Bound SynCom and photosynthetic graph claims by assay and strain (batch109)

[realmarcin]

Scope

Closes #1849.
Closes #1850.
Closes #1851.
Closes #1852.
Closes #1853.
Closes #1854.
Non-graph follow-up #1855 remains open.

• Retain comparator-specific chemical outcomes; remove construction nodes, unsupported interaction types and two design-order arrows.
• Retain assay-specific reciprocal biofilm growth and qualify its proposed downstream mediation.; Retain measured FA tolerance and pot biocontrol as community outcomes, not a second mutualism.; Separate positive supplementation from transfer and correct modeling input/version provenance.; Retain predicted return with the reported negative supplementation endpoint and corrected provenance.
• Retain exporter-dependent carbon support without transport-rate or PHB-tracing claims.; Retain omission-context mutualism; qualify nitrogen-to-PHB mediation and substrate role.; Retain PHB production as a community endpoint and distinguish potential alginate production.
• Retain cyanobacterial carbon support with explicit 168-versus-3610 scope.; Retain bounded Bacillus growth support and the positive168 assay; remove unestablished long-term stability.
• Retain carbon supply while distinguishing early non-sucrose dependence and removing the invalid concentration.; Retain strain-specific growth/persistence, not sucrose-exclusive growth or syntrophy.; Retain conditional reciprocal growth benefit; mediator of cyanobacterial stimulation is unresolved.
• Retain donor-to-W303Clump sucrose provision, not a generic yeast claim.; Retain long-term continuous persistence separately from batch decline and the negative parental control.; Retain conditional reciprocal growth benefit; qualify the proposed contribution of sucrose-supported yeast.

Adversarial Review

• Whole original targets and all changed graph/discussion diffs reviewed. All19 original nodes/12 arrows have dispositions:retain16 nodes/nine existing directions,remove three nodes/three arrows,rename three. No new topology or Edison spend.
• Challenge overcorrection: retain measured flavor outcomes, reciprocal biofilm-associated abundance, FA tolerance/pot biocontrol, omission-context mutualism/PHB, photosynthate-supported growth and conditional cyanobacterial benefits. Qualification does not erase source-supported positive effects.
• Fuqu: construction rationale is not measured niche separation or metabolite exchange. SC2 did not monotonically increase the flavor diversity metric; large-scale ethanol was not significantly different. Preserve SC3 comparator outcomes and source-proposed bacterial-fungal synergy without adding an organism-specific mechanism or any cultivation optimization.
• SynComY: reciprocal biofilm growth has species-specific qPCR support and stays MUTUALISM, whereas the FA/pot endpoint is untyped. Forward additions support response,not direct transfer. Reverse additions were tested and did not significantly enhance LSQ16 biofilm; this does not refute all possible exchange. Keep both existing mediation arrows hypothetical. The SRA range belongs to RNA-seq,not verified genome input;source-named tools stay but unsupported versions are removed. Root-colonization synergy remains unverified.
• Azotobacter: exporter dependence and failure of either partner alone under carbon/nitrogen omission support the growth-context mutualism. They do not quantify PHB mediation,identify a nitrogen transfer product or establish PHB assay conditions. Keep initial glutamate experiments separate. PHB is demonstrated;alginate is potential. Abstract-limited review is explicit,not a claim that full text does not exist.
• Bacillus: main Figure4 plus supplementS2/S5/S9 identify3610 in growth/perturbation assays. Strain168 production and supplementS4 inhibition do not establish months-long persistence. Remove the unsupported stabilization node/arrow without adding a new alpha-amylase node;positive168 evidence remains as bounded context. The two remaining nodes retain PARTIAL strain-specific support.
• Ecoli: early W and W delta-cscR growth is insensitive to induced sucrose export,so retain carbon support without sucrose exclusivity. Other photosynthates are inferred,not chemically identified.85% background carbon-export capability is not a concentration. Preserve more-than-two-week continuous persistence and conditional reciprocal benefit;carbon feeding alone is not product-removal syntrophy.
• Yeast: preserve Synechococcus_Yarrowia_SPC: the cited paper never studied Yarrowia #605 corrected W303Clump identity,parentalW303 negative result,no yeast bioproduct,and batch decline. The two-month constant-light persistence is distinct from diurnal experiments;source supplementS8 confirmed this distinction. Uptake is an organism phenotype,not a reverse donor arrow. Metabolite return/byproduct absorption remains a proposed mediator of cyanobacterial stimulation.
• All28 graph plus six discussion quotations match independently retrieved primary text and unchanged caches. Three primary main bodies/captions and one abstract read;SPC supplement captionsS1-S12 and pixelsS2/S4/S5/S8 additionally inspected. Other supplements/images,mathematical framework and raw data were not certified. Large cache headers and literal quotations checked,not a whole-cache audit;literal matching remains separate from entailment.
• Six guarded writes produce six append-only histories. Other454 records,all923 caches,non-graph raw blocks and prior history/decision files are unchanged. Four phenotype-scope changes add eight taxa to the community-level survey denominator but no additional solely-credited taxa. Observational census bounds update to the measured407/132 counts with an exact regression;connectivity rules and the share guard are unchanged.
• Four in-memory control/mutation/restored-control probes reject transfer SUPPORT inflation,RNA-seq input misattribution,Bacillus168 persistence-arrow restoration and diurnal duration inflation. Mutation application and rejection were explicitly checked at scientific assertions. Canonical files are unchanged and probes do not inflate the pytest count.
• Twelve focused tests and987 combined regressions pass. Six full-record schema/strict/term/reference/snippet checks and six histories validate. Network retains56 baseline warnings with zero structural defects. Deterministic rendering and exact HTML parsing cover456 pages,1367 node descriptions and536 arrows;this is not screenshot QA.
• Repair issues1849-1854 are addressed but remain open until protected-main merge;non-graph follow-up1855 remains open. Existing loader1703,DOI-case1091,stub1093 and license949 are not certified. Denied/unanswered Edison scopes remain untouched. Self-review is not independent approval;no artificial CI,protection bypass or premature branch deletion.
• Corpus status:350 reviewed,58 pending,52 needs_research. The whole goal is not complete. Postcommit docs-current and exact-head publication require separate receipts and are not preasserted here.
• Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Verification And Output Records

