TraitMech

TraitMech › PHYSIOLOGY

extracellular-trail-based spatial memory

traitmech:000715 · CLASS · PROPOSED

A physiological phenotype in which a microorganism's subsequent spatial exploration is guided by persistent extracellular trails deposited during earlier movement.

Trait evidence (3)

  • DOI:10.1073/pnas.1215037109
    When one arm contained extracellular slime, 39 of 40 plasmodia chose the blank agar arm

    Reid et al. 2012, PMID:23045640, PMC3491460; Results opening paragraph, printed page 17490 / PDF page 1. Cultured Physarum polycephalum avoided previously deposited slime in a Y maze. Same-stock coatings do not demonstrate individual recognition of one's own trace. In the separate U-trap experiment, 23/24 plasmodia on blank agar versus 8/24 on slime-coated agar reached the target within 120 hours. Coating masks newly informative trails; it does not abolish secretion or lesion internal memory. Success, completion time among successful trials, speed, path length and revisitation are distinct endpoints. No-trap and speed controls do not exclude every environmental confound. Main Methods, Results, Discussion and all four figures were inspected in an author-hosted publisher-formatted PDF bearing a 2012 download stamp, not verified as the current corrected VoR. Supplements and raw data were not assessed. Southern Biological Supplies culture provenance remains unresolved. The contiguous result span was text-matched and visually checked.

  • DOI:10.1088/1361-6463/aa87df
    Our results suggest that the external memory has an adaptive advantage in ‘open’ and simple bounded environments.

    Smith-Ferguson et al. 2017; scientific abstract, printed page 1 / PDF page 2. This is the authors' interpretation of maze performance, not a measured fitness or natural-selection endpoint. Within 72 hours, blank versus extracellular-slime conditions yielded success in 24/24 versus 9/24 open trials, 12/15 versus 4/12 simple-maze trials and 11/17 versus 11/13 complex-maze trials; the last comparison showed no significant benefit. Completion times conditional on success were not significantly different. Escaped trials were excluded; split decisions used the dominant front. Printed page 6 pairs the same chi-square 0.802 with P=0.004 and P=0.371; this discrepancy is unresolved. Figure 8 is illustrative, not quantified trajectory evidence. Main Methods, Results, Discussion, Conclusion and all eight figures were inspected; supplements were not. The author-hosted PDF bears a 2017 download stamp, not verified current VoR equivalence. This study shares authors with Reid 2012, not an independent-laboratory replication.

  • DOI:10.1073/pnas.2312611121
    In accordance with the literature, we observe that plasmodia generally avoid previously visited areas marked by their slime trail

    Troger et al. 2024, PMID:38517977, PMC10990088; Results, Quantifying Run-and-Tumble and Self-Avoiding Behavior, page 3. The authors report their own Physarum observations, not only a background citation. Actual trajectories, including Figure 2A, are distinct from simulated-model panels. Page 5 describes 14 trajectories divided into groups of nine each; Figure 4 instead gives seven small and seven large. The discrepancy remains unresolved. The 0.65 square-millimeter median is a cohort split, not a universal threshold. Small plasmodia can cross trails; a modeled three-hour forgetting time is not a measured chemical half-life or internal-memory duration. Main text, Methods and all four main figures were inspected in the author-hosted publisher-formatted PDF with a March 2024 download stamp, not verified current corrected VoR equivalence. Publisher supplements and raw data were not reanalyzed. This different laboratory's assay is not a replication of the earlier maze experiments; no universal molecular receptor is established.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1073/pnas.1215037109

Parent traits (1)

kg-microbe context

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

Discussions and Knowledge Gaps (3)

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

Keep external trace-guided exploration distinct from internal memory and universal trail avoidance.

CURATION TODO OPEN trail-memory-scope-and-hierarchy · raised by codex · 2026-10-13

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 operational phenotype concerns spatial information persisting outside the microorganism. It does not require always avoiding a trail, improved navigation in every setting, individual self-recognition, or internal recall. Carbon-source memory (traitmech:000706), acquired stress-resistance memory (traitmech:000712), enhanced transcriptional reactivation memory (traitmech:000713) and behavioral habituation (traitmech:000714) have different endpoints. Negative autotropism (traitmech:000603) concerns germ-tube or hyphal orientation. Collective bacterial predation (traitmech:000701) concerns coordinated killing and feeding, despite a trail mention. Contact-dependent outer membrane exchange (traitmech:000650) concerns actual intercellular exchange. METPO:1000059 phenotype is the conservative parent pending hierarchy review; local chemotaxis has a flagellar-specific definition and is not a universal parent. Generic memory, learning, stigmergy and extracellular polymer production are not exact synonyms. Psl-biased visitation and community growth history require separate scope and evidence assessments.

Resolve source versions, assay discrepancies and culture provenance before assigning taxa or mechanisms.

KNOWLEDGE GAP OPEN trail-memory-source-and-mechanism-limits · raised by codex · 2026-10-13

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.

Coated-versus-blank substrates manipulate spatial trace information along with the environment, not exclusively a memory molecule. The 2017 significance-statistic discrepancy and 2024 group-size discrepancy remain visible source gaps. The 2024 arXiv v1 was posted after journal publication; its seven-per-group wording and differing illumination details do not silently correct the publisher-formatted PDF. Supplement illustrations do not establish crossing frequencies. Bounded Crossref/MED and publisher checks do not establish exhaustive absence of notices or corrected-version equivalence. The evidence concerns cultured Physarum, not species-wide possession or all microbes. Natural culture provenance remains unverified. No canonical taxa, exact external mappings, protein examples or molecular causal graph are asserted. Unknown trail components, sensory mechanisms, unread supplements and raw-data reanalysis remain research gaps. Source hashes, access limits and actual native snippet-verifier outcomes are retained in the source-verification sidecar.

Retain unresolved historical adaptation and chemotaxis identity without reviving deprecated identifiers.

CURATION TODO OPEN trail-memory-historical-identity · raised by codex · 2026-10-13

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.

Pinned and inspected current METPO graphs mark METPO:0000248 and METPO:000249 Microbial Adaptation, METPO:1000004 adaptation and METPO:1000062 chemotaxis deprecated. Inspected subjects have no replacement or consider annotations; OMO:0001000 reasons are provisional under open METPO issue 521. Original historical scopes remain unresolved. Neither biological invalidity nor exact equivalence follows from their labels or deprecation reasons. This qualified external-trace phenotype is accepted independently from primary evidence. Ignored and hidden current files, available tracked history, independent copies, pending changes and inspected ontology graphs revealed no exact active record within the documented scope. No historical exact mapping is asserted. Existing records and the pinned ontology remain unchanged; discovery is not exhausted.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added extracellular-trail-based spatial memory with three primary DOI sources and contiguous snippets. Retained assay, version, mechanism and historical-identity limits. Reserved 000715, v591 and 1066800-1066899 after scoped ignored/hidden, retained-history, independent-copy and pending-PR checks; numeric false positives were explicitly adjudicated. No canonical taxa or causal graph; existing records unchanged. Timestamp is the observed UTC post-audit confirmation, not an estimated write time.

Recorded curation sessions

  • · codex
    • CREATE — Add extracellular-trail-based spatial memory

      Added traitmech:000715 as PROPOSED under phenotype, with three DOI-backed contiguous snippets, qualified assay/version/provenance limits and three open discussions. Added cohort v591, reserving METPO:1066800-1066899 with only 1066800 populated. No canonical taxa, graph, proteins or exact mappings; existing records unchanged.

    Read this curation session