identifier: traitmech:000591
label: pH taxis
definition: A motile phenotype in which active locomotion is directionally biased
  in response to an external pH gradient.
definition_source: DOI:10.1128/jb.00491-19
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- METPO:1000702
evidence:
- reference: DOI:10.1128/jb.00491-19
  snippet: This bacterium was found to perform bidirectional taxis in response to
    external pH gradients, enabling it to preferentially migrate to neutral environments.
  notes: Abstract, exact-matched at Europe PMC (PMID:31685537). The antecedent is
    Bacillus subtilis. This observation supports external-gradient-directed movement,
    including responses from both acidic and alkaline environments in this study.
    It does not establish neutral pH as a universal preferred destination. Full text
    was not systematically inspected; receptor-chimera findings in the abstract are
    not converted into a molecular causal graph or an unqualified natural-strain example.
- reference: DOI:10.1128/jb.188.7.2656-2665.2006
  snippet: Bacteria in more-alkaline regions did not swim toward the acid, suggesting
    the pH taxis is a form of negative chemotaxis.
  notes: Abstract, exact-matched at Europe PMC (PMID:16547053); full text not inspected.
    The preceding observation describes Helicobacter pylori moving away from strong
    acid in a microscope-slide pH gradient. This supports an acid-avoidance response
    without requiring every pH-tactic organism to show bidirectional attraction to
    a neutral optimum. Strain-specific mutant, receptor and host-colonization findings
    are not generalized into the trait definition or mechanism.
discussions:
- discussion_id: ph-taxis-scope-and-mapping-boundaries
  prompt: Preserve directional scope and verify external equivalents.
  kind: CURATION_TODO
  status: OPEN
  rationale: Growth pH preference, acid or alkali tolerance, intracellular pH homeostasis
    and changes in speed alone do not establish pH-directed locomotion. Neither neutral-pH
    attraction nor bidirectional response is required universally. The local chemotaxis
    definition specifies flagellar motor switching; motile is the verified broader
    METPO parent without imposing that apparatus. No external xref or exact synonym
    is asserted before authority resolution and organismal-scope comparison.
  posed_by: codex
  posed_date: '2026-10-04'
- discussion_id: ph-taxis-mechanism-and-canonical-strains
  prompt: Verify natural strain provenance and protein-resolved mechanisms.
  kind: CURATION_TODO
  status: OPEN
  rationale: The primary abstracts establish pH-tactic behavior, not a single universal
    receptor mechanism. Before adding canonical examples, verify the unperturbed reference
    strains against primary strain-provenance sources and resolve their NCBI taxon
    identities. Before adding a causal graph, inspect the full studies and relevant
    supplements, distinguish observed perturbation effects from proposed sensing models,
    and resolve taxon-paired protein accessions. A NONMECHANISTIC graph must not bypass
    those requirements.
  posed_by: codex
  posed_date: '2026-10-04'
curation_history:
- timestamp: '2026-10-04T08:03:18Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added pH taxis with two primary DOI citations and exact abstract snippets.
    Ignored-and-hidden searches and structured OWL review found no exact live record
    or METPO term. Reserved METPO:1054500 in v468. Deferred unverified strain examples,
    molecular graph grounding and external equivalents; retained directional scope
    without universal neutral-pH or bidirectionality requirements.
  llm_assisted: true