987 passed in 328.40s (0:05:28); twelve new focused tests. Six full-record schema, strict, ontology-term, reference and snippet checks passed; six append-only histories validated. 55 recorded gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Sixteen nodes and nine existing directions remain, with three renames. Three nodes and three arrows are removed. All 34 reviewed graph/discussion quotations match fresh primary text and unchanged caches; literal matching is not entailment. All 454 other records, all 923 caches and non-graph raw blocks are unchanged. Corpus: 350 reviewed, 58 pending, 52 needs_research. Network: 56 existing warnings, zero structural defects. Four phenotype scope changes yield 407 community-level and 132 mixed records with no additional solely-credited taxa. Observational census bounds are updated with an exact regression; connectivity rules and share guard are unchanged.

Four in-memory control/mutation/restored-control probes reject direct-transfer SUPPORT inflation, RNA-seq model-input misattribution, Bacillus168 persistence-arrow restoration and yeast diurnal-duration inflation. Canonical files remain unchanged; these probes are not added to the pytest count.

Decisions, cache provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 259b68aab908650ebf8a445a102c8518a17deff1878f5f180f285fcf3042d5d2. Deterministic rendering and HTML parser checks are not screenshots. Six full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.

Review covers independently retrieved Sesame, SynComY and SPC primary main texts/captions, the Azotobacter primary abstract, and SPC supplement captions S1-S12 plus selected figure pixels S2/S4/S5/S8. Other supplements/images, the mathematical framework and raw data are not certified. No access bypass, new topology, Edison spend or experimental protocols. Non-graph SPC follow-up #1855 remains open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.

