Variovorax SynCom28 graph: separate compartment enrichment, competition hypothesis and CF313 mutant assay #1471

CommunityMech:000028; GLBRC_Populus_Variovorax_SynCom28.yaml; PMID:41543249, doi:10.1128/msystems.01605-25.

Source-based self-adversarial review found three connected overclaims. The 28-strain experiment measures relative endosphere/rhizosphere DNA enrichment after three weeks, not absolute colonization efficiency or reduced competition caused by spatial separation. Isolates span putative species; this is not an established single-species competition experiment. Resource competition is an author-proposed strategy supported by growth/enrichment associations, not selectively measured partner harm or demonstrated mediation of compartment partitioning.

The CF313 deletion of PMI12_01353 abolishes sole-fucose growth and reduces recovered root CFUs in P. deltoides (reported P=0.0022). It does not establish priority effects, facilitation of other strains, a general benefit of pathway possession, or causation of the 28-member compartment-enrichment pattern. Several intact-pathway strains did not grow on fucose; only CF313/OV700/YR750 showed the reported growth. The paper did not quantify host fucose. Keep this existing node as a bounded intrinsic CF313 result with its exact canonical preferred name, not a genus-only self-edge or community-wide facilitation type. Remove both unsupported downstream arrows rather than attach the mutant assay to the community enrichment outcome.

Acceptance: bound all three existing nodes; preserve positive observations and qualify competition as HYPOTHESIZED; explicitly name the canonical community participants while assigning only CF313 to the mutant result; reuse the existing L-fucose grounding; remove unsupported biological-process/category assignments and causal arrows; add a focused knowledge gap, append-only history, tests, generated page and hash-bound review/validation outputs. No new causal structure or provider spend is required. Non-graph metadata remains outside this repair and is not certified.

The record doubles as a shared-CURIE auditor fixture. Preserve the original synthetic all-community-level behavior tests separately from the changing scientific record; retain exact-name versus CURIE-only canaries, add a live CF313 precision test, and measure the connectivity census before changing its upper bound. Do not weaken auditor matching semantics or invent species IDs.

Scope: whole record and complete cached primary main body/Methods/captions read, despite stale abstract_only front matter. PMC public browser access presented reCAPTCHA; no bypass. No figure images, separate supplementary files, raw data, or analysis code independently inspected. No complementation rescue or full-panel mutant-replacement result is claimed.

Dedup: 788 all-state issue titles/bodies and ignored/hidden-inclusive reports, research, history, tests, scripts and workflows. All eight matched issue bodies read (#1251/#762/#615/#524/#485/#312/#18/#12); no exact source-specific duplicate in that scope. #524 remains a broader ambiguity question, not fixed by this curation. The initial local scan used nonexistent data/history and failed; corrected scan used history/ and retained 178 lines. Not every comment or PR review inspected. This review is not independent approval.