The Biogeography of New Zealand Fungi: A Study of Community Processes Along Spatial, Ecological, and Agricultural Gradients

Abstract

Microbial communities are vital components of natural, agricultural, and biotechnological ecosystems. Microbial species play a particularly important role in viticulture and winemaking by modulating the health, productivity, and development of grape vines and converting grape sugars into alcohol and other flavour and aroma compounds during commercial fermentation. Understanding how microbial community ecology can impact wine production is of great interest to industry, and exploring the ecological behaviour of microbes can be done using tools such as next-generation sequencing. While next-generation sequencing techniques have transformed the way in which we study the ecology and biogeography of microbes, we still know very little about the patterns and processes that shape microbial diversity. is thesis aims to elucidate the biogeography of New Zealand fungal species and test ecological and biogeographical concepts using human-managed vineyard ecosystems. To do this I use next-generation sequencing to characterise fungal diversity within and across vineyard ecosystems, quantify the natural and artificial processes shaping this diversity, explore the relationship between vineyard and winery diversity, and explore their implications for winemaking. This thesis goes on to explore the potential of co-evolution and microbial interactions operating within these communities to modify the sensory properties of wines seeded with interacting yeasts. In the second chapter I quantify the relative strength of natural selection and neutral processes in shaping fungal diversity, I and use next-generation sequencing to evaluate 106 contemporaneous fungal communities inhabiting adjacent soil, bark, and fruit niches across six New Zealand regions spanning a thousand kilometres. The data show that species richness and community structure are not homogenous but significantly varied with vineyard habitat and region. Across all vineyard samples, habitat explained the greatest proportion of the variation in community structure compared to region, indicating that selection is the primary driver of fungal diversity in vineyards. In the third chapter I examine the diversity of commercial NZ ferments and quantify the microbial links between various winery communities and cultivated and uncultivated ecosystems. Here I analyse the fungal diversity of a further 44 samples collected from NZ wineries as well as those associated with the fruit and soil of 36 native plants from nearby uncultivated areas. The data show that microbial communities in ferments vary significantly across regions, and that while vineyard fungi account for a sizeable fraction of the source of this diversity, uncultivated ecosystems outside of vineyards also provide a significant source. The data also show that species richness and community structure significantly shift over the course of the ferment, and while communities initially resemble those found on grapes, these increasingly resemble fungi present on vine bark. In the fourth chapter, I examine the impact of human agriculture on fungal diversity in vineyards and ascertain whether these impacts translate to the diversity found in pressed juice, or to commercially important metabolites in the resultant wines. I compare the fungal diversity present in six conventionally managed and seven biodynamically managed vineyards in the Wairau Valley. To test whether these agricultural practices translate to their respective wineries, I compare the fungal diversity of juices harvested from sampled vineyard blocks as well as the concentrations of commercially important metabolites —varietal thiols — in wines produced from these juices. The data show that the method of management significantly affects communities in soil, on plant structures, and on the developing crop in subtle but importantly different ways in terms of number, type, and abundance of species. However, management approach has no effect on communities in the final harvested juice, nor on product traits aligned with quality. This shows that while management approach affects different habitats in the environment in different ways, this does not automatically flow onto the harvested crop. In the fifth chapter I use experimental evolution of two yeast species, Candida glabrata and Pichia kudriavzevi, to examine how co-evolution and the generation of novel microbial interactions can impact upon the products of commercial winery fermentation. In this chapter I successfully reapplied the experimental design of Lawrence et al. (2012) to generate co-evolved strains through serial transfers of polyculture of these yeasts to fresh grape juice for ∼65 generations. I explore the nature of interactions between co-evolved strains by estimating the relative fitness of co-evolved and mono-cultured strains by analysing the growth rates and cell densities using Bioscreen CTM spectrophotometry. The metabolite profiles of the inoculated wines — comprising 38 sensory compounds — were then quantified and compared across co-evolved, mono-cultured, and ancestral strains. The data also show that coculture strains of C. glabrata and P. kudriavzevi exhibited significantly different growth rates and metabolic activity than their mono-culture equivalents. Furthermore, unlike the findings of Lawrence et al. (2012), I found no evidence of mutualistic cross-feeding and suggest that the apparent interactions are antagonistic in nature. The data and analyses presented in this thesis represent one of the most extensive sampling of multiple plant-associated microbial communities through space and provide a major advance in how these communities can vary within respective habitats. As such, this study expands our understanding of the nature and connection of various natural microbial communities in a landscape, and how agricultural products and processes might be affected by these communities.