Bound syntrophic feedback, energetic constraints and ES5 effects (batch112)

[realmarcin]

Scope

Closes #1871.
Closes #1872.
Closes #1873.
Closes #1874.
Closes #1875.
Closes #1876.
Non-graph #1877/#1878 and validator #622 remain open.

• Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain carrier-removal feedback with physical units and flux uncertainty explicit.; Retain coupled community conversion without duplicate exchange typing.
• Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain carrier-removal feedback with physical units and flux uncertainty explicit.; Retain coupled community conversion without duplicate exchange typing.
• Retain substrate-bounded syntrophic growth and qualify the existing growth-to-ratio inference.; Retain population convergence as an outcome and remove misplaced reverse causality.; Retain reciprocal attraction and aggregation without one-way colonization or proven metabolic mediation.
• Retain butyrate oxidation with substrate-bounded dependence.; Retain hydrogen feedback without an uncited pressure threshold or duplicate evidence.; Retain the conversion endpoint without an additional exchange claim.
• Retain coculture benzoate metabolism without importing other-partner enzyme assays.; Bound hydrogen-user dependence to the syntrophic product route.; Rename mineralization as conversion and correct graph benzoate grounding.
• Retain exact-pair benzoate conversion and correct benzoate grounding.; Assign inferred energy availability to the fermenter without a spurious recipient.; Retain product inhibition without competition typing or treatment-system conflation.
• Bound stimulation to exact-pair lag and statistical comparisons at community scope.; Retain three-member spatial association without directed colonization or DIET proof.; Retain differential proteomics without enzyme-activation or signaling-causality overstatement.

