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methanotrophic

METPO:1000650 · CLASS · REVIEWED

A trophic type in which an organism uses methane as the primary carbon and energy source through oxidation of methane to carbon dioxide.

Aerobic methanotrophic methane oxidation mechanism

DOI-backed graph for aerobic methane oxidation from methane to methanol, formaldehyde assimilation, and carbon dioxide production.

Aerobic methanotrophic methane oxidation mechanism Interactive directed graph showing evidence-backed causal relationships for methanotrophic.

Edge evidence

  • methanotrophic uses substrate methane

    Methane is the defining carbon and energy source for methanotrophy.

    • DOI:10.1039/D3CY00737E methane as carbon and energy sources Review places methane among C1 compounds used by methanotrophs.
  • methane monooxygenase oxidizes methane METPO:2007803

    Methane monooxygenase catalyzes methane oxidation.

    • DOI:10.1039/D3CY00737E methane oxidation ... catalyzed by two types of methane monooxygenases Supports MMO as the enzyme for the first oxidation step.
  • methane monooxygenase uses oxidant molecular oxygen

    Aerobic methane monooxygenases activate oxygen during methane oxidation.

    • DOI:10.1039/D3CY00737E activation of molecular oxygen Supports oxygen involvement in MMO catalysis.
  • methane oxidized to methanol METPO:2007405

    The first aerobic methane oxidation product is methanol.

    • DOI:10.1039/D3CY00737E convert methane to methanol Supports methane-to-methanol conversion by MMO.
  • methane monooxygenase located in intracellular membrane biolink:located_in

    Particulate methane monooxygenase is membrane associated in methanotrophs.

    • DOI:10.1039/D3CY00737E pMMO is located in the characteristic intracellular membrane Supports subcellular localization for pMMO.
  • methanol dehydrogenase oxidizes methanol METPO:2007803

    Methanol dehydrogenase converts methanol onward to formaldehyde.

    • DOI:10.1039/D3CY00737E Methanol is oxidized to formaldehyde Supports methanol dehydrogenase as the next step.
  • formaldehyde participates in formaldehyde assimilation biolink:participates_in

    Formaldehyde can be assimilated through RuMP or serine pathways.

    • DOI:10.1039/D3CY00737E RuMP pathway and the serine pathway Supports formaldehyde assimilation routes in methanotrophs.
  • methanotrophic produces carbon dioxide METPO:2007800

    Methane oxidation can continue to carbon dioxide for energy metabolism.

    • DOI:10.1039/D3CY00737E methane cycle between ... methane and CO2 Supports methane oxidation in the methane-carbon dioxide cycle; graph focuses on aerobic methanotrophy.
  • copper positively regulates particulate methane monooxygenase (pMMO) RO:0002213

    High copper favors pMMO expression (the copper switch).

    • DOI:10.1039/D3CY00737E high copper favors pMMO and represses sMMO
  • copper negatively regulates soluble methane monooxygenase (sMMO) RO:0002212

    High copper represses sMMO; low copper favors sMMO (the copper switch).

    • DOI:10.1039/D3CY00737E high copper favors pMMO and represses sMMO; low copper/biomass favors sMMO
  • pmoCAB operon encodes PmoA/PmoB/PmoC subunits METPO:2007813

    pmoCAB operon encodes the PmoA, PmoB and PmoC subunits of pMMO.

    • DOI:10.1039/D3CY00737E pMMO ... composed of subunits PmoA, PmoB, and PmoC, encoded by the pmoCAB operon
  • mmoXYZ genes encodes MmoX/MmoY/MmoZ (MMOH alpha/beta/gamma) METPO:2007813

    mmoXYZ genes encode the MMOH alpha/beta/gamma hydroxylase subunits of sMMO.

    • DOI:10.1039/D3CY00737E MMOH is a dimer of heterotrimers encoded by the mmoXYZ genes
  • methanobactin binds Cu(I)

    Methanobactin binds Cu(I) with high affinity.

    • DOI:10.1021/acs.chemrev.3c00727 Mbns are ribosomally synthesized ... that bind Cu(I) with particularly high affinity
  • methanobactin enables copper acquisition RO:0002327

    Methanobactin-mediated copper chelation enables copper uptake.

    • DOI:10.1039/D3CY00737E some methanotrophs produce methanobactin (high affinity for Cu(I)) for copper collection
  • copper acquisition promotes particulate methane monooxygenase (pMMO) RO:0002213

    Copper acquisition supplies the cofactor required for pMMO activity.

    • DOI:10.1021/acs.chemrev.3c00727 As a required cofactor for pMMO activity ... copper is central to methanotroph physiology

Provenance

Source
METPO (2025-11-25)
Author
Luke Wang
Definition source
DOI:10.1039/D3CY00737E

Parent traits (1)

Synonyms (1)

  • methanotroph RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000650 [-1.873, -2.718, -3.631, -1.154, …]

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/methanotrophic-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: methanotrophic

