Bioprospecting Australian microbial genetic diversity
An important aspect of terroir, particularly where spontaneous fermentations are performed, is very likely to be related to differences in wine microbiota. Focused microbiological research has shown that both vineyards and spontaneous fermentations contain diverse mixtures of microbial species (often with species being represented by multiple strains). However, the inability to transition this traditional methodology to efficiently and accurately assess the large numbers of samples required to tackle such a complex problem, has so far limited subsequent insights into this important question. This lack of information is therefore a major impediment to the exploitation of native microbial germplasm and spontaneous fermentation, by the Australian wine industry.
However, recent advances in metagenomics (genomic sequencing of mixed microbial communities), can address these issues by providing detailed identification of the species, and their proportions which comprise complex microbial mixtures, in a high throughput manner. In addition, by adopting and developing new genomic approaches, such as single cell high throughput sequencing, the genetic make-up of individual strains within these mixtures can also be obtained, to provide direct links between novel genetic and phenotypic characteristics. This type of metagenomic analysis has been initiated and refined for studies of wine fermentation at the AWRI, and now provides the technical platform to answer important questions regarding Australian wine microbial terroir.
This project builds on an existing project where the contributions of various species of fungi, yeast and bacteria are being elucidated in vineyard-to-wine time course experiments, using samples sourced from the spectrum of Australian wine regions, highlighting both the temporal and geographic dynamics of the microbial populations. Once these regional differences are identified, key microbes will be isolated in pure culture to assess their contributions to the unique terroir or wine style(s) of the region. In addition to regional wine isolates sourced from the metagenomics project, wild yeast strains will be sought from non-winemaking areas of Australia, as potential reservoirs of new and desirable winemaking characteristics, and uniquely Australian germplasm.
The thousands of strains that are isolated by this project, in addition to those already present in the AWRI Wine Microorganism Culture Collection, will be then assessed by high-throughput screening for desirable winemaking properties such as the production of key aroma compounds, the production of enzymes, and the ability to produce lower alcohol concentrations.
In addition, common winemaker interventions in wild fermentations will be explored by subjecting fermentations to various external factors (e.g. sulfite, oxygen, temperature, and/or high solids juice), to determine if it is possible to rationally influence or shape the performance or style of wild fermentations.
Strains that exhibit desirable phenotypes will progress to laboratory-scale fermentation and potentially to winery-scale and external trials, depending on their behaviour. These characterised strains will therefore provide a key resource for wineries to enhance the expression of regional terroir through inoculation of existing microbes either in the vineyard or within individual ferments.
Microbial composition of wild ferments
More than 2,000 samples from uninoculated ferments have been collected from 34 wineries around Australia across the 2016-2018 vintages. In addition to these samples, 7,200 yeast isolates (Saccharomyces and non-Saccharomyces) have been added to the AWRI Wine Microorganism Culture Collection. These provide an important reservoir of Australian wine microbial biodiversity for future bioprospecting studies.
Analysis of samples from the 2016 and 2017 vintages showed that there is significant diversity in the species of fungi and yeast present in uninoculated ferments across Australia and that individual ferments can have markedly different microbial communities. Whole genome sequencing of hundreds of Saccharomyces cerevisiae strains isolated from these ferments found that uninoculated ferments also harbour significant diversity of this species. Interestingly, it appears that commercial strains do not generally dominate these fermentations, even when wineries are performing conventional ferments at the same location. ‘Wild’ and/or ‘feral’ (once domesticated) strains of S. cerevisiae are therefore responsible for carrying out the bulk of these fermentations, with many strains being specific to particular wineries and also appearing across multiple vintages.