Bound mercury B12 and methane causal claims (batch70)

[realmarcin]

Scope

Closes #1596.
Closes #1597.
Closes #1598.
Closes #1599.
Related non-graph metadata #1600 remains OPEN after graph repair merge.

• Retain sampled-community and historical contamination context, not isolated selection.; Retain bounded EFPC methylation potential; separate external positive methanogen culture evidence.; Retain 27/28 putative resistance/efflux annotations, not measured phenotype or persistence.; Retain 17/28 selenium-capacity annotations with the canonical subset explicit.
• Retain salinity-associated Microcystis disappearance, not later-assay causality.; Retain relative compositional changes without competition or extinction claims.; Retain source-proposed B12 provision with pellet non-detection and unresolved delivery.; Retain spatial association and explicitly hypothetical facilitation.; Retain temporal transcript profiles without absolute output or transfer inference.; Retain positive B12-limited growth rescue and the supplementation control.
• Retain simultaneous positive endpoints and reported division of labor, not obligatory reciprocal dependence.; Retain SIP-associated EET assignment with incomplete genus-specific causality.; Retain reported diazotroph assignment, not individually quantified fixation.; Retain positive 15N2 incorporation and net ammonium accumulation at enrichment scope.; Retain positive current, cytochrome inhibitor evidence and labeled protein without a new nitrogen-to-current causal claim.
• Retain MAG-associated hypoxic methane oxidation without exclusive genus attribution.; Retain alternative proposed EET routes, not an obligatory serial partner chain.; Retain positive chromium removal and inhibition coupling, not omics-proven mediation.

