Qualify cross-study and omics claims in four community graphs (batch106)

[realmarcin]

Scope

Closes #1829.
Closes #1830.
Closes #1831.
Closes #1832.
Non-graph #1833 remains open.

• Retain aggregate suppression, removing reciprocal-competition typing not established by aggregate endpoints.; Retain study-specific contact-associated fungal suppression without reciprocal-competition typing or a cross-study mechanism arrow.; Retain the authors mutualism proposal as HYPOTHESIZED/PARTIAL, separating proteomic inference from aggregate biomass.; Retain the source-supported scaffold facilitation without importing another study requirement.; Retain context-dependent observations without universal mutualism or a cross-study hyphal-requirement arrow.; Retain transcript and ontology associations; remove demonstrated-virulence/genotype and colonization interpretations.
• Retain archaeal encoded potential and transcripts with canonical participant scope; remove unsupported syntrophy and unrelated catalog evidence.; Retain bacterial encoded potential and transcripts with canonical participant scope; remove categorical cross-feeding and the acetate-to-methylotrophic route error.; Retain source-proposed fen niche partitioning and its existing functional direction as HYPOTHESIZED/PARTIAL, not measured uptake or reduced competition.; Retain habitat-associated transcript patterns with computational provenance; remove niche typing and activity-restatement arrows.
• Retain exact-mixture non-antagonism and aggregate biomass, removing reciprocal-mutualism typing and excluding other source formulations.; Retain herbicide-catabolism gene detection as genetic potential, with the existing outcome direction HYPOTHESIZED/PARTIAL.; Retain observed atrazine growth/removal without mineralization or reciprocal-benefit claims; qualify the existing toxicity direction.; Retain positive tested phytotoxicity reversal without claiming its sole causal mediator or universal detoxification.
• Retain field perturbation input with its existing relative-abundance direction HYPOTHESIZED/PARTIAL, not aggregate restructuring as a proven mediator.; Retain observed relative-abundance decline without inferring absolute loss, mortality or fitness.; Retain CODH-associated genomic potential with computational provenance, not a demonstrated physiological switch.; Retain potential carbon/electron-flow implications and their existing direction as HYPOTHESIZED/PARTIAL, not measured flux.

