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oxygen preference

METPO:1000601 · CLASS · REVIEWED

A phenotype that is relating to an organism's oxygen requirements or tolerance for growth.

Oxygen-preference O2-availability axis

DOI-backed graph linking ambient molecular-oxygen availability to the four child oxygen-preference phenotypes (aerobic, anaerobic, microaerophilic, facultative) that classify how organisms use or tolerate O2.

Oxygen-preference O2-availability axis Interactive directed graph showing evidence-backed causal relationships for oxygen preference.

Edge evidence

  • ambient molecular oxygen defines oxygen preference METPO:2007500

    Ambient molecular-oxygen concentration is the quantitative axis defining oxygen-preference phenotypes.

    • DOI:10.3389/fmicb.2014.00674 various capacities in their utilization of molecular oxygen Supports molecular oxygen utilization as the classification axis for oxygen-preference phenotypes.
  • aerobic is a oxygen preference rdfs:subClassOf

    Aerobic is a child oxygen-preference phenotype.

    • DOI:10.3389/fmicb.2014.00674 aerobic ... respiration capacities Supports aerobic as an oxygen-use phenotype within oxygen-preference classification.
  • anaerobic is a oxygen preference rdfs:subClassOf

    Anaerobic is a child oxygen-preference phenotype.

    • DOI:10.3389/fmicb.2014.00674 aerobic, microaerobic, and anaerobic reductases Supports anaerobic as a distinct oxygen-preference classification.
  • microaerophilic is a oxygen preference rdfs:subClassOf

    Microaerophilic is a child oxygen-preference phenotype.

    • DOI:10.3389/fmicb.2014.00674 aerophilic, microaerophilic, or anaerobic Supports microaerophilic as a low-O2 setting on the oxygen-preference axis.
  • facultative oxygen preference is a oxygen preference rdfs:subClassOf

    Facultative oxygen preference is a child oxygen-preference phenotype.

    • DOI:10.1111/cmi.13338 cope with changing oxygen levels Supports facultative organisms as a mixed-O2 setting on the oxygen-preference axis, switching between aerobic and anaerobic metabolism.
  • O2 as terminal electron acceptor confers aerobic METPO:2007700

    Obligate aerobic growth depends on molecular oxygen as terminal electron acceptor.

    • DOI:10.1371/journal.ppat.1012084 Obligate aerobes use only oxygen as the terminal electron acceptor, defining aerobic oxygen-preference.
  • molecular oxygen serves as O2 as terminal electron acceptor

    Molecular oxygen functions as the terminal electron acceptor in aerobic respiration.

    • DOI:10.1371/journal.ppat.1012084 Oxygen is used as the terminal electron acceptor of the aerobic respiratory chain.
  • oxygen / reactive oxygen species stress upregulates detoxifying-enzyme gene expression

    O2 or H2O2 stress upregulates detoxifying-enzyme genes.

    • DOI:10.1128/aem.00606-23 Expression of genes encoding detoxifying enzymes was upregulated in response to O2 or H2O2 stress.
  • detoxifying-enzyme gene expression increases oxygen preference RO:0002213

    A larger detoxifying-enzyme repertoire increases survival under oxygen exposure.

    • DOI:10.1128/aem.00606-23 Cells with more detoxifying genes survived longer than those with few scavenging enzymes.
  • catalase degrades hydrogen peroxide METPO:2007809

    Catalase rapidly degrades hydrogen peroxide, a reactive oxygen species.

    • DOI:10.1038/s43705-023-00251-7 Catalase is the most prominent enzyme for H2O2 degradation at higher concentrations.
  • superoxide dismutase increases oxygen preference RO:0002213

    Higher superoxide dismutase activity is associated with higher oxygen tolerance.

    • DOI:10.1038/s43705-023-00251-7 Higher Sod activity corresponded to higher oxygen tolerance.

Provenance

Source
METPO (2025-11-25)
Definition source
PMID:21413255

Parent traits (1)

Children (10)

Synonyms (2)

  • Physiology and metabolism.oxygen tolerance.oxygen tolerance RELATED_SYNONYM · metpo.owl
  • metabolism RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000601 [-1.145, -2.522, -2.827, -0.321, …]

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/environment/oxygen_preference-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-focused research report: microbial oxygen preference

## 1. Scope and recommended interpretation

**Target trait:** oxygen preference  
**Identifier:** **METPO:1000601**  
**Category/kind:** ENVIRONMENT / CLASS  
**Reviewed definition:** “A phenotype that is relating to an organism's oxygen requirements or tolerance for growth.”

For TraitMech, oxygen preference should be modeled primarily as an **observed growth phenotype along an environmental O2-availability/concentration axis**, rather than as the mere presence of an O2-reactive enzyme. Operational states include obligate aerobic, microaerophilic, facultatively anaerobic, aerotolerant anaerobic, and obligately anaerobic growth. The phenotype is conditional on O2 concentration, exposure duration, medium, electron donors and alternative acceptors, redox state, temperature, pressure, and growth phase.

The central mechanistic balance is:

1. **Benefit:** O2 serves as a high-potential terminal electron acceptor, enabling respiratory energy conservation.
2. **Cost:** O2 directly damages oxygen-labile enzymes and indirectly produces reactive oxygen species (ROS).
3. **Adaptation:** terminal oxidases, oxygen sensors, metabolic switching, O2-reducing enzymes, and ROS-defense systems alter the O2 range over which growth remains possible.

