SynCom35 metadata: verify strain roster, control identity and assay-specific cultivation conditions #1378

Non-graph follow-up for Dangl_SynComm_35.yaml (CommunityMech:000022). Primary main body and author-submitted GEO protocol.

The current taxonomy aggregates overlapping taxonomic ranks rather than enumerating 35 strains, assigns syntrophic/cross-feeder roles without matching measurements, and calls E. coli DH5alpha a root negative control. Verify Dataset S1 and supplementary methods before revising canonical identities; the main body does not substantiate that control phenotype. Distinguish SynCom35 members, smaller suppressor/nonsuppressor communities and challenge strains.

Current MS/sucrose/22 C/16-hour-light cultivation metadata differs from the GEO root transcriptome protocol (Johnson medium, 21/18 C, 9-hour-light/15-hour-dark). These may be different assays; do not silently harmonize them. Root-length, acute reporter and chronic RNA-seq outcomes have different denominators and times. Check the 10+13+11 strain-count summary against the source's assay-specific counts. Background MAMP examples and generic nutrient-role prose should not be presented as exact treatments or demonstrated mechanisms. Graph-only edits leave these fields unchanged.

Deduplication: 706 all-state issue titles/bodies and ignored/hidden-inclusive local reports, research, history, tests and scripts; relevant #401 and #754 read. Not every issue comment was searched.