lethal nematicidal activity

traitmech:000720 · CLASS · PROPOSED

A physiological capability of a microorganism to kill nematodes.

Trait evidence (2)

DOI:10.1038/s41598-023-33669-z
T. asperellum FbMi6 at 80% concentration had the highest (90.3%) juvenile mortality compared to control.

Saharan et al. 2023, PMID:37088805, Results in vitro activity; native NOT_IN_ABSTRACT, direct publisher HTML match. Actual Figure 4 inspected. This is culture filtrate, not live fungal inoculum: 100 newly hatched M. incognita J2, water/PDB controls, 72 h endpoint, 25 +/- 2 degrees C, two repeats. Methods reports fresh-water recovery confirmation without its duration or scoring criterion. The quote's percentage is source-reported, not independently recalculated. Supplement text/tables and its embedded image were inspected, not rendered document pages. Strain/accession discrepancies prevent a canonical taxon assignment; pot/field efficacy is not imported.
DOI:10.1128/spectrum.02577-21
In this study, three secondary metabolites (SMs) with nematicidal activities were isolated from in vitro cultures of P. luminescens sonorensis strain Caborca

Producer-origin supporting evidence, not definition authority. The self-contained excerpt establishes microbial origin of nematicidal metabolites; its wording alone does not distinguish death from paralysis. The independently cited Saharan mortality result supplies explicit lethal definition support. Kusakabe et al. 2022, PMID:35138171, Discussion opening clause, printed/PDF page 12; native NOT_IN_ABSTRACT and direct XML/typeset PDF match. The producer is Photorhabdus. Culture-supernatant fractionation links the isolated metabolites to this microorganism. t-CA and PPA caused mortality; indole mainly caused reversible paralysis at lower doses, with killing only at high concentrations. Equipotent synthetic standards were used for dose-response assays. Actual Figures 2/3 and Table 4 inspected. Needle response and morphology distinguished death from paralysis; recovery used washing and 24 h in water. Table 4 tests lower-dose indole, not t-CA/PPA survival. No live-culture lethal concentration is inferred. Some numerical prose conflicts with tables; no potency, selectivity or significance values are adopted. Linked supplemental NMR/statistics files were not audited; figure inspection is not raw-data verification.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1038/s41598-023-33669-z

Parent traits (1)

phenotype METPO:1000059

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.

Refine the hierarchy while preserving the lethal, microbial-actor endpoint.

CURATION TODO OPEN lethal-nematicidal-scope-and-mappings · 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.

Killing susceptible nematodes is required; reversible paralysis, repellence, reduced egg hatch, host defense induction and a sequence annotation alone are insufficient. The label is qualified because nematicidal usage can include nonlethal readouts. Neither all nematode species/stages nor all producing strains are implied. Fungal nematophagy (traitmech:000719) requires feeding, and trap formation (traitmech:000718) is structural; neither is an exact parent. Predatory bacterium (traitmech:000054) requires consuming bacterial prey. Animal pathogen METPO:1004002 requires infection, unnecessary for culture-derived toxicity. Phenotype METPO:1000059 is the conservative parent. Pinned/current METPO inspection found no exact active or deprecated counterpart. CHEBI:25491 denotes a nematicide chemical, not this microbial capability, and is not an xref. No exact synonyms or organism-level disjointness are asserted; v596 proposes the class. The methodological context below cautions against equating immobility or a negative NaOH response with death under all conditions. It is not evidence of microbial killing or definition support.

Evidence

DOI:10.3725/jjn.45.51 NO EVIDENCE
The J2s inactivated by low temperature showed no reaction to the NaOH treatment.
Harada and Yoshiga 2015, scientific abstract, printed page 51. Direct publisher HTML/PDF match; actual pages 51-54, Table 1 and Figure 1 inspected. Second-stage M. incognita juveniles could recover after warming or removal of some chemicals. This supports condition-dependent viability-assay caution, not microbial killing or an additional phenotype replication. Native UNRESOLVED: exact DOI query returned zero results; publisher and Crossref verify identity. This citation is discussion-only context, not supporting evidence for the trait or its definition.

