Root and Rhizosphere Microbiome of Tomato Plants Grown in the Open Field in the South of West Siberia under Mineral Fertilization

Agricultural practices can affect root-associated microbiota, but the effect of fertilization is still poorly examined. The aim of this study was to obtain 16S and ITS metagenomic profiles of tomato rhizosphere and root endosphere under mineral (NPK) fertilization in the open field experiment in the south of West Siberia. We found 6 bacterial and 3 fungal phyla in the roots and 24 bacterial and 16 fungal phyla in the rhizosphere. Proteobacteria and Actinobacteria together contributed 90% of the total number of sequence reads in roots and 50% in the rhizosphere, whereas Ascomycota ultimately prevailed in OTUs’ richness and abundance in both biotopes. Fertilization changed the relative abundance of 32 bacterial and 14 fungal OTUs in the rhizosphere and of 7 bacterial and 3 fungal OTUs in roots. The revealed root bacteriobiome response to conventional mineral NPK fertilization by the dominant taxa at the high taxonomic level (class) illustrates well the role of NPK-changed plant metabolism in shaping endophytic microbiota and hence fertilization potential in enhancing plant growth-promoting microorganisms and mitigating plant pathogens. Using fertilization rate gradient in further research may bring a more detailed understanding of how to modify and even fine-tune root-associated microbiomes in order to enhance crops’ health and yields.