TraitMech

TraitMech › METABOLISM

Methanogenesis

METPO:1000844 · CLASS · REVIEWED

A metabolism in which methane is produced as the primary end product through the reduction of carbon-containing compounds, formate, methanol, or acetate, exclusively performed by methanogenic archaea under strictly anaerobic conditions.

Trait evidence (2)

Methanogenesis C1 reduction mechanism

Evidence-backed causal sketch linking anoxic C1 reduction, methyl-coenzyme M reductase, and methane formation.

MECHANISTIC · Represents hydrogenotrophic C1 reduction and the terminal methyl-coenzyme M reductase reaction, with branch labels for alternative methanogenic substrates; the exemplar is explicitly the McrA component, not the entire complex.

Methanogenesis C1 reduction mechanism Interactive directed graph showing evidence-backed causal relationships for Methanogenesis.

Edge evidence

  • Methanogenesis occurs in anoxic habitat biolink:occurs_in

    Hydrogenotrophic methanogenesis is associated with anoxic habitats.

  • carbon dioxide reduced with electron donor molecular hydrogen

    Carbon dioxide is reduced using electrons derived from hydrogen.

  • methyl-coenzyme M reductase has prosthetic group coenzyme F430

    Methyl-coenzyme M reductase contains nickel coenzyme F430.

  • methyl-coenzyme M reductase catalyzes formation of methane biolink:catalyzes

    Methyl-coenzyme M reductase catalyzes the terminal methane-forming reaction.

    • DOI:10.1021/acs.biochem.9b00164 catalyzes the reversible reduction of methyl-coenzyme M Source describes methane formation by methyl-coenzyme M reductase.
  • Methanogenesis produces methane METPO:2007800

    The defining output of methanogenesis is methane.

  • acetate serves as substrate for acetoclastic methanogenesis

    Acetate is the substrate split to methane and CO2 in acetoclastic methanogenesis.

  • methylated compounds serves as substrate for methyl-based methanogenesis

    Methylated compounds are the substrates for methyl-based methanogenesis.

  • coenzyme B is required for methane

    Coenzyme B reacts with methyl-CoM in the terminal step to yield methane.

    • DOI:10.1021/ja906367h It converts the thioether methyl-coenzyme M and the thiol coenzyme B into methane and the heterodisulfide of coenzyme M and coenzyme B. methyl-CoM reacts with coenzyme B (CoB) to yield methane.
  • coenzyme M carries methyl group in Methanogenesis

    Methyltransferases transfer methyl groups to coenzyme M to form methyl-CoM.

    • DOI:10.1128/mmbr.00024-22 the methyl group first transferred to a substrate-specific corrinoid protein and then to coenzyme M (CoM) to produce methyl-CoM methyltransferases transfer methyl groups ultimately to CoM to form methyl-CoM.
  • coenzyme F420 (F420H2) donates electrons to carbon dioxide METPO:2007403

    Reduced coenzyme F420 donates electrons for reduction of C1 intermediates derived from CO2.

    • DOI:10.3389/fmicb.2023.1296008 Reduced coenzyme F420 (F420H2), generated by an F420-reducing [NiFe]-hydrogenase (Frh) with H2, serves as a direct electron donor for the reduction of methenyl and methylene forms. Reduced coenzyme F420 (F420H2) donates electrons for reductions of methenyl/methylene intermediates.
  • carbon dioxide participates in Methanogenesis biolink:participates_in

    CO2 is the carbon substrate of hydrogenotrophic methanogenesis.

    • DOI:10.3389/fmicb.2017.01198 Three major methanogenic pathways are known based on the type of carbon sources catabolized, i.e., hydrogenotrophic methanogenesis using CO2 and H2 Verified against the freely available article full text.
  • acetoclastic methanogenesis part of Methanogenesis biolink:part_of

    Acetoclastic methanogenesis is an acetate-using branch.

    • DOI:10.3389/fmicb.2017.01198 hydrogenotrophic methanogenesis using CO2 and H2, acetoclastic methanogenesis using acetate Verified against the freely available article full text.
  • methyl-based methanogenesis part of Methanogenesis biolink:part_of

    Methyl-based methanogenesis is a methyl-substrate branch.

