identifier: traitmech:000720 label: lethal nematicidal activity definition: A physiological capability of a microorganism to kill nematodes. definition_source: DOI:10.1038/s41598-023-33669-z trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - METPO:1000059 evidence: - reference: DOI:10.1038/s41598-023-33669-z snippet: T. asperellum FbMi6 at 80% concentration had the highest (90.3%) juvenile mortality compared to control. notes: '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.' - reference: DOI:10.1128/spectrum.02577-21 snippet: In this study, three secondary metabolites (SMs) with nematicidal activities were isolated from in vitro cultures of P. luminescens sonorensis strain Caborca notes: 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. discussions: - discussion_id: lethal-nematicidal-scope-and-mappings prompt: Refine the hierarchy while preserving the lethal, microbial-actor endpoint. kind: CURATION_TODO status: OPEN rationale: 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. posed_by: codex posed_date: '2026-10-13' evidence: - reference: DOI:10.3725/jjn.45.51 supports: NO_EVIDENCE evidence_source: scientific abstract; publisher HTML and PDF snippet: The J2s inactivated by low temperature showed no reaction to the NaOH treatment. explanation: '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.' - discussion_id: lethal-nematicidal-provenance-and-mechanisms prompt: Reconcile strain provenance and establish taxon-paired mechanisms before expanding the record. kind: KNOWLEDGE_GAP status: OPEN rationale: 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. posed_by: codex posed_date: '2026-10-13' curation_history: - timestamp: '2026-10-13T17:31:43Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true - timestamp: '2026-10-13T18:14:01Z' curator: codex action: CORRECTED_EVIDENCE_ROLE changes: '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.' llm_assisted: true - timestamp: '2026-10-13T18:54:48Z' curator: codex action: CORRECTED_PRODUCER_EXCERPT changes: '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.' llm_assisted: true - timestamp: '2026-10-13T19:40:13Z' curator: codex action: CORRECTED_LETHAL_ENDPOINT_EXCERPTS changes: '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.' llm_assisted: true - timestamp: '2026-10-13T20:27:02Z' curator: codex action: CORRECTED_DEFINITION_AUTHORITY changes: '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.' llm_assisted: true