**Trait:** `METPO:1000650`  
**Category:** PHYSIOLOGY · **Kind:** CLASS · **Status:** REVIEWED

## 1. Scope summary

`METPO:1000650` should denote the physiological capacity to use methane as a primary carbon and energy source through methane oxidation. The canonical aerobic route is **CH₄ → methanol → formaldehyde → formate → CO₂**, with methane carbon assimilated principally at the formaldehyde level. Methanotrophs are a methane-using subset of the broader methylotrophs; possession of methanol-dehydrogenase or other methylotrophy genes alone is therefore insufficient. A 2024 floodplain study found methanol-dehydrogenase-containing MAGs that lacked methane monooxygenase and should not be classified as methanotrophs. (rasmussen2024diverseandunconventional pages 7-10, semrau2018metalsandmethanotrophy pages 3-5, ahmadi2024recentfindingsin pages 1-2)

The supplied definition is broadly correct but is too narrow if the class is intended to include anaerobic methanotrophic archaea and NC10/Methylomirabilis bacteria. ANME archaea activate methane with methyl-coenzyme M reductase (MCR), not methane monooxygenase, and couple oxidation to external electron acceptors. *Ca. Methylomirabilis* performs “intra-aerobic” methane oxidation: nitrite-derived nitric oxide is dismutated to N₂ and O₂, and the internally generated O₂ supports pMMO. (wissink2024probingdenitrifyinganaerobic pages 1-2, dinh2024towardtheuse pages 2-4, dinh2024towardtheuse pages 1-2)

### Boundaries

- **Methanotroph versus methylotroph:** methane utilization is defining; methanol or methyl-compound utilization without methane activation is methylotrophy, not methanotrophy. The evolutionary evidence is consistent with methanotrophy arising from methylotrophy after acquisition of MMO genes. (rasmussen2024diverseandunconventional pages 7-10, kang2019theoriginof pages 1-1)
- **Facultative methanotrophs remain in scope:** methane need not be the organism’s exclusive carbon source. Some recognized methanotrophs also grow on acetate or other multicarbon compounds. Thus “primary carbon and energy source” should be interpreted as an assayed capacity, not an obligate nutritional restriction. (ahmadi2024recentfindingsin pages 7-9)
- **Methanogenesis is out of scope:** methane production is not methanotrophy, although MCR catalyzes methane formation in methanogens and the initial reverse reaction in ANME. (dinh2024towardtheuse pages 2-4, dinh2024towardtheuse pages 1-2)
- **Cometabolic oxidation alone is insufficient:** oxidation of methane or other hydrocarbons without methane-supported carbon assimilation and energy conservation should not automatically confer the trait.
- **Genotype is not phenotype:** `pmoA/pmoCAB`, `mmoX/mmoXYBZDC`, or `mcrA/mcrABG` supports mechanistic potential, but incomplete MAGs, promiscuous monooxygenases, and pathway directionality require activity or sufficiently complete pathway evidence. (rasmussen2024diverseandunconventional pages 7-10)
- **Aerobic versus anaerobic should be represented as alternative mechanistic branches**, not collapsed into one universal linear graph.

## 2. Candidate nodes

### Trait and processes

- `METPO:1000650` — methanotrophic
- aerobic methane oxidation
- anaerobic oxidation of methane (AOM)
- reverse methanogenesis
- nitrate-/nitrite-dependent anaerobic methane oxidation (N-DAMO)
- sulfate-dependent AOM
- extracellular electron transfer (EET)
- RuMP pathway
- serine cycle
- H₄MPT/H₄F-linked formaldehyde oxidation
- fermentation-based methanotrophy — **provisional**
- denitrification / partial denitrification — taxon-specific

### Chemicals and environmental inputs

Verified high-value chemical candidates are:

- `CHEBI:16183` — methane
- `CHEBI:17790` — methanol
- `CHEBI:16842` — formaldehyde
- `CHEBI:15740` — formate
- `CHEBI:16526` — carbon dioxide
- `CHEBI:15379` — dioxygen

Additional label-only candidates pending identifier verification include nitrate, nitrite, nitric oxide, dinitrogen, sulfate, sulfide, copper, calcium, lanthanides, NADH/NADPH, PQQ, coenzyme M, coenzyme B, coenzyme F430, iron oxide, manganese oxide, humic substances, electrodes, ammonium, lead, nickel, and cadmium.

### Enzymes, complexes, and genes

- particulate methane monooxygenase, **pMMO**; genes `pmoCAB`
- soluble methane monooxygenase, **sMMO**; genes commonly represented by `mmoXYBZDC`
- calcium-dependent methanol dehydrogenase, **MxaFI**; `mxaFI`
- lanthanide-dependent methanol dehydrogenase, **XoxF**; `xoxF`
- formaldehyde-oxidation modules linked to H₄MPT/H₄F
- formate dehydrogenase
- methyl-coenzyme M reductase, **MCR**; `mcrABG`
- nitrate reductase; nitrite reductase

Showing the first 60 of 281 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 aerobic methane oxidation by methane monooxygenase and downstream C1 metabolism.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000016×2, METPO:2000202×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

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

  5. · GROUND_CAUSAL_PREDICATES · claude

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

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0A3YNQ7×1, UniProtKB:A0A010SCY7×1).

  7. · RENAME_PREDICATE_LABELS · claude

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

  8. · GROUND_CAUSAL_PREDICATES · claude

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

  9. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019649×1).

  10. · ENRICH_CAUSAL_GRAPH · claude

    Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.

  11. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:encodes×2, RO:0002327×1, RO:0002213×1).

  12. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031090×1, CHEBI:222862×1).

  13. · 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)

  14. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0015050×1).

  15. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×1, RO:0002212×1).

  16. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to oxidizes, 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.

  17. · 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.