Bound Trichodesmium helper hypotheses and remove cross-study causal arrows #1882

Finding

CommunityMech:000147: conserved colonization does not prove commensal neutrality; comparative gene complements do not prove mutualistic fitness effects; field co-expression does not demonstrate metabolite transfer. The proposed B12 direction is Trichodesmium to Alteromonas, and the 2017 genome permits facultative use rather than obligate B12 dependence. Remove habitat-setting and comparative-genome-to-field-expression arrows without demonstrated causal mediation. Restrict the field node to the canonical microbiome guild, not an asserted exact IMS101 field strain. Preserve the distinct ROS compound/process choice from #297.

Sources And Limits

https://pubmed.ncbi.nlm.nih.gov/28440800/
https://pubmed.ncbi.nlm.nih.gov/29382945/

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.