PhD defense: Sarah Mak

Riesling, ferments, microbes − The development and application of NGS tools in the context of winemaking

Supervisors: Tom Gilbert & Anders Hansen (Evolutionary Genomics)

Examiners: Nina Lundholm (Chair), Frank Møller Aarestrup (DTU), Patrick Lucas (U. Bordeaux)

Winemaking, the art of producing wine, has been practiced for thousands of years in many different human civilizations. The most essential component in winemaking is the microbial activity, especially that of yeasts, that convert sugar to alcohol and in doing so turn grape must into wine during alcoholic fermentation. Characterising the microbial diversity, and understanding how they interact is critical for controlling and predicting the complex microbial processes in winemaking. Traditionally, such research was routinely done with isolation by culturing, followed by enzymatic screening and characterization. With the advancement of next-generation sequencing tools (NGS), we can improve our understanding of these microbial communities and their interactions during alcoholic fermentation. Riesling was used as the model cultivar in this thesis, owing to its well-known high aromatic capability that reflects climatic and soil conditions, and viticultural practices. Furthermore, its microbial communities and their interactions remain understudied.

Since the use of NGS in winemaking is a tool in development, this thesis centred around exploring and developing different laboratory methods of relevance to ferment samples with which to generate the NGS data and their applications. With the refinement of laboratory methods in Chapters 1 and 2, we examined the microbial diversity (particularly fungi) during spontaneous fermentation using metabarcoding and metagenomic approaches in Chapter 3. In addition, the applicability of applying the recently launched sequencing platform BGISEQ-500 to palaeogenomics was explored, by comparing its performance against the Illumina HiSeq 2500 platform in Chapter 2. We found data generated on the BGISEQ-500 to be highly comparable, thus this was used to generate the metagenomic data from the fermented samples. Furthermore, given that integrating different ‘omics approaches will provide exceptional insights into winemaking should we wish to fully understand the microbial interactions, in Chapter 4 we evaluated the role and future potential of these approaches in wine production, and highlighted the potential challenges.