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obligately aerobic

METPO:1000606 · CLASS · REVIEWED

An oxygen preference that requires molecular oxygen (O₂) for growth.

Obligate aerobe oxygen-dependent respiration mechanism

Evidence-backed causal sketch linking obligate aerobic growth to oxygen-dependent terminal oxidase respiration.

Obligate aerobe oxygen-dependent respiration mechanism Interactive directed graph showing evidence-backed causal relationships for obligately aerobic.

Edge evidence

  • obligately aerobic depends on molecular oxygen RO:0002502

    Obligate aerobic growth depends on oxygen availability.

    • DOI:10.1016/j.celrep.2023.112444 obligate aerobe ... exposed to hypoxia, stops growing Mycobacterium tuberculosis example supports oxygen requirement in an obligately aerobic bacterium.
  • terminal respiratory oxidases reduces molecular oxygen METPO:2007802

    Terminal oxidases use oxygen as the respiratory electron acceptor.

    • DOI:10.1016/j.celrep.2023.112444 transfer electrons from the ETC to O2 Supports oxygen reduction by terminal oxidases in an obligate aerobe.
  • electron transport chain includes terminal respiratory oxidases biolink:has_part

    Oxygen-dependent respiratory chains terminate in oxygen reductases.

    • DOI:10.1016/j.bbabio.2011.06.016 respiratory quinol:O2 oxidoreductase Review supports terminal oxygen reductases as respiratory chain enzymes.
  • terminal respiratory oxidases contributes to proton motive force RO:0002326

    Oxygen reductases contribute to proton motive force generation.

    • DOI:10.1016/j.bbabio.2011.06.016 production of a proton motive force Supports bioenergetic coupling by cytochrome bd oxygen reductases.
  • molecular oxygen enables aerobic respiration RO:0002327

    Molecular oxygen enables aerobic respiration.

    • DOI:10.1111/cmi.13338 Aerobic respiration is identified as the main cause of bacterial oxygen consumption.
  • absence of oxygen (anoxia) interrupts flux through electron transport chain

    Anoxia interrupts electron flux through the electron transport chain.

    • DOI:10.1128/JB.00797-19 Interrupted flux through the electron transport chain (ETC) due to the absence of oxygen.
  • electron transport chain maintains proton motive force

    Electron transport chain flux maintains the proton motive force; anoxic interruption impairs it.

    • DOI:10.1128/JB.00797-19 Obligate aerobes must maintain redox balance and the proton motive force (PMF) despite interrupted flux through the electron transport chain.
  • superoxide dismutase activity mitigates superoxide METPO:2007407

    Superoxide dismutase mitigates superoxide stress in aerobes.

    • DOI:10.1016/j.tim.2020.10.001 Aerobes deploy scavenging enzymes (SOD, catalase, other peroxidases).
  • catalase / catalase-peroxidase activity mitigates hydrogen peroxide METPO:2007407

    Catalase/catalase-peroxidase mitigates hydrogen peroxide stress in aerobes.

    • DOI:10.1016/j.tim.2020.10.001 Aerobes deploy scavenging enzymes (SOD, catalase, other peroxidases).
  • superoxide inactivates Fe-S cluster enzymes

    Superoxide and H2O2 oxidize and inactivate exposed Fe-S cluster enzymes.

    • DOI:10.1016/j.tim.2020.10.001 Rate constants for cluster oxidation given (~1e6 M-1 s-1 for superoxide and ~1e4 M-1 s-1 for H2O2), explaining ROS-defense need in aerobes.

Provenance

Source
METPO (2025-11-25)
Definition source
https://www.ncbi.nlm.nih.gov/books/NBK482349/

Parent traits (1)

Synonyms (2)

  • obligate aerobe RELATED_SYNONYM · metpo.owl
  • obligate aerobic RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000606 [-9.610, +1.401, -2.576, -1.238, …]

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/obligately_aerobic-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 Research Report: Obligately Aerobic

**Trait:** obligately aerobic  
**Identifier:** `METPO:1000606`  
**Category / term kind / status:** ENVIRONMENT / CLASS / REVIEWED  
**Definition supplied:** “An oxygen preference that requires molecular oxygen (O₂) for growth.”  
**Parent:** `METPO:1000601`

## 1. Scope summary

`METPO:1000606` should denote an **assay-observed growth phenotype**: reproducible growth requires molecular oxygen. In the strongest mechanistic form, the organism uses O₂ as its sole terminal respiratory electron acceptor, so removal of O₂ prevents sustained energy conservation and cell multiplication. The 2024 *Bordetella* study provides an unusually direct modern example: *B. pertussis* and *B. bronchiseptica* are described as obligate aerobes that use “only oxygen as the terminal electron acceptor” for electron-transport-coupled oxidative phosphorylation. (mckay2024cytochromeoxidaserequirements pages 1-2)

This term should not imply that an organism requires atmospheric 21% O₂. *B. bronchiseptica* grew at both 5% and 2% O₂, although more slowly than in ambient air; thus an obligate aerobe can persist and grow under hypoxia if trace O₂ remains available. (s.2024adaptationofbordetella pages 122-126, mckay2024cytochromeoxidaserequirements pages 18-20)