Adversarial Review

• All 21 original nodes and 17 directions have dispositions: 21 nodes and 16 arrows retained, one misplaced reverse direction removed, and one conversion outcome renamed. No new biological topology or Edison submission.
• Challenge overcorrection: preserve exact-pair propionate and butyrate syntrophy,thermodynamic carrier-removal feedback,reciprocal spatial attraction,benzoate conversion,energy/product constraints and positive ES5 lag stimulation. Qualified mechanisms do not erase measured effects.
• Propionate: hydrogen pressure differs from formate concentration. Both exact pairings are present in the comparative proteomic study,where main-text Fdh1/Hox assignments remain qualified. Protein abundance and homology are not selective enzyme demonstrations or carrier-flux fractions. Cooperation is reciprocal without bidirectional carrier donation. Reuse and amend the existing formicicum source-attribution discussion.
• Coordination: manipulated starting ratios differ from the converged ratio. The former reverse arrow described aggregation rather than its population source. Retain the forward growth-to-ratio inference as PARTIAL and retain reciprocal attraction as a community observation. Physical disturbance changed activity without detectable aggregation changes,so mediation is unresolved. The nanomaterial study explicitly withholds decisive DIET attribution.
• Butyrate: the accessible1981abstract names M.hungatei and reports added-hydrogen inhibition. Preserve directly implied feedback,but remove an unsupported graph pressure threshold,duplicate evidence and substrate-wide obligacy. Do not certify detailed exact-pair perturbation conditions from the abstract.
• Benzoate: acetate remains organic carbon,so conversion is not complete mineralization. The pure-culture experiment explicitly demonstrates partner-free benzoate metabolism with a different product balance. Other-partner enzymology is not imported into the methanogenic pair. Benzoate graph grounding uses officially verified CHEBI16150,not neutral benzoic acid.
• Gentianae: fermenter energy is not a second directed exchange;product inhibition is not intertaxon competition. Preserve the source-supported constraint chain while distinguishing approximate growth energy,dense suspensions,propionate addition and expanded-community rescue. The product arrow changes available free energy,not a fixed intrinsic threshold.
• ES5: preserve the exact M.hungatei lag response;Table1 marks lag significant,not fitted rate/final concentration,and Discussion reports similar butyrate slopes. Do not transfer abstract-wide120%/150% to exact-triculture increases. Three-member outcomes include both syntrophic partners;their proteomes,not ES5,are assayed. Candidate methanogen signaling proteins were often more abundant in biculture,not uniformly activated by ES5. Both existing mediation arrows remain hypothetical.
• Source-access challenge: four fresh extracted main bodies plus five older primary abstracts were read. Two 2024 transcription quotes remain grounded only in existing curator-supplied publisher text; fresh retrieval failed. All 53 quotes match unchanged caches; 51 match fresh primary artifacts. Matching is not entailment. No original pixels, separate supplements or raw data were certified; read spans and retrieval failures are explicit.
• Seven guarded records and eight append-only histories preserve 453 other records, 923 caches, raw non-graph blocks and prior decision/history artifacts. The second benzoate history records a shorter contiguous quote after bracket-stripping issue validate-references silently strips [bracketed] text from snippets before matching #622; the compound-or-CoA qualification remains in its explanation. Initial ledger, failed output and mutation proof are preserved. Exact canonical identity-only participants are used. Measured census gains three community-level records, two mixed and one community-only; seven denominator taxa and three solely-credited ES5 members. Connectivity logic and share guard remain unchanged.
• Five real in-memory control/mutation/restored-control probes reject enzyme certainty,reverse ratio causality,competition typing,inflated exact-triculture rates and proven proteomic mediation. Each logs actual changed values and the rejecting assertion. Canonical hashes remain unchanged;these probes do not inflate pytest counts.
• Eleven focused tests and 1014 combined regressions pass. Seven schema/strict/term/local-snippet checks and eight histories pass. Six full-record reference CLI checks pass; coordination has one unchanged bracket-stripping validate-references silently strips [bracketed] text from snippets before matching #622 failure, proved byte-identical on parent and matched to fresh primary text. It is an exception, not a pass. The 70 outputs include six superseded outputs: five from before the quote correction, plus the initial regression failure. The new bracket quote was corrected and revalidated; the exact participant-user test was updated for the three intentionally added records after the measured census. Neither failed run is counted as a pass. All 56 existing network warnings are unchanged; zero structural defects. Deterministic rendering and exact HTML-description matching cover 456 pages, 1366 nodes and 535 arrows, not screenshots. Full-corpus snippets remain informational, not clean-corpus certification.
• Graph repairs Bound propionate carrier feedback and enzyme inference to exact syntrophic partners #1871-Bound ES5 stimulation by exact-triculture statistics and distinguish proteomic correlates #1876 await protected-main merge; non-graph metadata follow-ups Reconcile syntrophic-record culture metadata with vessel volume and generation time #1877-Reconcile residual non-graph syntrophy and ES5 kinetic claims with assay scope #1878 remain open. Source-based self-review is not independent approval. Reference-loader, DOI-case and preexisting snippet-rendering issues remain outside scope; macOS reference success is not Linux certification. No artificial CI, access/protection bypass or premature branch deletion.
• Corpus status: 362 reviewed, 45 pending, 53 needs_research across 460 records. The overall goal is incomplete. Exact-head publication and postcommit docs-current remain separate gates, not preasserted in this report.
• Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Verification And Output Records

1014 passed in 381.37s (0:06:21); eleven focused tests and five real in-memory mutation probes. Seven schema, strict, term and local-snippet checks and eight histories pass. Six full-record reference CLI checks pass; one unchanged cultivation quote reproduces bracket-stripping issue #622 byte-for-byte on the parent. This is a recorded exception, not a pass. Six full-record reference CLI passes;one expected preexisting failure in unchanged coordination cultivation_setup due to bracket stripping622 and misleading abstract note496,proven byte-identical on parent and matched to fresh primary text. Seven local snippet audits pass. macOS,not Linux certification;DOI-case1091,ligature1863 and loader1703 remain outside scope. Literal matches do not establish entailment. CLI Total checks counts issues,not checks.