Reconcile strain provenance and establish taxon-paired mechanisms before expanding the record.

KNOWLEDGE GAP OPEN lethal-nematicidal-provenance-and-mechanisms · 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.

Saharan's claimed FbMi6 accession MT529846.1 resolves in GenBank to clone SF_570, not FbMi6. Its supplement compares strain 6 with MT529837.1, clone SF_561, but labels the table SF_570 and the mortality image FbMi-4. No corrected accession is inferred. Caborca's primary strain-provenance reference has not been reconciled either. Retain these qualified observations without canonical examples. No common molecular mechanism, natural lethal dose, nutritional benefit or environmental safety is established; graphs and proteins remain unset. Culture-derived activity does not restrict the entire class to secretion. Crossref/publisher/indexing notice checks are bounded, not comprehensive clearance. Source hashes, assay limits and native verification outcomes are retained in the source-verification sidecar.

Curation history

2026-10-13T17:31:43Z · MINTED_TRAITMECH_ID · codex
Added lethal nematicidal activity with two primary microbial-product studies and one viability-method citation, each with a directly matched snippet. Distinguished death from reversible paralysis and feeding; retained strain and assay caveats. Reserved 000720, v596 and 1067300-1067399 after ignored/hidden current-file, retained history and open/draft PR checks, with numeric false positives adjudicated. No exact active METPO counterpart identified. Other records unchanged. Timestamp records observed post-audit acceptance.
2026-10-13T18:14:01Z · CORRECTED_EVIDENCE_ROLE · codex
Addressed review issue #1916: moved the Harada viability-method citation and exact excerpt from supporting evidence into the scope discussion. Retained its source/resolver provenance as context. The two microbial-killing studies remain supporting evidence; the context-only DOI no longer enters proposal definition annotations. Preserved original history, identity, hierarchy and other records.
2026-10-13T18:54:48Z · CORRECTED_PRODUCER_EXCERPT · codex
Addressed review issue #1917: replaced the compound-only excerpt with a directly matched producer-linked Discussion result and retained the actual NOT_IN_ABSTRACT outcome and assay limits. Moved the unchanged Harada excerpt into structured discussion evidence with NO_EVIDENCE role for native verification. Preserved #1916's two-source definition support, prior events, identity, hierarchy and other records.
2026-10-13T19:40:13Z · CORRECTED_LETHAL_ENDPOINT_EXCERPTS · codex
Addressed review issue #1918: stored separate producer-origin and explicit mortality spans from Kusakabe, totaling 25 words. Preserved the high-concentration non-target and synthetic-standard assay qualifiers. IMPORTANCE matches native VERIFIED but is not the scientific Abstract; the mortality span is NOT_IN_ABSTRACT. Three evidence items still represent only two supporting studies. Preserved #1916/#1917 fixes, all prior events, fungal evidence, discussion-only context, identity, hierarchy and other records.
2026-10-13T20:27:02Z · CORRECTED_DEFINITION_AUTHORITY · codex
Addressed review issue #1919: selected the unchanged Saharan mortality result as definition authority and first evidence item. Restored the complete 22-word Kusakabe producer-linked clause as origin support, not definition authority. Removed the subjectless origin and anaphoric mortality spans. This supersedes #1918's two-span correction: explicit mortality support now comes from the selected fungal source. Proposal definition annotations cite only that source and the local record; two distinct primary studies remain supporting evidence. Both excerpts retain native NOT_IN_ABSTRACT outcomes. Preserved all prior events, assay limitations, structured context, identity, hierarchy and other records.

