Separate transfer, prediction and mediation in four community graphs (batch107)

[realmarcin]

Scope

Closes #1837.
Closes #1838.
Closes #1839.
Closes #1840.
Identity #1841 remains open.

• Retain recruitment, distinguishing chemotaxis from motility and qualifying its necessity for the cue response.; Retain the measured cue response without asserting nutrient uptake or resolved bacterial benefit.; Preserve experimentally supported thiamine transfer and growth rescue; qualify in-plant mediation.; Preserve fungal and host benefits and the source mutualism interpretation without exclusive mediator or flux claims.
• Preserve sulfur-granule observations; remove commensalism and redundant source, explicitly leaving species grounding unresolved.; Preserve the source episymbiosis hypothesis without confirmed cell identity or fitness interpretation; remove the spatial causal arrow.; Preserve lineage-specific genomic/structural predictions with provenance, not measured flux or host exchange.
• Preserve predicted exchange and measured metabolite production with iNAP provenance and an explicitly partial upstream mechanism.; Preserve supported Th17 induction; remove colonization typing and the mismatched innate-only GO annotation.; Preserve positive host-protection endpoints without competition, eradication or exclusive SFB mediation.
• Retain protective fungal/aflatoxin endpoints with the storage-time boundary, without reciprocal competition.; Retain rhizobia-dependent nodulation facilitation with participant scope excluding the fungal target.; Retain combined positive outcomes, qualifying causal coupling and removing misplaced colonization/host-defense typing.

Adversarial Review

• Whole original targets and changed graph/discussion diffs reviewed. All 13 original nodes and nine directions have dispositions: retain 13 nodes and seven qualified existing directions, remove two spatial arrows and rename five nodes. No new topology or Edison spend.
• Challenge removal versus lost evidence: retain demonstrated bacterial-to-fungal vitamin transfer, fungal/host benefits, sulfur-granule imaging, tentative CPR associations and lineage-specific predictions, immune induction and protective host/plant outcomes. Preserve qualified source hypotheses rather than rejecting positive observations.
• Suillus: distinguish ureidosuccinate chemotaxis from pregnenolone motility. Cue response does not establish nutrient uptake or resolved bacterial benefit. Labeled thiamine in fungal hyphae supports direct transfer; preserve CROSS_FEEDING and host mutualism interpretation. Qualify recruitment necessity and exclusive in-plant vitamin mediation. Preserve thiamine-free P20 and prior Five records where the growth medium is defined by what it omits, and naming its contents would be wrong #583 context.
• Spring: remove unestablished commensalism and spatial arrows. Proximity does not cause attachment or encoded metabolic capacity. Failed FISH leaves imaged-cell identity tentative; predicted genes and structures are not measured flux or exchange. The legacy Thiothrix species grounding exceeds the source 51% average amino-acid similarity and is explicitly uncertified. Keep needs_research under Resolve sulfide-spring Thiothrix participant identity before certifying its causal graph #1841, not completed review.
• Adversarial correction: HydDB was initially copied onto sulfur-enzyme provenance. Narrow that evidence to METABOLIC and AlphaFold2; retain HydDB only for hydrogenases. Add a second spring curation event and fifth append-only history without rewriting the first. Interrupt the first verification with SIGINT/exit130 for this factual correction, archive its partial report/logs and run all final gates afresh. This was not a timeout. A separate in-memory control/mutation/restore probe passes, rejects reinserting HydDB at the exact tool-set assertion, then passes again; canonical files remain unchanged.
• Chicken: iNAP2.0 predicted exchange and measured supernatant metabolites do not prove recipient uptake or exclusive mediation. Preserve supported immune induction and host protection; remove mismatched colonization/competition typing and innate-only GO annotation. Keep both existing directions explicitly partial. No pathogen-enhancement procedures, challenge protocols, strain-selection advice or genetic designs are added.
• ARC: retain reduced aflatoxin after 12 months of storage, not an immediate field endpoint. ARC alone did not induce nodulation; preserve the rhizobia-dependent comparison and identity-only node scopes. Remove reciprocal-competition and aggregate colonization/host-defense annotations. Parallel positive endpoints and omics do not isolate the proposed carbon/nitrogen feedback. Preserve Genus-level grounding conflates included and excluded strains in SynCom ARC (000314) #300/Counter-selection (candidates deliberately excluded) has no machine-readable home in the schema #307 counter-selection and #183 second triage: the constructed-community signal is also exhausted, and names three distinct blockers #653 supplement context; no toxin-production or optimization procedures.
• Twenty-five graph and six discussion quotations match fresh primary text and unchanged caches. Four independently retrieved primary XML sources have bounded actual read spans recorded in the ledger. No figure-pixel, separate-supplement, raw-data or full-pipeline certification. Cache headers with abstract_only labels can contain body text; no cache imports or global absence claims. Literal matching is distinct from entailment.
• Four guarded initial writes plus one guarded provenance correction produce five append-only histories. All 456 other records, all 923 caches, non-graph raw blocks and prior history/decision files remain byte-identical. No schema, validator, census-threshold or runtime-rule changes. The global participant census is unchanged; legacy spring identity links are not certified.
• Eight focused tests and 967 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks and all five histories validate. The network retains 56 baseline warnings and zero structural defects. Deterministic rendering and exact HTML parsing cover 456 pages, 1372 node descriptions and 543 arrows, not screenshots. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.
• Repair issues Separate Suillus recruitment and vitamin transfer from untested causal mediation #1837-Bound ARC outcome graph to protective assays and distinguish nodulation from aggregate yield #1840 are addressed but remain open until protected-main merge. Identity Resolve sulfide-spring Thiothrix participant identity before certifying its causal graph #1841 stays open. Existing license The paywalled-text gate exempts a whole cache file on any CC substring, and the licence is still not recorded #949, loader Generated MicrobialCommunity loader fails on inlined TaxonDescriptor and CultureCollectionEnum keys #1703 and DOI-cache case On Linux, linkml-reference-validator 0.1.7 finds none of the 107 committed doi_ caches: #690 renamed them to a casing it cannot read #1091 are not certified. Denied and unanswered Edison scopes remain untouched. Self-review is not independent approval; no artificial CI, protection bypass or premature branch deletion.
• Corpus status is 341 reviewed, 68 pending and 51 needs_research, not completion. Postcommit docs-current and exact-head publication require separate receipts and are not preasserted here.

