Mapping Microbes in California Wine Country

Sommeliers touting a wine’s aroma, body, and acidity may eventually add “microbial community” to what makes a vintage unique. Researchers at the University of California, Davis sampled grapes from nearly 300 locations in California’s famous wine country and found that the bacteria and fungi living on the fruit show patterns based on location, climate, and grape variety. The findings set the stage for future studies that investigate how these microbial communities influence the regional characteristics of wine. Nick Bokulich, lead author of the study, spoke with Science Friday about the work, which was published today in PNAS Online Early Edition.

In a nutshell, what did your results show?
What we saw in the study is that the microbial communities—both bacterial and fungal—on the surfaces of grapes from different regions in California have specific community structures. Grapes grown from the Napa region—from a Napa vineyard—have different bacterial and fungal communities than grapes from a Central Valley or a Central Coast vineyard. In effect, we’re seeing different regional fingerprints. The different growing conditions, the different environmental features, and the grape host itself all appear to shape the microbial community on the grape surface.

Has anyone ever looked at these microbe cultures on this scale?
This is the largest study of its kind in terms of studying grapes or wine, as far as I know. For the most part, research that’s been looking at grapes and at wine have studied much smaller areas—single vineyards and single wineries. Before we undertook this work, no one knew for sure whether the microbes were randomly distributed on grape surfaces or not—no one as far as I know.

What was the smallest region that had a unique culture of microbes?
What we see is almost kind of a fractal relationship, where if you look at these large-scale regions you see large-scale differences in the types and amounts of fungi and bacteria populating the surface of the grapes, but then as you look at the more fine-tuned detail, you see more fine-tuned differences. For example, between different growing regions, like Napa and Central Valley, we see entirely different phylogenetic groups of bacteria and fungi dominating the grape ‘musts’ [crushed grapes]. Between some vineyards in the same region, the musts are dominated by the same groups of bacteria and fungi, but have different abundances of different species within these groups.

While we didn’t really look at it in this study, one could even speculate further that you could study how different blocks within an individual vineyard might support different microbial communities based on the so-called microclimate in those different blocks.

Your team identified the different bacteria and fungi using a very modern DNA sequencing technique. Can you tell me a little bit about it?
The method we use here is commonly known as high-throughput marker-gene sequencing, or next generation sequencing. In the past, you had to grow those organisms in isolation. So you had to pull them off of the surface of the grape, grow them up in an isolated container, extract their DNA, and look at the DNA sequence individually. This new sequencing approach allows us to look at the DNA sequence of many different organisms simultaneously.

Your research did not look at how these microbes affect the quality or taste of the wine. Will that be the next step?
That would be the hope. This study answers that first critical question: Are microbial communities on grape surfaces randomly formed, or is there some rhyme and reason behind the different groupings of these organisms? And answering that question serves as a platform to ask many more questions about how these different community structures specifically improve or influence the sensory characteristics of the wine or the health of the grape vines.

We already know quite a good deal about a lot of the different bacteria and fungi that differentiate these regions. A lot of them are organisms that relate to grape vine health and a lot of them organisms that relate to wine quality. So we know, for example, that Botrytis cinerea and other fungi like that are plant pathogens, and they can diminish the yield and quality of grapes. And we know that things like acetic acid bacteria can spoil wine.

What I’d like to know is, based on what we learn from these microbial patterns, can we take a must sample and determine: Is this going to make good wine or is it going to make bad wine? That’s the biggest question that I want to hunt down next.