East River core graph: separate core gene capacity from one-floodplain transcription #1418

East_River_Floodplain_Core_Microbiome.yaml, PMID:34022966, https://doi.org/10.1186/s40168-020-00957-z.

The reservoir-to-capacity arrow is a part/whole restatement. Reservoir-to-low-carbon activity conflates conserved genomic inventory with a one-time transcription snapshot; the paper explicitly says gene abundance did not predict transcription. Remove both arrows and categorical niche partitioning. The operational core comprises 42 genomes detected in >=89/94 samples; 2016 RNA was sampled only in floodplain L, notwithstanding broader abstract wording. Transcripts are not measured reaction flux or a carbon manipulation.

Narrow core participants to canonical Betaproteobacteria and Gemmatimonadota groupings supported as core members. Do not propagate a phylum-level Nitrospirae observation into the canonical Nitrospira genus ID or credit non-core Acidobacteriota to these core/low-carbon claims. Any newly exposed disconnected warnings must be reported, not repaired with fabricated links. Taxonomy and non-graph scope need a separate follow-up; existing #401 concerns GTDB withholding, not correction of the NCBI rank mismatch.

Deduplication: 742 all-state issue titles/bodies and ignored/hidden-inclusive local review, research, history, tests, scripts and workflow files. Relevant #401, #573, #594 and #595 read; no exact duplicate in that scope. Not every issue comment searched. Source review used cached primary main-body text; no visual figures, raw-data analysis or external supplement review.