Clarify Dehalococcoides recipient processes and conditional cofactor support (batch 30)

[realmarcin]

Scope

Three complete record-level graph reviews: Dhc195/DvH lactate coculture, Dhc195/DvH/PfR7 triculture and BAV1/Fusaro cofactor coculture. Corpus: 135 reviewed / 321 pending / 4 needs_research across all 460 records in both roots.

Closes #1382. Closes #1383. Closes #1384. Separate non-graph follow-ups #1385 and #1386 remain open.

Changes And Adversarial Review

Preserve all ten nodes and seven arrows. Assign recipient dechlorination and remodeling to the recipient instead of duplicate or reversed nutrient transfers. Separate sulfide-associated inhibition under donor excess from hydrogen competition and from donor-limited butyrate-triculture experiments. The roughly threefold rate comparison is not generalized to cell yield.

Make external DMB a coinput throughout the corrinoid triculture. Preserve positive hydrogen and corrinoid transfer, donor cobalamin production as a possible contribution, and recipient remodeling without an exclusive-route claim. Classify measured transcript evidence as IN_VITRO, not merely computational; induction is not proof of gene necessity.

For BAV1/Fusaro preserve positive DMB-associated support and negative native-cobamide compatibility. A missing adequate cofactor is not active factor-III toxicity, and BAV1 activity is not reverse cross-feeding. Distinct strain and donor results are not pooled.

Verification

348 passed in 189.71s (0:03:09); six new focused tests. Schema, strict, term, reference, independent snippet and history checks passed. Raw reference diagnostics and actual snippet counts are recorded separately. Exact targets, one rename and discussion anchors checked.

Zero structural errors; all 31 prior network warnings unchanged. Measured connectivity survey unchanged. Exact participant registry 173 to 174 users, only the corrinoid triculture added; no numeric bounds or algorithms changed.

Three guarded edits, llm-assisted events, append-only histories and regenerated pages. All non-graph raw blocks, 457 other records and 920 reference caches are byte-preserved. Repeat rendering is deterministic and exact descriptions are checked on all 456 pages. Actual post-commit docs-current passed with a clean tree. No screenshot QA is claimed.

Committed decision, validation and adversarial-review records are under reports/causal_graph_review, dated 20261006, batch30. This is source-based self-adversarial review, not independent approval. Source access is explicit per paper: 2014/2017 main text read, 2012 abstract-bounded, 2013 abstract plus partial indexed primary excerpts. No figure images or supplements inspected; no new article body/PDF or Edison job.

Stacking

Draft dependency on #1381. Do not merge into the topic parent. Require exact-head protected main checks/queue after parents merge; move dependents before branch deletion. This batch does not complete the full-corpus goal.

[realmarcin]

Source-based self-adversarial review at exact head 5988d5a; not independent approval.

Addressed #1382, #1383 and #1384 after reading the actual diffs against primary sources at the documented access scope. All ten nodes and seven arrows remain. Recipient capabilities are source-only, not reverse/duplicate nutrient transfers. Sulfide toxicity under donor excess is separated from competition and other community experiments. All corrinoid-triculture arrows expose external DMB; donor cofactor synthesis and recipient remodeling are not falsely made exclusive. Native factor-III insufficiency is not active inhibition.

348 passed in 189.71s (0:03:09); six new tests; schema, strict, terms, reference, independent snippet and history checks passed. Zero structural errors, all 31 prior warnings unchanged. Exact participant registry 173 to 174, measured connectivity unchanged, no numeric bounds or algorithms altered. Deterministic rendering, exact descriptions across 456 pages and actual post-commit docs-current passed.

Three guarded writes/histories; 457 other records and 920 caches unchanged. Source-only and partial-full-text limits are explicit, as are uninspected figures/supplements. No new article bodies/PDFs or paid research. Metadata #1385/#1386 remains open, not certified by graph curation.

Decisions, validation and self-adversarial output are committed. Protected CI/main merge and full-corpus completion are not claimed; preserve the dependency stack until main merges.

[github-actions]

Network integrity findings

Warnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build.

Network Integrity Audit Report
================================================================================

0 error, 31 warning across 12 records with findings
Only error-severity findings fail the build.