Adversarial Review

• Read all four whole records,18 original nodes and12 arrows. Read three complete public primary bodies/Methods/captions and the EFPC MAG table, plus complete primary abstracts for both methane studies. Public publisher requests failed; no access-control bypass. No separate supplements, original images, raw data or executable models audited.
• EFPC is two depths from one core and28 MAGs, not a controlled Hg-selection experiment or complete seven-phylum community. Preserve the sampled genomic observations and author selection interpretation but qualify its causal link to resistance capacity. Do not infer niche partitioning from functional annotations.
• EFPC methylation potential is explicit prior-study environmental background, not measured hgcAB or flux in the28 MAGs. The removed selection-to-methylation arrow is not retargeted to a invented pathway. The independent methanogen culture study remains positive comparative context: eight of nine strains methylated above matched controls, while fused-hgcAB M.methylutens did not. Do not silently credit canonical Thermoproteota with those external methanogen results.
• Preserve27/28 putative metal-resistance/ATPase annotations and17/28 Se-assimilatory annotations without measured resistance, expression, uptake or community persistence. Eisenbacteria is an explicitly represented subset; Rokubacteria is source-mentioned but not added through an unverified canonical mapping. No selenium-to-mercury arrow invented.
• Syn7002 salinity-associated Microcystis disappearance and later relative sorting are real observations. They are not a tested interspecies competition mechanism, proof of PseTH extinction or absolute viable growth. Remove three assembly/analysis-order arrows without deleting the observations. Preserve source-inoculum versus stable-partner distinctions and prior genus grounding.
• Syn7002 coculture growth rescue and B12-positive controls remain positive results under B12-free BG11. Do not turn uncertainty about the mechanism into absence of benefit. Washed precultures do not by themselves establish zero carryover or intracellular stores. Growth/absorbance is not a direct photosynthetic-flux assay or reciprocal-fitness test.
• MesTH B12 provision, proximity-facilitated transfer and biosynthetic/transport contribution remain source-consistent hypotheses with direction and biological mechanism stated. The day20 pellet LC-MS/MS non-detection is not an extracellular measurement or proof of rapid uptake. SEM rods are not cell-resolved identity or a contact-requirement test. No donor perturbation or delivery route was selectively isolated.
• Figure4 transcript values are fold changes relative to an initial stage, not absolute cross-species B12 output or matched monoculture induction. Retain positive temporal transcriptional observations; nitrogen-related expression is not direct fixation/assimilation. Separate TableS1 was not read and its numerical assay limits are not invented.
• Methane MFC isotope results are stronger than ammonium accumulation alone: retain15N2-derived biomass13.55%,aqueous ammonium7.15%,0.22+/-0.01mg/L over30days. Retain1.17+/-0.18mA and78.1% Coulombic efficiency. Whole-enrichment outcomes are not six separately proven fixation or electrode-transfer phenotypes.
• MFC DNA-SIP guild assignments remain attributed as reported. Qualify both guild-to-endpoint arrows rather than erasing positive isotope and inhibitor evidence. Raman15N in cytochrome shows incorporation, not a selective causal test that fixation increases current. No obligatory reciprocal dependence, exclusive route, new methane node or nitrogen-to-current arrow claimed.
• Methane-CrVI retains maximum20.63mg/L/d removal and the positive inhibition result linking methane oxidation to reduced CrVI reduction. MAG-assigned Methylocystis6.30% is not exclusive taxon flux. Hypoxic aerobic methanotrophy is not automatically oxygen-independent oxidation.
• CrVI source proposes cytochrome/pilus routes or partner-associated transfer, not one proven serial chain. Keep twoPARTIAL arrows; inhibitor specificity and route-specific controls remain unavailable. Differential quorum-sensing/ABC/porin expression is not selective mediation. Chromate is the preserved canonical representation, not exact challenge-salt validation. Three named genera are a subset, not a defined three-isolate consortium.
• All changed top-level fields are graph/discussions/curation_history only. Verify raw preservation of non-graph blocks,456 other records and920 caches. Preserve upstream id001 aliases for CrVI engineering/taxonomy/environment evidence while detaching changed graph evidence. Exactly one append-only history/event per record, all discussion anchors resolve.
• Measure both-root participant census unchanged460/391/123/268/1507/1240. Add EFPC to exact participant USERS registry only; no taxonomy or auditor-rule changes. All44 network warnings match baseline exactly. Coarse solely-rule counts are not proof of member-resolved mechanisms or precise participant credit.
• Actual schema/strict/terms/references/snippets/history, inventory/rank/network, repeat-render and combined regression outputs retained with hashes. Exact description parser covers456 pages, not browser screenshots. A preflight lint complaint about the new test lambda was fixed before the recorded full run; all recorded final gates refer to the corrected test. Post-commit docs-current remains a separate gate.
• Deduplication includes886 all-state issue titles/bodies and23 scoped ignored/hidden local matches. Matching issue bodies#713,#183's cue-ranked candidate list is exhausted: 7 of the last 8 cannot be enriched, each for a documented reason #650,Five records where the growth medium is defined by what it omits, and naming its contents would be wrong #583,Editing a taxon after GTDB grounding silently leaves it ungrounded, indistinguishable from never-attempted #314,Add Mercury SFA East Fork Poplar Creek Hg methylator community #16 read, not all PR comments/historical local matches. Repairs#1596-Methane-CrVI graph conflates omics associations with resolved electron-transfer mediation #1599 addressed but OPEN until protected-main merge; metadata#1600 remains OPEN afterward. Self-review is not independent approval or whole-corpus completion.

Verification And Output Records

634 passed in 259.03s (0:04:19); seven new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 70 record snippets match selected caches;23 graph excerpts independently match fresh primary text with whitespace-only normalization.920 caches unchanged. CLI Total checks counts reported issues, not executed checks. Cache MATCH is not scientific entailment or historical provenance certification. All920 caches unchanged;23 graph excerpts independently match fresh primary text after whitespace normalization. #1600 metadata remains OPEN. Two methane full texts unavailable. Broader #476/#1091/#1095 source limitations persist.

All18 nodes retained;8 arrows qualified and4 cross-study/workflow arrows removed. No new structure or provider spend. Canonical taxonomy and raw non-graph blocks preserved, not recertified.456 other records unchanged. Zero structural defects;all44 baseline network warnings preserved exactly. Coarse scope census remains460 records,391 with community-level nodes,123 mixed,268 community-only,1507 taxa and1240 solely-rule count; no taxonomy or auditor-rule change. This census does not measure exact participant credit.

Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Post-commit just check-docs-current passed with clean tree; log SHA256 5b9f12481362cbfcab8f60bb9d1aee0904f858ba06c4c7b701fbfa8991d3d359. Every-node/every-arrow decisions,39 actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch70. Corpus224 reviewed /212 pending /24 needs_research: unfinished, not independent approval. Metadata #1600 remains OPEN.

