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Quantifying the effect of human practices on S. cerevisiae vineyard metapopulation diversity

Abstract : Saccharomyces cerevisiae is the main actor of wine fermentation but at present, still little is known about the factors impacting its distribution in the vineyards. In this study, 23 vineyards and 7 cellars were sampled over 2 consecutive years in the Bordeaux and Bergerac regions. The impact of geography and farming system and the relation between grape and vat populations were evaluated using a collection of 1374 S. cerevisiae merlot grape isolates and 289 vat isolates analyzed at 17 microsatellites loci. A very high genetic diversity of S. cerevisiae strains was obtained from grape samples, higher in conventional farming system than in organic one. The geographic appellation and the wine estate significantly impact the S. cerevisiae population structure, whereas the type of farming system has a weak global effect. When comparing cellar and vineyard populations, we evidenced the tight connection between the two compartments, based on the high proportion of grape isolates (25%) related to the commercial starters used in the cellar and on the estimation of bidirectional geneflows between the vineyard and the cellar compartments. Vineyards and wineries are ecological habitats that house a community of molds, yeasts and bacteria 1. The yeast species present on the grape berry are related to a fruit microflora (including mainly Hanseniaspora sp., Aureobasidium pullulans, Pichia sp., Metschnikowia pulcherima, Torulaspora delbrueckii, Starmerella bacillaris 2,3. By contrast, the yeast community in the cellar changes drastically during fermentation with the gradual increase in ethanol and temperature 4,5 , as well as with the use of sulfites for wine making, leading to the domination of Saccharomyces sp. Saccharomyces cerevisiae has been associated with human fermentations since the dawn of the civilization 6,7 ; its diversity is shaped by human activities, especially by winemaking 8-10. Because of the key role of S. cerevisiae in wine production, its genetic diversity has been widely analyzed in the wake of the technological advances in the molecular tools designed to reveal yeast diversity. Since the first exploration of wine S. cerevisiae diversity with mtDNA restriction analysis 11 , many more studies have been performed using this technique 12-15. Almost simultaneously, the polymorphism of the karyotypes of wine yeast revealed by pulsed field electrophoresis has been used as an alternative technique 16-19. Later inter-delta analysis 20-24 and more recently microsatellite analysis 25-27 have been used. Several parameters that could impact the genetic diversity and population structure of wine S. cerevisiae have been investigated by different authors. Geographical distance has been the most widely studied environmental parameter, often covering large areas and comparing different regions in a given country. Many species are organized into a metapopulation (i.e., a group of local subpopulations that inhabit discrete habitat patches but interact through dispersal 28. Knight and Goddard 29 have shown that the diversity of regional S. cerevisiae metapopulations from vineyards were undergoing significant changes between distant areas. These authors have also shown differential migration of this species between regions that may be due in part to the human influence. At vineyard scale level, no spatial differentiation of the S. cerevisiae population isolated from spontaneous fermentation is evidenced 30. Over smaller distances, many vectors may favor the homogenization of diversity such as insects including wasps, bees and fruit flies 31-33 , or migratory birds 34. Finally, the influence of grape berry varieties on S. cerevisiae diversity seems to be low 27,35. open 1 UR Oenologie EA 4577, USC 1366 INRAE,
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Marine Börlin, Olivier Claisse, Warren Albertin, Franck Salin, Jean-Luc Legras, et al.. Quantifying the effect of human practices on S. cerevisiae vineyard metapopulation diversity. Scientific Reports, Nature Publishing Group, 2020, 10 (1), 14 p. ⟨10.1038/s41598-020-73279-7⟩. ⟨hal-02983511⟩

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