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DVM graph: separate conditional substrate supply, methane pathways and sulfate competition #1530

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@realmarcin

DVM_Triculture.yaml (CommunityMech:000021) retains four nodes and two substrate-supply arrows, but needs exact-system and conditional-mechanism repair.

The 2019 primary study distinguishes no-added-sulfate, 7.5 mM and 15 mM sulfate treatments. Lactate conversion and enhanced tri-culture methane production are supported; complete acetate utilization is not. H2-pressure perturbations in Mb monocultures and mass balances in Dv-Mb pairs support H2 co-utilization, but do not resolve pathway shares in the tri-culture. Carbon dioxide and some initial hydrogen are also present in culture headspace, so exclusive donor origin is not established. The older 1981 pair experiments cannot substitute for exact 2019 tri-culture measurements. Preserve observed positive effects, distinguish co-/tri-/monoculture assays and bound competition and pathway inference. Do not add new causal structure during this repair.

Acceptance: review every original node and arrow against the whole record and primary Methods/Results; preserve canonical taxonomy; use source-context evidence and exact discussion anchors; retain append-only curation history, focused regression tests, full gates, regenerated pages and committed output/review records. Keep this repair issue open until protected-main merge. Existing #1364 tracks non-graph protocol/metadata and remains unresolved separately.

Primary: https://pmc.ncbi.nlm.nih.gov/articles/PMC6544901/ (Results2.1-2.4, Discussion, Methods4.1-4.8, Tables1-2, main captions read; no original images, supplements or raw-data audit). PMID16345708 cached abstract only.

Dedup: 833 all-state issue titles/bodies searched, 14 matching ignored/hidden-inclusive local files (excluding generated docs/site and separately inspected reference caches). Relevant #1364, #1398-1400 and #496 inspected; not every historical comment or PR. Self-adversarial review is not independent approval.

Activity

  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1531 at 762a708; exact-head self-review:#1531 (review). 531 passed in 203.79s (0:03:23); post-commit docs-current passed. Every-node/arrow decisions and actual output digests committed with explicit primary-source limits. Not independent approval. Close only after protected-main merge.

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