Bound nitrogen mediation and separate gallium bioleaching evidence (batch73)

[realmarcin]

Scope

Closes #1614.
Closes #1615.
Closes #1616.
Research #1617 and non-graph #1618 remain OPEN after graph repair merge.

• Retain supported selective mutualistic growth; distinguish shared growth from resolved organic-carbon identities or fluxes.; Retain urea cross-feeding as convergent PARTIAL mechanism, including positive release/growth assays and explicit donor uncertainty.; Correct the responding organism and motility process; retain experimental signaling, natural-versus-culture and high-GABA boundaries.
• Reviewed unchanged: the single community-level net respiration/MBC node, four canonical participants and both OPEN mechanism/carbonate discussions already preserve the primary-source boundaries. No member-resolved causal arrow is supported by the measured aggregate outcomes.
• Retain nitrogen-cycle capability; name existing grouped participants and bound its contribution to AN reduction.; Retain positive AN reduction and plant-alone comparator; qualify removal-to-growth mediation as HYPOTHESIZED.; Retain live-versus-dead biomass gains and enrichment without converting them to strain-resolved uptake or mutual fitness.
• Retain reported sulfuric-acid production with explicit source limits; remove unsupported fitness and unbalanced chemistry.; Replace single-strain ferric evidence with the existing exact-consortium excerpt; no pH niche or equal-contribution claim.; Retain joint acid/ferric production, not untested synergy or optimized ratios; preserve the production-to-recovery connection.; Recast procedural design as the measured non-contact recovery endpoint, preserve the contact comparison, and defer adsorption extension.

Adversarial Review

• Baseline before research; read all four whole records and every original node/arrow, including the one-node zero-edge mineral-litter graph. Signaling, urea and mineral-litter primary main bodies, captions and embedded tables read. No separate supplements, raw-data or figure-pixel audit claimed. Native-cyanosphere context was retrieved but not used to expand the exact pair.
• Retain demonstrated selective carbon-for-nitrogen growth rather than erasing mutualism because the carrier is unresolved. CO2 is a fixation substrate, not the asserted transferred organic-carbon molecule.
• Urea evidence includes increased extracellular release, coordinated exact-pair expression and supplied-urea growth at5 but not2micromolar. The primary explicitly acknowledges unresolved absolute donor attribution; rates use total coculture biomass. Do not convert pool measurements into isotope-traced transfer or exclusive-carrier proof.
• The signaling source experimentally perturbs compounds and cyanosphere abundance. Preserve direct cyanobacterial motility/bundling causality. Correct the arrow that previously implied Massilia recruitment: the observed responding organism is Microcoleus. Remove true-chemotaxis annotation because PCC9802 showed no true Glu chemotaxis.
• Distinguish natural bundles from the long-cultured strain with diminished reversal response. Retain concentration-dependent GABA effects, including high-GABA destabilization, rather than asserting monotonic improvement. Nutrient-exchange optimization remains a mechanistic interpretation. No untested feedback self-loop is added.
• Mineral-litter graph is already appropriately aggregate: net respiration/MBC, four canonical participants, unpartitioned carbonate CO2 and unmeasured enzyme-sorption/stabilization mechanisms. Preserve the record byte-for-byte and closed1011/1012 fixes; no fabricated missing edge or gratuitous curation event.
• Preserve Miscanthus positive AN reductions24.8% alone,32.6% with plants and25.5% plants alone. Preserve shoot/root gains39.8%/49.7% relative to dead SynCom. Nitrogen-cycle capability supports a contribution, but no quantitative partition or selective removal-to-growth mediation follows from the abstract.
• Plant growth can also increase nitrogen uptake; enrichment of seven strains is not a direct causal mediation experiment. Name the five canonical grouped entries without claiming ten resolved strain identities or equal member activity. Preserve the Sinomonas taxon mismatch for metadata1618.
• Gallium2019 source is an adapted A.ferrooxidans-only system at20g/L, not the2025 three-member15g/L system. Remove it from exact-consortium graph support. Use existing2025 component excerpts with PARTIAL provenance boundaries; do not equate a full-labeled cache with a complete primary article.
• Preserve joint acid/ferric production and the direct production-to-non-contact-recovery link. Remove unbalanced GaN/Cu equations, pH niche partition, untested synergistic/optimal ratios, mutualism/commensalism and continuous recycling. Move the terminal node from procedural design to its already-reported recovery endpoint, without adding topology.
• Preserve99.5% non-contact and45.59% contact gallium recovery and reported adsorption up to21.43%. Existing correct CHEBI84043 resolves the graph atom/ion confusion without asserting measured aqueous speciation. Separate B-EPS component roles and total-Ga accounting remain research1617.
• One-community Edison LITERATURE dry run completed, zero provider calls or credits. Scoped authorization question remains pending; do not treat a preselected answer or earlier generic permission as this run authorization. No new adsorption structure. Gallium remains needs_research.
• Guarded dry run caught a capitalized This where the primary abstract has lowercase this; corrected only the graph snippet and revalidated. Other raw sections and YAML anchors remain byte-preserved. Three append-only curation events/histories;457 records and920 caches unchanged. Canonical taxonomy and auditor rules unchanged.
• Actual schema, strict, term, references, snippets, history, both-root inventory/network/rank, repeat rendering, regression and lint outputs are retained with digests. Connectivity census unchanged. All44 pre-existing warnings preserved exactly; zero structural defects. Exact descriptions parsed across456 generated pages, not browser screenshots.
• Dedup901 all-state issue titles/bodies and ignored/hidden scoped local search; read1011,1012,596. Broader source-filename search had permission errors and truncated output, so it does not establish global absence. Scoped repository filename/PDF search included ignored files. No exhaustive historical PR-comment audit claimed.
• Tasks1614-1616 remain OPEN until protected-main merge; research1617 and metadata1618 remain OPEN afterward. Self-adversarial COMMENT is not independent approval. Postcommit docs-current is a separate publication gate; full corpus remains unfinished.
• The gallium full-record reference gate is NOT green: the untouched duration quotation at environmental_factors[2].evidence[0].snippet raises one identical error on parent and repaired records. Preserve the initial failed check, explicit baseline comparison and issue1618 follow-up. No graph reference errors and no new validator regression. Do not edit a faithful quoted snippet merely to satisfy a cache extraction boundary.