Algal_Methanotroph_Biogas_Valorization_Coculture
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Leptolyngbya' has no interactions

Total: 1 issues (0 error, 1 warning)

At_RSPHERE_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Flavobacterium sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhodococcus sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptomyces sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Variovorax sp.' has no interactions

Total: 5 issues (0 error, 5 warning)

Australian_Lead_Zinc_Polymetallic
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidithiobacillus ferrooxidans' has no interactions
  [warning] DISCONNECTED: Taxon 'Leptospirillum ferriphilum' has no interactions

Total: 2 issues (0 error, 2 warning)

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Brocadia_Low_Nitrogen_Anammox_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Ca. Kuenenia early-acclimation lineage' has no interactions

Total: 1 issues (0 error, 1 warning)

Dangl_SynComm_35
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Escherichia coli DH5α' has no interactions
  [warning] DISCONNECTED: Taxon 'Flavobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Stenotrophomonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Xanthomonadales members' has no interactions

Total: 5 issues (0 error, 5 warning)

Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylophaga' has no interactions

Total: 1 issues (0 error, 1 warning)

Mangrove_Benzene_MFC_Bioanode_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Pelobacter' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas' has no interactions

Total: 2 issues (0 error, 2 warning)

Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Legionella MAGs' has no interactions

Total: 1 issues (0 error, 1 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.

[realmarcin]

Self-adversarial review refreshed at exact head 3b4f54dd705d288c37e52ca173f372a8cc8572dc
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 6f7947a8bdf7f2d7491b551f88a63911eb00e0cd
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head d11c413201d5f4389312aa2f0470414f209605ea
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 1d413bf389704b17dfc67af616c167a53cad8f3f
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 0248e7251ab60e600718774ccbb00f05a9ba003d
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 6006515a3a03000098bdbd9c4c912fc9377dd3ed
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 9d2eceb63c68ef9506b6ce8c8479a348eaa9facf
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 3680053b918391ca1939c3f4066a278bea439cc6
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 20868a1cf45a111ecc94b5b9e6817ceb4bbe7f65
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head c34b76ca31173f09b929082b52cf85b9381d8325
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4b39c126a27eb25a16ef82af9440641f55832cd0.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial integration review at exact head a66f315ccdacde92979962e77342df1414f896a2. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head c34b76ca31173f09b929082b52cf85b9381d8325, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.

Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.

An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.

Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.

[realmarcin]

Self-adversarial review refreshed at exact head be022f67e3b3bcca237d2561f067cb0d4c1c52bd
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 8e621c68a314607021c1c344efe588197b89085f.
The batch-owned binary patch is byte-identical
(SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial governance integration review at exact head 4e0b6870cc9942383dd90b71c138adb1cedfed58. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head be022f67e3b3bcca237d2561f067cb0d4c1c52bd, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.

Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.

Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.

Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.

[realmarcin]

Exact-head self-adversarial restack review at 85860d0d6b56b133ce2b2b9032f21af5e0953e0b.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 4ea591fb96bd6c6a83000c118387a9cef73a4af48e73b12faaf37f71118d7d47.
Tree f7d3dd6a38f1634527861d8aeee853c3656f5696 matches the independently computed clean merge.
Compared with historical tree 112cf985a4db6e00dc5fe18fd166738aa541f043, only scripts/.vendored_canon_ref
changes, incorporating main PR #1834's pin 849f336e025510316a5f235eb0af8547b8bd50cc.
All curated records, source caches, review outputs, histories, regression tests, and rendered
pages remain unchanged. No new primary-source review or local scientific-test rerun is claimed.

This PR is now part of native stack #1973, rooted at #1363 on main. No protected merge
has occurred. Fresh eligible PR/merge-group CI remains mandatory. No rule bypass, fabricated
status, merge into a topic parent, or premature branch deletion.

[realmarcin]

Superseded by the protected cumulative merge #1975 at 42959bef2549f9a42c3e3303a0e10fd5be99f30e. This PR's reviewed source head df0fe6289f22075eabf0abc139d7672ad78a11f8 was included in the cumulative branch; the final squash tree matches the reviewed integration tree exactly, and all seven required merge-group checks passed.

Patch-inclusion receipt. Existing issue-closing links were transferred to #1975; unresolved research and non-graph gaps are not closed by this action. This PR is being closed as superseded, not represented as individually merged. Archival provenance tags retain source commits; cleanup removes branch refs only and preserves worktree files.