New insights into phylogeny and function of the agricultural soil microbiome

Soil is a habitat that hosts an abundant and diverse microbial community. At the same time, the soil microbiome plays a crucial role in ecosystem processes, such as biogeochemical cycles, and has been a main source for novel compound discovery, e.g. antimicrobials. In agricultural fields, the soil microbiome impacts soil fertility and plant health. Despite its significance, the soil microbiome remains poorly characterized, with few members being cultured and a small fraction of soil communities being represented in public genome collections even through culture independent characterization. Nevertheless, comprehensive understanding of the agricultural soil microbiome is key for providing sustainable solutions for crop production.

In this study, we aimed to better characterize the agricultural soil microbiome through deep metagenomic sequencing and genome resolved metagenomics. We sequenced 455 soil samples collected in two depths of two agricultural fields in Denmark, with different physical properties. The above yielded ~70 TB of raw sequencing data, which resulted in 58,831 medium to high quality metagenome-assembled genomes (MAGs), which could be further clustered in 9,090 species level genomes (SGBs) spanning 46 different bacterial and 3 archaeal phyla. Our genome catalogue covers unexplored diversity as 96.2% of the SGBs have not been previously reported. Characterization of the functional potential of the genomes revealed their role in a range of physicochemical pathways, such a nitrogen and sulfur cycling. In addition, we illustrated the broad and diverse biosynthetic potential of soil microbiome with the identification of > 46k biosynthetic gene clusters (BGCs), across 8,182 genomes. In general, our catalogue greatly expands the known soil prokaryotic diversity and provides a valuable genetic and genomic resource for understanding the role of microbes in soil ecosystem processes. This information can be used to study the response of agricultural soil in a changing environment and may be leveraged to design sustainable microbiome-based strategies to improve crop production and resilience.