Eutypa dieback of grapevine is an important disease caused by the generalist Ascomycete fungus Eutypa lata. Despite the relevance of this species to the global wine industry, its genomic diversity remains unknown, with only a single publicly available genome assembly. Whole-genome sequencing and comparative genomics was performed on forty Australian E. lata isolates to understand the genome evolution, adaptation, population size and structure of these isolates. Phylogenetic and linkage disequilibrium decay analyses provided evidence of extensive gene flow through sexual recombination between isolates obtained from different geographic locations and hosts. Investigation of the genetic diversity of these isolates suggested rapid population expansion, likely as a consequence of the recent growth of the Australian wine industry. Genomic regions affected by selective sweeps were shown to be enriched for genes associated with secondary metabolite clusters and included genes encoding proteins with a role in nutrient acquisition, degradation of host cell wall and metal and drug resistance, suggesting recent adaptation to both abiotic factors and potentially host genotypes. Genome synteny analysis using long-read genome assemblies showed significant intraspecific genomic plasticity with extensive chromosomal rearrangements impacting the secondary metabolite production potential of this species. Finally, k-mer based GWAS analysis identified a potential locus associated with mycelia recovery in canes of Vitis vinifera that will require further investigations.

Uninoculated wines are regarded as having improved mouthfeel and texture and more complex flavor profiles when compared to wines inoculated with commercial S. cerevisiae strains. Uninoculated fermentation involves a complex microbial succession of yeasts and bacteria during fermentation. Microbial population dynamics are affected by several factors that can ultimately determine if a particular species or strain contributes to wine aroma and flavor. In this work, we have studied the effect of aeration, a common winemaking practice, on the yeast microbiota during uninoculated Chardonnay wine fermentation. The timing of aeration and then aeration intensity were evaluated across two successive vintages. While the timing of aeration significantly impacted fermentation efficiency across oxygen treatments, different levels of aeration intensity only differed when compared to the non-aerated control ferments. Air addition increased the viable cell population size of yeast from the genera Hanseniaspora, Lachancea, Metschnikowia and Torulaspora in both vintages. While in 2019, a high relative abundance was found for Hanseniaspora species in aerated ferments, in 2020, T. delbrueckii was visibly more abundant than other species in response to aeration. Accompanying the observed differences in yeast community structure, the chemical profile of the finished wines was also different across the various aeration treatments. However, excessive aeration resulted in elevated concentrations of ethyl acetate and acetic acid, which would likely have a detrimental effect on wine quality. This work demonstrates the role of aeration in shaping yeast population dynamics and modulating a volatile profile in uninoculated wines, and highlights the need for careful air addition to avoid a negative sensory impact on wine flavor and aroma.

Uninoculated wine fermentations are conducted by a consortium of wine yeast and bacteria that establish themselves either from the grape surface or from the winery environment. Of the additives that are commonly used by winemakers, sulphur dioxide (SO2) represents the main antimicrobial preservative and its use can have drastic effects on the microbial composition of the fermentation. To investigate the effect of SO2 on the resident yeast community of uninoculated ferments, Chardonnay grape juice from 2018 and 2019 was treated with a variety of SO2 concentrations ranging up to 100 mg/L and was then allowed to undergo fermentation, with the yeast community structure being assessed via high-throughput meta-barcoding (phylotyping). While the addition of SO2 was shown to select against the presence of many species of non-Saccharomyces yeasts, there was a clear and increasing selection for the species Hanseniaspora osmophila as concentrations of SO2 rose above 40 mg/L in fermentations from both vintages. Chemical analysis of the wines resulting from these treatments showed significant increases in acetate esters, and specifically the desirable aroma compound 2-phenylethyl acetate, that accompanied the increase in abundance of H. osmophila. The ability to modulate the yeast community structure of an uninoculated ferment and the resulting chemical composition of the final wine, as demonstrated in this study, represents an important tool for winemakers to begin to be able to influence the organoleptic profile of uninoculated wines.

Cultural exchange of fermentation techniques has driven the spread of Saccharomyces cerevisiae across the globe, establishing wild populations in many countries. Despite this, most modern commercial fermentations are inoculated using monocultures, rather than relying on natural populations, potentially impacting wild population diversity. Here we investigate the genomic landscape of 411 wild S. cerevisiae isolated from spontaneous grape fermentations in Australia across multiple locations, years, and grape cultivars. Spontaneous fermentations contained highly recombined mosaic strains that commonly exhibited aneuploidy of chromosomes 1, 3, 6 and 9. Assigning wild genomic windows to putative ancestral origin revealed that few closely related commercial lineages have come to dominate the genetic landscape, contributing most of the genetic variation. Fine-scale phylogenetic analysis of loci not observed in strains of commercial wine origin identified widespread admixture with the Beer2 clade along with three independent admixture events from potentially endemic Oceanic lineages that last shared an ancestor with modern East Asian S. cerevisiae populations. Our results illustrate how commercial use of microbes can affect local microorganism genetic diversity and demonstrates the presence of non-domesticated, non-European derived lineages of S. cerevisiae in Australian ecological niches that are actively admixing.