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pH tropism

traitmech:000602 · CLASS · PROPOSED

A phenotype in which polarized growth is directionally biased in response to a spatial gradient of external pH.

Trait evidence (2)

  • DOI:10.1128/mbio.00285-23
    F. oxysporum hyphae exposed to a pH gradient displayed robust tropism toward acid.

    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.

  • DOI:10.1371/journal.pbio.3002726
    These outcomes indicate that the hyphae exhibit chemotropism towards pH 4 within the pH range of 3 to 8.

    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.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1128/mbio.00285-23

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Keep pH-directed growth distinct from taxis, tolerance and growth rate.

CURATION TODO OPEN ph-tropism-growth-direction-and-assay-boundaries · raised by codex · 2026-10-04

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Resolve strain identity and the spatial-sensing mechanism before enrichment.

CURATION TODO OPEN ph-tropism-strain-provenance-and-spatial-mechanism · raised by codex · 2026-10-04

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.