Microbial terroir emerges through ripening, fermentation and cellar choices

A changing ecosystem, not a fixed fingerprint

Research reviewed by María Carmen Portillo and colleagues places bacteria, yeasts and filamentous fungi alongside soil, climate, grape variety and vineyard management in the study of terroir. Rather than moving intact from vineyard to bottle, microbial communities change with ripening, weather and farming conditions, then encounter further ecological filters during harvest, crushing, pressing and the initial hours of fermentation. Harvest timing, processing speed, fruit health and the method used to begin fermentation can therefore affect which organisms remain active and potentially influence the wine.¹

DNA-sequencing advances over the past 20 years revealed recurring geographic patterns and encouraged the idea of microbial terroir. Geography, however, operates together with temperature, water availability, soil chemistry, topography, grape variety and vineyard practices. Vineyard microbes can also originate in soil, air, insects, rain and other plant tissues.¹

Place, time and berry condition

In Spain's Priorat region, Portillo and co-authors examined bacterial communities on Grenache and Carignan from 5 vineyards. Communities varied by vineyard and were associated with origin, orientation and variety; among Carignan sites, nearby vineyards tended to be more similar. A 2019 study across 4 Australian vineyards likewise found that origin affected fungal communities more strongly than grape variety or harvest timing. The most abundant fungi were not always the most useful indicators of origin, showing that geographic signals can reflect the balance among many groups rather than the presence of a dominant organism.¹

Time can alter that starting point even within the same vineyard block. As berries ripen, sugar increases, acidity changes and skins soften, transforming the habitat on the grape surface. Grapes harvested on different dates may consequently enter the winery with different communities.¹

Berry health creates another important divide. Portillo's group compared healthy Macabeo with grapes affected by sour rot or Botrytis and found different bacterial and fungal communities as well as distinct spontaneous-fermentation patterns. Must from damaged fruit contained higher levels of certain fungi and acetic acid bacteria, and the differences persisted beyond pressing. These fermentations retained greater microbial diversity for longer, followed different yeast successions and later affected organisms including Oenococcus oeni, a bacterium important in winemaking.¹

The cellar as an ecological filter

Crushing produces the sharpest ecological disruption. Breaking the skins transfers surface organisms into sugar- and nutrient-rich juice, while oxygen, acidity and alcohol begin changing rapidly. Must is therefore not merely a carrier for vineyard microbes: it is a new environment that selects which organisms can grow.¹

Spontaneous Grenache fermentations demonstrate this succession. Hanseniaspora and Issatchenkia were common initially, Candida increased later, and Saccharomyces gained importance toward the end. Acetic acid bacteria persisted through much of fermentation, while lactic acid bacteria increased later. Organisms prominent on intact grapes are thus not necessarily those that eventually dominate fermentation.¹

Nutrient conditions and inoculation timing further influence the outcome. In microvinification trials, nitrogen and sugar levels changed the balance between Saccharomyces cerevisiae and non-Saccharomyces yeasts. Low nitrogen slowed fermentation and prolonged the persistence of non-Saccharomyces yeasts, while the timing of S. cerevisiae inoculation affected community stability and diversity. Interest in non-Saccharomyces yeasts has grown because of their roles in aroma and acid production, but their effects depend on interactions with S. cerevisiae and on the conditions governing mixed fermentations.¹

What the 2026 study found

The 2026 study in the International Journal of Food Microbiology followed bacteria and fungi on Muscat of Alexandria grapes and through early winemaking using DNA metabarcoding. Fruit was harvested at 3 ripeness levels corresponding to about 10%, 12% and 13% potential alcohol.¹

Sampling stage was the strongest overall influence: movement from grape to processing and early fermentation changed the microbiome more than any other measured factor, as environmental and surface organisms were gradually replaced by groups suited to must and fermentation conditions. Yet among samples taken specifically at the start of fermentation, ripeness was the leading factor associated with both bacterial and fungal differences, while the immediate effect of inoculation strategy was smaller. Ripening can therefore leave a detectable signal after processing has imposed its stronger filter.¹

That signal did not amount simply to a gain or loss of diversity. Fungal richness and Shannon diversity showed no major differences among ripeness levels; instead, the identity and relative abundance of community members changed. A terroir-related pattern may therefore appear in microbial composition without increasing total diversity.¹

Function, fermentation choices and the research gap

Geographic microbial differences do not by themselves demonstrate a functional terroir effect. To contribute to wine identity, organisms must reach the must, remain metabolically active long enough to matter, interact with other populations and produce compounds that alter fermentation or wine chemistry. A widely cited 2016 study of more than 200 commercial fermentations in Napa and Sonoma found that microbial and metabolic profiles could distinguish wine-growing areas and individual vineyards. It also reported associations between fermentation microbiota and finished-wine chemistry, but those correlations do not establish causation.¹

Winemakers consequently face tradeoffs in how fermentation is initiated. Spontaneous fermentation may retain more local diversity but can be more variable. A commercial S. cerevisiae strain generally offers greater control and repeatability while potentially restricting the contribution of native microbes. Local starter cultures and pied de cuve provide intermediate approaches; pied de cuve is a small pre-fermentation prepared from native grapes and juice and later used to seed the main tank.¹

Studies reviewed by Portillo and colleagues indicate that pied de cuve can serve as an ecological-selection tool. Sulfur dioxide, temperature and small ethanol additions during its preparation can alter which yeasts develop. In the researchers' latest work, pied-de-cuve fermentations preserved more indigenous S. cerevisiae strain diversity than fermentations inoculated with a commercial strain and were more reliable than fully spontaneous fermentations.¹

The evidence ultimately describes microbial terroir as a local probability shaped by vineyard conditions and narrowed by winery decisions, rather than a fixed collection of organisms unique to a place. DNA detection alone cannot show whether an organism was alive or active. The researchers therefore call for sequencing to be combined with metagenomics, transcriptomics, metabolomics, culture-based methods and sampling over multiple years so that persistent regional signals can be separated from effects confined to 1 season.¹