Adversarial Review

• Whole original targets and all changed graph/discussion diffs reviewed. All19 original nodes and10 directions have dispositions: retain18nodes and5qualified existing directions, remove1analysis-workflow node and5cross-study/wrong-route/restatement arrows, rename8nodes. No new topology or provider spend.
• Challenge removal versus lost evidence: retain the six separate Staphylococcus-Candida observations, mire encoded potential/expression/metabolite findings, exact four-member pesticide outcomes and aquifer relative-abundance/genomic-potential findings. Retain qualified source hypotheses rather than deleting all topology or rejecting positive results.
• Staphylococcus-Candida: species composition is not one fixed experimental system. Remove cross-study mechanism/requirement arrows; aggregate biomass and one-way inhibition do not demonstrate reciprocal competition. Preserve copper authors mutualism as HYPOTHESIZED/PARTIAL and direct scaffold facilitation. RNA/ontology associations do not establish virulence, altered genotype or colonization. No new pathogen enhancement procedures, genetic designs, strain-selection advice or partner mechanisms.
• Mire: source distinguishes acetate-to-acetoclastic routing from methylotrophic methanogenesis. Remove the wrong-route arrow without importing another mechanism. Product-removal feedback and traced exchange are not established by omics co-occurrence. Retain source-proposed fen niche partitioning and its existing direction HYPOTHESIZED/PARTIAL, not reduced competition or direct uptake. Preserve genomic/transcript/metabolite support and canonical identity-only scope; the gradient remains an observation, not its own causal driver.
• Pesticide: non-antagonism and greater mixed biomass do not establish reciprocal benefit. Preserve exact A2-A5-A11-M7 observations without transferring six-member immobilized-culture results. Gene detection supports potential, not expression/flux; removal is not mineralization. Keep both existing directions HYPOTHESIZED/PARTIAL because the accessible abstract does not isolate gene activity or parent depletion as mediators. Positive phytotoxicity endpoints remain.
• Aquifer: remove the genome-resolution workflow node and preserve prior analysis-edge repair. Field perturbation is the upstream abiotic input, not aggregate restructuring as a demonstrated mediator. Relative abundance is not absolute loss or fitness. CODH analysis supports inferred potential, not a physiological switch; carbon/electron flow is a source implication, not measured flux. Keep both existing directions qualified and do not invent methods.
• Twenty-nine graph and seven discussion quotations match fresh primary text and unchanged caches. Eleven independent primary retrievals: nine whole abstracts plus bounded mire2023/pesticide2013 main-text coverage. Available Staphylococcus-Candida PMCID leads were not read; copper cache PMCID differs from fresh metadata. Failed aquifer/pesticide publisher requests were Internal Error, not verified HTTP403. No global full-text absence claim, bypass, cache import, supplement/figure-pixel or raw-data certification.
• Four guarded writes and four append-only histories;456 other records/all923 caches and prior history/decision files byte-identical. Non-graph raw blocks unchanged. Identity-only mire scopes do not change the global census because the whole-community gradient observation remains. No census threshold, schema or runtime-rule changes. The pre-write guard rejected unsupported discussion provenance fields; provenance remains on interaction evidence without changing the shared schema.
• Eight focused tests and959 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks and four histories validate. Network equals56 baseline warnings with zero structural defects. Deterministic rendering and exact HTML parser cover456pages/1372descriptions/545arrows, not screenshots. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked.
• Repairs1829-1832 addressed but remain open until protected-main merge; non-graph1833 remains open. Prior691/763 and aquifer analysis repairs preserved. The caches requested by764 are present, so no duplicate cache issue/import. Existing license949, loader1703, DOIcache1091, denied and unansweredEdison scopes are not resolved. Self-review is not independent approval; no artificial CI, protection bypass or premature cleanup.
• Corpus338reviewed/72pending/50needs_research is not completion. Postcommit docs-current and exact-head publication require separate receipts, not preasserted here.

Verification And Output Records

959 passed in 793.39s (0:13:13); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; four append-only histories validated. 41 recorded gate outputs/digests. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Explicit-runtime non-incremental mypy passed. All36 reviewed graph/discussion quotations match fresh primary text and existing caches; literal matching is not entailment.

Eighteen nodes remain, with eight renames; five qualified existing directions remain. One analysis-workflow node and five cross-study, wrong-route or restatement arrows are removed. All four targets changed; 456 other records, all923 caches, taxonomy and non-graph raw blocks preserved. Corpus338reviewed/72pending/50needs_research. Network56existingwarnings/zero structural defects. Mire archaeal/bacterial observations gain canonical identity-only participant scope; the community-level census and its thresholds are unchanged.

Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with four append-only history records. Postcommit docs-current passed clean, SHA256 d2a4d50906e8bde6f7fe0e459780343a94bfc848ec927f3c4c90061faeb92b84. Deterministic rendering and HTML parser checks are not screenshots. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.

Staphylococcus-Candida, mire2018, pesticide2026 and aquifer independent evidence is abstract-bounded. Mire2023 and pesticide2013 primary-body coverage is bounded, not whole-paper/supplement/figure/raw-data certification. No new topology or Edison spend. Non-graph1833 stays open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.

