Transcriptomics provides a genetic signature of vineyard site with insight into vintage-independent regional wine characteristics

Abstract

In wine fermentations, the metabolic activity of both Saccharomyces cerevisiae and non-Saccharomyces organisms impact wine chemistry. Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur non-randomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. We used ribosomal DNA amplicon sequencing of grape must and RNA sequencing of primary fermentations to profile fermentations from 15 vineyards in California and Oregon across two vintages. We find that the relative abundance of fungal organisms detected by ribosomal DNA amplicon sequencing did not correlate with transcript abundance from those organisms within the RNA sequencing data, suggesting that the majority of the fungi detected in must by ribosomal DNA amplicon sequencing are not active during these inoculated fermentations. Additionally, we detect genetic signatures of vineyard site and region during fermentation that are predictive for each vineyard site, identifying nitrogen, sulfur, and thiamine metabolism as important factors for distinguishing vineyard site and region.ImportanceThe wine industry generates billions of dollars of revenue annually, and economic productivity is in part associated with regional distinctiveness of wine sensory attributes. Microorganisms associated with grapes and wineries are influenced by region of origin, and given that some microorganisms play a role in fermentation, it is thought that microbes may contribute to the regional distinctiveness of wine. We show that while the presence of microbial DNA is associated with wine region and vineyard site, the presence of microbial DNA is not associated with gene expression of those microorganisms during fermentation. We further show that detected gene expression signatures associated with wine region and vineyard site provide a means to address differences in fermentations that may drive regional distinctiveness.

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

“…Microbial communities colonizing grapevine compartments change in composition throughout the growing season in response to phenological and environmental changes (Martins et al, 2012). Grapevine microbiomes also exhibit interannual variation (probably in response to weather), but remain semistable between regions and across vintages (Bokulich et al, 2014;Cheng et al, 2020;Reiter et al, 2021). How do we account for these findings in understanding the microbial source-sink relationships between vines and the site-defined regional pool?…”

“…The potential impacts by specific microbiota derive from interactions among vineyard site, variety, and viticultural practices (Bokulich et al, 2014(Bokulich et al, , 2016. Similarly, microorganisms exert both positive and negative effects on wine quality before, during, and following fermentation (Domizio et al, 2014(Domizio et al, , 2017Blanco-Ulate et al, 2015;Belda et al, 2017;Hall et al, 2017;Reiter et al, 2021), spurring recent interest in the use of non-Saccharomyces yeasts in winemaking (Jolly et al, 2003(Jolly et al, , 2014.…”

“…Geographic distance is often a primary factor correlated with these differences, though it is unclear if it is merely a proxy for these other drivers (Burns et al, 2015;Miura et al, 2017). For example, microbiota in musts appear to correlate with vineyard and regional level climate and weather patterns (Bokulich et al, 2014;Reiter et al, 2021;Steenwerth et al, 2021), human activity, and human transport between vineyards in the case of S. cerevisiae (Goddard et al, 2010;Gayevskiy et al, 2016). Site, encompassing the specific environmental constraints of a single place (e.g., vineyard or block), is commonly the most explanatory variable in studies of microbiome assembly in other plants, suggesting that vineyard-specific microbiomes should not come as a surprise (Knief et al, 2010;Rastogi et al, 2012;Coleman-Derr et al, 2016;Wagner et al, 2016).…”