Verification And Output Records

655 passed in 204.54s (0:03:24); seven new focused tests. Schema, strict, term, snippet and history checks passed. Gallium full-record reference validation is NOT fully green: one unchanged non-graph quotation error reproduces identically on the parent and repaired records (exit1), tracked in #1618. No graph-reference errors; the other three record reference validators exit0. Gallium reference validation is NOT fully passed: one unchanged error at environmental_factors[2].evidence[0].snippet reproduces identically on the parent record (both exit1); tracked in1618. Graph reference errors are zero. Other three record reference validators exit0. CLI Total checks counts reported issues, not executed checks. Cache MATCH is not entailment or provenance authentication. All17 graph excerpts match selected caches;13 match fresh primary XML/abstracts with whitespace-only normalization, one gallium abstract sentence was visually matched to publisher-indexed text, and three gallium component excerpts remain provenance-limited. All920 caches unchanged, not recertified. Research1617 and metadata1618 remain OPEN.

All11 original nodes and7 arrows retained. Three records repaired; mineral-litter reviewed byte-for-byte unchanged. Positive mutualistic growth, urea release/growth, causal cyanobacterial signaling, plant gains and gallium recovery remain. No new structure or paid provider run. One-community Edison LITERATURE dry run completed; scoped approval pending. Gallium stays needs_research for adsorption/source provenance #1617. Non-graph #1618 remains OPEN.

All457 unchanged records (including mineral-litter),920 caches and raw non-graph blocks verified. Canonical taxa/auditor rules unchanged. Zero structural defects; all44 baseline warnings preserved exactly. Both-root connectivity census unchanged:460 records,393 community-level,125 mixed,268 community-only,1511 existing taxa in community-scope records and1240 solely-rule count. Grouped participants are not resolved strain contributions.

Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Postcommit just check-docs-current passed with clean tree; log SHA256 55fc25a2b20c2737f46b572029da0a58d87355108985a1d192d9bf50e68d8a03. Every-node/every-arrow decisions,40 actual check outputs/digests, the explicit baseline reference exception and self-adversarial review are committed under reports/causal_graph_review, batch73. Final focused rerun:16 passed. Corpus:235 reviewed,200 pending,25 needs_research. Not independent approval or corpus completion.

