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MICROWINE - Microbial metagenomics and the modern wine industry

Periodic Reporting for period 2 - MICROWINE (MICROWINE - Microbial metagenomics and the modern wine industry)

Reporting period: 2017-01-01 to 2018-12-31

A diverse, complex, and poorly characterised community of microorganisms lies at the heart of the wine – an industry worth over €220 billion globally. These microorganisms play key roles at all stages of the viniculture and vinification processes, from helping the plants access nutrients from the soil, driving the plants’ health through protection against pathogens, to the fermentation process that transforms the must into wine with its complex array of aromas and flavours. Given this importance, an improved understanding of the microbial community and its interplay will have significant effects on the wine industry.

In recent years, the 'Next Generation' DNA sequencing revolution has revolutionised many areas of biology, including microbiology, in particular through conferring the ability to characterise microbes on the deep community scale, through both ’shotgun’ and ’deep amplicon’ sequencing approaches. To exploit the power of such approaches for the benefit of the wine industry, we have initiated MICROWINE, a Marie Curie Actions European Training Network including 15 early stage researchers (ESRs). The network is constructed as a close collaboration between industry and academic partners, around the theme of the role of the microbial community in the wine production process.

Through combining microbial metagenomic sequencing with powerful computation analyses, with metadata generated using techniques such as metabolomics and geochemistry, we will study the action of microbes from the plant protection and nutrition, through to wine fermentation process, using samples collected from both Europe and beyond. We will further train the ESRs within a wide range of relevant disciplines, and maximise information transfer through multiple host and academic-industry cosupervision and secondments. In this way, we anticipate contributing to the strength and scientific progress of the wine industry through training of a cohort of leading, interdisciplinary and tightly interconnected scientists at the forefront of modern microbiological, genomic, computational and related techniques.
The MicroWine network was initiated to support a new generation of researchers to develop tools and gather knowledge for a modern DNA-based approach to European winemaking. Having a network like this provided the opportunity to uncover and interpret microbial contributions to several levels of winemaking, from microbial influence to plant health to the microbial role in fermentation processes and influence on wine aroma and sensory perception. This was done by bringing together experienced scientists and ESRs from a range of disciplines such as microbial ecology, DNA forensics, fermentation biotechnology, chemistry, mathematical modelling and bioinformatics. Between 2015 and 2019, the network supported 15 ESRs (www.microwine.eu) all dedicated to gather and interpret information related to metagenomics and the wine industry.

During the four years, MicroWine’s research and training activities featured a large number of workshops (www.microwine.eu) that focused on both on general dissemination skills (media training and communication workshops) and scientific discipline topics ranging from Wine sensory analyses, metagenomics and fermentation techniques. This has produced 15 highly skilled ESRs who are determined to or already contributing to the wine industry specifically or to the European research environment. The network has throughout enjoyed the strong support from several industrial partners from and surrounding the wine industry.

From the network start we took measures to ensure a coherent, tightly knit network that would last throughout the 4-year period and would enable the ESRs and the experienced scientists to collaborate and use each other’s competences and infrastructure in a synergistic manner. This was headed by a management team at Aarhus University and supported by an executive steering committee encompassing key PIs that held regular meetings throughout the project’s duration. Hence, we succeeded in establishing a close community spirit that was particularly born from a planned activity structure that started with two training events following immediately the kickoff meeting in Rungsted, Denmark. From here, the ESRs and PIs met at regular timepoints for multi-day training events and social events that allowed the build-up of both professional and personal relationships.

The ESRs all started within 2.5 months of each other, ensuring that all followed the full training program planned in the network. The training was important for both professional and personal development reasons and we therefore focused 75% of the training activities in the first 18 months. Here in this first period the ESRs acquired personal skills related to communication, project management, career development media and professional networking.

The scientific training events were clustered into three distinct themes: ‘Background’. ‘Genomics and Analytic Tools’ and ‘General Vine and Wine Science’. These were held within the network as closed intensive workshops/courses. These were often coupled to symposia that involved other academic visitors, guest speakers and members of the wine industry. These events were all held with the coordination and funding provided by the network and often greatly aided by our main industrial partner Chr. Hansen. The external and internal input have been key tools to broaden the horizons of the fellows and improve networking activities (www.microwine.eu). The events were held at varying geographical sites in Europe that reflects very different traditions and approaches to winemaking. These included Germany, Georgia, Portugal, France, Denmark and Holland.

The final event was held at Cité du Vin in Bordeaux, where the fellows over a course of two days were offered a chance to present their scientific findings to a very broad range of decision makers from the wine industry and to their academic peers. Here, a number of invited speakers were also presenting their views on wine science to the
With regards to research outcomes, at the time of network completion, the fellows report attendance at a 53 conferences and symposia, as well as 39 academic articles that are either published already or in late preparation stages. Some of the major research highlights so far include (i) a microbial variation map of global vineyards highlighting the differences between wine fields at either country scale or region scale (ii) Discovery of new genera of viruses that control or impede the use of certain bacterial strains used in wine fermentation or as bio-control agents in vineyards, (iii) Deciphering genomic variations between malolactic fermentation microbes Oenococcus Oenii, and (iv) new strategies to control serious diseases of Vines such as esca and Pierce’s disease. We expect these outcomes to increase, but even without these final papers we are very proud of our ESR achievements.

The societal impact of providing state of the arts training for 15 young scientists to revolutionize the European wine industry will undoubtedly show itself in the coming years as increased business competitiveness, job creation and increase wine quality and therefore quality of life in general.
The MicroWine ESRs visiting vineyard in Portugal