TraitMech

TraitMech › METABOLISM

Anaerobic respiration

METPO:1000802 · CLASS · REVIEWED

A respiration in which an organism uses electron acceptors other than oxygen for energy production.

Anaerobic respiration with nitrogen oxide acceptors

Evidence-backed causal sketch using denitrification as a representative anaerobic respiratory process.

Anaerobic respiration with nitrogen oxide acceptors Interactive directed graph showing evidence-backed causal relationships for Anaerobic respiration.

Edge evidence

  • denitrification occurs in anaerobic or microaerophilic condition biolink:occurs_in

    Denitrification can occur under anaerobic and microaerophilic conditions.

    • DOI:10.1128/mmbr.61.4.533-616.1997 under anaerobic, microaerophilic, and occasionally aerobic conditions Supports low-oxygen context for denitrification.
  • nitrogen oxides acts as terminal electron acceptor

    Nitrogen oxides serve as terminal electron acceptors.

    • DOI:10.1128/mmbr.61.4.533-616.1997 N oxides as terminal electron acceptors Supports the terminal electron acceptor role.
  • denitrification uses nitrogen oxides

    Denitrification uses nitrogen oxides in respiratory bioenergetics.

    • DOI:10.1128/mmbr.61.4.533-616.1997 making use of N oxides Supports nitrogen oxides as denitrification substrates.
  • denitrification conserves cellular energy conservation

    Denitrification is a respiratory route for energy conservation.

    • DOI:10.1128/mmbr.61.4.533-616.1997 distinct means of energy conservation Supports energy conservation via denitrification.
  • Anaerobic respiration exemplified by denitrification

    Denitrification is a representative anaerobic respiratory process.

    • DOI:10.1128/mmbr.61.4.533-616.1997 terminal electron acceptors for cellular bioenergetics Supports denitrification as non-oxygen respiratory bioenergetics.
  • oxygen limitation / anoxic transition increases activity of denitrification reductases

    Onset of anoxia drives early transcription and activity of denitrification reductases.

    • DOI:10.1038/s41467-024-51688-w early transcription of NAR (and sometimes NOS) at the cusp of anoxia; environmental driver activating denitrification reductases.
  • respiratory nitrate reductase (NarGHI) catalyzes reduction of nitrate

    Respiratory nitrate reductase NarGHI catalyzes the reduction of nitrate to nitrite.

    • DOI:10.1128/msystems.00967-23 the narGHI nitrate reductase cluster; NarGHI catalyzes nitrate reduction to nitrite, the canonical first step of nitrate respiration.
  • respiratory nitrate reductase (NarGHI) produces nitrite METPO:2007800

    Reduction of nitrate by NarGHI yields nitrite.

    • DOI:10.1128/msystems.00967-23 NarGHI nitrate reductase produces nitrite from nitrate.
  • nitrous oxide reductase (NosZ) reduces nitrous oxide METPO:2007802

    NosZ reduces nitrous oxide to dinitrogen, the terminal step of complete denitrification.

    • DOI:10.1128/msystems.00967-23 NosZ reduces N2O to N2; canonical terminal denitrification step.
  • nitrous oxide reductase (NosZ) produces dinitrogen METPO:2007800

    NosZ-catalyzed reduction of nitrous oxide produces dinitrogen.

    • DOI:10.1128/msystems.00967-23 NosZ reduces N2O to N2; produces dinitrogen as denitrification end product.

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1128/mmbr.61.4.533-616.1997

Parent traits (1)

Children (5)

Synonyms (2)

  • Anoxic respiration RELATED_SYNONYM · metpo.owl
  • Dissimilatory respiration (non-O₂) RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000802 [-0.426, -1.069, -1.023, +1.207, …]

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/anaerobic_respiration-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. 
# TraitMech Curation Report: Anaerobic Respiration

## 1. Trait record and scope

- **Trait label:** Anaerobic respiration
- **Trait identifier:** **METPO:1000802**
- **Category / kind / status:** METABOLISM / CLASS / REVIEWED
- **Parent:** METPO:1000800
- **Synonyms:** anoxic respiration; dissimilatory respiration (non-O₂)

### Operational definition

Anaerobic respiration is an energy-conserving respiratory process in which electrons from an organic or inorganic donor pass through an electron-transport chain to a terminal electron acceptor other than molecular oxygen. Electron transfer generates a transmembrane electrochemical gradient that drives ATP synthesis. This mechanistic criterion—not merely growth without oxygen—is the recommended defining feature for TraitMech (little2024dietaryandhostderived pages 1-3, bueno2012bacterialadaptationof pages 1-2).

