Metagenomic Study of the Grapevine Decline Detected a Cocktail of Fungi Associated with Grapevine Trunk Diseases

This study analyzed the microbiome of three varieties differing in genotype and technical purpose: Cristal, Riesling, and Avgustin, all exhibiting decline symptoms of unknown etiology. A total of 92 symptomatic and asymptomatic grapevines were analyzed using ITS and 16S rRNA amplicon sequencing and molecular genetic methods. Phytoplasmas and the pathogenic bacteria <i>Xylella fastidiosa</i> and <i>Xylophilus ampelinus</i> were not present in the samples. The decline symptoms were associated with a cocktail of fungal pathogens that cause grapevine trunk diseases. In particular, the analysis revealed the causative agents of Botryosphaeria dieback (<i>Sphaeropsis</i> spp. and <i>Botryosphaeria</i> spp.), fungi associated with the Esca complex (<i>Phaeomoniella</i> spp., <i>Phaeoacremonium</i> spp., <i>Inonotus</i> spp., <i>Seimatosporium</i> spp., <i>Stereum</i> spp., and <i>Cadophora</i> spp.), and the causative agents of Phomopsis dieback (<i>Diaporthe</i> spp.). The symptoms of decline may be increased by several facultative grapevine pathogens that have been identified in microbiome (genera <i>Stemphylium</i>, <i>Alternaria</i>, <i>Aspergillus</i>, <i>Penicillium</i>, <i>Talaromyces</i>, and <i>Fusarium</i>). The metagenomic data of the grapevine microbiome provides opportunities for developing disease control strategies, which is important for the sustainable management of vineyards.