identifier: traitmech:000674 label: necridium formation definition: A morphological phenotype in which a filamentous cyanobacterium forms degenerating separation cells called necridia whose disintegration permits trichome fragmentation. definition_source: DOI:10.1127/1864-1318/2005/0117-0239 trait_category: MORPHOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - METPO:1000059 evidence: - reference: DOI:10.1127/1864-1318/2005/0117-0239 snippet: Trichome breakage and hormogonia liberation were caused by the disintegration of such necridia notes: 'Hernandez-Marine and Roldan (2005), scientific abstract on article page 239, visually checked in the published article reproduced in Roldan''s university thesis: https://diposit.ub.edu/server/api/core/bitstreams/6ce8a85f-d68f-402d-8c13-882f128e4a7f/content (PDF page 106). Article pages 239-247, including Methods, Results, Discussion and actual Figures 1-4, were inspected. Natural cave/catacomb biofilms contain Leptolyngbya and Scytonema; microscopy associates cell degeneration with fragmentation and terminal polysaccharide pads. The proposed adhesive function is not a demonstrated universal requirement. No exact strain exemplar is assigned from these mixed samples.' - reference: DOI:10.1111/mmi.12506 snippet: Necridia formation inhibits further molecular exchange, determining the fate of a branch likely to become a hormogonium. notes: Nurnberg et al. (2014), scientific abstract directly retrieved from DOI-matched Europe PMC record PMID:24383541. Publisher full-text Results and Methods were read; actual Figures 5-6 were inspected in the accepted manuscript at https://idus.us.es/bitstreams/05b873c9-9775-45f4-a6d6-2b6c54f97978/download (PDF pages 41-42), with final publisher captions cross-checked. Figure 5 follows 5-CFDA fluorescence for 24 seconds across a necridium; this is not proof of permanent exclusion of every molecule. Figure 6 shows terminal cell remnants and sealed neighboring membranes. Supplements were not inspected. - reference: DOI:10.3389/fmicb.2015.00278 snippet: necridic (dead) cells are SYTOX Green-positive and CTC-negative notes: Publisher full-text Methods, Results, Figure 2 caption and actual panels A-I were inspected. The quoted caption identifies dead cells operationally by membrane permeability and lack of CTC reduction. Panels D-F concern Microcoleus vaginatus 858 CCALA after a week at 4 degrees C, before desiccation; Results report frequent necridia and trichome splitting in cold cultures. Injured double-positive cells and nitrogen-starved bleached but active cells are distinguished. Neither cold exposure nor this stain combination defines the entire class. Supplements and strain provenance were not inspected. canonical_examples: - taxon_id: NCBITaxon:447715 taxon_label: Mastigocladus laminosus SAG 4.84 reference: DOI:10.1111/mmi.12506 note: Necridium-forming stage of the study strain, not a claim that every cell is a necridium. Methods report Castenholz D liquid culture at 40 degrees C under constant white light and fresh medium growth before communication assays. Natural origin from an Icelandic thermal spring in 1967 is independently confirmed by the culture collection at https://sagdb.uni-goettingen.de/detailedList.php?str_number=4.84. NCBI Taxonomy efetch for 447715 confirms this current name and rank strain. These authorities support identity/provenance, not additional phenotype experiments. discussions: - discussion_id: necridium-formation-scope prompt: Review a closer parent and separation-cell terminology. kind: CURATION_TODO status: OPEN rationale: Use active phenotype METPO:1000059 below quality METPO:1000188. Hormogonium formation traitmech:000651 denotes production of short dispersal filaments, not the degenerating separation cell. The 2005 Introduction describes additional fragmentation routes, so neither trait is asserted a subclass or exact synonym of the other. Filament-shaped morphology concerns elongated cell shape, not this multicellular separation stage. Do not equate all dead cells, all trichome fragmentation or all hormogonium formation with necridia. No exact synonyms, xrefs, SSSOM equivalences or organism-level disjointness are asserted pending review of historical separation-disc usages. posed_by: codex posed_date: '2026-10-08' - discussion_id: necridium-formation-mechanism prompt: Resolve the formation mechanism without inferring protein causality. kind: KNOWLEDGE_GAP status: OPEN rationale: Cell degeneration, communication loss and fragmentation are observed, but the inspected evidence does not establish a protein-resolved necridium-formation mechanism. SepJ sequence similarity and septal localization in the 2014 paper do not establish its causal role in necridium formation. Programmed cell death is an interpretation, not proof of conserved apoptosis machinery. Do not impose a fixed cell shape, spacing, cold trigger, adhesion function or fitness benefit. A causal graph is deferred pending direct mechanism evidence and authority-verified protein examples; the mechanism is not claimed biologically absent. posed_by: codex posed_date: '2026-10-08' curation_history: - timestamp: '2026-10-08T05:29:42Z' curator: codex action: MINTED_TRAITMECH_ID changes: Added necridium formation with three primary DOI references, three verbatim snippets and a source-qualified SAG 4.84 example. Ignored-and-hidden novelty and current-main/worktree/complete-open-PR reservation checks support 000674 and v550 block 1062700-1062799. Kept separation-cell morphology distinct from hormogonium formation, generic cell death and inferred protein mechanisms; existing records unchanged. Timestamp is observed UTC curation time. llm_assisted: true