    • DOI:10.3389/fmicb.2017.01198 acetoclastic methanogenesis using acetate, and methylotrophic methanogenesis using methylated compounds, such as methanol, methylamines Verified against the freely available article full text.

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
methyl-coenzyme M reductase UniProtKB:Q58256
Methyl-coenzyme M reductase I subunit alpha (mcrA) 		Methanocaldococcus jannaschii DSM 2661
NCBITaxon:243232 		REVIEWED
retrieved 2026-08-23 · entry v146 · sequence v2

Alpha subunit of methyl-coenzyme M reductase I, the multisubunit enzyme catalyzing the terminal methane-forming step; this accession is not presented as the complete McrABG complex.

  • DOI:10.1074/jbc.M503492200 MJ0846 (McrA, 61227 Da) The primary M. jannaschii study identifies the exact McrA component used in its methyl-coenzyme M reductase preparation; UniProtKB Q58256 verifies the reviewed strain-level entry.
  • DOI:10.1016/S0076-6879(05)97026-2 catalyzes the last step in methanogenesis The mechanistic methods paper establishes the terminal pathway role of methyl-coenzyme M reductase while the first citation establishes the exact M. jannaschii component identity.

Provenance

Identifier source
METPO (2026-06-12)
Author
Luke Wang
Definition source
DOI:10.1146/annurev-micro-011720-122807

Parent traits (1)

Children (3)

Synonyms (5)

  • Biological methanation RELATED_SYNONYM · metpo.owl
  • Biomethanation RELATED_SYNONYM · metpo.owl
  • Carbonate respiration RELATED_SYNONYM · metpo.owl
  • methane biosynthesis EXACT_SYNONYM · http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo
  • methane biosynthetic process EXACT_SYNONYM · http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo

Cross-references

  • GO:0015948

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000844 [+2.183, -3.599, -0.641, +0.610, …]

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/metabolism/methanogenesis-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. 
# Methanogenesis (`METPO:1000844`): TraitMech curation report

## Executive summary

**Methanogenesis** is the net anaerobic biological production of methane by methanogenic archaea. For TraitMech, the class should cover hydrogenotrophic, acetoclastic/aceticlastic, methylotrophic, and H₂-dependent methyl-reducing routes. These routes differ in substrate entry and electron supply but converge on methyl-coenzyme M (methyl-S-CoM), whose reduction by methyl-coenzyme M reductase (MCR) is the terminal methane-forming reaction. The reviewed trait identifier should be retained verbatim as **`METPO:1000844`**, with parent **`METPO:1000060`** and category **METABOLISM**. (borrel2013phylogenomicdatasupport pages 1-2, thauer2019methyl(alkyl)coenzymem pages 1-2)

The recommended graph backbone is therefore:

**anaerobic environment + methanogenic archaeon + pathway-specific substrate/electron donor → methyl-S-CoM → MCR reaction → CH₄**, with heterodisulfide reductase recycling coenzymes M and B. Environmental controls such as H₂ availability, competing electron acceptors, temperature, substrate loading, and inhibitors should be represented as regulatory/contextual branches rather than defining reactions. (thauer2019methyl(alkyl)coenzymem pages 1-2, yang2022effectofbiochar pages 81-86, tveit2015fromthecover pages 1-2, mackie2024—invitedreview pages 1-2)

## 1. Trait scope and boundaries

### 1.1 Included phenotype

The trait denotes a **physiological capacity for net methane production**, not merely possession of a marker gene. Its direct assay-level readout is methane accumulation or production rate under anoxic conditions with an appropriate substrate and controls. Classical routes are:

