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Cable-bacteria biofilm: reconcile diatom source with Chlorophyta roster before graph certification #1267
Description
Cable_Bacteria_Photosynthetic_Biofilm_Sediment (CommunityMech:000145), PMID:25416774 / doi:10.1128/AEM.02682-14: the primary main text describes a diatom-dominated biofilm, while taxonomy and explicit graph participants use NCBITaxon:3041 Chlorophyta.
Graph-only Batch 8 repair will remove the unsupported explicit Chlorophyta assignments, retain bounded oxygen-supply cross-feeding and the two supported perturbation-response arrows, and remove CROSS_FEEDING from intrafilament conduction and geochemical response nodes. This is only a partial repair: community-level graph expansion still draws on the uncorrected roster. Keep the record needs_research and this issue OPEN until whole-record taxonomy, connectivity and related sulfide(2-) metadata are reconciled against primary evidence and canonical grounding.
Further limits: repeated light cycles are not independent cores; exact redox-site, motility and regulation mechanisms are hypotheses. Inspect reported sulfide-depth statistical inconsistency rather than claiming significance. Main text through conclusions read; images and supplements not inspected. Source: https://journals.asm.org/doi/10.1128/aem.02682-14
Acceptance: consistent evidence-backed roster and graph membership, no unsupported green-algal identity, term/network/reference gates and updated review certification. Issue titles/bodies across all states and current recent issues checked; comments not exhaustive.
Activity
realmarcin commentedon Oct 5, 2026
Partial graph repair is in PR #1269 at 149106e. Explicit Chlorophyta participants were removed, but the unchanged roster and resulting community-level expansion still require reconciliation. The committed ledger marks 000145 needs_research. Keep this issue OPEN after merge; green schema/snippet/network checks do not resolve organism identity.
realmarcin commentedon Oct 8, 2026
The identity/chemical dependency repair is in #1974 at
6f062d2eb68fedab336b700c758cd21622fabbb6.Primary Methods support the corrected diatom roster and H2S measurement; calculated total sulfide, species resolution, reciprocal benefit and mechanistic uncertainty remain distinct. All three nodes and two arrows are retained. The old batch8 ledger remains unchanged; the batch125 ledger explicitly supersedes its record hash.
Eight focused tests include five mutation probes; schema/strict/terms/references/snippets/history/network and deterministic publication gates passed within the recorded scopes. Existing57network warnings remain, with zero structural defects. Self-review: #1974 (review) (not independent approval).
Keep this issue OPEN until the PR is actually merged to protected main. #1268 is unchanged.