Source Limits

• Fresh both-root baseline before source reads: 460 records, 923 caches, 56 existing warnings, zero structural defects. Four whole records and all19 original nodes/10 directions reviewed;18 nodes and five qualified existing directions retained, one workflow node and five arrows removed, eight renames. No new topology or Edison submission/spend.
• Eleven primary sources independently retrieved. All nine abstract-only retrievals were read whole, including the six Staphylococcus-Candida studies, 2018 mire catalog, 2026 pesticide study and aquifer study. Available full-text leads were not fetched for Staphylococcus-Candida: fresh PMCID leads exist for three and the pre-existing copper cache lists PMC13306210 despite missing fresh PMCID metadata. This is an abstract-bounded metadata correction, not an assertion of full-text absence.
• Fresh EuropePMC full-body XML retrieved for mire2023 and pesticide2013. Mire abstract1-33, results/discussion238-477 and methods528-676 read; pesticide2013 results182-246 read. Other spans were indexed or not read, not whole-paper review. No figure-pixel, supplement, raw-data or full-pipeline certification. Mire CC BY4.0 and pesticide2013 CC BY3.0 metadata retained.
• Existing six Staphylococcus-Candida caches, pesticide2026, both aquifer caches and both lindane abstract caches read whole. Large mire2023, mire2018 and pesticide2013 caches used for bounded context and normalized claim matching, not exhaustive duplicated full-text review. Wiley aquifer and Elsevier pesticide2026 web requests returned Internal Error with no HTTP code reported; no bypass or global full-text-absence assertion. No cache imports, license949/loader1703/DOI-case1091 certification.
• Staphylococcus-Candida: retain six separate-study observations; remove cross-study arrows and categorical reciprocal competition/universal mutualism. Preserve the copper authors mutualism interpretation as HYPOTHESIZED/PARTIAL and source-supported scaffold facilitation. Transcript/ontology associations are not demonstrated virulence, genotype change or colonization. No new growth, biofilm, survival, resistance, virulence or colonization enhancement procedures, genetic designs, strain-selection advice or partner mechanisms.
• Mire: preserve encoded potential, transcripts and metabolite observations with canonical identity-only archaeal/bacterial scope and computational provenance. Remove unestablished syntrophic product-removal feedback and traced cross-feeding. Acetate supports an acetoclastic route, not the removed methylotrophic target; no replacement mechanism/node added. Preserve source-proposed fen niche partitioning and its existing direction as HYPOTHESIZED/PARTIAL; no measured substrate flux or competition reduction. Remove redundant habitat arrows and unrelated catalog support for specific syntrophy.
• Pesticide: retain the exact four-member non-antagonism, aggregate growth, gene detection, removal and phytotoxicity results. Remove reciprocal-mutualism typing and qualify both existing directions; gene presence is not expression/flux, removal is not mineralization or an isolated toxicity mediator. Do not transfer six-member immobilized-culture results or claim universal consortium superiority. Existing22840534/31430718 caches requested by open764 are present; no duplicate cache issue/import.
• Aquifer: remove only the genome-resolution workflow node and preserve prior2026-10-02 analysis-edge removal. Retain field perturbation and relative-abundance observation without absolute loss or fitness claims. Gene-based CO-oxidation potential and carbon/electron-flow implications receive computational provenance and HYPOTHESIZED/PARTIAL causal descriptions. No invented methods or measured flux.
• Graph issues1829-1832 addressed here and remain open until protected-main merge; non-graph1833 remains open. Fresh all-state title/body dedup matches294/691/763/764. Hidden/ignored local search excludes.git/docs/site/references_cache with relevant caches separately covered. PRs/comments not exhaustively searched. Non-graph role, abundance, placeholder taxonomy, habitat-note and substrate extrapolations remain separately scoped and byte-preserved, not certified.
• Four guarded writes and append-only histories;456 other records and all923 caches unchanged. Every unrelated raw block preserved. No schema/runtime/audit rule changes. Self-adversarial review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication not preasserted.

Dependency

Draft depends on #1828. Do not merge into the topic parent. Require exact-head checks and independent approval through protected main. Move dependents before deleting parent branches.

[realmarcin]

Source-based self-adversarial review at exact head 2d931ac; not independent approval.

• Retain aggregate suppression, removing reciprocal-competition typing not established by aggregate endpoints.; Retain study-specific contact-associated fungal suppression without reciprocal-competition typing or a cross-study mechanism arrow.; Retain the authors mutualism proposal as HYPOTHESIZED/PARTIAL, separating proteomic inference from aggregate biomass.; Retain the source-supported scaffold facilitation without importing another study requirement.; Retain context-dependent observations without universal mutualism or a cross-study hyphal-requirement arrow.; Retain transcript and ontology associations; remove demonstrated-virulence/genotype and colonization interpretations.

