Distinct Vineyard Microbiomes Persist Through Winemaking, Study Finds

Researchers from Zurich and Davis, California, have conducted a detailed study on the role of microbiota in vineyards and wineries, focusing on how these microbial communities influence wine fermentation. The study took place in Davis, California, where two neighboring vineyards, both planted with Chardonnay grapes and managed under the same agricultural practices, were selected for analysis. The main goal was to determine whether the specific microbial profiles of each vineyard persist during the winemaking process, even when grapes are processed in the same winery.

The research team collected more than 200 samples from grapes, fruit flies (Drosophila), and various surfaces of winery equipment that come into contact with the grapes, such as destemmers, crushers, and presses. Sampling took place during the 2013 harvest season. The grape samples were taken from different rows and vines within each vineyard to ensure a representative overview of the microbial diversity present. Equipment surfaces were swabbed before processing began, and fruit flies were trapped inside the winery during harvest.

To analyze the bacterial and fungal communities, including yeasts, researchers used advanced DNA sequencing techniques. They amplified and sequenced specific genetic regions: the V4 region of the 16S rRNA gene for bacteria and the ITS1 locus for fungi. This allowed them to identify and compare the microbial populations present on grapes, in fruit flies, and on winery equipment.

The results showed that each vineyard had its own distinct microbial signature, even though they were located just over three kilometers apart and managed identically. These differences in microbiota were linked to subtle variations in soil type and microclimate between the sites. Importantly, when grapes from both vineyards were processed in the same winery using the same equipment, their unique microbial profiles remained detectable through the early stages of winemaking.

The study also found that the winery environment itself contributes additional microorganisms to the fermentation process. Surfaces of equipment that come into direct contact with grapes harbored their own microbial communities, which differed from those found on the grapes themselves. Fruit flies present in the winery carried yet another set of microbes. Notably, some fermentative yeasts that are rare or absent in vineyard environments were found on equipment and in fruit flies, suggesting these sources play a role in seeding fermentations with important yeast species.

Despite this contribution from the winery environment, it did not erase or override the original differences between vineyard microbiomes. Instead, it added another layer of complexity to the microbial community involved in fermentation. This supports the concept of “microbial terroir,” where site-specific microbiota contribute to regional wine characteristics.

The findings highlight that wine fermentation is shaped by a combination of microbes originating from both vineyard and winery environments. While intentional inoculation with commercial yeast strains is common practice in many wineries, spontaneous fermentations rely heavily on these native microbial populations. The persistence of vineyard-specific microbiota through processing suggests that even small-scale differences between neighboring vineyards can influence wine character.

This research provides new insight into how microbial diversity is maintained from vineyard to bottle and underscores the importance of considering both vineyard management and winery hygiene practices when aiming to preserve or enhance regional wine identity. The study also opens avenues for further investigation into how specific microbes contribute to flavor development during fermentation and how their interactions might be managed for quality control or stylistic purposes.

By tracking changes in microbial communities from grape harvest through initial processing steps, this work offers a clearer understanding of how environmental factors shape wine fermentation at a microbial level. It also demonstrates that while wineries introduce new microbes into fermentations—through equipment surfaces and insect vectors like fruit flies—the unique signature of each vineyard’s microbiome remains an important factor in defining wine character.

The research was published by Griggs R.G., Flörl L., Swadener M., Hernández-Velázquez R., Mills D.A., Bokulich N.A., underlining its significance for both scientific understanding and practical winemaking applications. Their work lays a foundation for future studies on managing microbiomes in viticulture and enology to optimize wine quality and expressiveness.