Source Limits

• All18 original nodes and12 arrows reviewed. Retain18 bounded observations, qualify8 arrows and remove4 unsupported cross-study/workflow arrows. No new nodes/arrows or paid research submission.
• Three complete public primary main bodies and captions read, including EFPC Table1. MFC and CrVI studies available only at primary-abstract scope after public publisher requests failed. Separate supplements, raw data/genomes, original images and executable analyses not audited.
• EFPC methylation is explicitly background potential from prior studies, not measured carriage/flux in the sampled MAGs. Separate methanogen culture results remain positive external context in a focused discussion. Resistance/selenium are annotation-based capacities.
• Syn7002 positive growth rescue remains; B12 delivery, contact facilitation and expression-to-provision are hypotheses. Pellet non-detection is not an extracellular assay or proof of rapid utilization. Relative PseTH decline is not extinction, competition or absolute viable growth.
• MFC positive 15N2 incorporation, current and cytochrome inhibitor/Raman results remain at enrichment scope. Reported guild assignments do not isolate each genus or establish nitrogen fixation as a cause of greater current.
• CrVI positive removal and methane-inhibition effects remain. MAG/multi-omics route alternatives do not establish an exclusive serial pathway, exact challenge species or quorum-sensing mediation.
• All920 caches and all non-graph raw blocks unchanged, not recertified. Canonical phylum/genera and unresolved Hyphomicrobium IDs remain unchanged. Follow-up Batch70 non-graph follow-up: EFPC scope, Syn7002 B12 claims and methane consortium metadata #1600 stays OPEN after graph repairs; Five records where the growth medium is defined by what it omits, and naming its contents would be wrong #583 guidance and prior Editing a taxon after GTDB grounding silently leaves it ungrounded, indistinguishable from never-attempted #314 grounding preserved.
• Ignored/hidden-inclusive local search and all886 issue titles/bodies used for deduplication; matching issue bodies An evidence snippet can support a claim about an organism it never names, and nothing checks that #713,#183's cue-ranked candidate list is exhausted: 7 of the last 8 cannot be enriched, each for a documented reason #650,Five records where the growth medium is defined by what it omits, and naming its contents would be wrong #583,Editing a taxon after GTDB grounding silently leaves it ungrounded, indistinguishable from never-attempted #314,Add Mercury SFA East Fork Poplar Creek Hg methylator community #16 read. No claim to exhaustive PR-comment or historical-local-match review.
• Self-review is not independent approval. Repair issues EFPC graph conflates external methanogen assays with sampled sediment MAGs #1596-Methane-CrVI graph conflates omics associations with resolved electron-transfer mediation #1599 remain OPEN until protected-main merge. Reviewed status means bounded existing-graph review, not experimentally complete mechanisms or whole-record certification.

Dependency

Draft depends on #1595. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after the parent merges. Move dependents before deleting parent branches.

[realmarcin]

Source-based self-adversarial review at exact head 7c62dbe; not independent approval.

Repairs #1596-#1599 addressed; non-graph #1600 unresolved.

• Retain sampled-community and historical contamination context, not isolated selection.; Retain bounded EFPC methylation potential; separate external positive methanogen culture evidence.; Retain 27/28 putative resistance/efflux annotations, not measured phenotype or persistence.; Retain 17/28 selenium-capacity annotations with the canonical subset explicit.

• Retain salinity-associated Microcystis disappearance, not later-assay causality.; Retain relative compositional changes without competition or extinction claims.; Retain source-proposed B12 provision with pellet non-detection and unresolved delivery.; Retain spatial association and explicitly hypothetical facilitation.; Retain temporal transcript profiles without absolute output or transfer inference.; Retain positive B12-limited growth rescue and the supplementation control.

• Retain simultaneous positive endpoints and reported division of labor, not obligatory reciprocal dependence.; Retain SIP-associated EET assignment with incomplete genus-specific causality.; Retain reported diazotroph assignment, not individually quantified fixation.; Retain positive 15N2 incorporation and net ammonium accumulation at enrichment scope.; Retain positive current, cytochrome inhibitor evidence and labeled protein without a new nitrogen-to-current causal claim.

• Retain MAG-associated hypoxic methane oxidation without exclusive genus attribution.; Retain alternative proposed EET routes, not an obligatory serial partner chain.; Retain positive chromium removal and inhibition coupling, not omics-proven mediation.

