Assessment of Soil Health Through Metagenomic Analysis of Bacterial Diversity in Russian Black Soil

Abstract

Soil health is a critical determinant of agricultural productivity and environmental sustainability. Traditional assessment methods often fail to provide a comprehensive understanding of soil microbial communities and their functions. This study addresses this challenge by employing metagenomic techniques to assess the functionality of soil microbiomes in Russian black soil, renowned for its high fertility. We utilized shotgun metagenomic sequencing to analyze soil samples from Western Siberia subjected to different degrees of agro-soil disturbance. We identified functional genes involved in carbon (accA, argG, acsA, mphE, miaB), phosphorus (phoB, ppa, pstB, pnp, phnJ), and nitrogen (queC, amiF, pyrG, guaA, guaB, napA) metabolic pathways and associated with changes in microbial diversity, in general, and higher representation of certain bacterial species-Bradyrhizobium spp. The results demonstrated significant differences in microbial composition and functional potential between tillage treatments. No-Till technology and conventional tillage practices promoted beneficial microbial communities and enhanced soil health compared to long-term fallow soil. This work underscores the potential of metagenomic analysis in providing a comprehensive understanding of soil health, marking a significant advancement in the field.

Keywords: Russian black soil; agricultural productivity; no-till technology; shotgun sequencing; soil metagenome.

Figure 1

Comparison of median values of relative abundance of top-20 species for groups of leached black earths. Relative abundance of species in % is located on Y-axis. On X-axis, there are subgroups of soil samples.

Figure 2

The alpha diversity of the taxonomic composition of the leached black earths. The values of the Shannon index are located on the Y-axis. The X-axis shows the subgroups of the soil samples. The shape of the graph represents the distribution density of the Shannon index. The boxplot shows the median, quartiles, and spread of the Shannon index among the data.

Figure 3

The beta diversity of the taxonomic composition of the leached black earths at the level of species. The NMDS graph shows the clustering of soil samples (dots on the figure). The blue dots represent soil samples from the sample subgroups with long-term fallow, the green dots are for the soil samples with conventional tillage, and the red dots are for the soil samples with No-Till technology.

Figure 4

A comparison of the median values of the relative representation of genes for the groups of leached black earths. The logarithm of relative abundance is located on the Y-axis. Gene names with statistically significant differences in relative abundance between the soil groups are located on the X-axis. The blue bars represent abundance for the long-term fallow group, the green bars represent the abundance for the conventional tillage group, and the red bars represent the abundance for the No-Till technology group.

Figure 5

The heatmap for signature pairs, compiled according to their median relative abundance. The center of the scale is set at 500 readcounts. ‘Bradyrhizobium sp. CCBAU 051011|acsA’ and ‘Bradyrhizobium sp. 200|pstB’ represent the highest abundance.