Separate Ruegeria transcript responses from colonization and reverse cross-feeding #1881

Finding

CommunityMech:000162: recognition-related transcription is not a measured colonization benefit; chitin/lipid transcription is not substrate transfer from bacterium to diatom. The two arrows to the transcription node either restate response or use shared chitin-related vocabulary without demonstrating mediation. Preserve diatom carbon-supported bacterial growth and distinguish DMSP/GlcNAc expression evidence from proline/guanosine net drawdown in Table 1 of the 2020 paper. The 2017 B12-limited assay and 2020 L1 assay must not be conflated.

Sources And Limits

https://pubmed.ncbi.nlm.nih.gov/28631440/
https://pubmed.ncbi.nlm.nih.gov/33097854/

Three whole canonical records read. Fresh primary abstracts and DOI metadata for nine source identities; complete extracted main bodies for the 2014 climate, HP15 genome and 2020 partitioning papers; full extracted 2011 aggregation, 2017 recognition and 2017 consortium PDFs. Selected figures visually inspected. The 2018 diel main body was read from existing curator text, not independently retrieved full text. Chemotaxis is bounded to the abstract; MEPS full PDF returned HTTP 401 and was not bypassed. No new publication bodies or cache changes.

All-state issue title/body dedup and ignored/hidden-inclusive local searches were recorded. Nine matching existing issues were read; historical PR comments were not exhaustively searched.

Lifecycle

Address existing-graph correction in batch113; close only after protected-main merge. Source-based self-adversarial review is not independent approval.