A tale of two vineyards: parsing site-specific differences in bacterial and fungal communities of wine grapes from proximal vineyards, and their changes during processing in a single winery

Wine is a microbial product, naturally transformed through fermentation by a consortium of fungi and bacteria that originate from the vineyard and the cellar, in addition to any microorganisms that are intentionally inoculated. Previous work has shown that grapevine-associated microbiota follow distinct biogeographic patterns, associated with climate and soil properties, and that even neighboring vineyards can harbor distinct microbial communities, but it is unclear whether these differences persist when controlling for variations in farming practices, cultivar, and climate, and whether site-specific microbial profiles change during processing in the winery. Here we investigated the bacterial and fungal microbiota of fruit pre- and post-harvest from two nearby vineyards planted to a single variety, geographically close to one another, and farmed the same way, and then processed in a single winery. These communities subtly changed during processing yet retained distinct site-specific signatures, indicating a partial contribution of the winery environment to the microbiota of grape must and juice pre-fermentation. We also profiled the microbiota of key microbial sources in the winery environment, including fruit flies and processing equipment, demonstrating that the microbiota at these sites reflect contact with plant material, harbor communities distinct from fruit, and appear to partially contribute to the fermentation assemblage, especially via the contribution of fermentative yeasts that are rare or missing in the vineyard environment. These results bolster previous reports of site-specific microbial signatures in winegrowing and make a first estimation of the changes to the grape-associated microbiome during early processing. ImportanceNative wine fermentations are driven by microbes carried over from the vineyard or introduced in the winery. In this study, we tracked the microbiome dynamics of wine fermentations from two Chardonnay vineyards planted in close proximity to examine the relative contribution of vineyard- and winery-resident microbiota on microbial succession during wine fermentation. By tracking microbial changes from vineyard to winery, we show that the winery environment, including processing equipment and fruit flies, contributes to the fermentation microbiome but does not override vineyard-specific microbial differences. These findings support the concept of microbial terroir and highlight the importance of vineyard microbiomes in shaping wine fermentation. This work advances our understanding of how microbial diversity influences wine production and provides insight into the ecological dynamics of fermentation. By identifying key microbial sources and their contributions, this study lays the groundwork for future microbiome research in viticulture and wine making.