1. **Hydrogenotrophic methanogenesis:** CO₂ is reduced through formyl-, methenyl-, methylene-, and methyl-level C1 intermediates; H₂ supplies reducing equivalents. Formate can also support this metabolism in organisms able to oxidize it to provide electrons and CO₂.
2. **Acetoclastic methanogenesis:** acetate is activated and cleaved; its methyl carbon is transferred through the methanogenic carrier system to methyl-S-CoM, while oxidation of the carboxyl carbon supplies reducing equivalents.
3. **Methylotrophic methanogenesis:** substrate-specific methyltransferases transfer methyl groups from methanol, methylamines, or methyl sulfides to CoM.
4. **H₂-dependent methyl-reducing methanogenesis:** external H₂ supplies the reducing equivalents for reduction of methyl compounds; this is characteristic of Methanomassiliicoccales and related organisms. (borrel2013phylogenomicdatasupport pages 1-2)

All four route classes converge on MCR. MCR is an α₂β₂γ₂-type complex built from McrA, McrB, and McrG subunits and uses nickel-containing coenzyme F₄₃₀. It reduces methyl-S-CoM with coenzyme B to methane and CoM-S-S-CoB; Hdr subsequently regenerates the free thiols. (thauer2019methyl(alkyl)coenzymem pages 1-2)

### 1.2 Boundary cases

- **Anaerobic methane oxidation (AOM) is not methanogenesis.** MCR homologues also catalyze the first step of methane oxidation in ANME archaea. Methanogen MCR can run in reverse in vitro, although the reported oxidation activity is only about 0.01% of its methane-formation rate; enzyme presence therefore does not determine net physiological direction. (dinh2024towardtheuse pages 2-4)
- **Alkyl-CoM reductase-mediated ethane, propane, or butane activation is not this trait.** Divergent ACRs are related to MCR but support anaerobic non-methane alkane metabolism. Claims that such enzymes produce alkanes remain partly prospective and should not be folded into `METPO:1000844`. (sarno2024beyondmethanenew pages 1-3)
- **Methanotrophy is distinct.** Methane-consuming bacteria or archaea should not be assigned the methanogenesis trait without independent evidence of net methane formation. mcrA can occur in methane oxidizers, and nitrate reduction or N₂ production alone does not prove methane-dependent metabolism. (ahmadi2024recentfindingsin pages 2-4)
- **Anaerobic digestion is broader than methanogenesis.** Hydrolysis, acidogenesis, acetogenesis, syntrophy, and fermentation furnish methanogenic substrates but are upstream community processes, not themselves instances of the trait.
- **Methane accumulation alone is not taxonomic proof.** Abiotic methane, carry-over methane, and methane produced by another consortium member must be excluded. Appropriate no-cell, killed, substrate-free, and inhibitor controls are needed.
- **“Exclusively Euryarchaeota” is historically useful but taxonomically outdated as a rigid graph constraint.** Recent phylogenomic work finds canonical and divergent MCR systems across broader archaeal lineages; curate the producer as Archaea/methanogenic archaeon and add narrower taxonomic scope only when the source demonstrates it. (sarno2024beyondmethanenew pages 1-3)

## 2. Candidate nodes grouped by type

### 2.1 Trait and pathway/process nodes

- Methanogenesis — **`METPO:1000844`**
- Hydrogenotrophic methanogenesis — label-only candidate
- Acetoclastic/aceticlastic methanogenesis — label-only candidate
- Methylotrophic methanogenesis — label-only candidate
- H₂-dependent methyl-reducing methanogenesis — label-only candidate
- CO₂ reduction to methyl-S-CoM — label-only candidate
- Terminal methane formation — label-only candidate
- CoM/CoB heterodisulfide recycling — label-only candidate
- Anaerobic digestion — contextual process, not synonymous with the trait
- Direct interspecies electron transfer — contextual process; curate only with system-specific evidence
- Anaerobic methane oxidation — explicit exclusion/contrast node

### 2.2 Chemicals and cofactors

Conservative candidate grounding includes methane **CHEBI:16183**, carbon dioxide **CHEBI:16526**, dihydrogen **CHEBI:18276**, acetate **CHEBI:30089**, methanol **CHEBI:17790**, and formate **CHEBI:15740**. Other important label-only candidates are methyl-S-CoM, coenzyme M/HS-CoM, coenzyme B/HS-CoB, CoM-S-S-CoB, methanofuran, tetrahydromethanopterin/H₄MPT, coenzyme F₄₂₀, coenzyme F₄₃₀, ferredoxin, methylamines, and dimethyl sulfide. Exact ChEBI records for protonation states and conjugates should be resolved during implementation rather than inferred from names.