Recorded curation sessions

2026-10-13T17:35:40Z · codex
- CREATE — Add lethal nematicidal activity
  Added one proposed physiological capability backed by two microbial-product studies and one methodological citation. Three directly matched excerpts retain lethal-versus-paralytic assay boundaries and unresolved strain/accession provenance. No canonical examples, exact xrefs, protein examples or causal graphs are asserted. Local/remote novelty and full-block reservation checks include ignored/hidden files and available retained tracked history; all numerical false positives are adjudicated. Other trait records and protected spore germination are unchanged. v596 reserves the upstream placeholder; source receipts and focused tests accompany the guarded writer.
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2026-10-13T18:16:56Z · codex
- EDIT — Separate method context from trait support
  Addressed #1916 by moving the Harada viability-method citation and verified excerpt into the scope discussion. Only two microbial-killing studies remain supporting evidence and definition citations. Preserved the original minting event and CREATE history; appended CORRECTED_EVIDENCE_ROLE. Source receipt separates context from support and retains historical native outcomes. Guarded writer accepts only the reviewed preimage or corrected result; tests cover migration and replay. No identity, hierarchy, example, protein, graph or other-record changes.
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2026-10-13T18:57:52Z · codex
- EDIT — Link the excerpt to its microbial producer
  Addressed #1917 by replacing the compound-only excerpt with a directly matched producer-linked Discussion clause. Preserved actual NOT_IN_ABSTRACT and assay qualifications. Moved the unchanged Harada context snippet into structured discussion evidence with NO_EVIDENCE role; it remains excluded from trait support and definition annotations. Preserved the original CREATE and first EDIT history; appended CORRECTED_PRODUCER_EXCERPT. Guarded migrations and replay retain earlier events. No identity, hierarchy, example, protein, graph or other-record changes.
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2026-10-13T19:41:47Z · codex
- EDIT — Quote microbial origin and an explicit lethal endpoint
  Addressed #1918 with two separately located Kusakabe excerpts totaling 25 words: culture origin and high-concentration mortality in non-target nematodes. Native VERIFIED matches IMPORTANCE, not the scientific Abstract; mortality remains NOT_IN_ABSTRACT. Three evidence items represent two supporting studies. Preserved #1916/#1917 corrections, fungal evidence, structured discussion context and all prior events. Appended CORRECTED_LETHAL_ENDPOINT_EXCERPTS; guarded migration and replay reject unknown drift. No identity, hierarchy, example, protein, graph or other-record changes.
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2026-10-13T20:29:11Z · codex
- EDIT — Select explicit lethal definition authority and self-contained evidence
  Addressed #1919 by selecting the unchanged Saharan mortality result as definition authority and restoring the complete 22-word Kusakabe producer-linked clause as origin support, not definition authority. Removed subjectless/anaphoric excerpts. Supersedes the #1918 two-span correction in 2026-10-13T194147Z-codex-8e2a91.yaml by placing explicit mortality support with the selected fungal source. Proposal definition annotations now cite only Saharan and the local record; two primary studies remain supporting evidence. Preserved all prior events, source receipts, assay limits and discussion-only context. Appended CORRECTED_DEFINITION_AUTHORITY; guarded migration accepts four historical preimages and rejects unknown drift. No identifier, hierarchy, example, protein, graph or other-record changes.
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2026-10-13T21:06:24Z · codex
- AUDIT — Link prior nematicidal corrections to structured review issues
  Addressed #1921 by appending structured issue and PR links for prior immutable correction records: 2026-10-13T181656Z-codex-7e97a3.yaml, 2026-10-13T185752Z-codex-bb2ac8.yaml, 2026-10-13T194147Z-codex-8e2a91.yaml, 2026-10-13T202911Z-codex-c477c5.yaml. These EDIT records named #1916, #1917, #1918 and #1919 only in prose. This audit adds queryable provenance without changing their bytes or claiming they originally had structured links. The initial CREATE predates those review issues and is not retroactively attributed to them. #1920 separately corrected the companion proposal narrative. No TraitRecord fact, curation event, identifier, hierarchy, source receipt or biological evidence changed. The generated page gains this audit as its sixth history link.
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