Source Limits

• All11 original nodes and7 arrows retained; three node names corrected with exact targets/anchors. Mineral-litter graph reviewed unchanged, not overlooked. Three record edits and histories only.
• Baseline covered460 records and920 caches in both roots before paper research. All44 pre-existing warnings remain; source quality is separate from structural validity.
• Full primary main bodies, captions and embedded tables read for signaling, urea and mineral-litter. Separate supplements, original figure pixels and raw data not audited. Natural cyanosphere context source retrieved but not fully reviewed or used to extend the exact pair.
• Trading and Miscanthus supported by fresh primary abstracts. Trading XML returned500 after three attempts and public PMC HTML presented reCAPTCHA. Miscanthus metadata lists subscription-required full text. Abstract-only access is not evidence no selective controls exist.
• Gallium2025 primary abstract visually matched against publisher-indexed text. Its cached selected full-text excerpts are not a complete article or independently verified provenance; three graph excerpts remain explicitly PARTIAL. Full publisher access returned403. Earlier broad ignored-file search had permission errors/truncated output; narrower CommunityMech ignored/hidden filename/PDF search found no gallium PDF, not proof none exists anywhere.
• All17 retained graph excerpts match selected caches;13 also match freshly retrieved primary XML/abstract by whitespace normalization, plus one gallium abstract sentence visually matched to indexed publisher text. Three gallium component excerpts have unresolved provenance, tracked in1617; do not call all17 independently authenticated.
• Keep positive carbon-for-nitrogen growth, coculture urea release and low-concentration urea growth. Donor origin and exclusive carrier remain bounded. Keep causal cyanobacterial signaling while distinguishing true chemotaxis, natural-bundle reversals and high-GABA destabilization from unmeasured exchange optimization.
• Mineral-litter aggregate net respiration/MBC and two existing discussions already capture unpartitioned carbonate CO2 and unmeasured mineral mechanisms. Preserve closed1011/1012 fixes; no fabricated member-level arrows or gratuitous record history.
• Keep Miscanthus AN reductions and dead-inoculum biomass comparator. Removal-to-growth mediation is HYPOTHESIZED; plant uptake can also depend on growth. Five canonical grouped entries do not resolve ten strain contributions; no taxonomy or audit-rule changes.
• Gallium2019 abstract explicitly concerns adapted A.ferrooxidans alone, removed from exact-consortium graph evidence. Keep joint production and positive non-contact output; no unsupported synergy, pH partition, mutualism/commensalism, balanced-chemistry invention or recycling. Existing Ga ion identifier replaces atom/ion confusion without claiming aqueous speciation.
• Gallium adsorption extension remains needs_research in1617. One-record Edison LITERATURE dry run completed at zero cost; scoped authorization question pending, no paid submission and no new node/arrow. Earlier denied or pending authorizations are unchanged.
• Dedup read901 all-state issue titles/bodies with33 ignored/hidden local matches and prior1011/1012/596 bodies. No exhaustive historical PR-comment audit claimed. Tasks1614-1616 stay OPEN until protected-main merge;1617 research and1618 metadata remain OPEN afterward.
• All920 caches and raw non-graph blocks preserved, not recertified;457 records unchanged including reviewed mineral-litter. Self-adversarial COMMENT is not independent approval; corpus work is unfinished.

Dependency

Draft depends on #1613. 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 b46d627; not independent approval.

Repairs #1614-#1616 addressed; research #1617 and non-graph #1618 unresolved.

• Retain supported selective mutualistic growth; distinguish shared growth from resolved organic-carbon identities or fluxes.; Retain urea cross-feeding as convergent PARTIAL mechanism, including positive release/growth assays and explicit donor uncertainty.; Correct the responding organism and motility process; retain experimental signaling, natural-versus-culture and high-GABA boundaries.

• Reviewed unchanged: the single community-level net respiration/MBC node, four canonical participants and both OPEN mechanism/carbonate discussions already preserve the primary-source boundaries. No member-resolved causal arrow is supported by the measured aggregate outcomes.

• Retain nitrogen-cycle capability; name existing grouped participants and bound its contribution to AN reduction.; Retain positive AN reduction and plant-alone comparator; qualify removal-to-growth mediation as HYPOTHESIZED.; Retain live-versus-dead biomass gains and enrichment without converting them to strain-resolved uptake or mutual fitness.