All 21 nodes and 16 of 17 existing directions remain; one misplaced reverse arrow is removed and one outcome renamed. All 53 graph/discussion quotations match unchanged caches; 51 match fresh primary artifacts and two retain existing curator-supplied publisher-text provenance. Four fresh extracted main bodies and five older abstracts were reviewed. No original figure pixels, separate supplements or raw datasets were certified. All 453 other records and 923 caches are unchanged. The 70 gate outputs and digests include six superseded outputs: five from before the quote correction, plus the initial regression failure. Eight append-only histories include a shorter contiguous benzoate quote after the newly introduced bracket failure. The exact participant-user test was updated for the three intentionally added records after the measured census. Both failed outputs, the original ledger and pre-correction mutation proof remain recorded; neither failed run is counted as a pass.

Corpus: 362 reviewed, 45 pending, 53 needs_research. There are 56 existing warnings and zero structural defects. Participant census: 412 community-level records, 136 mixed, 276 community-only, 1563 taxa, 1273 solely credited. The three additional sole credits are the community-scoped ES5 members. Connectivity and share logic are unchanged. Postcommit docs-current passed clean, SHA256 c66e229e63e63353a84c09e27b046a42ce6b271570e2ccd52bd5c2b593ac8540. Deterministic rendering and HTML-description parsing are not screenshots. Full-corpus snippet auditing remains informational, not clean-corpus certification. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Decisions, provenance, validation and self-adversarial records are committed under reports/causal_graph_review. Metadata follow-ups #1877 and #1878, and existing validator issue #622, stay open. No new topology, Edison spend, experimental optimization or access/protection bypass. This COMMENT is self-review, not independent approval.

Source Limits

• Fresh pre-source baseline across both roots:460 records,923 caches,56 existing warnings,zero structural defects. Review all21 original nodes/17arrows; retain21nodes/16directions,remove one misplaced reverse arrow,rename one outcome. No new topology or Edison spend.
• Whole seven canonical records, schema scope/type definitions and existing discussion evidence read. Four fresh extracted main bodies read:propionate proteome1-187,coordination1-147,trichococcus1-133,nanomaterials1-161,including abstracts,Methods and embedded captions/tables. Extraction is not original figure-pixel or separate supplement/raw-data review.
• Fresh primary abstracts and exact Crossref DOI metadata read for1998propionate type,1981butyrate type,1997gentianae,and both2001benzoate studies. Older fullTextXML endpoints failed for1981 and both2001papers. PMC93338 web main-body excerpts were available through Results,not a complete independently archived full-text read. Gentianae publisher rendered abstract only; no PDF audit. Graph claims for these sources use fresh abstracts, not inaccessible detailed assays.
• 2024formate publisher retrieval failed403/429. Existing curator-supplied cached publisher text main content lines1-735 read; contains duplicated extraction passages and prepublication page headers. Its two retained transcription snippets are cache-matched,not fresh independently retrieved full-text matches. Existing dose discussion preserved and amended; sludge and coculture are distinguished. Reference-list tail and separate supplements not audited.
• All graph/discussion quotations are normalized contiguous cache matches. Fresh primary matches are counted separately from the two2024cache-only graph quotes; matching does not establish entailment. Other caches were quotation-checked,not read in full. Official ChEBI16150 identity confirmed; no new taxon groundings.
• Propionate: preserve real carrier-removal feedback, bound enzyme homology/abundance inference and carrier partitioning, distinguish gas pressure from aqueous concentration. Butyrate: preserve reported hydrogen inhibition but do not certify exact perturbation conditions,universal obligacy or an uncited pressure threshold.
• Coordination: initial ratio perturbations are distinct from endpoint convergence; remove aggregation-described reverse arrow. Reciprocal attraction and unchanged aggregation under activity-changing disturbance are retained. Nanomaterial acceleration does not prove DIET.
• Benzoate: acetate+CH4 is conversion,not complete mineralization; pure-culture fermentation disproves universal partner dependence. Other-partner enzyme assays are not imported. Gentianae: approximate growth energy and product effects are not competition or a fixed threshold across dense-suspension and added-partner treatments.
• ES5: exact M.hungatei lag is significant in Table1; fitted rate/final concentration are not marked significant and Discussion reports similar butyrate slopes. Preserve stimulation without abstract-wide120%/150% exact-triculture attribution. All three members remain in outcome scope; measured proteomes are two partners. Aggregation/protein mediation remains hypothetical,not enzyme activation or DIET proof.
• Ignored/hidden-inclusive local path index read,not all historical file bodies. Fresh all-state issue title/body dedup matched1392,1389,795,583,496,259;fullbodies and related529/183 read. PR comments not exhaustively searched. Broad metadata issues are followups,not addressed by graph scope.
• Preserve453otherrecords,923caches,rawnon-graph blocks and prior history/decision artifacts. Participant census measured,not guessed;rules/share guard unchanged. No schema/validator/runtime change. MacOS full-record CLI is not Linux certification;reference-loader,DOI-case and rendering caveats remain.
• Repair issues remain open until protected-main merge;metadata followups remain open afterward. Self-review is not independent approval or full-corpus completion. Denied/unanswered Edison scopes untouched;no artificial CI,protection bypass or premature branch deletion.
• Post-write validation correction: a new benzoate quote triggered bracket-stripping622. Replace it with a shorter contiguous excerpt and keep the compound-or-CoA qualification in explanation;append a second history for that record. The initial ledger,failed output and pre-correction mutation proof are preserved. Eight histories total;one unchanged coordination metadata622 failure remains explicitly excepted.

