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Bound Stordalen methylotrophy graphs to omics evidence and correct the acetate-route arrow #1830

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@realmarcin

Finding

CommunityMech:000254, PMID:38063415. Preserve methylotrophic genomic potential, expression and substrate observations, but remove categorical SYNTROPHY without product-removal feedback and bacterial CROSS_FEEDING without traced exchange. The acetate arrow points to methylotrophic methanogenesis even though the paper assigns acetate to the acetoclastic route; do not repair it by inventing a new recipient node or importing another mechanism. Retain the source-proposed fen substrate niche interpretation and its existing functional direction only as HYPOTHESIZED/PARTIAL. Habitat-expression patterns do not themselves establish causal arrows to the same activities. Add canonical identity-only archaeal/bacterial scope and bounded computational provenance. The 2018 catalog abstract reports broad correlations, not the specific methylotrophic syntrophy claimed by the graph.

Lifecycle

Address in the dependent batch106 PR; close only after protected-main merge. Self-adversarial review is not independent approval. No paid provider submission or new topology is part of this repair.

Activity

  1. realmarcin commented on Oct 8, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1835 at 2d931ac; self-review: #1835 (review). 959 passed in 793.39s (0:13:13); postcommit docs-current passed.41gate outputs/digests, decisions, provenance and four append-only histories committed.18nodes/5qualified directions retained;1workflow node and5unsupported/restatement arrows removed; all36reviewed quotations match fresh primary text and unchanged caches. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Non-graph1833 stays open. Not independent approval; close only after protected-main merge.

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