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Bound Mushroom Spring transcription, nitrogen-fixation potential and spatial causal claims #1632
Description
Scope
Mushroom_Spring_Hot_Spring_Phototrophic_Mat_Community
Preserve measured diel transcripts and uneven mat structure. The storage-polymer-to-photomixotrophy link is a proposed model, not measured flux. Thermodesulfovibrio nitrogen fixation is inferred from genes; source/target fields imply unsupported transfer. Vertical distribution is context, not a demonstrated causal arrow. Bound gene absence by incomplete genomes and preserve overlapping layers. PMID:23575369 abstract; PMID:28634470 complete main body reviewed.
Deduplication
916 all-state issue titles/bodies and 27 ignored/hidden-inclusive matching local files examined; existing #1197, #1198, #939 and #396 read and preserved. No exhaustive PR-comment audit.
Acceptance
Source-bound graph repair, guarded write and append-only history; every-node/arrow decision, regression tests, actual validation outputs and self-adversarial review. Keep OPEN until protected-main merge.
Activity
realmarcin commentedon Oct 7, 2026
Addressed in #1636 at a74e8e8; exact-head self-review:#1636 (review). 677 passed in 244.49s (0:04:04); post-commit docs-current passed. Every-node/every-arrow decisions and actual output digests committed. Not independent approval; close only after protected-main merge. Metadata #1635 remains unfinished; all four current reference gates passed.