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S. wolfei/Dhc195 graph: separate recipient respiration from modeled aggregation support #1389

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@realmarcin

Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml (000183).

Recipient dechlorination is labelled as reverse CROSS_FEEDING. Aggregation is a joint observation, not demonstrated unidirectional COLONIZATION_FACILITATION. Primary PMID:25576615 reports SEM aggregates and calculates hydrogen flux using a diffusion model; it does not selectively perturb aggregation to prove necessity. Preserve three nodes and two arrows, with the aggregation mechanism PARTIAL and its modeling evidence COMPUTATIONAL, distinct from measured microscopy.

Keep butyrate-fed syntrophy distinct from crotonate comparisons; VC-to-ethene conversion is cometabolic, and donor-limited hydrogen thresholds are separate assays. The 2016 follow-up has exact-Dhc qRT-PCR but uses M. hungatei for protein/complex assays; do not pool them or infer gene necessity. Any new carbon-monoxide structure is a separate open research task.

Deduplication: 717 all-state issue titles/bodies, broader organism/biochar/acetylene/CO synonyms and ignored/hidden-inclusive scoped local review/history/research/tests/scripts. Relevant #1305, #1245, #1236, #900, #883, #765, #754, #561, #389, #384 and #383 were read; no duplicate exact graph defect in the searched material. Not all issue comments were searched.

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  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Existing graph defect addressed in #1393 at e62e9da; exact-head self-adversarial COMMENT #1393 (review). 354 passed in 182.27s (0:03:02); actual post-commit docs-current passed. Committed decisions/validation retain source limits. CO #1392 and metadata #765/#1391 remain open. This issue closes only after protected main merge.

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