This framing is preferable to a strict aerobic/anaerobic binary. Microorganisms can respire O2 at nanomolar concentrations, and aerobic and anaerobic respiration can coexist up to at least 25 µM O2. The estimated theoretical lower limit for aerobic respiration ranges from approximately 0.1 nM to several hundred nanomolar depending on cell size and growth efficiency. High-affinity oxidases are preferentially expressed below roughly 1–10 µM O2. (berg2022howlowcan pages 5-7)

### Boundary cases

- **Oxygen utilization is not automatically oxygen preference.** Anaerobes may express O2-reducing enzymes solely for detoxification.
- **Oxygen tolerance is not aerobic growth.** Survival after air exposure, ROS resistance, or reversible inhibition should not be curated as growth in O2 unless biomass increase or cell division was measured.
- **Microaerophily is not simply possession of cytochrome bd or cbb3 oxidase.** High-affinity oxidases support low-O2 respiration, but their genes also occur in facultative organisms and may serve stress-defense functions.
- **Aerotolerance differs from facultative anaerobiosis.** Aerotolerant organisms survive or grow fermentatively in O2 without using it as the terminal acceptor; facultative anaerobes can switch between aerobic and anaerobic energy metabolism.
- **Obligate anaerobiosis is graded.** Some nominal obligate anaerobes grow at low O2 or endure substantial transient exposure. Reported examples range from a 0.02–0.04% O2 preference in *Desulfovibrio vulgaris* to microoxic growth or tolerance at considerably higher concentrations in selected clostridia and archaea. (lu2021whenanaerobesencounter pages 3-4)
- **Assay atmosphere is not dissolved O2.** Headspace percentage, dissolved concentration, redox potential, and diffusion geometry must be stored separately.

## 2. Candidate causal-graph nodes

### A. Trait and phenotype nodes

- oxygen preference — **METPO:1000601**
- obligate aerobic growth — label-only pending verified phenotype CURIE
- microaerophilic growth — label-only
- facultative anaerobic growth — label-only
- aerotolerant anaerobic growth — label-only
- obligate anaerobic growth — label-only
- oxygen tolerance/survival — label-only; keep separate from growth preference
- oxygen-inhibited metabolic activity — label-only

### B. Environmental and experimental factors

- dioxygen — **CHEBI:15379**
- O2 availability; dissolved O2 concentration; O2 partial pressure — label-only measurement/context nodes
- oxic, microoxic/hypoxic, and anoxic environment — use ENVO terms only after identifier verification
- duration and periodicity of O2 exposure
- medium redox potential
- electron-donor availability
- alternative electron acceptors: nitrate, fumarate, sulfate and related compounds; ground individual chemicals only after validation
- temperature, pH, hydrostatic pressure, agitation, gas-transfer rate, biofilm diffusion, cell density, and growth phase
- inhibitors: cyanide, carbon monoxide, sulfide, nitric oxide; context modifiers rather than universal determinants

### C. Chemicals and metabolites

- water — **CHEBI:15377**
- superoxide — **CHEBI:18421**
- hydrogen peroxide — **CHEBI:16240**
- hydroxyl radical — label/CHEBI grounding to verify
- quinol/quinone pool — label-only unless the specific ubiquinone or menaquinone species is known

Showing the first 60 of 256 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. · CURATED_CAUSAL_GRAPH · claude

    Added DOI-backed causal graph framing oxygen preference as the O2-availability axis with child aerobic, anaerobic, microaerophilic, and facultative phenotypes.

  3. · IMPROVED_CAUSAL_GRAPH_EVIDENCE · codex

    Replaced PMID fallback CausalEdge references with DOI-backed oxygen-utilization and facultative oxygen-response citations.

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×4).

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500×1).

  6. · ENRICH_CAUSAL_GRAPH · claude

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

  7. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×2, RO:0002327×1).

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15379×1, UniProtKB:A0A071MK53×1, UniProtKB:A0A009QPW9×1).

  9. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16240×1).

  10. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000007×1).

  11. · 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)

  12. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004096×1, GO:0004784×1).

  13. · MIGRATE_ENABLES_TRAIT_EDGES · claude

    Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), 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.

  14. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

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

  15. · MERGE_CAUSAL_NODE · claude

    Merged node oxygen_tolerance into oxygen_preference_trait and repointed its edges. Issue 352. A SIXTH restatement (#360). METPO:1000601's own definition is 'an organism's oxygen requirements OR TOLERANCE for growth', so 'capacity of a cell to survive exposure to molecular oxygen' is part of what the anchor already says. I had grounded it METPO:1000609 (aerotolerant), which METPO defines as 'does NOT USE O2 for growth but tolerates its presence' -- the aerotolerant-anaerobe phenotype, false of the obligate aerobes this node also covers -- and which is itself sub METPO:1000601, making it a sixth child phenotype in a graph that wires the other four in with `is a` and left this one unlinked. aerotolerant.yaml, the record FOR 1000609, has no such node at all: it models the same biology as detoxification processes. Merging attaches the ROS-defence island to the trait, which unlike a retype is a real connectivity gain.

  16. · NORMALISE_NODE_SENSE · claude

    One node_id per SENSE (issues 356, 384): ambient_oxygen is the chemical sense here. Already the ambient sense. Listed so a re-run still normalises the label and still retracts ENVO:01001495 if it has been re-applied — the grounder keys on (label, node_type), so an un-normalised label is what lets the retracted CURIE come back.