Understanding the Importance of Microbial Biogeography to Australian Winemaking

Abstract

Microbes are a vital part of ecosystems and play key roles in the essential processes of the functioning. In agriculture, microbial ecology has wide reaching impacts on crop growth and quality commodity production. As a high value agricultural product, wine is a useful model for elucidating the effects of microbial ecology from the vineyard to the winery. Microbial growth and metabolism is an inherent component of wine production, influencing grapevine health and productivity, conversion of sugar to ethanol during fermentation, and the flavour, aroma and quality of finished wines. Recent advances in genetic sequencing and metagenomic approaches has extended our understanding of microbial distribution patterns and established the unique biogeography model in viticulture. While the contributions of microbial biogeography to wine metabolites and regional distinctiveness (known as terroir, a well-recognised and celebrated character in wine industry), and by which mechanisms, remain tenuous. This thesis focuses on the microbial biogeography of wine, the interplay between microbial patterns and affecting factors, and how these patterns drive wine quality and styles.

I begin by investigating the distribution patterns of bacteria and fungi at large scale, and their roles in shaping wine characteristics. Samples were collected from vineyard soil, grape must, and wine ferments across six geographically separated wine-producing regions in southern Australia (~ 400 km). Soil and grape must microbiota exhibited distinctive regional patterns, as well as wine aroma profiles. Associations among soil and wine microbiota, abiotic factors (weather and soil properties), and wine regionality were modelled, highlighting that fungal communities was the most important driver of wine aroma profiles. Source tracking wine-related fungi in the vineyard suggests that soil is a source reservoir of grape- and must-associated fungi which might be translocated via xylem sap.

I then move on to elucidate the fungal ecology within vineyards. Fungal communities were characterised over space and time that associated with the grapevine (grapes, flowers, leaves, roots, root zone soil) during the annual growth cycle (flowering, fruit set, veraison, and harvest). Fungi were significantly influenced by the grapevine habitat and plant development stage, with little influences from the geographic location (<5 km). The developmental stage of veraison, where grapes undergo a dramatic change in metabolism and start ripening process, saw a distinct shift in fungal communities. A core fungal microbiota of grapevines (based on abundance-occupancy models) existed over space and time which drove the seasonal community succession. Beyond coinciding with the changing plant metabolism and physiology, strong correlations with solar radiation and water status suggests that the core microbiota changes with respect to the changing environments during plant development.

I further investigate fungal contributions to wine aroma profiles by quantifying multiple layers of fungi, combining metagenomics and population genetics. Fungal communities were characterised associated with Pinot Noir and Chardonnay grape must/juice and ferments coming from three wine estates (including 11 vineyards) in the Mornington Peninsula wine region. At this scale (< 12 km), fungal communities, yeast populations, and Saccharomyces cerevisiae populations differentiated between geographic origins (estate/vineyard), with influences from the grape variety. During spontaneous fermentation, growth and dominance of S. cerevisiae reshaped the fungal community and structured the biodiversity at strain level. Associations between fungal microbiota and wine metabolites highlights the primary role of S. cerevisiae in determining wine aroma profiles at sub-regional scale.

Overall, this thesis provides a significant body of knowledge to the microbial ecology field. Using vineyards, grapes, and wine as a model system, these findings relate microbial biogeography, environments, and quality agricultural commodity production. It provides fundamental perspectives to conserve the biodiversity and functioning for sustainable agriculture under the changing climate.