• Retain reported sulfuric-acid production with explicit source limits; remove unsupported fitness and unbalanced chemistry.; Replace single-strain ferric evidence with the existing exact-consortium excerpt; no pH niche or equal-contribution claim.; Retain joint acid/ferric production, not untested synergy or optimized ratios; preserve the production-to-recovery connection.; Recast procedural design as the measured non-contact recovery endpoint, preserve the contact comparison, and defer adsorption extension.

• Baseline before research; read all four whole records and every original node/arrow, including the one-node zero-edge mineral-litter graph. Signaling, urea and mineral-litter primary main bodies, captions and embedded tables read. No separate supplements, raw-data or figure-pixel audit claimed. Native-cyanosphere context was retrieved but not used to expand the exact pair.

• Retain demonstrated selective carbon-for-nitrogen growth rather than erasing mutualism because the carrier is unresolved. CO2 is a fixation substrate, not the asserted transferred organic-carbon molecule.

• Urea evidence includes increased extracellular release, coordinated exact-pair expression and supplied-urea growth at5 but not2micromolar. The primary explicitly acknowledges unresolved absolute donor attribution; rates use total coculture biomass. Do not convert pool measurements into isotope-traced transfer or exclusive-carrier proof.

• The signaling source experimentally perturbs compounds and cyanosphere abundance. Preserve direct cyanobacterial motility/bundling causality. Correct the arrow that previously implied Massilia recruitment: the observed responding organism is Microcoleus. Remove true-chemotaxis annotation because PCC9802 showed no true Glu chemotaxis.

• Distinguish natural bundles from the long-cultured strain with diminished reversal response. Retain concentration-dependent GABA effects, including high-GABA destabilization, rather than asserting monotonic improvement. Nutrient-exchange optimization remains a mechanistic interpretation. No untested feedback self-loop is added.

• Mineral-litter graph is already appropriately aggregate: net respiration/MBC, four canonical participants, unpartitioned carbonate CO2 and unmeasured enzyme-sorption/stabilization mechanisms. Preserve the record byte-for-byte and closed1011/1012 fixes; no fabricated missing edge or gratuitous curation event.

• Preserve Miscanthus positive AN reductions24.8% alone,32.6% with plants and25.5% plants alone. Preserve shoot/root gains39.8%/49.7% relative to dead SynCom. Nitrogen-cycle capability supports a contribution, but no quantitative partition or selective removal-to-growth mediation follows from the abstract.

• Plant growth can also increase nitrogen uptake; enrichment of seven strains is not a direct causal mediation experiment. Name the five canonical grouped entries without claiming ten resolved strain identities or equal member activity. Preserve the Sinomonas taxon mismatch for metadata1618.

• Gallium2019 source is an adapted A.ferrooxidans-only system at20g/L, not the2025 three-member15g/L system. Remove it from exact-consortium graph support. Use existing2025 component excerpts with PARTIAL provenance boundaries; do not equate a full-labeled cache with a complete primary article.

• Preserve joint acid/ferric production and the direct production-to-non-contact-recovery link. Remove unbalanced GaN/Cu equations, pH niche partition, untested synergistic/optimal ratios, mutualism/commensalism and continuous recycling. Move the terminal node from procedural design to its already-reported recovery endpoint, without adding topology.

• Preserve99.5% non-contact and45.59% contact gallium recovery and reported adsorption up to21.43%. Existing correct CHEBI84043 resolves the graph atom/ion confusion without asserting measured aqueous speciation. Separate B-EPS component roles and total-Ga accounting remain research1617.

• One-community Edison LITERATURE dry run completed, zero provider calls or credits. Scoped authorization question remains pending; do not treat a preselected answer or earlier generic permission as this run authorization. No new adsorption structure. Gallium remains needs_research.

• Guarded dry run caught a capitalized This where the primary abstract has lowercase this; corrected only the graph snippet and revalidated. Other raw sections and YAML anchors remain byte-preserved. Three append-only curation events/histories;457 records and920 caches unchanged. Canonical taxonomy and auditor rules unchanged.

• Actual schema, strict, term, references, snippets, history, both-root inventory/network/rank, repeat rendering, regression and lint outputs are retained with digests. Connectivity census unchanged. All44 pre-existing warnings preserved exactly; zero structural defects. Exact descriptions parsed across456 generated pages, not browser screenshots.