### Boundary cases

- **Facultative anaerobe:** grows with or without O₂ by switching to anaerobic respiration or fermentation. This excludes it from `METPO:1000606`; the defining contrast is not oxygen tolerance but anaerobic growth capacity. (andre2021theselectiveadvantage pages 2-4)
- **Microaerophile:** requires or preferentially grows at O₂ below atmospheric concentration. A microaerophile may also be obligately oxygen-dependent, so “microaerophilic” and “obligately aerobic” can overlap along different axes: optimum concentration versus absolute requirement.
- **Aerotolerant anaerobe:** tolerates O₂ but does not use it as the required terminal acceptor and generally obtains energy fermentatively. Oxygen tolerance alone does not support this trait.
- **Obligate aerobe surviving anoxia without growth:** dormancy, persistence, or maintenance viability under anoxia does not disprove the trait. Curators should use demonstrated cell multiplication—not CFU persistence alone—as the endpoint.
- **Oxygen-dependent biosynthesis without obligate aerobiosis:** an O₂-requiring enzyme or biosynthetic reaction does not establish the whole-organism phenotype if an anaerobic bypass or nutrient salvage route exists.
- ***Pseudomonas aeruginosa*:** should not be used as a canonical obligate aerobe. It can support anaerobic growth by denitrification and, under some conditions, fermentation; older descriptions as “obligately aerobic” are therefore misleading.

## 2. Current mechanistic model

The most defensible trait-wide causal chain is:

**environmental O₂ availability → terminal oxygen reductase activity → four-electron reduction of O₂ to water → respiratory electron flow/electrochemical gradient → ATP synthase activity → ATP supply sufficient for growth → obligately aerobic growth phenotype.**

Bacterial terminal oxygen reductases include heme-copper oxidases, such as aa₃-type enzymes, alternative oxidases, and cytochrome-bd-family oxidases. They accept electrons through carriers such as quinol or cytochrome *c* and reduce dioxygen to water. (andre2021theselectiveadvantage pages 2-4)

This is a **minimal mechanistic backbone**, not a universal gene signature. Respiratory chains are branched and taxon-specific. In *B. bronchiseptica*, no individual oxidase was necessary in ambient air: strains retaining only Cyd1, Cta1, or Cyo1 had approximately wild-type growth, demonstrating functional redundancy. (mckay2024cytochromeoxidaserequirements pages 8-10) The three oxidases conserved in *B. pertussis*—`cydAB1`, `ctaCDFGE1`, and `cyoABCD1`—were sufficient for ambient-air and low-O₂ growth, while CyoABCD1 alone supported wild-type-level murine burden. (mckay2024cytochromeoxidaserequirements pages 18-20, mckay2024cytochromeoxidaserequirements pages 1-2)

## 3. Candidate nodes grouped by type

### Trait and environmental nodes

- obligately aerobic — `METPO:1000606`
- oxygen preference — parent `METPO:1000601`
- molecular oxygen — **CHEBI:15379**
- oxic environment — candidate ENVO term; verify the exact release-specific CURIE before insertion
- hypoxic/low-oxygen environment — label-only pending ENVO verification
- anoxic condition — label-only pending ENVO verification
- oxygen concentration / oxygen partial pressure
- ambient air, 21% O₂
- experimental low oxygen, 5% O₂ and 2% O₂

### Chemicals and energetic products

- water — **CHEBI:15377**
- proton — **CHEBI:15378**
- ATP — **CHEBI:15422**
- ADP — **CHEBI:16761**
- phosphate — **CHEBI:18367**
- ubiquinone/ubiquinol pool — ground to the exact quinone species only where experimentally known
- cytochrome *c*
- superoxide anion radical — **CHEBI:18421**
- hydrogen peroxide — **CHEBI:16240**
- reactive oxygen species — **CHEBI:26523**
- bedaquiline — use ChEBI/drug identifier only after release verification

Showing the first 60 of 245 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_WITH_LITERATURE · codex

    Added definition source and evidence for obligate oxygen requirement.

  3. · ADDED_ORGANISM_EXAMPLE · codex

    Added Mycobacterium tuberculosis organism example with PMID-backed evidence.

  4. · ADDED_CAUSAL_GRAPH · codex

    Added DOI-backed causal graph for obligate aerobic respiration and oxygen-reducing terminal oxidases.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326×1).

  6. · GROUND_CAUSAL_NODES · claude

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

  7. · 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.

  8. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: requires → depends on ×1.

  9. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002502×1).

  10. · GROUND_CAUSAL_PREDICATES · claude

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

  11. · GROUND_CAUSAL_PREDICATES · claude

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

  12. · ENRICH_CAUSAL_GRAPH · claude

    Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.

  13. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407×2, RO:0002327×1).

  14. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009060×1).

  15. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:18421×1, CHEBI:16240×1, GO:0004784×1).

  16. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

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

  17. · SPLIT_PROTEIN_FROM_ACTIVITY · claude

    Separated the protein sense from the activity sense so one node_id means one thing (issue 356): renamed superoxide_dismutase -> superoxide_dismutase_activity (MOLECULAR_FUNCTION sense); renamed catalase -> catalase_activity (MOLECULAR_FUNCTION sense). Described as 'Enzyme ACTIVITY that detoxifies hydrogen peroxide', while the four GENE_OR_PROTEIN occurrences describe the enzyme itself ('Enzyme that degrades hydrogen peroxide to water and oxygen'). catalase_activity already exists corpus-wide as a MOLECULAR_FUNCTION node. Described as 'Enzyme ACTIVITY that detoxifies superoxide' against 'Enzyme that dismutates superoxide' for the protein occurrences. It also carries GO:0004784, which IS 'superoxide dismutase activity' -- so the grounding was already describing a molecular function and only the id disagreed. The one new id in this migration, coined to the corpus's dominant _activity convention.

  18. · NORMALISE_NODE_TYPE · claude

    Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): electron_transport_chain is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes. Was 4 PATHWAY to 2 before this tranche.