Verification And Output Records

967 passed in 327.16s (0:05:27); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; five append-only histories validated. 42 recorded gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

All 13 nodes remain with five renames; seven existing directions are retained and qualified, two spatial arrows removed. All 31 reviewed graph/discussion quotations match fresh primary text and unchanged caches; literal matching is not entailment. All 456 other records, all 923 caches and non-graph raw blocks are unchanged. Corpus: 341 reviewed, 68 pending, 51 needs_research. Network: 56 existing warnings, zero structural defects. Participant census and thresholds are unchanged.

The adversarial pass found and corrected HydDB attribution on sulfur-enzyme evidence. A second spring curation event and fifth history preserve the original entry unchanged. Initial verification was interrupted for this factual correction, not a timeout; its partial logs are archived and all final gates were rerun.

Decisions, cache provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 b32a89283094b00cef0bbb5d819c7eedcef8809ad83c95b897438ec1601bb8af. Deterministic rendering and HTML parser checks are not screenshots. Four 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.

Four primary XML sources were independently retrieved; actual review spans are bounded in the ledger, not whole-paper/supplement/figure/raw-data certification. No new topology or Edison spend. No pathogen-enhancement or toxin-production procedures are added. Spring identity #1841 remains unresolved and its record stays needs_research. This COMMENT is self-review, not independent approval. Protected-main merge remains required.

