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Separate Streptomyces aggregate performance from mutualism and gene-mediated causation #1831

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Description

@realmarcin

Finding

CommunityMech:000335, PMID:41678860 and PMID:23865051. Preserve the exact four-strain growth, atrazine removal, gene-detection and phytotoxicity observations. Higher mixed-culture biomass and a non-antagonism screen do not establish reciprocal benefit to every member. Gene presence is catabolic potential, not measured expression, enzyme activity or isolated causal mediation. Qualify the two existing gene-to-removal and removal-to-phytotoxicity directions rather than treating them as demonstrated mediators. The 2013 source contains multiple formulations; do not transfer its six-member immobilized-culture results to A2-A5-A11-M7. Existing caches requested by open #764 are present in the current checkout; preserve them and the closed #691/#763 repairs rather than duplicating the old missing-cache findings.

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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