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diatom frustule production

traitmech:000691 · CLASS · PROPOSED

A biomineralization phenotype in which a diatom forms the siliceous valve and girdle-band elements of its cell wall (frustule).

Trait evidence (2)

  • DOI:10.1007/s00709-017-1199-4
    The basic stages of frustule morphogenesis characteristic of raphid pennate diatoms have been traced

    Bedoshvili et al., journal issue May 2018, online 2017-12-21, PMID:29270874. Scientific Abstract directly read at https://pubmed.ncbi.nlm.nih.gov/29270874/ and in Europe PMC CORE on 2026-10-10 using EXT_ID:29270874 AND SRC:MED; exact ID, source, title and DOI checked together. The abstract defines frustule components as silica valves and girdle bands and reports microscopy of morphogenesis in Encyonema ventricosum under the source name. This supports formation, not just an isolated shell's presence. Cytoskeletal proximity is not functional necessity. Full text, Methods, actual figures and supplements were not inspected; no canonical taxon or universal membrane-release mechanism is inferred.

  • DOI:10.1038/s41467-024-52211-x
    A diatom cell wall consists of two types of building blocks: two plate-shaped valves and several ring-shaped girdle bands.

    Aram et al. 2024, PMID:39251596, PMC11385223, Introduction. Scientific Abstract, Introduction, Results, Discussion and Methods directly read in official Europe PMC full-text XML on 2026-10-10; actual Figure 2 inspected, other actual figures and supplements unread. Source-qualified CORE lookup EXT_ID:39251596 AND SRC:MED confirmed ID, source, title and DOI. Silicon-starved CCMP1335 cultures were resupplied and imaged during valve formation. Figure 2 orders different cells by inferred maturation, not a live-cell time series. The paper retains historical Thalassiosira pseudonana naming while noting Cyclotella nana; this is not a current taxonomy assignment. Structural correlations support a membrane-mold hypothesis, not proven contact-site function or a universal molecular mechanism. The quote defines wall elements; the Results provide the production observations.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1007/s00709-017-1199-4

Parent traits (1)

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.

Keep frustule-element formation distinct from possession and other silica traits.

CURATION TODO OPEN diatom-frustule-production-scope-and-mappings · raised by codex · 2026-10-10

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 biomineralization traitmech:000690 as the broader phenotype because this endpoint entails formation of mineral cell-wall elements. It is not a material frustule, generic silicification, silica uptake, retention of an inherited valve or adsorption of preformed silica. Production of new wall elements does not require both valves to be synthesized anew in one cell cycle or every element to be formed simultaneously. Keep valve/girdle formation distinct from silica scales, auxospore coverings and setae; their observation alone does not establish this endpoint. The existing scale-production scope note distinguishes these phenotypes and is not an unresolved exact grounding. Do not infer organism-level disjointness or a universal geometry, cell-cycle schedule or fitness effect. Exact synonyms and external phenotype mappings remain unasserted pending authority review; process and material terms are not exact equivalents.

Resolve assay-strain provenance and production-specific causal evidence.

KNOWLEDGE GAP OPEN diatom-frustule-production-exemplars-and-mechanisms · raised by codex · 2026-10-10

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.

No canonical examples are assigned before reconciling study strains, collection provenance and current taxonomy. The two studies support wall-element formation but do not establish a conserved protein mechanism. The contact-site transport model and actin-associated expansion in Aram et al. remain proposals; unobserved vesicle fusion is not proof of its absence. Separate silica deposition, shaping, exocytosis and wall assembly when evaluating perturbation evidence. Functional evidence and taxon-paired accessions are required for protein edges; sequence features alone are insufficient. Mechanism is deferred, not claimed absent, and no universal intracellular route is imposed on all diatom silica structures.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added diatom frustule production beneath biomineralization with two primary DOI citations and directly checked short snippets. Ignored-and-hidden main/worktree/open-PR reservation checks support 000691 and v567 block 1064400-1064499. Existing trait records unchanged; mappings, canonical taxa and mechanisms remain open. Timestamp records the observed UTC curation decision.

Recorded curation sessions

  • · codex
    • CREATE — Add source-bounded diatom frustule production

      Added traitmech:000691 as a PROPOSED PHYSIOLOGY class beneath biomineralization traitmech:000690. Bedoshvili et al. DOI:10.1007/s00709-017-1199-4 scientific abstract defines frustule components and describes morphogenesis; Aram et al. DOI:10.1038/s41467-024-52211-x Introduction supplies the valve/girdle definition and its Results/Methods support valve formation. Short contiguous snippets checked directly. Aram main scientific sections and actual Figure 2 were inspected; other actual figures/supplements and the Bedoshvili full text remain unread. Reserved local 000691, cohort v567 and METPO block 1064400-1064499 after ignored-and-hidden main/all-worktree/current open-PR checks. Proposal uses released phenotype as ancestor and explicitly requests the biomineralization refinement with v566. No canonical taxa, xrefs, synonyms, protein accessions or causal graph added; two open discussions retain scope, provenance and mechanism questions. Existing trait YAMLs are unchanged. Written using the guarded dry-run-default validated writer; focused writer tests and dry run passed before application. Full corpus validation and review outcomes are recorded separately when completed.

    Read this curation session