Source Limits

• Fresh both-root baseline before source reads:460records,923caches,56existing warnings,zero structural defects. Whole four targets and all13nodes/9directions reviewed. Retain13nodes/7existing directions,remove2spatial arrows,rename5nodes. No new topology or Edison submission/spend.
• Four primary EuropePMC XML sources independently retrieved with CC BY4.0 metadata. Suillus abstract/introduction1-60 and results/discussion242-503 read; spring abstract/background1-65,methods193-268,results270-485 and513-662 read; chicken bounded immune/protection/prediction results260-393 and discussion427-522 read, plus abstract; ARC extracted main text1-217 read. Other spans were indexed or not read. No figure-pixel,separate-supplement,raw-data or full-pipeline certification.
• Existing caches used for headers,bounded context and normalized quote checks,not exhaustive duplicated full-text review. Suillus cache is PMID_41454778.md and contains body text despite abstract_only metadata. Chicken has two existing cache representations; no new cache imports. Large single-line cache output was truncated and is not claimed as read. No license949,loader1703 or DOI-case1091 certification.
• Suillus:preserve demonstrated bacterial-to-fungal thiamine transfer,auxotrophy rescue,recruitment and fungal/plant benefits. Distinguish pregnenolone motility from ureidosuccinate chemotaxis. Remove nutrient-consumption typing from cue response; preserve host mutualism interpretation but not measured host-fungal flux or exclusive thiamine mediation. Thiamine-free P20 and prior583 context remain unchanged.
• Spring:preserve sulfur-granule imaging,putative CPR association and lineage-specific metabolic predictions. Remove unestablished commensalism and both spatial arrows; add bounded genomic/structural provenance. Current canonical NCBITaxon:1031 link exceeds the source51%amino-acid similarity; legacy references remain explicitly uncertified pending coordinated identity repair1841. This record remains needs_research rather than being counted fully reviewed.
• Chicken:preserve measured immune induction,metabolite-production evidence and host protection. Predicted iNAP2.0 exchange is not measured recipient transfer; protective association is not exclusive mediation. Remove colonization/competition typing and misplaced innate-only GO annotation. Evidence correction only; no new pathogen enhancement,genetic designs,strain-selection advice,challenge methods,growth optimization or causal mechanisms.
• ARC:preserve protective fungal,nodulation,photosynthesis and yield outcomes. Attach85.6%aflatoxin decrease to12months storage and retain the rhizobia-dependent nodulation boundary. Remove reciprocal-competition and aggregate-colonization/host-defense annotations; narrow separate node participants. Both outcome-contribution directions remain qualified,not isolated mechanisms or a proven feedback loop. Prior300/307counter-selection and653supplement provenance remain unchanged. No toxin-production procedures or optimization advice.
• Graph repairs1837-1840remain open until protected-main merge. Identity1841remains open after repair merge. Fresh all-state issue-title/body search matched653/583/307/304/300; all five bodies read. Scoped local search includes ignored/hidden files,excluding.git/docs/site/references_cache and credentials; relevant caches separately covered. PRs/comments not exhaustively searched. No reusable taxon match found in ignored/hidden-inclusive kb/taxa search for the reviewed taxa/IDs.
• Only graphs,new focused discussions and curation events change. All456other records,923caches,non-graph raw blocks and prior histories/decisions preserved. No schema,validator,threshold or runtime-rule changes. Spring remaining identity uncertainty is explicit; other non-graph taxonomy,abundance,role,cultivation and evidence claims are not recertified. Self-review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication are not preasserted.
• Self-adversarial review corrected a too-broad computational tool chain before publication:HydDB removed from Doudnabacteria sulfur-enzyme provenance and retained for hydrogenases. A fifth append-only history and second spring curation event preserve the initial entry unchanged. Initial verification was deliberately interrupted with SIGINT/exit130 for this factual correction,not a timeout,and its partial logs are archived;all final gates run afresh.

Dependency

Draft depends on #1835. 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 f1c2170; not independent approval.

• Retain recruitment, distinguishing chemotaxis from motility and qualifying its necessity for the cue response.; Retain the measured cue response without asserting nutrient uptake or resolved bacterial benefit.; Preserve experimentally supported thiamine transfer and growth rescue; qualify in-plant mediation.; Preserve fungal and host benefits and the source mutualism interpretation without exclusive mediator or flux claims.

• Preserve sulfur-granule observations; remove commensalism and redundant source, explicitly leaving species grounding unresolved.; Preserve the source episymbiosis hypothesis without confirmed cell identity or fitness interpretation; remove the spatial causal arrow.; Preserve lineage-specific genomic/structural predictions with provenance, not measured flux or host exchange.

• Preserve predicted exchange and measured metabolite production with iNAP provenance and an explicitly partial upstream mechanism.; Preserve supported Th17 induction; remove colonization typing and the mismatched innate-only GO annotation.; Preserve positive host-protection endpoints without competition, eradication or exclusive SFB mediation.

• Retain protective fungal/aflatoxin endpoints with the storage-time boundary, without reciprocal competition.; Retain rhizobia-dependent nodulation facilitation with participant scope excluding the fungal target.; Retain combined positive outcomes, qualifying causal coupling and removing misplaced colonization/host-defense typing.

• Whole original targets and changed graph/discussion diffs reviewed. All 13 original nodes and nine directions have dispositions: retain 13 nodes and seven qualified existing directions, remove two spatial arrows and rename five nodes. No new topology or Edison spend.

• Challenge removal versus lost evidence: retain demonstrated bacterial-to-fungal vitamin transfer, fungal/host benefits, sulfur-granule imaging, tentative CPR associations and lineage-specific predictions, immune induction and protective host/plant outcomes. Preserve qualified source hypotheses rather than rejecting positive observations.

• Suillus: distinguish ureidosuccinate chemotaxis from pregnenolone motility. Cue response does not establish nutrient uptake or resolved bacterial benefit. Labeled thiamine in fungal hyphae supports direct transfer; preserve CROSS_FEEDING and host mutualism interpretation. Qualify recruitment necessity and exclusive in-plant vitamin mediation. Preserve thiamine-free P20 and prior #583 context.