Source Limits

• Fresh both-root baseline precedes source reads:460 records,923 caches,56 existing warnings,zero structural defects. Whole six records and all19 original nodes/12 arrows reviewed;retain16 nodes/nine existing directions,remove three nodes/three arrows,rename three. No new topology or Edison spend.
• Whole independently retrieved primary Sesame,SynComY and SPC abstract/main text/methods/results/discussion/captions read from EuropePMC XML;Azotobacter primary abstract read independently and checked against publisher index. Exact DOI metadata cross-checked. Azotobacter full article and supplements were not retrieved;bounded publisher/repository search is not proof of absence. No access bypass or author contact.
• Public SPC supplement retrieved through EuropePMC after CDN DNS failure. CaptionsS1-S12 read and pixelsS2/S4/S5/S8 inspected. S2/S5 confirm3610 growth/stimulation scope;S4 identifies168 inhibition;S8 long-duration yeast cultures used constant light,not the separate diurnal assay. Remaining images,mathematical framework and raw datasets were not reviewed. No separate Sesame/SynComY supplements or main-figure pixels inspected.
• Cache headers inspected and all graph quotations literal-checked against the three large caches;contextual reading used fresh primary text. Azotobacter cache read whole. Not a whole-cache audit. Every retained/new graph and discussion quotation matches fresh primary text and unchanged committed cache. Sesame/SynComY headers still say abstract_only despite additional text;metadata policy949/1093 is not repaired here.
• Sesame preserves comparator-specific flavor outcomes and source-proposed bacterial-fungal synergy,not exchange/niche partitioning/reciprocal growth. Remove two assembly nodes/arrows. No cultivation,optimization,organism identity or experimental design changes.
• SynComY retains positive reciprocal biofilm-associated qPCR abundance,EPS/activity,FA tolerance and pot outcomes. Positive forward supplementation is not direct transfer;negative reverse supplementation is not proof of no exchange. Correct RNA-seq-as-genome-input and unsupported COBRA version;do not invent model identifiers or genome accessions. Rhizosphere mediation remains explicitly unresolved.
• Azotobacter preserves abstract-supported exporter dependence and omission-context mutualism. PHB is a community endpoint;carbon/nitrogen-to-PHB mediation stays hypothetical. Dinitrogen is substrate,not a specified transfer product. Initial glutamate model and potential alginate are not promoted to omission-assay or demonstrated-production claims.
• SPC records retain positive partner-specific growth and conditional mutualism without universal stability. Bacillus168 production evidence cannot inherit3610 trajectories or other-partner weeks/months persistence. Ecoli early growth is not sucrose-exclusive and85% background export is not a concentration. W303Clump remains distinct from parentalW303 and no yeast bioproduct is invented. Reverse-benefit mechanism is source-proposed,not identified transfer.
• Repair issues[1849, 1850, 1851, 1852, 1853, 1854] stay open until protected-main merge;non-graph follow-up1855 stays open. Fresh all-state title/body dedup matched757,714,605,310;all read plus related529. Ignored/hidden local index inspected,not every matching report read;PRs/comments not exhaustively searched. No reusable taxon match in ignored/hidden kb/taxa name/identifier search. Whole reviewed B12 Syn7002 neighbor read for modeling patterns,not used as evidence for these targets.
• Only graph/discussions/events change. Other454 records,923 caches,non-graph raw blocks and prior histories/decisions preserved. Canonical identities reused as preferred_term+term only;no GTDB copies into graph. General growth metadata and narrative claims are not recertified. No schema,validator,configuration or runtime change. Participant census must be measured;any census test update must reflect actual scoped changes,not a relaxed connectivity rule. Loader1703,DOI-case1091,stub1093 and license949 remain separate. Self-review is not independent approval or corpus completion. Denied/unanswered Edison scopes remain untouched.

Dependency

Draft depends on #1848. Do not merge into the topic parent. Require 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 9b429a9; not independent approval.

• Retain comparator-specific chemical outcomes; remove construction nodes, unsupported interaction types and two design-order arrows.

• Retain assay-specific reciprocal biofilm growth and qualify its proposed downstream mediation.; Retain measured FA tolerance and pot biocontrol as community outcomes, not a second mutualism.; Separate positive supplementation from transfer and correct modeling input/version provenance.; Retain predicted return with the reported negative supplementation endpoint and corrected provenance.

