The Endophytic Microbiome of Wild Grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat Growing in the Russian Far East

Abstract

Many grape endophytic microorganisms exhibit high potential for suppressing the development of grape diseases and stimulating grapevine growth and fitness, as well as beneficial properties of the crop. The microbiome of wild grapevines is a promising source of biocontrol agents, which can be beneficial for domesticated grapevines. Using next-generation sequencing (NGS) and classical microbiology techniques, we performed an analysis of bacterial and fungal endophytic communities of wild grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat growing in the Russian Far East. According to the NGS analysis, 24 and 18 bacterial taxa from the class level were present in V. amurensis and V. coignetiae grapevines, respectively. Gammaproteobacteria (35%) was the predominant class of endophytic bacteria in V. amurensis and Alphaproteobacteria (46%) in V. coignetiae. Three taxa, namely Sphingomonas, Methylobacterium, and Hymenobacter, were the most common bacterial genera for V. amurensis and V. coignetiae. Metagenomic analysis showed the presence of 23 and 22 fungi and fungus-like taxa of class level in V. amurensis and V. coignetiae, respectively. The predominant fungal classes were Dothideomycetes (61–65%) and Tremellomycetes (10–11%), while Cladosporium and Aureobasidium were the most common fungal genera in V. amurensis and V. coignetiae, respectively. A comparative analysis of the endophytic communities of V. amurensis and V. coignetiae with the previously reported endophytic communities of V. vinifera revealed that the bacterial biodiversity of V. amurensis and V. coignetiae was similar in alpha diversity to V. vinifera’s bacterial biodiversity. The fungal alpha diversity of V. amurensis and V. coignetiae was statistically different from that of V. vinifera. The beta diversity analysis of bacterial and fungal endophytes showed that samples of V. vinifera formed separate clusters, while V. amurensis samples formed a separate cluster including V. coignetiae samples. The data revealed that the endophytic community of bacteria and fungi from wild V. amurensis was richer than that from V. coignetiae grapes and cultivated V. vinifera grapes. Therefore, the data obtained in this work could be of high value in the search for potentially useful microorganisms for viticulture.

Bacterial and Fungal Endophytes of Grapevine Cultivars Growing in Primorsky Krai of Russia

“…We also compared the biodiversity of the endophytic bacteria of grape varieties with the bacterial endophytic community of wild grapes V. amurensis; the data were obtained in previous research [39]. According to the analysis, in all samples of cultivated grapes, except for the cv.…”

“…Alpha from PRIM ORGANICA, while the representation of these bacterial genera in other varieties and the wild grape V. amurensis was less than 0.1% (Figure 2). amurensis-the sum of data for all V. amurensis grapevines obtained early [39]. The top 10 most abundant taxa from each grapevine are displayed.…”

“…Adele from commercial vineyard Makarevich; Muk-V. riparia × V. vinifera cv. Mukuzani; V.amurensis-the sum of data for all V. amurensis grapevines obtained early [39]: (a) class-level taxonomical bar plots for the fungal and fungi-like endophytic community depend on the variates of grapevines, and the sum of data for all V. amurensis grapevines obtained early [39]; (b) genus-level UpSet diagrams depicting overlapping taxa of NGS in different cultivars of grapevines. For each biocompartment, taxa were filtered based on relative abundance > 0.1%.…”

“…Adele from commercial vineyard Makarevich; Muk-V. riparia × V. vinifera cv. Mukuzani; V.amurensis-the sum of data for all V. amurensis grapevines obtained early [39]. The top 10 most abundant taxa from each grapevine are displayed.…”