Soil microbial dark matter explored from genome-resolved metagenomics

Abstract Soil contains a vast number of unidentified microbes, known as soil microbial dark matter. This is an important source of microbial biodiversity and genetic resources1,2, but has yet to be fully explored. 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.