• Retain exporter-dependent carbon support without transport-rate or PHB-tracing claims.; Retain omission-context mutualism; qualify nitrogen-to-PHB mediation and substrate role.; Retain PHB production as a community endpoint and distinguish potential alginate production.

• Retain cyanobacterial carbon support with explicit 168-versus-3610 scope.; Retain bounded Bacillus growth support and the positive168 assay; remove unestablished long-term stability.

• Retain carbon supply while distinguishing early non-sucrose dependence and removing the invalid concentration.; Retain strain-specific growth/persistence, not sucrose-exclusive growth or syntrophy.; Retain conditional reciprocal growth benefit; mediator of cyanobacterial stimulation is unresolved.

• Retain donor-to-W303Clump sucrose provision, not a generic yeast claim.; Retain long-term continuous persistence separately from batch decline and the negative parental control.; Retain conditional reciprocal growth benefit; qualify the proposed contribution of sucrose-supported yeast.

• Whole original targets and all changed graph/discussion diffs reviewed. All19 original nodes/12 arrows have dispositions:retain16 nodes/nine existing directions,remove three nodes/three arrows,rename three. No new topology or Edison spend.

• Challenge overcorrection: retain measured flavor outcomes, reciprocal biofilm-associated abundance, FA tolerance/pot biocontrol, omission-context mutualism/PHB, photosynthate-supported growth and conditional cyanobacterial benefits. Qualification does not erase source-supported positive effects.

• Fuqu: construction rationale is not measured niche separation or metabolite exchange. SC2 did not monotonically increase the flavor diversity metric; large-scale ethanol was not significantly different. Preserve SC3 comparator outcomes and source-proposed bacterial-fungal synergy without adding an organism-specific mechanism or any cultivation optimization.

• SynComY: reciprocal biofilm growth has species-specific qPCR support and stays MUTUALISM, whereas the FA/pot endpoint is untyped. Forward additions support response,not direct transfer. Reverse additions were tested and did not significantly enhance LSQ16 biofilm; this does not refute all possible exchange. Keep both existing mediation arrows hypothetical. The SRA range belongs to RNA-seq,not verified genome input;source-named tools stay but unsupported versions are removed. Root-colonization synergy remains unverified.

• Azotobacter: exporter dependence and failure of either partner alone under carbon/nitrogen omission support the growth-context mutualism. They do not quantify PHB mediation,identify a nitrogen transfer product or establish PHB assay conditions. Keep initial glutamate experiments separate. PHB is demonstrated;alginate is potential. Abstract-limited review is explicit,not a claim that full text does not exist.

• Bacillus: main Figure4 plus supplementS2/S5/S9 identify3610 in growth/perturbation assays. Strain168 production and supplementS4 inhibition do not establish months-long persistence. Remove the unsupported stabilization node/arrow without adding a new alpha-amylase node;positive168 evidence remains as bounded context. The two remaining nodes retain PARTIAL strain-specific support.

• Ecoli: early W and W delta-cscR growth is insensitive to induced sucrose export,so retain carbon support without sucrose exclusivity. Other photosynthates are inferred,not chemically identified.85% background carbon-export capability is not a concentration. Preserve more-than-two-week continuous persistence and conditional reciprocal benefit;carbon feeding alone is not product-removal syntrophy.

• Yeast: preserve #605 corrected W303Clump identity,parentalW303 negative result,no yeast bioproduct,and batch decline. The two-month constant-light persistence is distinct from diurnal experiments;source supplementS8 confirmed this distinction. Uptake is an organism phenotype,not a reverse donor arrow. Metabolite return/byproduct absorption remains a proposed mediator of cyanobacterial stimulation.

• All28 graph plus six discussion quotations match independently retrieved primary text and unchanged caches. Three primary main bodies/captions and one abstract read;SPC supplement captionsS1-S12 and pixelsS2/S4/S5/S8 additionally inspected. Other supplements/images,mathematical framework and raw data were not certified. Large cache headers and literal quotations checked,not a whole-cache audit;literal matching remains separate from entailment.

