Exploring how microbial communities on grapes are revolutionizing winemaking
In the world of winemaking, a silent revolution is brewing—one that unfolds at a microscopic level. Beyond the sun, soil, and grape variety lies an invisible world that profoundly shapes the wine in your glass: the grape microbiome. This complex ecosystem of bacteria, fungi, and yeasts living on grapevines is now recognized as a critical component of wine quality, health, and character.
Scientists are now exploring how we can harness these naturally occurring microorganisms as next-generation starter cultures—biological tools that could help winemakers tackle challenges like climate change and disease while consistently producing exceptional wine. This article delves into the fascinating world of grape-associated microbes and their promising future in sustainable viticulture.
The grape microbiome comprises the diverse community of microorganisms—including bacteria, fungi, viruses, and yeasts—that live in association with grapevines. These microbes inhabit every part of the plant, from the roots and leaves to the bark and, most importantly for winemaking, the berry surface 5 . Together, the grapevine and its microbial partners form what scientists call a "holobiont"—a collective ecological unit that functions in concert 9 .
These microbial communities are acquired through both vertical transmission (via seeds) and horizontal transmission from environmental reservoirs like soil and air 5 . The soil, particularly the rhizosphere (the area surrounding roots), serves as the most significant reservoir of plant-associated microbes 5 . Interestingly, research shows that while soil is a primary source of microorganisms, the microbial communities that eventually colonize grape berries are highly distinct from those found in soil, indicating specialized adaptation to the fruit environment .
The grape microbiome contains both core microbiota (a stable subset of microorganisms consistently associated with grapevines) and keystone taxa (highly connected members that exert disproportionate influence on the microbial community structure) 5 . Among the most common bacterial genera found on grape berries are Pseudomonas, Sphingomonas, Staphylococcus, and Bacillus, while dominant fungal genera often include Aureobasidium, Alternaria, and various yeasts .
| Microorganism | Type | Potential Function/Role |
|---|---|---|
| Gordonia alkanivorans | Bacterium | Breaks down smoke-derived compounds 1 |
| Aureobasidium | Fungus | Dominant on mature berries |
| Pseudomonas | Bacterium | Common on green berries |
| Bacillus | Bacterium | Common on mature berries |
| Zygosaccharomyces | Yeast | Associated with sour rot symptoms 6 |
| Gluconobacter | Bacterium | Associated with sour rot symptoms 6 |
| Streptococcus thermophiles | Bacterium | Considered a probiotic 2 |
As wildfires increasingly threaten wine-producing regions, particularly on the U.S. West Coast, smoke taint has become a multi-million dollar problem for the wine industry 1 . When grapes are exposed to wildfire smoke, they absorb unpleasant-tasting substances that eventually make their way into the wine, resulting in a smoky, ashy-tasting pour. One of the main compounds responsible for this off-flavor is guaiacol 1 .
In September 2025, Claudia Castro of the U.S. Department of Agriculture's Agricultural Research Service and her colleagues published groundbreaking research in PLOS One demonstrating a potential biological solution to this problem 1 .
The researchers collected leaves from two varieties of grape plants—Chardonnay and Cabernet Sauvignon—from vineyards 1 .
They tested these leaves in the laboratory for the presence of bacteria capable of breaking down guaiacol 1 .
The genomes of promising bacterial strains were analyzed to identify specific genes involved in the guaiacol degradation process 1 .
Through gene deletion experiments, the researchers confirmed the specific gene required for guaiacol degradation 1 .
The team exposed living Merlot plants to smoke produced by a culinary smoker—simulating wildfire smoke exposure—and analyzed how the grape microbiome changed before and after smoke exposure 1 .
The research yielded exciting results. The scientists discovered that grape leaves naturally harbored two strains of the bacterial species Gordonia alkanivorans that could break down guaiacol in the laboratory 1 . Through genetic analysis, they identified a specific gene called guaA that is required for this process—when this gene was experimentally deleted, the bacterium lost its ability to degrade guaiacol 1 .
Additionally, the smoke exposure experiment revealed that the grape microbiome changes significantly following smoke exposure, with a notable increase in bacteria from the Bacilli class, which are known to survive in extreme environments 1 .
"Working in the vineyard along with our collaborator Dr. Tom Collins and his team to set up the wildfire smoke simulation is one of my best memories of this study. Probably second best to finding a guaiacol-degrading microbe that lives on the surface of grapes."
| Research Phase | Methodology | Key Outcome |
|---|---|---|
| Sample Collection | Collected leaves from Chardonnay and Cabernet Sauvignon vines | Obtained natural grape microbiome for testing |
| Bacterial Screening | Laboratory tests for guaiacol degradation | Identified Gordonia alkanivorans strains capable of breaking down guaiacol |
| Genetic Analysis | Genome sequencing of bacterial strains | Discovered guaA gene involved in the degradation process |
| Gene Validation | Experimental deletion of guaA gene | Confirmed guaA is essential for guaiacol degradation |
| Smoke Response | Simulated wildfire exposure on Merlot plants | Documented microbiome shifts after smoke exposure |
Studying the grape microbiome requires sophisticated tools and techniques. Researchers use a combination of approaches to isolate, identify, and characterize microbial communities associated with grapevines.
Isolates microorganisms using growth media to test plant growth-promoting or antifungal properties of specific microbes 3 .
DNA sequencing without culturing provides detailed insights into microbial taxonomy and metabolic potential 3 .
Identifies and classifies bacterial communities to characterize bacterial diversity in grape berries 6 .
Identifies and classifies fungal communities to analyze fungal diversity in grape berries 6 .
Links genetic markers to traits to identify grape genome regions associated with microbial recruitment 8 .
Studies small molecule metabolites to understand how microbial activities influence grape and wine properties 5 .
The integration of multiple approaches—often called "culturomics"—has become increasingly important in advancing our understanding of grapevine microbial ecology 3 . This combined strategy helps researchers not only identify beneficial microorganisms but also discover previously uncultivated species 3 .
The application of grape microbiome research extends far beyond fixing smoke-tainted wine. Scientists are exploring multiple avenues for harnessing these natural microorganisms:
Grapevine Trunk Diseases (GTDs) represent a major threat to vineyards worldwide, causing significant economic losses. Research has shown that microbiome composition in symptomatic plants is modulated by genotype and region 4 . By identifying beneficial microorganisms that can compete with or suppress pathogenic fungi, researchers hope to develop effective biocontrol agents 4 .
Microbial fertilizers are emerging as alternatives to conventional chemicals, offering the potential for increased crop productivity and environmental sustainability 3 . Specific plant growth-promoting bacteria can enhance nutrient availability, improve disease resistance, and support vital physiological functions of grapevines 3 .
The concept of "microbial terroir" suggests that microbial communities contribute to the regional characteristics of wine . Studies have revealed that unique bacterial and fungal communities are associated with different vineyard habitats, and these communities correlate with specific volatile compounds in wines . This understanding could lead to starter cultures that help express specific regional characteristics more consistently.
The exploration of the grape microbiome represents a paradigm shift in how we approach viticulture and winemaking. No longer passive bystanders, the microorganisms living on grapevines are now recognized as active contributors to wine quality, character, and production.
As research advances, we can anticipate more targeted microbial solutions emerging—whether for combating the growing problem of smoke taint, managing devastating vine diseases, enhancing sustainability, or expressing the unique character of a vineyard's terroir. The development of specialized starter cultures from naturally occurring grape microbiota promises to provide winemakers with new tools that are both effective and environmentally friendly.
As the research progresses, the adage "great wine is made in the vineyard" is taking on a whole new meaning—one that extends deep into the microbial world.