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necridium formation

traitmech:000674 · CLASS · PROPOSED

A morphological phenotype in which a filamentous cyanobacterium forms degenerating separation cells called necridia whose disintegration permits trichome fragmentation.

Trait evidence (3)

  • DOI:10.1127/1864-1318/2005/0117-0239
    Trichome breakage and hormogonia liberation were caused by the disintegration of such necridia

    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.

  • DOI:10.1111/mmi.12506
    Necridia formation inhibits further molecular exchange, determining the fate of a branch likely to become a hormogonium.

    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.

  • DOI:10.3389/fmicb.2015.00278
    necridic (dead) cells are SYTOX Green-positive and CTC-negative

    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.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1127/1864-1318/2005/0117-0239

Parent traits (1)

kg-microbe context

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

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Mastigocladus laminosus SAG 4.84 NCBITaxon:447715 DOI:10.1111/mmi.12506 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 and Knowledge Gaps (2)

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

Review a closer parent and separation-cell terminology.

CURATION TODO OPEN necridium-formation-scope · raised by codex · 2026-10-08

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.

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.

Resolve the formation mechanism without inferring protein causality.

KNOWLEDGE GAP OPEN necridium-formation-mechanism · raised by codex · 2026-10-08

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.

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.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed cyanobacterial necridium formation

      Added traitmech:000674 with three primary DOI references and verbatim snippets, a natural SAG 4.84 strain example, explicit scope and mechanism discussions, and METPO v550 placeholder 1062700. Direct source inspection supports separation-cell morphology; protein mechanism is deferred without a graph. Existing records unchanged.

    Read this curation session