### 2.3 Enzymes, genes, and complexes

- Methyl-coenzyme M reductase; genes **mcrA, mcrB, mcrG**; **EC:2.8.4.1**
- Heterodisulfide reductase, especially soluble **HdrABC**; label-only pending complex-specific grounding
- Formylmethanofuran dehydrogenase, **Fwd/Fmd**
- Formylmethanofuran:H₄MPT formyltransferase, **Ftr**
- Methenyl-H₄MPT cyclohydrolase, **Mch**
- F₄₂₀-dependent methylene-H₄MPT dehydrogenase, **Mtd**

Showing the first 60 of 249 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (2)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Curation history

  1. · CURATE_PROTEIN_TAXON_EXAMPLE · codex

    Reviewed the graph as mechanistic, documented the mcrABG cluster as an exact reviewed label-only node, and added DOI-backed UniProtKB Q58256 as the M. jannaschii McrA component exemplar.

  2. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  3. · ADDED_CAUSAL_GRAPH · codex

    Added DOI-backed causal graph for anoxic C1 reduction to methane and the methyl-coenzyme M reductase terminal step.

  4. · GROUND_CAUSAL_PREDICATES · claude

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

  5. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A099T5Q9×1).

  6. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: occurs under → occurs in ×1.

  7. · GROUND_CAUSAL_PREDICATES · claude

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

  8. · GROUND_CAUSAL_PREDICATES · claude

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

  9. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:28265×1).

  10. · REMOVE_REDUNDANT_SYNONYM · claude

    Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).

  11. · ENRICH_CAUSAL_GRAPH · claude

    Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.

  12. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1, METPO:2007403×1).

  13. · 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.

  14. · REGROUND_CAUSAL_EDGE · claude

    Re-grounded causal edge(s) off enables/RO:0002327 onto encodes (biolink:encodes), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.

  15. · REGROUND_CAUSAL_EDGE · claude

    Correction to the REGROUND_CAUSAL_EDGE event above, issue 334 review. That event claimed "All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed". For biolink:encodes that justification was vacuous: the term is ABSENT from the pinned biolink 4.4.0 model, so it trivially declares nothing, and the check used could not distinguish absent from unconstrained. reports/biolink_coverage.tsv already recorded it as the only applied biolink: CURIE with no backing slot. The grounding is retained because a gene CLUSTER to protein COMPLEX edge does not fit `has gene product`'s range of gene product mixin, so repointing would trade a missing term for a wrong range; mappings/predicate_grounding.tsv now states plainly that it is a local coinage. Tracked in issue 342. The edge itself is unchanged and is still an improvement on enables, whose declared range it genuinely violated.

  16. · REGROUND_CAUSAL_EDGE · claude

    Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.

  17. · REVIEW_UNIPROT_INSTANCE_GROUNDINGS · codex

    Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).

  18. · ADD_EXACT_ONTOLOGY_MATCH · codex

    Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0015948; declared exact synonym(s): 'methane biosynthesis', 'methane biosynthetic process'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.

  19. · REVIEW_EVIDENCE_REFERENCE_CHURN · codex

    Offline review for issue 520 retained 3 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s00253-023-12700-3 -> DOI:10.3389/fmicb.2017.01198 (2 edges); DOI:10.1128/mmbr.00024-22 -> DOI:10.1021/ja906367h (1 edge).

  20. · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex

    Resolved issue #183 graph fragmentation (4 components to 1) using 3 public-source, verbatim-snippet-backed connector(s). No paid research service was called.

  21. · GROUND_CAUSAL_NODE · codex

    Grounded the acetoclastic methanogenesis causal node to traitmech:000191 after minting the same-scope acetate-using methanogenesis TraitRecord.

  22. · GROUND_CAUSAL_NODE · codex

    Grounded the methyl-based methanogenesis causal node to traitmech:000192 after minting the same-scope methyl-substrate methanogenesis TraitRecord.