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Qualify Prairie Pothole genomic guilds and unresolved viral causal effects #1718

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@realmarcin

CommunityMech:000256; PMID:30086797. Preserve positive marker genes, diverse MAGs and predicted host links. Genomic potential is not measured substrate flux, reaction direction or a demonstrated cross-feeding route. Full primary discussion explicitly leaves the sign of viral effects on ecosystem rates unresolved and warns of host-prediction false positives. Retain four nodes and two existing arrows with explicit proposed-mechanism scope; remove categorical CROSS_FEEDING, PREDATION and NICHE_PARTITIONING assertions, and use canonical guild participants. Do not invent new viral-lysis or partner-specific arrows. Close only after protected-main merge.

All-state issue titles/bodies searched by exact IDs, PMIDs, DOIs and stems. Closed #258 concerns prior dangling-edge repair; #419 mentions honest broad Prairie taxon grounding. Neither resolves these semantic findings. Local ignored/hidden files included, with .git/docs/site/references_cache exclusions; relevant caches separately checked. Comments and PRs not exhaustive. Self-adversarial source review, not independent approval.

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  1. realmarcin commented on Oct 7, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1723 at e5ce1f8; exact-head self-review: #1723 (review). 786 passed in 236.68s (0:03:56); postcommit docs-current passed. Decisions and actual output digests committed. Not independent approval; close only after protected-main merge. Non-graph1722remains unfinished.

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