Cyprus bioleaching graph: remove discovery-order arrows and qualify plasmid CRISPR inference #1369

Source review of kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml (CommunityMech:000217), including complete primary main body and Tables 1-3: Lane et al., PMID:41381092.

The composition-to-plasmid arrow describes where plasmids were recovered. The repertoire-to-CRISPR arrow describes a specific example within that repertoire. Neither is a demonstrated causal transition. Gene annotations do not establish commensal fitness or expressed sulphur/metal functions. CRISPR spacers match two unbinned Acidithiobacillus-like contigs with conjugation-related genes; they support a putative plasmid interference model, not observed plasmid elimination, confirmed co-residence, or reciprocal competition among the community taxa.

Remove both unsupported arrows, keep the positive mineral/fraction-associated composition findings and the annotated plasmid repertoire, distinguish known host groups from unresolved Alphaproteobacteria-related assignments, and qualify the CRISPR proposal using the canonical Acidithiobacillus host. Add an anchored mechanistic gap. Do not turn the literature-derived sulphur pathway diagram into experimentally resolved interspecies flux. Figure images and supplements were not inspected in this review.

Deduplication: 700 all-state issue titles/bodies, relevant prior issues, and ignored/hidden-inclusive local review/history searches. Not every issue comment was searched.