The Population Biology of New Zealand Wine Yeasts and Their Contribution to Wine Styles

Abstract

Microbes perform essential processes vital to the functioning of the biosphere and have wide reaching impacts on global economies for the roles they play in producing quality agricultural commodities. They are widely used as model systems to test fundamental hypotheses from a range of scientific disciplines, uncovering invaluable knowledge about biological processes. Despite their undisputed importance to both fundamental science and commercial enterprises, we have a poor understanding of microbial population biology and ecology and how these patterns and processes affect the production of quality agricultural goods. This thesis focuses on the model research eukaryote Saccharomyces cerevisiae and takes advantage of its and other fungal species’, commercial applications in wine making. I begin by quantifying the population processes occurring in the New Zealand (NZ) metapopulation of S. cerevisiae. I sampled over ten thousand isolates from a variety of native and vineyard associated niches from six different winemaking regions, spanning over 1 000 km across NZ. From these, hundreds of genotypes were obtained and used in a suite of comprehensive quantitative analyses of population structure and gene-flow. Within geographic regions, these reveal no differentiation between native or vineyard associate samples or between populations residing in different niches. Between regions (on scales larger than ~100 km), a complex picture of varying degrees of population differentiation and migration was revealed. These patterns are in line with the movement of fruit by the NZ wine industry and suggest human associated gene-flow may affect microbial population patterns and diversity. From here I investigate the ecology of S. cerevisiae and target my research away from the well understood fruit and ferment niches. As fruit is ephemeral, S. cerevisiae requires a strategy to survive when this energy rich resource is not available. While it has been isolated from soil and bark samples in previous studies, including the above population genetic analysis, what S. cerevisiae is doing in this ‘woodland’ niche is unknown. I hypothesised that S. cerevisiae employs a life history strategy targeted at self-preservation rather than growth outside of the fruit niche and thus resides in these alternate niches in a sporulated state. Using soil agar as a proxy for the soil niche, I provide evidence that S. cerevisiae is able to sporulate in the presence of soil nutrients and does so in a way that maximises its potential reproductive success upon germination. While there are many other aspects of this hypothesis that require experimental verification, this is the first step in understanding the ecology of S. cerevisiae outside of the fruit niche. I then move on to investigate the potential consequences these observed population patterns have on a commercially important agricultural commodity: wine. Agricultural products derived from the same genotype display differential geographic phenotypes in their physical and sensorial signatures, adding economic value and distinctiveness to products. Historically this has been attributed to complex interactions between local soils, climate and agricultural practices and is collectively known as terroir, or sense of place. The potential for microbes to contribute to this regional distinction has been ignored until recently; however there is growing evidence to suggest that microbial communities and populations vary with geography. Here I perform the first general test for a microbial aspect to terroir using wine as a model system and take advantage of the genetically well characterised S. cerevisiae population described in this thesis. I experimentally demonstrate significant differentiation of wine phenotypes by yeasts derived from different geographic regions, providing the first evidence that microbes contribute to the regional distinctiveness of wine and potentially agricultural products generally. This reveals the importance of microbial populations on the regional identity of agricultural commodities and suggests that long-term implementation of agricultural practices that maintain differential microbial diversity could have direct economic implications as well as being desirable in terms of employing agricultural practices that increase responsible environmental stewardship and maintain microbial biodiversity. Finally I investigated whether fungal species diversity in the grape juice and during fermentation is correlated with the final concentration of three volatile thiols important to wine aroma and flavour. The species of Saccharomyces driving the ferment was found to significantly correlate with thiol concentration, particularly 4MMP, with higher proportions of S. uvarum affording higher concentrations of 4MMP. Additionally, the fungal communities in the initial juice were found to correlate with the thiol concentrations in the wine. Genera identified as being the main drivers of this effect are known to influence vine and fruit health rather than contribute to fermentation itself, suggesting the effects of microbial populations on wine thiol concentration begins in the vineyard. This reiterates the need to have a better understanding of the interactions between microbial populations and agricultural products and has implications for the management of fungal diversity and disease in these systems. Overall, this thesis provides a significant body of knowledge to both fundamentally and commercially important fields. It highlights the need to better understand the ecology of microbial populations not only in a fundamental sense but also for commercial imperatives.