Dependency

Draft depends on #1870. Do not merge into the topic parent. Require actual exact-head checks through protected main; self-review is not independent approval. Root CI blocker #1836 remains separate. Move dependents before deleting parent branches.

[realmarcin]

Source-based self-adversarial review at exact head 7a92057; not independent approval.

• Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain carrier-removal feedback with physical units and flux uncertainty explicit.; Retain coupled community conversion without duplicate exchange typing.

• Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain carrier-removal feedback with physical units and flux uncertainty explicit.; Retain coupled community conversion without duplicate exchange typing.

• Retain substrate-bounded syntrophic growth and qualify the existing growth-to-ratio inference.; Retain population convergence as an outcome and remove misplaced reverse causality.; Retain reciprocal attraction and aggregation without one-way colonization or proven metabolic mediation.

• Retain butyrate oxidation with substrate-bounded dependence.; Retain hydrogen feedback without an uncited pressure threshold or duplicate evidence.; Retain the conversion endpoint without an additional exchange claim.

• Retain coculture benzoate metabolism without importing other-partner enzyme assays.; Bound hydrogen-user dependence to the syntrophic product route.; Rename mineralization as conversion and correct graph benzoate grounding.

• Retain exact-pair benzoate conversion and correct benzoate grounding.; Assign inferred energy availability to the fermenter without a spurious recipient.; Retain product inhibition without competition typing or treatment-system conflation.

• Bound stimulation to exact-pair lag and statistical comparisons at community scope.; Retain three-member spatial association without directed colonization or DIET proof.; Retain differential proteomics without enzyme-activation or signaling-causality overstatement.

• All 21 original nodes and 17 directions have dispositions: 21 nodes and 16 arrows retained, one misplaced reverse direction removed, and one conversion outcome renamed. No new biological topology or Edison submission.

• Challenge overcorrection: preserve exact-pair propionate and butyrate syntrophy,thermodynamic carrier-removal feedback,reciprocal spatial attraction,benzoate conversion,energy/product constraints and positive ES5 lag stimulation. Qualified mechanisms do not erase measured effects.

• Propionate: hydrogen pressure differs from formate concentration. Both exact pairings are present in the comparative proteomic study,where main-text Fdh1/Hox assignments remain qualified. Protein abundance and homology are not selective enzyme demonstrations or carrier-flux fractions. Cooperation is reciprocal without bidirectional carrier donation. Reuse and amend the existing formicicum source-attribution discussion.

• Coordination: manipulated starting ratios differ from the converged ratio. The former reverse arrow described aggregation rather than its population source. Retain the forward growth-to-ratio inference as PARTIAL and retain reciprocal attraction as a community observation. Physical disturbance changed activity without detectable aggregation changes,so mediation is unresolved. The nanomaterial study explicitly withholds decisive DIET attribution.

