Genome-resolved metagenomics reveals rare taxa and functional traits in two contrasting agricultural fields

Abstract Agricultural soils harbor highly diverse and functionally rich microbial communities, yet much of their genomic potential remains unexplored. Here, we present a genome-resolved metagenomic analysis of 455 soil samples collected at different depths and seasonal stages across two Danish agricultural fields representing sandy and clay soil types. Ultra-deep shotgun sequencing enabled the recovery of 58,831 medium to high-quality prokaryotic metagenome-assembled genomes (MAGs), which were dereplicated into 56,340 strain-level MAGs and 9,090 species-level genome bins (SGBs) spanning 49 prokaryotic phyla. The majority of the SGBs represented previously uncharacterized species. Functional annotation revealed extensive biosynthetic and metabolic potential, including 46,913 biosynthetic gene clusters and prevalent genes linked to nitrogen cycling. Notably, 378 MAGs harbored the nitrous oxide reductase gene nosZ. Soil type and depth strongly influenced microbial diversity and functional traits. These findings provide a resource for linking microbial traits to soil function of potential value for better sustainable agricultural practice.