### Boundaries

1. **Versus aerobic respiration:** aerobic respiration terminates electron flow at O₂; anaerobic respiration uses a non-O₂ acceptor. Low oxygen commonly induces anaerobic systems in facultative bacteria, but strict anaerobes need not possess the FNR/Arc regulatory architecture of *Escherichia coli* (price2021bacterialapproachesto pages 11-12, price2021bacterialapproachesto pages 6-8).
2. **Versus fermentation:** fermentation does not require an external terminal acceptor or a respiratory electron-transport chain. In *Desulfovibrio vulgaris*, a recent analysis estimated approximately **1 mol ATP per mol lactate** from fermentation versus **2.5 mol ATP per mol lactate** during sulfate respiration, illustrating the energetic distinction; these yields are organism- and model-specific, not universal constants (marbehan2024combiningmetabolicflux pages 1-2).
3. **Versus anaerobic growth:** anaerobic growth is broader and includes fermentation, disproportionation, acetogenesis and methanogenesis. Do not infer this trait solely from growth under N₂ or low O₂.
4. **Versus denitrification:** denitrification is one subtype, normally reducing nitrate/nitrite through NO and N₂O toward N₂. Nitrate respiration can instead end in nitrite or ammonium (DNRA), so nitrate reduction alone does not establish denitrification (bueno2012bacterialadaptationof pages 1-2).
5. **Assimilatory versus dissimilatory reduction:** assimilatory nitrate or sulfate reduction supplies biomass precursors; respiratory/dissimilatory reduction supports energy conservation. The trait should represent the latter.
6. **Detoxification boundary:** cytosolic detoxification reductases such as ArsC should not automatically be equated with respiratory arsenate reductase Arr. Evidence of growth, membrane electron transport, ATP production or an established respiratory complex is needed.

## 2. Candidate nodes grouped by type

### Trait, processes and pathways

- Anaerobic respiration — **METPO:1000802**; GO candidate **GO:0009061**
- Anaerobic electron-transport chain — GO candidate **GO:0019646**; verify against the project’s GO release
- Ion-motive force/proton gradient; oxidative phosphorylation; ATP synthesis
- Nitrate respiration; denitrification; DNRA
- Fumarate, TMAO and DMSO respiration
- Dissimilatory sulfate/sulfite reduction
- Extracellular Fe(III)/Mn(IV) reduction
- Arsenate, selenate, chlorate/perchlorate and organohalide respiration
- Organic-metabolite respiration in the gut

### Environmental and experimental factors

- Oxygen limitation/anoxia; nitrate, nitrite or other acceptor availability
- Electron-donor availability and donor:acceptor ratio
- Redox potential; pH; salinity; temperature
- Anoxic culture or microcosm; acceptor-dependent growth; ATP assay
- Mutant/complementation assay; reductase activity assay
- Transcriptomics/proteomics; isotope tracing; electrochemical current
- Anaerobic/anoxic reactor stage; poised electrode

### Electron donors and intermediates

- NADH, formate, H₂, lactate, pyruvate, acetate, ethanol, sulfide and reduced organic carbon
- Quinone/quinol pools, including menaquinone and ubiquinone
- Periplasmic or membrane-associated formate dehydrogenases and hydrogenases

Sulfate-reducing microorganisms couple sulfate reduction to oxidation of lactate, pyruvate, formate, ethanol or H₂; in the absence of sulfate, some can instead ferment organic substrates (marbehan2024combiningmetabolicflux pages 1-2).

### Terminal acceptors and products

- Nitrate (**CHEBI:17632**) → nitrite → NO → N₂O → N₂, or nitrite → ammonium
- Fumarate → succinate
- TMAO → trimethylamine; DMSO → dimethyl sulfide

Showing the first 60 of 258 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 anaerobic respiration using denitrification and nitrogen oxide terminal electron acceptors.

  3. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007504×1).

  4. · RENAME_PREDICATE_LABELS · claude

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

  5. · GROUND_CAUSAL_PREDICATES · claude

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

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:35196×1).

  7. · ENRICH_CAUSAL_GRAPH · claude

    Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.

  8. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×2, METPO:2000017×1).

  9. · GROUND_CAUSAL_NODES · claude

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

  10. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16301×1, CHEBI:17045×1, CHEBI:17997×1).

  11. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0050304×1).

  12. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces, 1 to reduces), 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.