• Butyrate: the accessible1981abstract names M.hungatei and reports added-hydrogen inhibition. Preserve directly implied feedback,but remove an unsupported graph pressure threshold,duplicate evidence and substrate-wide obligacy. Do not certify detailed exact-pair perturbation conditions from the abstract.

• Benzoate: acetate remains organic carbon,so conversion is not complete mineralization. The pure-culture experiment explicitly demonstrates partner-free benzoate metabolism with a different product balance. Other-partner enzymology is not imported into the methanogenic pair. Benzoate graph grounding uses officially verified CHEBI16150,not neutral benzoic acid.

• Gentianae: fermenter energy is not a second directed exchange;product inhibition is not intertaxon competition. Preserve the source-supported constraint chain while distinguishing approximate growth energy,dense suspensions,propionate addition and expanded-community rescue. The product arrow changes available free energy,not a fixed intrinsic threshold.

• ES5: preserve the exact M.hungatei lag response;Table1 marks lag significant,not fitted rate/final concentration,and Discussion reports similar butyrate slopes. Do not transfer abstract-wide120%/150% to exact-triculture increases. Three-member outcomes include both syntrophic partners;their proteomes,not ES5,are assayed. Candidate methanogen signaling proteins were often more abundant in biculture,not uniformly activated by ES5. Both existing mediation arrows remain hypothetical.

• Source-access challenge: four fresh extracted main bodies plus five older primary abstracts were read. Two 2024 transcription quotes remain grounded only in existing curator-supplied publisher text; fresh retrieval failed. All 53 quotes match unchanged caches; 51 match fresh primary artifacts. Matching is not entailment. No original pixels, separate supplements or raw data were certified; read spans and retrieval failures are explicit.

• Seven guarded records and eight append-only histories preserve 453 other records, 923 caches, raw non-graph blocks and prior decision/history artifacts. The second benzoate history records a shorter contiguous quote after bracket-stripping issue #622; the compound-or-CoA qualification remains in its explanation. Initial ledger, failed output and mutation proof are preserved. Exact canonical identity-only participants are used. Measured census gains three community-level records, two mixed and one community-only; seven denominator taxa and three solely-credited ES5 members. Connectivity logic and share guard remain unchanged.

• Five real in-memory control/mutation/restored-control probes reject enzyme certainty,reverse ratio causality,competition typing,inflated exact-triculture rates and proven proteomic mediation. Each logs actual changed values and the rejecting assertion. Canonical hashes remain unchanged;these probes do not inflate pytest counts.

• Eleven focused tests and 1014 combined regressions pass. Seven schema/strict/term/local-snippet checks and eight histories pass. Six full-record reference CLI checks pass; coordination has one unchanged bracket-stripping #622 failure, proved byte-identical on parent and matched to fresh primary text. It is an exception, not a pass. The 70 outputs include six superseded outputs: five from before the quote correction, plus the initial regression failure. The new bracket quote was corrected and revalidated; the exact participant-user test was updated for the three intentionally added records after the measured census. Neither failed run is counted as a pass. All 56 existing network warnings are unchanged; zero structural defects. Deterministic rendering and exact HTML-description matching cover 456 pages, 1366 nodes and 535 arrows, not screenshots. Full-corpus snippets remain informational, not clean-corpus certification.

• Graph repairs #1871-#1876 await protected-main merge; non-graph metadata follow-ups #1877-#1878 remain open. Source-based self-review is not independent approval. Reference-loader, DOI-case and preexisting snippet-rendering issues remain outside scope; macOS reference success is not Linux certification. No artificial CI, access/protection bypass or premature branch deletion.

• Corpus status: 362 reviewed, 45 pending, 53 needs_research across 460 records. The overall goal is incomplete. Exact-head publication and postcommit docs-current remain separate gates, not preasserted in this report.

• Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

1014 passed in 381.37s (0:06:21); eleven focused tests and five real in-memory mutation probes. Seven schema, strict, term and local-snippet checks and eight histories pass. Six full-record reference CLI checks pass; one unchanged cultivation quote reproduces bracket-stripping issue #622 byte-for-byte on the parent. This is a recorded exception, not a pass. Six full-record reference CLI passes;one expected preexisting failure in unchanged coordination cultivation_setup due to bracket stripping622 and misleading abstract note496,proven byte-identical on parent and matched to fresh primary text. Seven local snippet audits pass. macOS,not Linux certification;DOI-case1091,ligature1863 and loader1703 remain outside scope. Literal matches do not establish entailment. CLI Total checks counts issues,not checks.