• Six guarded writes produce six append-only histories. Other454 records,all923 caches,non-graph raw blocks and prior history/decision files are unchanged. Four phenotype-scope changes add eight taxa to the community-level survey denominator but no additional solely-credited taxa. Observational census bounds update to the measured407/132 counts with an exact regression;connectivity rules and the share guard are unchanged.

• Four in-memory control/mutation/restored-control probes reject transfer SUPPORT inflation,RNA-seq input misattribution,Bacillus168 persistence-arrow restoration and diurnal duration inflation. Mutation application and rejection were explicitly checked at scientific assertions. Canonical files are unchanged and probes do not inflate the pytest count.

• Twelve focused tests and987 combined regressions pass. Six full-record schema/strict/term/reference/snippet checks and six histories validate. Network retains56 baseline warnings with zero structural defects. Deterministic rendering and exact HTML parsing cover456 pages,1367 node descriptions and536 arrows;this is not screenshot QA.

• Repair issues1849-1854 are addressed but remain open until protected-main merge;non-graph follow-up1855 remains open. Existing loader1703,DOI-case1091,stub1093 and license949 are not certified. Denied/unanswered Edison scopes remain untouched. Self-review is not independent approval;no artificial CI,protection bypass or premature branch deletion.

• Corpus status:350 reviewed,58 pending,52 needs_research. The whole goal is not complete. Postcommit docs-current and exact-head publication require separate receipts and are not preasserted here.

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

987 passed in 328.40s (0:05:28); twelve new focused tests. Six full-record schema, strict, ontology-term, reference and snippet checks passed; six append-only histories validated. 55 recorded gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Sixteen nodes and nine existing directions remain, with three renames. Three nodes and three arrows are removed. All 34 reviewed graph/discussion quotations match fresh primary text and unchanged caches; literal matching is not entailment. All 454 other records, all 923 caches and non-graph raw blocks are unchanged. Corpus: 350 reviewed, 58 pending, 52 needs_research. Network: 56 existing warnings, zero structural defects. Four phenotype scope changes yield 407 community-level and 132 mixed records with no additional solely-credited taxa. Observational census bounds are updated with an exact regression; connectivity rules and share guard are unchanged.

Four in-memory control/mutation/restored-control probes reject direct-transfer SUPPORT inflation, RNA-seq model-input misattribution, Bacillus168 persistence-arrow restoration and yeast diurnal-duration inflation. Canonical files remain unchanged; these probes are not added to the pytest count.

Decisions, cache provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 259b68aab908650ebf8a445a102c8518a17deff1878f5f180f285fcf3042d5d2. Deterministic rendering and HTML parser checks are not screenshots. Six full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.

Review covers independently retrieved Sesame, SynComY and SPC primary main texts/captions, the Azotobacter primary abstract, and SPC supplement captions S1-S12 plus selected figure pixels S2/S4/S5/S8. Other supplements/images, the mathematical framework and raw data are not certified. No access bypass, new topology, Edison spend or experimental protocols. Non-graph SPC follow-up #1855 remains 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]

Self-adversarial review refreshed at exact head 1e4ed39 after propagating the real CI correction #1899. Not independent approval.

Original head: 9b429a9. Current parent: 5c3a892. 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 c67752772b6327c130ea21cca44b43ed5e7e996dfcc9892f1f72e0667e4ba17a).

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 23.88s
Test log SHA256: 7f914a11bd539f70d4db1e29cf6f956f9f594224edcc18e423feb11172641196. Fresh docs-current passed with a clean worktree; log SHA256 259b68aab908650ebf8a445a102c8518a17deff1878f5f180f285fcf3042d5d2.

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 ce26ebd7735eb5634f266522adddf619a63bdca7.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 39ca02efdc5f14a44fb4706e906f2d05ae62b92629c28022a1cdefbadd1dab3e.
Tree dd9b362e73c0b7c726f325ce87947b0872af13ca matches the independently computed clean merge.
Compared with historical tree 87b5cafab329801462365ec663c3f4522d505e82, 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 bb21ea2b0fbd9f26c7098288cc0cb3e50edb47c0 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.