• Read all four whole records,18 original nodes and12 arrows. Read three complete public primary bodies/Methods/captions and the EFPC MAG table, plus complete primary abstracts for both methane studies. Public publisher requests failed; no access-control bypass. No separate supplements, original images, raw data or executable models audited.

• EFPC is two depths from one core and28 MAGs, not a controlled Hg-selection experiment or complete seven-phylum community. Preserve the sampled genomic observations and author selection interpretation but qualify its causal link to resistance capacity. Do not infer niche partitioning from functional annotations.

• EFPC methylation potential is explicit prior-study environmental background, not measured hgcAB or flux in the28 MAGs. The removed selection-to-methylation arrow is not retargeted to a invented pathway. The independent methanogen culture study remains positive comparative context: eight of nine strains methylated above matched controls, while fused-hgcAB M.methylutens did not. Do not silently credit canonical Thermoproteota with those external methanogen results.

• Preserve27/28 putative metal-resistance/ATPase annotations and17/28 Se-assimilatory annotations without measured resistance, expression, uptake or community persistence. Eisenbacteria is an explicitly represented subset; Rokubacteria is source-mentioned but not added through an unverified canonical mapping. No selenium-to-mercury arrow invented.

• Syn7002 salinity-associated Microcystis disappearance and later relative sorting are real observations. They are not a tested interspecies competition mechanism, proof of PseTH extinction or absolute viable growth. Remove three assembly/analysis-order arrows without deleting the observations. Preserve source-inoculum versus stable-partner distinctions and prior genus grounding.

• Syn7002 coculture growth rescue and B12-positive controls remain positive results under B12-free BG11. Do not turn uncertainty about the mechanism into absence of benefit. Washed precultures do not by themselves establish zero carryover or intracellular stores. Growth/absorbance is not a direct photosynthetic-flux assay or reciprocal-fitness test.

• MesTH B12 provision, proximity-facilitated transfer and biosynthetic/transport contribution remain source-consistent hypotheses with direction and biological mechanism stated. The day20 pellet LC-MS/MS non-detection is not an extracellular measurement or proof of rapid uptake. SEM rods are not cell-resolved identity or a contact-requirement test. No donor perturbation or delivery route was selectively isolated.

• Figure4 transcript values are fold changes relative to an initial stage, not absolute cross-species B12 output or matched monoculture induction. Retain positive temporal transcriptional observations; nitrogen-related expression is not direct fixation/assimilation. Separate TableS1 was not read and its numerical assay limits are not invented.

• Methane MFC isotope results are stronger than ammonium accumulation alone: retain15N2-derived biomass13.55%,aqueous ammonium7.15%,0.22+/-0.01mg/L over30days. Retain1.17+/-0.18mA and78.1% Coulombic efficiency. Whole-enrichment outcomes are not six separately proven fixation or electrode-transfer phenotypes.

• MFC DNA-SIP guild assignments remain attributed as reported. Qualify both guild-to-endpoint arrows rather than erasing positive isotope and inhibitor evidence. Raman15N in cytochrome shows incorporation, not a selective causal test that fixation increases current. No obligatory reciprocal dependence, exclusive route, new methane node or nitrogen-to-current arrow claimed.

• Methane-CrVI retains maximum20.63mg/L/d removal and the positive inhibition result linking methane oxidation to reduced CrVI reduction. MAG-assigned Methylocystis6.30% is not exclusive taxon flux. Hypoxic aerobic methanotrophy is not automatically oxygen-independent oxidation.

• CrVI source proposes cytochrome/pilus routes or partner-associated transfer, not one proven serial chain. Keep twoPARTIAL arrows; inhibitor specificity and route-specific controls remain unavailable. Differential quorum-sensing/ABC/porin expression is not selective mediation. Chromate is the preserved canonical representation, not exact challenge-salt validation. Three named genera are a subset, not a defined three-isolate consortium.

• All changed top-level fields are graph/discussions/curation_history only. Verify raw preservation of non-graph blocks,456 other records and920 caches. Preserve upstream id001 aliases for CrVI engineering/taxonomy/environment evidence while detaching changed graph evidence. Exactly one append-only history/event per record, all discussion anchors resolve.

• Measure both-root participant census unchanged460/391/123/268/1507/1240. Add EFPC to exact participant USERS registry only; no taxonomy or auditor-rule changes. All44 network warnings match baseline exactly. Coarse solely-rule counts are not proof of member-resolved mechanisms or precise participant credit.

