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coccolith production

traitmech:000689 · CLASS · PROPOSED

A physiological phenotype in which a microbial cell produces the calcitic cell-covering elements known as coccoliths.

Trait evidence (2)

  • DOI:10.1038/ncomms11228
    Coccoliths are calcitic particles produced inside the cells of unicellular marine algae known as coccolithophores.

    Sviben et al. 2016, PMID:27075521, PMC4834641. Scientific Abstract and full article text directly read in Europe PMC XML on 2026-10-10; actual Figures 1 and 3 inspected. Calcium resupply to depleted AWI1516 cultures supports new calcite formation; imaging distinguishes forming coccoliths from a separate calcium-rich compartment. Its necessity, direct precursor identity and transfer route are not established. Figure 3's detector-panel caption repeats c in two pairs; no panel-specific detector assignment is imported. Other figures and supplements were not visually inspected. Historical Emiliania huxleyi is retained as the source name, not a current taxonomic or culture-collection phenotype assertion.

  • DOI:10.1111/nph.15272
    The continued production of malformed coccoliths could be observed on successive days

    Walker et al. 2018, PMID:29916209, PMC6175242, Results, time-lapse observations associated with Figure 8. Full article text and actual Figures 5 and 8 directly inspected on 2026-10-10; supplements and movies unread. This passage concerns Ge-treated Coccolithus braarudii PLY182g, not normal morphology. Production persists despite defective coccosphere integrity. Growth responses differ from the assayed E. huxleyi CCMP1516; neither growth dependence nor photosynthetic benefit is generalized. Preserve source discrepancies: Methods time-lapse stage 17 C versus Figure 5's 16 C; Methods/Results HEDP 50 micromolar versus Figure 1's 5 micromolar; Results low-Si threshold below 0.2 micromolar versus Discussion below 0.1. No unqualified quantitative claim depends on choosing between them.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/ncomms11228

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.

Resolve broader biomineralization placement without conflating endpoints.

CURATION TODO RESOLVED coccolith-production-scope-and-parent · 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 phenotype METPO:1000059 pending a source-backed broader biomineralization phenotype. Coccolith production is not mere possession, secretion or arrangement of preformed elements into a coccosphere. Defective elements still count as production; a complete covering is not required. It is not equivalent to generic calcification, urease-associated calcium carbonate precipitation, siliceous scale production, or magnetosome/ferrosome possession. The physiological trait is distinct from a material coccolith, its vesicle and a process-level ontology term. No exact synonyms, xrefs, common molecular pathway or organism-level disjointness are asserted.

Resolution: Added biomineralization traitmech:000690 as the direct broader phenotype. Production of the mineral elements specified by this record entails mineral formation; this is a definition-based hierarchy inference, not a new child experiment. Phenotype METPO:1000059 remains an ancestor. The historical rationale and endpoint distinctions are preserved; the separate exemplar and mechanism gap remains OPEN. The v566 proposal requests the additional child axiom without rewriting the historical proposal cohort.

Reconcile assay strains, life stages and production-specific mechanisms.

KNOWLEDGE GAP OPEN coccolith-production-exemplars-and-mechanism · 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 pending joint strain-provenance and current-taxonomy verification. Skeffington et al., DOI:10.1111/jpy.12942, p. 239, explicitly derives calcifying AWI1516 from CCMP1516; this does not make all descendants equivalent. The current collection https://ncma.bigelow.org/CCMP1516, read 2026-10-10, labels it Gephyrocapsa huxleyi and reports lost coccolith production. Keep historical assay observations separate from this current catalog state; loss alone does not establish engineering. PLY182g provenance remains unresolved here. No universal silicon requirement, ploidy restriction, growth dependence or protective function is inferred. Separate mineral deposition, transport, secretion and covering integrity before adding causal edges. A protein mechanism needs direct functional evidence and taxon-paired accessions; sequence features alone are insufficient. Mechanism is deferred, not claimed absent.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added coccolith production with two primary DOI citations and short directly checked snippets, retaining assay and source-conflict limits. Ignored-and-hidden main/worktree/open-PR reservation checks support 000689 and v565 block 1064200-1064299. Broader hierarchy, canonical exemplars and protein mechanism remain unresolved. Existing records unchanged. Timestamp records the observed UTC curation decision.

  2. · REFINE_BIOMINERALIZATION_PARENT · codex

    Refined the direct parent to biomineralization traitmech:000690 and resolved the temporary parent gap by definition-based inference. Preserved the definition, evidence, historical rationale, independent mechanism gap and prior curation history. No organism or molecular mechanism was added.

Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed coccolith production phenotype

      Added traitmech:000689 as PHYSIOLOGY/CLASS/PROPOSED under phenotype METPO:1000059 through the guarded add_coccolith_production_trait writer and record_curation_event. Two primary DOI citations (10.1038/ncomms11228 and 10.1111/nph.15272) and directly checked short scientific-abstract/Results snippets support production, including malformed elements, distinct from coccosphere integrity. Preserved source condition/caption discrepancies and historical strain limits. DOI:10.1111/jpy.12942 and the current CCMP1516 collection support qualified provenance context only. Left two explicit discussions for broader hierarchy, canonical exemplars and functional protein mechanism; no graph, xref or synonym inferred. Ignored-and-hidden searches across current main and 22 worktrees plus all five paginated open PR heads found no exact duplicate or competing allocation. Reserved full METPO block 1064200-1064299 in proposal v565, only 1064200 populated. Existing records, including protected spore germination, are unchanged. Validation and review results will be reported after execution, not presumed here.

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  • · codex
    • EDIT — Resolve coccolith production biomineralization parent gap

      Reparented traitmech:000689 to biomineralization traitmech:000690 by definition-based inference and resolved its parent TODO. Preserved definition, evidence, historical rationale, separate exemplar/mechanism discussion and prior history. Historical v565 template remains unchanged; v566 explicitly requests the additional upstream child axiom. No new experiment or molecular claim is asserted.

    Read this curation session