Understanding The Wine Microbiota: The Challenges and Opportunities

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Background

After decades of efforts on individual species or strains, wine yeast and bacteria have been characterized in terms of their main physiological and metabolic traits largely in pure culture analyses. Winemaking practices are derived from this basic knowledge and undoubtedly insure wine quality improvement. Phylogenetic studies and genome comparisons in extensive collections gradually reveal the evolution of the two main species, Saccharomyces cerevisiae and Oenococcus oeni. However, grapes and grape juice contain a variety of microorganisms and the principal agents of fermentation are in fact part of a complex microbial community that evolves dynamically in a special niche. Thanks to the new methods of analysis, the complexity of the microbiota can be measured in any sample of must or wine. In addition there is greater appreciation of diversity within the main species present in wine. Intraspecific diversity has been evaluated in yeast and bacteria species and strains can be typed even in the mixture of selected or indigenous strains. Descriptions of microbial profiles in all the regions of the world have multiplied and suggest that the microbiota is an element of terroir or regional signature.
But it is no longer enough to simply describe what is present. It is time to consider evolution, physiology and metabolisms taking into account the importance of microbial interactions within the community. Wine microbiologists have expanded our understanding of the actual participation and role of the non-Saccharomyces organisms in winemaking, and refined knowledge on microbial spoilage, but they are faced with major challenges to go from the simple description of the phenomena to their interpretation. The greatest difficulty is analyzing the functioning of the extraordinary complex system of yeast and bacteria. Interactions in the very particular environment of fermenting grape must induce alternations of populations’ dominances and declines and the subsequent impact on wine composition. Some mechanisms have been identified or suggested, but much remains to be done. In spite of abundant studies, starters’ results, which depend on the way they are added, pure or mixed, on time of inoculation and initial grape must, are not fully controlled. The recent advent of inoculation with non-Saccharomyces in oenological practice, sometimes leading to inconstant results, makes one aware of the profound gaps in knowledge, in terms of physiology and metabolism. While the major problems of bacterial alterations appear to be diminishing due to the early and practical detections adapted, that by Brettanomyces bruxellensis does not cease to spread. Damage is great. The reasons commonly mentioned to explain their dissemination, their persistence in cellars, their easy multiplication in wine today are not sufficient and do not make it possible to prevent the extension of the damage.

The aim of this Research Topic is to bring together several aspects of wine microorganisms biology: i) evolution / co-evolution of yeasts and bacteria in their process of domestication and adaptation to the oenological niche, including laboratory directed evolution. Ii) Mechanisms of interactions between species and strains, both on grapes and in grape must. Understanding how the microbial community works is expected to provide a sound basis before using fermentation helpers and starters, taking into account the indigenous microflora. Iii) Metabolism and physiology of yeast and bacteria in interactions with each other and with the environment, considering to what extent expected objectives (typicity, lower alcohol, etc…) can be reached by using selected strains. iv) diversity, ecology, physiology and metabolism of B. bruxellensis. Damage is not effectively prevented, because we do not fully understand the biology of this species, particularly in interaction with other yeast and bacteria. v) Development of novel technologies or approaches for the assessment of changes in a dynamic microbial community and the linking of such changes to wine flavor and aroma properties.

Keywords: Yeast, bacteria, adaptation, interactions, metabolisms

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