Unravelling the Diversity of Grapevine Microbiome

Abstract

Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.

Quantifying the relative roles of selective and neutral processes in defining eukaryotic microbial communities

“…However, fungal diversity in these 36 NZ vineyard soils appears much greater than estimates from just two Italian vineyards with around 300 MOTUs in Orgiazzi et al (2012), but one might expect greater diversity with a greater sampling area. Previous reports of fungal diversity found on vine bark derived from live culture only and yielded just five species (Sabate et al, 2002); however, next-generation sequencing of fungal communities from vine leaves reveals around a thousand MOTUs and is thus in line with our inferences from bark here (Pinto et al, 2014).…”

“…Direct sequencing of DNA from these niches reveals approximately the same extent of fungal diversity recovered from similar niches in the handful of other studies that have used this approach (Bokulich et al, 2014;Pinto et al, 2014;Taylor et al, 2014). These communities are not homogenous; they significantly vary in terms of species richness and community composition, and both niche and geographic location affect this variance.…”

“…Vineyards naturally harbour a range of microbial taxa including diverse fungal communities (Bokulich et al, 2014;Pinto et al, 2014;Taylor et al, 2014). The conserved design and management of vineyard ecosystems (which comprise the same clone of plant, with comparable associated habitats and niches) across large distances provide a powerful system to separately estimate the impact of selective and neutral processes.…”

Directed metabolomic approaches for the characterization and development of new yeast strains

“…It should be noted that some yeast species found in grapes and must, like Aureobasidium pullulans or Cryptococcus amylolentus, are enzymatically interesting showing a wide range and intensity of hydrolytic activities but have a low incidence on fermentation development. A. pullulans dominates the microbial consortia of grape [25,26], however, its null fermentative power and its low adaptation to fermentative environment bias their contribution to the fermentation process, making their interest in winemaking scarce [27]. There is a simple method to minimize the isolation of this yeast-like fungus by keeping the fresh grape must refrigerated overnight in order to greatly reduce the Aureobasidium population.…”

“…Classical molecular technics like t-RFLP [31,32] or DGGE [25], genomic approaches [28,33,34] and metagenomic tools [26,35] are culture independent techniques, but we cannot forget the importance of microorganism cultures for their further study and industrial usage. Knowledge about the vineyard and fermentation microbiomes are growing notably in recent years [26,35,36], so now we have quite enough information about yeast abundance and distribution in both grapes and fermentations. However, information about comparative genomics of different yeast strains is scarce, even more in the case of non-Saccharomyces species.…”