• Retain archaeal encoded potential and transcripts with canonical participant scope; remove unsupported syntrophy and unrelated catalog evidence.; Retain bacterial encoded potential and transcripts with canonical participant scope; remove categorical cross-feeding and the acetate-to-methylotrophic route error.; Retain source-proposed fen niche partitioning and its existing functional direction as HYPOTHESIZED/PARTIAL, not measured uptake or reduced competition.; Retain habitat-associated transcript patterns with computational provenance; remove niche typing and activity-restatement arrows.

• Retain exact-mixture non-antagonism and aggregate biomass, removing reciprocal-mutualism typing and excluding other source formulations.; Retain herbicide-catabolism gene detection as genetic potential, with the existing outcome direction HYPOTHESIZED/PARTIAL.; Retain observed atrazine growth/removal without mineralization or reciprocal-benefit claims; qualify the existing toxicity direction.; Retain positive tested phytotoxicity reversal without claiming its sole causal mediator or universal detoxification.

• Retain field perturbation input with its existing relative-abundance direction HYPOTHESIZED/PARTIAL, not aggregate restructuring as a proven mediator.; Retain observed relative-abundance decline without inferring absolute loss, mortality or fitness.; Retain CODH-associated genomic potential with computational provenance, not a demonstrated physiological switch.; Retain potential carbon/electron-flow implications and their existing direction as HYPOTHESIZED/PARTIAL, not measured flux.

• Whole original targets and all changed graph/discussion diffs reviewed. All19 original nodes and10 directions have dispositions: retain18nodes and5qualified existing directions, remove1analysis-workflow node and5cross-study/wrong-route/restatement arrows, rename8nodes. No new topology or provider spend.

• Challenge removal versus lost evidence: retain the six separate Staphylococcus-Candida observations, mire encoded potential/expression/metabolite findings, exact four-member pesticide outcomes and aquifer relative-abundance/genomic-potential findings. Retain qualified source hypotheses rather than deleting all topology or rejecting positive results.

• Staphylococcus-Candida: species composition is not one fixed experimental system. Remove cross-study mechanism/requirement arrows; aggregate biomass and one-way inhibition do not demonstrate reciprocal competition. Preserve copper authors mutualism as HYPOTHESIZED/PARTIAL and direct scaffold facilitation. RNA/ontology associations do not establish virulence, altered genotype or colonization. No new pathogen enhancement procedures, genetic designs, strain-selection advice or partner mechanisms.

• Mire: source distinguishes acetate-to-acetoclastic routing from methylotrophic methanogenesis. Remove the wrong-route arrow without importing another mechanism. Product-removal feedback and traced exchange are not established by omics co-occurrence. Retain source-proposed fen niche partitioning and its existing direction HYPOTHESIZED/PARTIAL, not reduced competition or direct uptake. Preserve genomic/transcript/metabolite support and canonical identity-only scope; the gradient remains an observation, not its own causal driver.

• Pesticide: non-antagonism and greater mixed biomass do not establish reciprocal benefit. Preserve exact A2-A5-A11-M7 observations without transferring six-member immobilized-culture results. Gene detection supports potential, not expression/flux; removal is not mineralization. Keep both existing directions HYPOTHESIZED/PARTIAL because the accessible abstract does not isolate gene activity or parent depletion as mediators. Positive phytotoxicity endpoints remain.

• Aquifer: remove the genome-resolution workflow node and preserve prior analysis-edge repair. Field perturbation is the upstream abiotic input, not aggregate restructuring as a demonstrated mediator. Relative abundance is not absolute loss or fitness. CODH analysis supports inferred potential, not a physiological switch; carbon/electron flow is a source implication, not measured flux. Keep both existing directions qualified and do not invent methods.