• Actual schema/strict/terms/references/snippets/history, inventory/rank/network, repeat-render and combined regression outputs retained with hashes. Exact description parser covers456 pages, not browser screenshots. A preflight lint complaint about the new test lambda was fixed before the recorded full run; all recorded final gates refer to the corrected test. Post-commit docs-current remains a separate gate.

• Deduplication includes886 all-state issue titles/bodies and23 scoped ignored/hidden local matches. Matching issue bodies#713,#650,#583,#314,#16 read, not all PR comments/historical local matches. Repairs#1596-#1599 addressed but OPEN until protected-main merge; metadata#1600 remains OPEN afterward. Self-review is not independent approval or whole-corpus completion.

634 passed in 259.03s (0:04:19); seven new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 70 record snippets match selected caches;23 graph excerpts independently match fresh primary text with whitespace-only normalization.920 caches unchanged. CLI Total checks counts reported issues, not executed checks. Cache MATCH is not scientific entailment or historical provenance certification. All920 caches unchanged;23 graph excerpts independently match fresh primary text after whitespace normalization. #1600 metadata remains OPEN. Two methane full texts unavailable. Broader #476/#1091/#1095 source limitations persist.

All18 nodes retained;8 arrows qualified and4 cross-study/workflow arrows removed. No new structure or provider spend. Canonical taxonomy and raw non-graph blocks preserved, not recertified.456 other records unchanged. Zero structural defects;all44 baseline network warnings preserved exactly. Coarse scope census remains460 records,391 with community-level nodes,123 mixed,268 community-only,1507 taxa and1240 solely-rule count; no taxonomy or auditor-rule change. This census does not measure exact participant credit.

Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Post-commit just check-docs-current passed with clean tree; log SHA256 5b9f12481362cbfcab8f60bb9d1aee0904f858ba06c4c7b701fbfa8991d3d359. Every-node/every-arrow decisions,39 actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch70. Corpus224 reviewed /212 pending /24 needs_research: unfinished, not independent approval. Metadata #1600 remains OPEN.

Protected-main merge pending.

[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, 44 warning across 16 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)

East_River_Floodplain_Core_Microbiome
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidobacteriota floodplain representatives' has no interactions
  [warning] DISCONNECTED: Taxon 'Nitrospirae core floodplain members' has no interactions

Total: 2 issues (0 error, 2 warning)

GLBRC_UFMP_Fermentation_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'RUG023 sp. (MAG SPH2)' has no interactions

Total: 1 issues (0 error, 1 warning)

KBase_Models_for_Zahmeeth_Original_PLOS
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Klebsiella' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas fluorescens' has no interactions

Total: 2 issues (0 error, 2 warning)

Lake_Washington_Methane_Oxygen_Methylotroph_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylosarcina' has no interactions

Total: 1 issues (0 error, 1 warning)

Lotus_LjSC3
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Burkholderiaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule210' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule215' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule218' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Oxalobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Phyllobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonadaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobiaceae bacterium' has no interactions

Total: 9 issues (0 error, 9 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 integration review at exact head 2e667fe6a56cbc78fd0b64026c8e5b614eab05eb. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 7c62dbeb49b807960bfe3bc82765e91e98125d4c, 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 d90ff05040b75614147371616c14b7818515344c2454d9f3588323994337af25). 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 20dd6ba0f88c333e1c73b71d370c988a60dbf965
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 1b9ee18910bf8271827b6d33e1f1053a5f6044f3.
The batch-owned binary patch is byte-identical
(SHA-256 d90ff05040b75614147371616c14b7818515344c2454d9f3588323994337af25); 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 3563cc9dfb84ee3204b63d9f244d2f29d48967b6. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 20dd6ba0f88c333e1c73b71d370c988a60dbf965, 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 d90ff05040b75614147371616c14b7818515344c2454d9f3588323994337af25). 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 9579ad0a53d5fa1376ad89bc23c5c2422ac235b5.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 d90ff05040b75614147371616c14b7818515344c2454d9f3588323994337af25.
Tree 796e343ba54edf834892014401c9d3cbb5a1359c matches the independently computed clean merge.
Compared with historical tree b18e29b31dd1c066950a9d446bcecd9bf4e342b0, 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 ab810860db6003f7bac1f7094d2f2b529c00198f 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.