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.

Phytopathogenic bacteria belonging to the Pectobacterium and Dickeya genera (soft-rot Pectobacteriaceae) are in the focus of agriculture-related microbiology because of their diversity, their substantial negative impact on the production of potatoes and vegetables, and the prospects of bacteriophage applications for disease control. Because of numerous amendments in the taxonomy of P. carotovorum, there are still a few studied sequenced strains among this species. The present work reports on the isolation and characterization of the phage infectious to the type strain of P. carotovorum. The phage Arno 160 is a lytic Podovirus representing a potential new genus of the subfamily Autographivirinae. It recognizes O-polysaccahride of the host strain and depolymerizes it in the process of infection using a rhamnosidase hydrolytic mechanism. Despite the narrow host range of this phage, it is suitable for phage control application.