• Dedup901 all-state issue titles/bodies and ignored/hidden scoped local search; read1011,1012,596. Broader source-filename search had permission errors and truncated output, so it does not establish global absence. Scoped repository filename/PDF search included ignored files. No exhaustive historical PR-comment audit claimed.

• Tasks1614-1616 remain OPEN until protected-main merge; research1617 and metadata1618 remain OPEN afterward. Self-adversarial COMMENT is not independent approval. Postcommit docs-current is a separate publication gate; full corpus remains unfinished.

• The gallium full-record reference gate is NOT green: the untouched duration quotation at environmental_factors[2].evidence[0].snippet raises one identical error on parent and repaired records. Preserve the initial failed check, explicit baseline comparison and issue1618 follow-up. No graph reference errors and no new validator regression. Do not edit a faithful quoted snippet merely to satisfy a cache extraction boundary.

655 passed in 204.54s (0:03:24); seven new focused tests. Schema, strict, term, snippet and history checks passed. Gallium full-record reference validation is NOT fully green: one unchanged non-graph quotation error reproduces identically on the parent and repaired records (exit1), tracked in #1618. No graph-reference errors; the other three record reference validators exit0. Gallium reference validation is NOT fully passed: one unchanged error at environmental_factors[2].evidence[0].snippet reproduces identically on the parent record (both exit1); tracked in1618. Graph reference errors are zero. Other three record reference validators exit0. CLI Total checks counts reported issues, not executed checks. Cache MATCH is not entailment or provenance authentication. All17 graph excerpts match selected caches;13 match fresh primary XML/abstracts with whitespace-only normalization, one gallium abstract sentence was visually matched to publisher-indexed text, and three gallium component excerpts remain provenance-limited. All920 caches unchanged, not recertified. Research1617 and metadata1618 remain OPEN.

All11 original nodes and7 arrows retained. Three records repaired; mineral-litter reviewed byte-for-byte unchanged. Positive mutualistic growth, urea release/growth, causal cyanobacterial signaling, plant gains and gallium recovery remain. No new structure or paid provider run. One-community Edison LITERATURE dry run completed; scoped approval pending. Gallium stays needs_research for adsorption/source provenance #1617. Non-graph #1618 remains OPEN.

All457 unchanged records (including mineral-litter),920 caches and raw non-graph blocks verified. Canonical taxa/auditor rules unchanged. Zero structural defects; all44 baseline warnings preserved exactly. Both-root connectivity census unchanged:460 records,393 community-level,125 mixed,268 community-only,1511 existing taxa in community-scope records and1240 solely-rule count. Grouped participants are not resolved strain contributions.

Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Postcommit just check-docs-current passed with clean tree; log SHA256 55fc25a2b20c2737f46b572029da0a58d87355108985a1d192d9bf50e68d8a03. Every-node/every-arrow decisions,40 actual check outputs/digests, the explicit baseline reference exception and self-adversarial review are committed under reports/causal_graph_review, batch73. Final focused rerun:16 passed. Corpus:235 reviewed,200 pending,25 needs_research. Not independent approval or corpus completion.

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 b960ecc335df961561222aba48121baa5e9e7853. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head b46d6272aa24de28b7e31995b74f7a306b387fff, 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 7e49f46dc03b220ddc820a7cfe55fa1473d60839cf75cb8a0ad4a993e52f3405). 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 e174bf705065b209400579cc62819404ef563326
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 97af02e7e359195bd4b610fcd3e7c4997c61bc2c.
The batch-owned binary patch is byte-identical
(SHA-256 7e49f46dc03b220ddc820a7cfe55fa1473d60839cf75cb8a0ad4a993e52f3405); 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 252534b3fa6998cf10e2b9ead07c2f2b080758b3. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head e174bf705065b209400579cc62819404ef563326, 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 7e49f46dc03b220ddc820a7cfe55fa1473d60839cf75cb8a0ad4a993e52f3405). 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 3b77c0e30caec3f7a08b3058e0def230ef1da7c3.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 7e49f46dc03b220ddc820a7cfe55fa1473d60839cf75cb8a0ad4a993e52f3405.
Tree 1dea7247f62b6033c24b02ad5281d5fbe4b8d06d matches the independently computed clean merge.
Compared with historical tree 18ee7bd281c440f4ec9a2657fc307cf259c20e59, 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 8afb66c357834d8cd98e769d46b6d10d3d9789d5 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.