All 21 nodes and 16 of 17 existing directions remain; one misplaced reverse arrow is removed and one outcome renamed. All 53 graph/discussion quotations match unchanged caches; 51 match fresh primary artifacts and two retain existing curator-supplied publisher-text provenance. Four fresh extracted main bodies and five older abstracts were reviewed. No original figure pixels, separate supplements or raw datasets were certified. All 453 other records and 923 caches are unchanged. The 70 gate outputs and digests include six superseded outputs: five from before the quote correction, plus the initial regression failure. Eight append-only histories include a shorter contiguous benzoate quote after the newly introduced bracket failure. The exact participant-user test was updated for the three intentionally added records after the measured census. Both failed outputs, the original ledger and pre-correction mutation proof remain recorded; neither failed run is counted as a pass.

Corpus: 362 reviewed, 45 pending, 53 needs_research. There are 56 existing warnings and zero structural defects. Participant census: 412 community-level records, 136 mixed, 276 community-only, 1563 taxa, 1273 solely credited. The three additional sole credits are the community-scoped ES5 members. Connectivity and share logic are unchanged. Postcommit docs-current passed clean, SHA256 c66e229e63e63353a84c09e27b046a42ce6b271570e2ccd52bd5c2b593ac8540. Deterministic rendering and HTML-description parsing are not screenshots. Full-corpus snippet auditing remains informational, not clean-corpus certification. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Decisions, provenance, validation and self-adversarial records are committed under reports/causal_graph_review. Metadata follow-ups #1877 and #1878, and existing validator issue #622, stay open. No new topology, Edison spend, experimental optimization or access/protection bypass. This COMMENT is self-review, not independent approval.

[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]

Self-adversarial review refreshed at exact head 5238663 after propagating the real CI correction #1899. Not independent approval.

Original head: 7a92057. Current parent: f97306e. Only tests/test_datamodel.py changes in the tree for batches109-114; batch115's whole tree is unchanged. Scientific records, prior histories/decisions, caches, renderings and all other files are byte-identical to the respective reviewed trees. Each batch-owned patch excluding this test is byte-identical (SHA256 17a50bce447b3dc891394011cf9d086283ee514223cc1c6df58e745aa5ca5ee1).

The stale smoke test now requires the reviewed source and target names, resolving target, canonical pairwise taxa, qualified sucrose mediation and both SUPPORT/PARTIAL evidence. No graph was reverted or test skipped. The batch115 CI artifact records the original failed strict run, reproduction, 24 related test passes and seven rejecting counterfactual probes.

Fresh tests at this head: ............. [100%]
13 passed in 17.98s
Test log SHA256: 91fb1be8e46ba6faee58264935f6033685aa15aae0fcd38887ae9748d3fc6c59. Fresh docs-current passed with a clean worktree; log SHA256 c66e229e63e63353a84c09e27b046a42ce6b271570e2ccd52bd5c2b593ac8540.

The propagation-pending entries in batch115's immutable publication report describe the earlier publication state; this exact-head review records the subsequent propagation. Focused tests are not a new full-suite pass. Real exact-head protected CI remains required; #1836 independently blocks the upstream root PR. #1899 remains open until protected-main integration. No artificial CI, protection bypass, merge or branch deletion was performed.

[realmarcin]

Exact-head self-adversarial restack review at 271b02265e59ea1af21584d137c2c22c8c61d2a2.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 17a50bce447b3dc891394011cf9d086283ee514223cc1c6df58e745aa5ca5ee1.
Tree 21b6512428c1996f69266a5aed361594aa55a79d matches the independently computed clean merge.
Compared with historical tree 9341e9d3948ef327838d474d3dbed950f0557fbc, 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 885b8ef16a9cb609d09c3adbf71ee804f27a8248 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.