identifier: traitmech:000602
label: pH tropism
definition: A phenotype in which polarized growth is directionally biased in response
  to a spatial gradient of external pH.
definition_source: DOI:10.1128/mbio.00285-23
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000597
evidence:
- reference: DOI:10.1128/mbio.00285-23
  snippet: F. oxysporum hyphae exposed to a pH gradient displayed robust tropism toward
    acid.
  notes: Fernandes et al. (2023), Discussion; exact span in directly retrieved Europe
    PMC JATS, PMC10128062 (PMID:36861989). Results and Methods were read; Figure 1B
    and Table S1 (10.1128/mbio.00285-23.7) were visually inspected. Opposing 25 mM
    HCl/NaOH wells tested germ-tube direction after 8 h, with at least three experiments
    and 500 germ tubes per experiment. Mpk1 deletion reversed direction; complementation
    restored acidward growth, not necessarily wild-type magnitude. Panel A measures
    invasion, not tropism. The assay does not by itself resolve the local pH profile
    or exclude every co-varying ionic effect. The higher-pH response is an engineered-mutant
    observation, not a natural exemplar.
- reference: DOI:10.1371/journal.pbio.3002726
  snippet: These outcomes indicate that the hyphae exhibit chemotropism towards pH
    4 within the pH range of 3 to 8.
  notes: Yamamoto et al. (2024), Results, Chemotropism to low pH; exact span in directly
    retrieved Europe PMC JATS, PMC11288418 (PMID:39078817). Figure 3 and Table S1
    (10.1371/journal.pbio.3002726.s002) were visually inspected. Aspergillus nidulans
    tip trajectories near the pH 6.5/8 interface support reorientation. Figure 3D
    reports n=1 experiment with 40-50 hyphae; hypha counts are not independent experimental
    replication. Growth inhibition at pH 3 confounds the 3/4 comparison. The separate
    summary abstract's acidic-pH avoidance wording conflicts with the main Results.
    This is not a universal pH-4 setpoint. Strains are engineered; movies and remaining
    supplements were not inspected.
discussions:
- discussion_id: ph-tropism-growth-direction-and-assay-boundaries
  prompt: Keep pH-directed growth distinct from taxis, tolerance and growth rate.
  kind: CURATION_TODO
  status: OPEN
  rationale: This is a pH-specific child of chemotropism, not another name for all
    chemical-gradient growth. It includes growth toward lower or higher pH without
    requiring both in one organism; mutant direction reversal does not establish a
    natural higher-pH-seeking strain. pH taxis denotes active locomotion. pH optimum,
    acid tolerance, intracellular pH homeostasis, biomass and extension rate alone
    are insufficient. Retain the source-specific replication and growth-inhibition
    limitations; resolve external equivalents and alternative labels before adding
    synonyms or xrefs. The local chemotropism parent (traitmech:000597) has a pending
    v474 proposal, METPO:1055100, not a released term. The v479 proposal uses released
    METPO:1000059 phenotype; reconcile the narrower hierarchy when v474 is accepted.
  posed_by: codex
  posed_date: '2026-10-04'
- discussion_id: ph-tropism-strain-provenance-and-spatial-mechanism
  prompt: Resolve strain identity and the spatial-sensing mechanism before enrichment.
  kind: CURATION_TODO
  status: OPEN
  rationale: Fernandes Methods identify Fol4287 (FGSC 9935), whereas Table S1 labels
    its wild type FGSC 4287. Reconcile the collection label and verify natural provenance
    and NCBI identity before canonical examples. Yamamoto Table S1 lists engineered
    backgrounds including TH122. Keep spatial-gradient orientation separate from uniform
    pH shifts, cytosolic-pH regulation and invasion assays. Kinase perturbations support
    context-specific contributions, not a universal receptor or a complete spatial-sensing
    chain. Resolve native, taxon-paired protein accessions and direct causal links
    before adding a mechanism graph; NONMECHANISTIC is not a grounding bypass.
  posed_by: codex
  posed_date: '2026-10-04'
curation_history:
- timestamp: '2026-10-04T19:11:26Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added pH tropism under local chemotropism with two primary DOI citations
    and exact raw-JATS snippets. Ignored-and-hidden novelty searches and structured
    OWL review found no exact term; the parent's pH example has broader class scope.
    Reserved METPO:1055600 in v479 under released phenotype. Visually inspected both
    key figures and strain tables. Recorded assay replication, growth confounds, mutant
    direction scope, source discrepancies and pending hierarchy; deferred canonical
    strains and accession-level causal mechanisms.
  llm_assisted: true