The Saline Lake Microbiome Resource: a genome-resolved atlas for biosynthetic discovery

Saline lakes harbor unique microbial diversity and biosynthetic potential, yet remain largely unexplored genomically. We constructed the Saline Lake Microbiome Resource (SLMR), a genome-resolved atlas built from 567 water and sediment samples (paired by lake) from 76 lakes spanning salinities of 0.29–595.84 g/L and pH 6.15–10.38, covering brackish to hypersaline conditions. The resource comprises 48,830 metagenome-assembled genomes and ~140,000 predicted biosynthetic gene clusters (BGCs), most showing substantial divergence from characterized reference clusters. Its 24,780 species representatives span 151 phyla; 94.69% lack species-level annotation and 89.77% are absent from existing genome catalogs. Water and sediment harbor distinct, complementary microbial and biosynthetic profiles along the salinity gradient, with biosynthetic richness comparable to marine and coral microbiomes. Catalog mining identified the poorly characterized, BGC-rich order Multivoradales, and enrichment cultivation yielded 53 additional MAGs. Its candidate family UBA5704 has an exceptionally large biosynthetic repertoire, exemplified by a complete, novel 21.4-kb ranthipeptide cluster resolved by structural modeling. SLMR provides an open resource for biosynthetic discovery in extreme environments.