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Repair cross-study and taxon conflations in the Panzhihua causal graph #1676

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@realmarcin

CommunityMech:000051. The six-node graph conflates 2014 bulk-soil isolates, 2023 nodule isolates, 2018 Sinorhizobium saheli/Leucaena results, an external Polaromonas system and 2024 soil-carbon community measurements. Remove the ungrounded nitrogen/carbon feedback and unsupported vanadium and redundancy nodes. Preserve positive nodulation/N enrichment, isolate metal tolerance and Ochrobactrum IAA/siderophore phenotypes, with explicit strain/species uncertainty and no interbacterial mutualism/cross-feeding claim. Preserve the positive carbon result in an evidence-backed discussion pending community identity repair; do not grant all canonical members carbon activity to conceal disconnected taxa. No new taxon identities. Close only after protected-main merge.

Searched 954 all-state issue titles/bodies; read all five matches (#1077-1079, #497, #258), the previous milk review, and the existing Polaromonas author-request lead. Local hidden/ignored-inclusive search found 64 matching files, excluding .git/docs/site/references_cache. Four whole records and four fresh complete primary main texts/captions read; seven further abstracts checked. No original figure pixels or separate supplements audited. Self-adversarial review, not independent approval.

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  1. realmarcin commented on Oct 7, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1684 at 72da5ae; exact-head self-review:#1684 (review). 736 passed in 494.44s (0:08:14); 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 #1683 remains unfinished; all four current reference gates passed.

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