Soil microbial dark matter explored from genome-resolved metagenomics

<strong>Soil contains a vast number of unidentified microbes, known as soil microbial dark matter. This is an important source of microbial biodiversity and genetic resources</strong><strong>, but has yet to be fully explored.</strong><strong> In this study, we conducted the first large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalog) from 3,463 soil metagenomes. We identified 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which greatly expand archaeal and bacterial diversity across the tree of life. The uSGBs identified substantially increased the functional landscape and intra-species genome diversity of the soil microbiome, and provided large proportions of the 43,169 biosynthetic gene clusters and 8,544 CRISPR-Cas genes mined from the SMAG catalog. This suggests their potential for genetic resource exploitation. In addition, we determined that uSGBs contributed 84.6% of novel viral-host associations identified from the SMAG catalog. Our results demonstrate the richness of microbial dark matter in soil and highlight its potential. Furthermore, the SMAG catalog will serve as a valuable genomic database for understanding soil microbial biodiversity and exploiting novel genetic resources.</strong>