• Twenty-nine graph and seven discussion quotations match fresh primary text and unchanged caches. Eleven independent primary retrievals: nine whole abstracts plus bounded mire2023/pesticide2013 main-text coverage. Available Staphylococcus-Candida PMCID leads were not read; copper cache PMCID differs from fresh metadata. Failed aquifer/pesticide publisher requests were Internal Error, not verified HTTP403. No global full-text absence claim, bypass, cache import, supplement/figure-pixel or raw-data certification.

• Four guarded writes and four append-only histories;456 other records/all923 caches and prior history/decision files byte-identical. Non-graph raw blocks unchanged. Identity-only mire scopes do not change the global census because the whole-community gradient observation remains. No census threshold, schema or runtime-rule changes. The pre-write guard rejected unsupported discussion provenance fields; provenance remains on interaction evidence without changing the shared schema.

• Eight focused tests and959 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks and four histories validate. Network equals56 baseline warnings with zero structural defects. Deterministic rendering and exact HTML parser cover456pages/1372descriptions/545arrows, not screenshots. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked.

• Repairs1829-1832 addressed but remain open until protected-main merge; non-graph1833 remains open. Prior691/763 and aquifer analysis repairs preserved. The caches requested by764 are present, so no duplicate cache issue/import. Existing license949, loader1703, DOIcache1091, denied and unansweredEdison scopes are not resolved. Self-review is not independent approval; no artificial CI, protection bypass or premature cleanup.

• Corpus338reviewed/72pending/50needs_research is not completion. Postcommit docs-current and exact-head publication require separate receipts, not preasserted here.

959 passed in 793.39s (0:13:13); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; four append-only histories validated. 41 recorded gate outputs/digests. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Explicit-runtime non-incremental mypy passed. All36 reviewed graph/discussion quotations match fresh primary text and existing caches; literal matching is not entailment.

Eighteen nodes remain, with eight renames; five qualified existing directions remain. One analysis-workflow node and five cross-study, wrong-route or restatement arrows are removed. All four targets changed; 456 other records, all923 caches, taxonomy and non-graph raw blocks preserved. Corpus338reviewed/72pending/50needs_research. Network56existingwarnings/zero structural defects. Mire archaeal/bacterial observations gain canonical identity-only participant scope; the community-level census and its thresholds are unchanged.

Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with four append-only history records. Postcommit docs-current passed clean, SHA256 d2a4d50906e8bde6f7fe0e459780343a94bfc848ec927f3c4c90061faeb92b84. Deterministic rendering and HTML parser checks are not screenshots. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.

Staphylococcus-Candida, mire2018, pesticide2026 and aquifer independent evidence is abstract-bounded. Mire2023 and pesticide2013 primary-body coverage is bounded, not whole-paper/supplement/figure/raw-data certification. No new topology or Edison spend. Non-graph1833 stays open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.

[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, 56 warning across 20 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)

Panzhihua_Vanadium_Titanium_Tailings
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Polaromonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobium pisi' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobium selenitireducens' has no interactions

Total: 3 issues (0 error, 3 warning)

Phormidium_Alkaline_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Bacteroidota members' has no interactions

Total: 1 issues (0 error, 1 warning)

Polaromonas_Vanadium_Reduction_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Desulfitobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Desulfovibrio species' has no interactions
  [warning] DISCONNECTED: Taxon 'Geobacter species' has no interactions

Total: 3 issues (0 error, 3 warning)

Pseudomonas_Aeruginosa_EightStrain_Full_Factorial_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa MDR6-CAZ' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa NfxB-CAZ' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa OrfN' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa PA14' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa mexZ' has no interactions

Total: 5 issues (0 error, 5 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]

Exact-head self-adversarial restack review at 0532c2f57060f645c622691d5b3bdcd7dab21ab9.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 2004a60a5da3db6e19f7659ab984fe3e49c622afc0e8d9b09348e4d13ce46604.
Tree c9aec76cc905a1d28b845460b4c05f0d04525ca9 matches the independently computed clean merge.
Compared with historical tree 9bb3e7d09f2a5234432adf83c9509773b19635a4, 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 02611f4d2b8b4a867327091304300a591aff7452 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.