identifier: traitmech:000601
label: aerotropism
definition: A phenotype in which polarized growth is directionally biased in response
  to a spatial oxygen concentration gradient.
definition_source: DOI:10.1016/S0168-6496(03)00161-2
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000597
evidence:
- reference: DOI:10.1016/S0168-6496(03)00161-2
  snippet: Conidia also germinated close to air-filled Teflon tubes and exhibited
    germ-tube tropism, but not as distinctly as on living reed roots.
  notes: 'Abstract, exact-matched at Europe PMC (PMID:19719598). Publisher HTML methods,
    results and discussion were read at https://academic.oup.com/femsec/article/45/3/293/549782.
    Section 3.2 reports Microdochium bolleyi germ-tube orientation toward air-filled
    Teflon root dummies (60% +/- 12%) and stronger orientation toward living roots.
    This is qualified supporting evidence: oxygen-dependent germination and root-derived
    chemicals complicate attribution, and the tube result alone does not establish
    significance against random orientation. Figure 3 measures germination, not orientation.
    Figures were not visually verified. No strain accession or molecular mechanism
    is asserted.'
- reference: DOI:10.1155/2012/517529
  snippet: C. albicans responds to other external stimuli in vitro, displaying aerotropism
    under hypoxic conditions and galvanotropism, where hyphae germinate and orient
    towards the cathode in an applied electric field (Figure 2(c)(iii)) [94, 97, 98].
  notes: Brand (2012), Hyphal Growth in Human Fungal Pathogens and Its Role in Virulence;
    published online in 2011, volume 2012. Review, not independent experimental replication.
    Full text directly retrieved as Europe PMC JATS XML (PMC3216317), https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3216317/fullTextXML.
    The complete sentence exact-matches the XML text and is quoted under its Creative
    Commons Attribution license. It supports use of aerotropism for hyphal responses
    under hypoxia, not a quantified oxygen-gradient experiment or a mechanism. The
    cathode and Figure 2(c)(iii) clauses describe galvanotropism, not aerotropism;
    no figure-based oxygen claim is made. Its cited Aoki paper remains an unverified
    primary-source lead in the discussion.
discussions:
- discussion_id: aerotropism-direction-and-stimulus-boundaries
  prompt: Keep oxygen-directed growth distinct from oxygen demand, taxis and flow.
  kind: CURATION_TODO
  status: OPEN
  rationale: 'The class includes positive or negative directional growth, without
    requiring both in one organism. This is a polarity-neutral scope decision, not
    verification of a negative response: the avoidance lead below is unread. Aerotaxis
    denotes locomotion, not growth orientation. Oxygen tolerance, oxygen requirement,
    biomass, germination and extension rate alone are insufficient. This record uses
    the oxygen-gradient sense of aerotropism; air-flow-directed growth belongs to
    rheotropism, not this class solely because air supplies oxygen. Resolve external
    phenotype mappings and variant-label scopes before adding xrefs or synonyms. The
    local parent is chemotropism (traitmech:000597); its v474 METPO:1055100 proposal
    is not released. The v478 proposal therefore uses the existing METPO:1000059 phenotype
    parent; reconcile the narrower hierarchy when chemotropism is accepted.'
  posed_by: codex
  posed_date: '2026-10-04'
- discussion_id: aerotropism-controls-and-native-mechanism
  prompt: Resolve gradient controls, strain provenance and native causal mechanisms.
  kind: CURATION_TODO
  status: OPEN
  rationale: 'Unverified research leads: Aoki et al. (1998), DOI:10.1007/BF02464003,
    and Carlile and Tew (1988), DOI:10.1016/S0007-1536(88)80071-8. Crossref and Elsevier
    API retrievals confirmed metadata only; publisher retrieval returned 403. Search-index-limited
    summaries suggest positive Candida hyphal reorientation and negative aerotropism
    in Phytophthora germ tubes, respectively. Original wording, full text, figures
    and controls remain unverified. These are research leads, not definition authority
    or counted trait evidence (#1680, #1681). Inspect the older full texts and orientation
    readouts, and discriminate tip reorientation from preferential growth or survival
    in oxygen-rich regions. Resolve natural strain provenance and NCBI identity before
    canonical examples. The current evidence does not establish a universal oxygen
    sensor or a taxon-independent protein mechanism. Do not transfer pheromone chemotropism
    or aerotaxis mechanisms without direct evidence. Defer causal graphs until native
    causal evidence and taxon-paired protein accessions support them; NONMECHANISTIC
    is not a grounding bypass.'
  posed_by: codex
  posed_date: '2026-10-04'
curation_history:
- timestamp: '2026-10-04T17:35:43Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added polarity-neutral oxygen-gradient-directed growth under local chemotropism,
    supported by three primary DOI citations and source snippets. Ignored-and-hidden
    novelty searches and structured OWL review found no exact term. Reserved METPO:1055500
    in v478 under the released phenotype parent. Recorded indexed abstract access
    limits, growth confounds and pending narrower METPO hierarchy; deferred canonical
    strains and causal graphs.
  llm_assisted: true
- timestamp: '2026-10-04T17:43:50Z'
  curator: codex
  action: EVIDENCE_CORRECTION
  changes: 'Addressed #1676: replaced the margin-reorientation abstract quote with
    a contiguous oxygen-gradient passage so the definition snippet identifies the
    stimulus. Retained reorientation evidence, source-access limits and growth confounds
    in notes.'
  llm_assisted: true
- timestamp: '2026-10-04T18:01:14Z'
  curator: codex
  action: REVIEW_CORRECTION
  changes: 'Addressed #1678 and #1679: removed the two snippets obtained only from
    indexed publisher text. Prior history describes those now-withdrawn quotes, not
    directly verified source wording. Retained qualified DOI-backed interpretations
    in notes and the directly verified Damm snippet. Changed the definition genus
    to phenotype to match the released proposal parent, preserving the local chemotropism
    parent and pending hierarchy explanation.'
  llm_assisted: true
- timestamp: '2026-10-04T18:27:57Z'
  curator: codex
  action: REVIEW_CORRECTION
  changes: 'Addressed #1680 and #1681: moved unread Aoki and Carlile papers from counted
    evidence to qualified discussion leads. Replaced Aoki as definition authority
    with directly read Damm. Added directly retrieved Brand review with an exact full-sentence
    quote under its Attribution license; labeled its terminology role, not independent
    experimental replication. Negative direction remains unverified. Withdraws the
    prior histories'' evidence-authority claims for the two unread papers; earlier
    events remain unchanged. No new snippet-baseline exceptions.'
  llm_assisted: true