Bound URL genomic functions and remove contextual causal arrows #1501

Source-based self-adversarial finding

kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml, PMID:39696556, four nodes and two arrows.

The graph presents the two-site lithology association as an isolated driver, shared genome annotations as cross-feeding, and cross-depth genotype similarity as colonization facilitation. Its two incoming arrows to proposed hydrogen transfer are contextual inclusion links rather than demonstrated causal mechanisms; one asserts simultaneous sulfate reduction and hydrogen production more strongly than the primary discussion.

Resolution

Retain the observed community/genotype comparisons and positive genomic results. Identify functions as coding potential, qualify the authors' proposed hydrogen transfer, and distinguish iRep replication estimates from direct growth-rate, migration or mutation measurements. Remove the two contextual arrows. Use both canonical habitat placeholders with their distinct labels, limiting Horonobe-only claims to its own participant. Preserve non-graph data, add focused exact-node knowledge gaps and regression coverage.

Complete cached primary main text, Methods and embedded captions read; no original figure images, supplementary files, raw data or code audited. Publisher main text corroborated. No new causal structure is required for these repairs. Self-adversarial review is not independent approval.

Keep open until the repaired PR merges through protected main.