identifier: traitmech:000689
label: coccolith production
definition: A physiological phenotype in which a microbial cell produces the calcitic
  cell-covering elements known as coccoliths.
definition_source: DOI:10.1038/ncomms11228
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000690
evidence:
- reference: DOI:10.1038/ncomms11228
  snippet: Coccoliths are calcitic particles produced inside the cells of unicellular
    marine algae known as coccolithophores.
  notes: 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.
- reference: DOI:10.1111/nph.15272
  snippet: The continued production of malformed coccoliths could be observed on successive
    days
  notes: '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.'
discussions:
- discussion_id: coccolith-production-scope-and-parent
  prompt: Resolve broader biomineralization placement without conflating endpoints.
  kind: CURATION_TODO
  status: RESOLVED
  rationale: 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.
  posed_by: codex
  posed_date: '2026-10-10'
  resolved_date: '2026-10-10'
  resolution_note: 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.
- discussion_id: coccolith-production-exemplars-and-mechanism
  prompt: Reconcile assay strains, life stages and production-specific mechanisms.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: 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.
  posed_by: codex
  posed_date: '2026-10-10'
curation_history:
- timestamp: '2026-10-10T06:31:15Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: 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.
  llm_assisted: true
- timestamp: '2026-10-10T08:03:12Z'
  curator: codex
  action: REFINE_BIOMINERALIZATION_PARENT
  changes: 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.
  llm_assisted: true