + 2 CO2 → acetate + H+ + 2 H2O`, with ΔG°′ approximately −104 kJ per reaction as represented by the authors (frolov2023obligateautotrophyat pages 1-2).
* Methanogens performing `4 H2 + CO2 → CH4 + 2 H2O` while assimilating inorganic carbon (culp2023crossfeedinginthe pages 7-9, pichechoquette2019molecularhydrogena pages 8-9).

### Exclude or annotate as boundary cases

* **Hydrogen oxidation without autotrophy.** H2-supported fumarate, nitrate, or sulfate respiration is not by itself sufficient if biomass carbon comes predominantly from organics.
* **Atmospheric-H2 scavenging for persistence or mixotrophy.** High-affinity H2 oxidizers account for about 70% of atmospheric H2 uptake in soils, but atmospheric H2 is generally insufficient to sustain growth; many use it as ancillary maintenance energy. This is “H2 scavenging/mixotrophy,” not strict hydrogenotrophy unless CO2-primary growth is shown (pichechoquette2019molecularhydrogena pages 11-13).
* **Hydrogenogenic organisms.** Microbes producing H2 through fermentation, nitrogenase, or reversible hydrogenases have the opposite net flux and should not inherit the trait on that basis.
* **Hydrogen-dependent methylotrophic methanogenesis.** H2 reduces a methyl compound, but CO2 is not necessarily the primary carbon substrate or catabolic acceptor; curate separately unless autotrophic CO2 assimilation is demonstrated.
* **CO or formate utilization.** Acetogens and methanogens may use these substrates, but that does not establish H2 dependence. Syngas cultures containing CO/H2/CO2 are especially ambiguous because CO can supply both carbon and electrons (neto2024exploringthepotential pages 1-2).
* **Genomic potential alone.** A hydrogenase plus a carbon-fixation pathway supports a prediction, not an observed phenotype. Form-IV Rubisco-like proteins are not evidence of a functional CBB cycle; absence of phosphoribulokinase and the Rubisco small subunit can argue against CBB function (jiao2021insightintothe pages 6-7).

## 2. Candidate graph nodes

Identifiers below are restricted to high-confidence CURIEs. Labels are deliberately retained where an exact database identifier was not verified.

### Trait and processes

| Candidate node | Grounding | Curation note |
|---|---|---|
| hydrogenotrophic | `METPO:1000646` | Target trait; quote CURIE verbatim in YAML |
| parent trait | `METPO:1000631` | Supplied parent |
| molecular-hydrogen oxidation | Label only | Net H2-consuming process |
| chemolithoautotrophic growth | Label only | Assay-level phenotype |
| CBB-cycle CO2 fixation | Label only | Principal aerobic/Knallgas branch |
| reductive Wood–Ljungdahl pathway | Label only | Acetogenic and methanogenic carbon branch |
| hydrogenotrophic methanogenesis | Label only | H2-dependent CO2 reduction to methane |
| homoacetogenesis | Label only | H2-dependent CO2 reduction to acetate |
| hydrogenotrophic respiration | Label only | Must be paired with autotrophic carbon assimilation |
| oxidative phosphorylation | Label only | Respiratory energy-conservation module |
| flavin-based electron bifurcation | Label only | Important in HydABC and methanogenic systems |

### Chemicals and physicochemical entities

| Node | Suggested grounding |
|---|---|
| molecular hydrogen | `CHEBI:18276` |
| carbon dioxide | `CHEBI:16526` |
| water | `CHEBI:15377` |
| dioxygen | `CHEBI:15379` |
| methane | `CHEBI:16183` |
| acetate | `CHEBI:30089` |
| nitrate | `CHEBI:17632` |

Showing the first 60 of 231 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 hydrogenase-mediated H2 oxidation, membrane-linked energy conservation, and CO2 fixation.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009×1, METPO:2000016×1, METPO:2000202×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

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

  5. · GROUND_CAUSAL_PREDICATES · claude

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

  6. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405×1, METPO:2007404×1).

  7. · GROUND_CAUSAL_NODES · claude

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

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A059XQG3×1).

  9. · GROUND_CAUSAL_NODES · claude

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

  10. · 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.

  11. · ENRICH_CAUSAL_GRAPH · claude

    Added 7 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 (biolink:produces×1).

  13. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17632×1, CHEBI:16189×1).

  14. · 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.

  15. · 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).

  16. · 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.

  17. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

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

  18. · NORMALISE_NODE_SENSE · claude

    One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition — the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).