• Spring: remove unestablished commensalism and spatial arrows. Proximity does not cause attachment or encoded metabolic capacity. Failed FISH leaves imaged-cell identity tentative; predicted genes and structures are not measured flux or exchange. The legacy Thiothrix species grounding exceeds the source 51% average amino-acid similarity and is explicitly uncertified. Keep needs_research under #1841, not completed review.

• Adversarial correction: HydDB was initially copied onto sulfur-enzyme provenance. Narrow that evidence to METABOLIC and AlphaFold2; retain HydDB only for hydrogenases. Add a second spring curation event and fifth append-only history without rewriting the first. Interrupt the first verification with SIGINT/exit130 for this factual correction, archive its partial report/logs and run all final gates afresh. This was not a timeout. A separate in-memory control/mutation/restore probe passes, rejects reinserting HydDB at the exact tool-set assertion, then passes again; canonical files remain unchanged.

• Chicken: iNAP2.0 predicted exchange and measured supernatant metabolites do not prove recipient uptake or exclusive mediation. Preserve supported immune induction and host protection; remove mismatched colonization/competition typing and innate-only GO annotation. Keep both existing directions explicitly partial. No pathogen-enhancement procedures, challenge protocols, strain-selection advice or genetic designs are added.

• ARC: retain reduced aflatoxin after 12 months of storage, not an immediate field endpoint. ARC alone did not induce nodulation; preserve the rhizobia-dependent comparison and identity-only node scopes. Remove reciprocal-competition and aggregate colonization/host-defense annotations. Parallel positive endpoints and omics do not isolate the proposed carbon/nitrogen feedback. Preserve #300/#307 counter-selection and #653 supplement context; no toxin-production or optimization procedures.

• Twenty-five graph and six discussion quotations match fresh primary text and unchanged caches. Four independently retrieved primary XML sources have bounded actual read spans recorded in the ledger. No figure-pixel, separate-supplement, raw-data or full-pipeline certification. Cache headers with abstract_only labels can contain body text; no cache imports or global absence claims. Literal matching is distinct from entailment.

• Four guarded initial writes plus one guarded provenance correction produce five append-only histories. All 456 other records, all 923 caches, non-graph raw blocks and prior history/decision files remain byte-identical. No schema, validator, census-threshold or runtime-rule changes. The global participant census is unchanged; legacy spring identity links are not certified.

• Eight focused tests and 967 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks and all five histories validate. The network retains 56 baseline warnings and zero structural defects. Deterministic rendering and exact HTML parsing cover 456 pages, 1372 node descriptions and 543 arrows, not screenshots. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

• Repair issues #1837-#1840 are addressed but remain open until protected-main merge. Identity #1841 stays open. Existing license #949, loader #1703 and DOI-cache case #1091 are not certified. Denied and unanswered Edison scopes remain untouched. Self-review is not independent approval; no artificial CI, protection bypass or premature branch deletion.

• Corpus status is 341 reviewed, 68 pending and 51 needs_research, not completion. Postcommit docs-current and exact-head publication require separate receipts and are not preasserted here.

967 passed in 327.16s (0:05:27); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; five append-only histories validated. 42 recorded gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

All 13 nodes remain with five renames; seven existing directions are retained and qualified, two spatial arrows removed. All 31 reviewed graph/discussion quotations match fresh primary text and unchanged caches; literal matching is not entailment. All 456 other records, all 923 caches and non-graph raw blocks are unchanged. Corpus: 341 reviewed, 68 pending, 51 needs_research. Network: 56 existing warnings, zero structural defects. Participant census and thresholds are unchanged.

The adversarial pass found and corrected HydDB attribution on sulfur-enzyme evidence. A second spring curation event and fifth history preserve the original entry unchanged. Initial verification was interrupted for this factual correction, not a timeout; its partial logs are archived and all final gates were rerun.

Decisions, cache provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 b32a89283094b00cef0bbb5d819c7eedcef8809ad83c95b897438ec1601bb8af. Deterministic rendering and HTML parser checks are not screenshots. Four 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.

Four primary XML sources were independently retrieved; actual review spans are bounded in the ledger, not whole-paper/supplement/figure/raw-data certification. No new topology or Edison spend. No pathogen-enhancement or toxin-production procedures are added. Spring identity #1841 remains unresolved and its record stays needs_research. 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 3807f528ce04f9e9f410f2948acedb89feee0914.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 30dbdefc5c0c4e16da21cedc89dbfb918d06f16db09e444da4b0880f4ee95c47.
Tree 793ad54ce37db1d97ad3a006c4610179a4d17e93 matches the independently computed clean merge.
Compared with historical tree f67514fe657a504bbfbe4825943558b24b7f50e5, 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 08d44b9bdfd649007ef715601f08c5f0a3f44061 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.