Distribution of <i>Plasmopara viticola</i> Causing Downy Mildew in Russian Far East Grapevines

Downy mildew is a severe disease that leads to significant losses in grape yields worldwide. It is caused by the oomycete <i>Plasmopara viticola</i>. The study of the distribution of this agent and the search for endophytic organisms that inhibit the growth of <i>P. viticola</i> are essential objectives to facilitate the transition to sustainable and high-yield agriculture, while respecting the environment. In this study, high-throughput sequencing of the <i>ITS</i> (ITS1f/ITS2 region) and <i>16S</i> (V4 region) amplicons was employed to analyze 80 samples of leaves and stems from different grapevine species and cultivars grown in the Russian Far East (<i>Vitis amurensis</i> Rupr., <i>Vitis coignetiae</i> Pulliat, and several grapevine cultivars). The analysis revealed the presence of <i>P. viticola</i> in 53.75% of the grape samples. The pathogen <i>P. viticola</i> was not detected in <i>V. amurensis</i> samples collected near Vladivostok and Russky Island. Among the <i>P. viticola</i>-affected samples, only two (out of the eighty analyzed grape samples) from the Makarevich vineyard in Primorsky Krai exhibited disease symptoms, while the majority appeared visually healthy. We also found six distinct <i>P. viticola</i> ASVs in our metagenomic data. Based on phylogenetic analysis, we hypothesize that the <i>P. viticola</i> population in the Russian Far East may have originated from the invasive <i>P. viticola</i> clade <i>aestivalis</i>, which has spread around the world from North America. To identify putative microbial antagonists of <i>P. viticola</i>, a differential analysis of high-throughput sequencing data was conducted using the DESeq2 method to compare healthy and <i>P. viticola</i>-affected samples. The in silico analysis revealed an increased representation of certain taxa in healthy samples compared to <i>P. viticola</i>-affected ones: fungi—<i>Kabatina</i> sp., <i>Aureobasidium</i> sp., and <i>Vishniacozyma</i> sp.; bacteria—<i>Hymenobacter</i> spp., <i>Sphingomonas</i> spp., <i>Massilia</i> spp., <i>Methylobacterium-Methylorubrum</i> spp., and <i>Chryseobacterium</i> spp. This in-silico-obtained information on the potential microbial antagonists of <i>P. viticola</i> serves as a theoretical basis for the development of biocontrol agents for grapevine downy mildew.