DNA sequencing and metagenomics of cultivated and uncultivated chernozems in Russia

Abstract In this study, we analyzed the microbiomes of uncultivated (virgin) and cultivated (cropland) soils from the southern part of Russia using DNA shotgun deep sequencing and metagenomic studies. The processed reads were mapped to the nucleotide sequences of bacteria, fungi, archaea, and viruses extracted from the non redundant database of NCBI. Our data indicate that Archaea and Fungi are more abundant in the virgin soil. The analysis of the top ten most abundant taxa from phylum to species levels revealed only slightly statistically significant differences between the microbial communities of the soils. In contrast, among the less abundant organisms at all taxa levels, we detected considerable differences between the virgin soil and the cropland microbiomes. The higher biodiversity of the virgin soil was confirmed by functional annotation and abundance analysis using the eggNOG and KEGG databases. Collectively, our data strongly indicate that the biodiversity of virgin soil is much higher, suggesting that intensive farming reduces the microbial biodiversity and causes specific changes in the pattern of less abundant microbiome taxa.