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An Indigenous Saccharomyces Uvarum Population with High Genetic Diversity Dominates bioRxiv preprint doi: https://doi.org/10.1101/838268; this version posted November 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 An indigenous Saccharomyces uvarum population with high genetic diversity dominates 2 uninoculated Chardonnay fermentations at a Canadian winery 3 4 Garrett C. McCarthy1¶, Sydney C. Morgan1¶*, Jonathan T. Martiniuk2, Brianne L. 5 Newman1, Vivien Measday2, Daniel M. Durall1 6 7 1Irving K. Barber School of Arts and Sciences, Department of Biology, The University of 8 British Columbia, Kelowna, British Columbia, Canada 9 2Wine Research Centre, Faculty of Land and Food Systems, The University of British 10 Columbia, Vancouver, British Columbia, Canada 11 12 ¶ These authors contributed equally to this work 13 14 * Corresponding author 15 Email: [email protected] (SCM) 16 17 Short title: Genetic diversity of Saccharomyces uvarum 18 19 20 21 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/838268; this version posted November 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 24 Abstract 25 Saccharomyces cerevisiae is the primary yeast species responsible for most 26 fermentations in winemaking. However, other yeasts, including Saccharomyces uvarum, 27 have occasionally been found conducting commercial fermentations around the world. 28 S. uvarum is typically associated with white wine fermentations in cool-climate wine 29 regions, and has been identified as the dominant yeast in fermentations from France, 30 Hungary, northern Italy, and, recently, Canada. However, little is known about how the 31 origin and genetic diversity of the Canadian S. uvarum population relates to strains from 32 other parts of the world. In this study, a highly diverse S. uvarum population was found 33 dominating uninoculated commercial fermentations of Chardonnay grapes sourced from 34 two different vineyards. Most of the strains identified were found to be genetically 35 distinct from S. uvarum strains isolated around the world. Of the 106 strains of S. 36 uvarum identified in this study, four played a dominant role in the fermentations, with 37 some strains predominating in the fermentations from one vineyard over the other. 38 Furthermore, two of the dominant strains were previously identified as dominant strains 39 in uninoculated Chardonnay fermentations at the same winery two years earlier, 40 providing evidence for a winery-resident population of indigenous S. uvarum. This 41 research provides a valuable insight into the diversity and persistence of non- 42 commercial S. uvarum strains in North America, and provides a stepping stone for 43 future work into the enological potential of an alternative Saccharomyces yeast species. 44 Key words 45 Saccharomyces uvarum; spontaneous fermentation; microsatellite; indigenous yeast; 46 phylogenetic tree; low-temperature fermentation 2 bioRxiv preprint doi: https://doi.org/10.1101/838268; this version posted November 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 47 Introduction 48 Modern winemaking often involves the inoculation of grape must with one or 49 more commercial yeast strains, usually belonging to the dominant winemaking yeast 50 species Saccharomyces cerevisiae. However, single-strain fermentations have been 51 shown to produce less complex wines than fermentations conducted by multiple yeast 52 species and strains [1–3]. Furthermore, the commercial S. cerevisiae strains used in 53 these inoculated single-strain fermentations may be aggressively competitive towards 54 indigenous yeasts. The loss of indigenous yeast strains during the winemaking process 55 can result in the reduction of regional character, because the local consortium of 56 microorganisms can contribute to the expression of terroir in wine [3,4]. In recent years, 57 many winemakers have become interested in conducting uninoculated (spontaneous) 58 fermentations in an attempt to encourage a diversity of yeast species and strains to 59 participate in alcoholic fermentation. Although vineyard-derived yeasts were originally 60 thought to be the ones conducting uninoculated fermentations, a growing body of 61 evidence has shown that uninoculated fermentations are actually conducted by winery- 62 resident yeast strains [5–8]. These yeasts may be of commercial or indigenous origin, 63 but have established themselves as residents of the winery environment, and are 64 capable of entering and conducting fermentations over multiple vintages. 65 Although most uninoculated fermentations at commercial wineries are conducted 66 by strains of S. cerevisiae [5–8], some wineries contain established populations of 67 Saccharomyces uvarum that are able to conduct and complete alcoholic fermentation 68 [9–12]. S. uvarum belongs to the Saccharomyces sensu stricto clade, and is the furthest 69 relative from S. cerevisiae within this clade [13]. The Holarctic S. uvarum population, 3 bioRxiv preprint doi: https://doi.org/10.1101/838268; this version posted November 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 70 which originated in the northern hemisphere [14–16], includes both natural S. uvarum 71 strains isolated from Quercus (oak) trees as well as all industrial strains isolated from 72 cider, beer, and wine fermentations. It is believed that this population evolved alongside 73 other Saccharomyces species, as 95% of Holarctic S. uvarum strains possess 74 introgressed regions from Saccharomyces eubayanus, Saccharomyces kudriavzevii, 75 and S. cerevisiae throughout their genome [14,15]. However, the history of S. uvarum 76 research is difficult to trace, because S. uvarum has had many names, and has even 77 shared names with now distinct species. In the past, S. uvarum has been referred to as 78 Saccharomyces bayanus var. uvarum [10,11,17,18] or simply Saccharomyces bayanus 79 [19,20]. To complicate matters, many commercial S. cerevisiae strains have been 80 marketed incorrectly as strains of S. bayanus [21]. However, S. uvarum is now known to 81 be a pure species, distinct from S. bayanus, which itself is a hybrid of the pure species 82 S. uvarum and S. eubayanus [13,15,22,23]. 83 S. uvarum is a cryotolerant yeast usually found in association with white wine 84 fermentations in cool-climate wine regions [9,10,12,24], but has also been associated 85 with cider production [19,20] and some traditional fermentations [25,26]. During 86 fermentation, S. uvarum produces lower levels of ethanol, acetic acid, and 87 acetaldehyde, and higher levels of glycerol, succinic acid, malic acid, isoamyl alcohol, 88 isobutanol, and ethyl acetate, as compared to S. cerevisiae [27–30]. Additionally, 89 because of its ability to conduct fermentation at lower temperatures, S. uvarum may 90 produce wines with more balanced aroma profiles [31]. However, few studies have been 91 conducted to investigate the origins, genetic diversity, and enological potential of this 92 yeast, thus more research is needed on this topic. 4 bioRxiv preprint doi: https://doi.org/10.1101/838268; this version posted November 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 93 The overall objective of this study was to identify the presence and genetic 94 diversity of S. uvarum strains conducting uninoculated fermentations at a commercial 95 winery in the Okanagan Valley wine region of British Columbia, Canada, and place this 96 population within the context of S. uvarum strains from around the world. Two years 97 before this current study was conducted, a highly diverse, indigenous population of S. 98 uvarum was identified at this same commercial winery [12]. We were interested in 99 investigating the persistence of S. uvarum strains in the winery environment over 100 multiple vintages. A secondary objective involved sampling fermentations containing 101 grape must from two different vineyards, to investigate whether the geographical origin 102 or chemistry of the grapes played a role in determining the fungal communities and S. 103 uvarum populations present in the fermentations. 104 Materials and methods 105 Experimental design and sampling 106 This study was conducted in association with Mission Hill Family Estate Winery 107 during the 2017 vintage. The fungal diversity and community composition of grapes 108 from two different vineyards were followed from the vineyard into the winery and 109 throughout alcoholic fermentation. Samples for high-throughput amplicon sequencing 110 (Illumina MiSeq) were taken from grapes in the vineyard just prior to harvest, as well as 111 at four stages of fermentation in the winery. Samples for Saccharomyces uvarum 112 population analysis were taken
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