The wild, cold-adapted parent of hybrid lager-brewing yeasts, Saccharomyces eubayanus, has a complex and understudied natural history. The exploration of this diversity can be used both to develop new brewing applications and to enlighten our understanding of the dynamics of yeast evolution in the wild. Here, we integrate whole genome sequence and phenotypic data of 200 S. eubayanus strains, the largest collection known to date. S. eubayanus has a multilayered population structure, consisting of two major populations that are further structured into six subpopulations. Four of these subpopulations are found exclusively in the Patagonian region of South America; one is found predominantly in Patagonia and sparsely in Oceania and North America; and one is specific to the Holarctic ecozone. Plant host associations differed between subpopulations and between S. eubayanus and its sister species, Saccharomyces uvarum. S. eubayanus is most abundant and genetically diverse in northern Patagonia, where some locations harbor more genetic diversity than is found outside of South America, suggesting that northern Patagonia east of the Andes was a glacial refugium for this species. All but one subpopulation shows isolation-by-distance, and gene flow between subpopulations is low. However, there are strong signals of ancient and recent outcrossing, including two admixed lineages, one that is sympatric with and one that is mostly isolated from its parental populations. Using our extensive biogeographical data, we build a robust model that predicts all known and a handful of additional regions of the globe that are climatically suitable for S. eubayanus, including Europe where host accessibility and competitive exclusion by other Saccharomyces species may explain its continued elusiveness. We conclude that this industrially relevant species has rich natural diversity with many factors contributing to its complex distribution and natural history. The mysterious wild parent of hybrid-lager brewing yeasts, Saccharomyces eubayanus, has been known for less than 10 years. In this time, it has become clear that lager hybrids arose from a subpopulation that has only been isolated in Tibet and North Carolina, USA; but the global diversity of this species has been less explored. Here, we use whole genome sequencing data for 200 strains (174 newly sequenced) to investigate the genetic diversity and geographical distribution of S. eubayanus. We find that its extensive wild diversity is largely centered in northern Patagonia, which likely was a glacial refugium for this species as three of six subpopulations are endemic to this region. In contrast, S. eubayanus is rarely isolated outside of Patagonia. In North America, isolates are dominated by an invasive, near-clonal admixed lineage; the result of an outcrossing and migration event. All subpopulations are well-differentiated, with low gene flow between them. This genetic isolation of subpopulations could be due to ecological factors, such as plant host associations. With modeling, we find that many areas of the world are climatically suitable to S. eubayanus, including Europe, where it has never been isolated. We propose complex ancestries and rich ecologies underlie the global distribution and diversity of this elusive and industrially important species.

Different species can find convergent solutions to adapt their genome to the same evolutionary constraints, although functional convergence promoted by chromosomal rearrangements in different species has not previously been found. In this work, we discovered that two domesticated yeast species, Saccharomyces cerevisiae, and Saccharomyces uvarum, acquired chromosomal rearrangements to convergently adapt to the presence of sulfite in fermentation environments. We found two new heterologous chromosomal translocations in fermentative strains of S. uvarum at the SSU1 locus, involved in sulfite resistance, an antimicrobial additive widely used in food production. These are convergent events that share similarities with other SSU1 locus chromosomal translocations previously described in domesticated S. cerevisiae strains. In S. uvarum, the newly described VII^XVI and XI^XVI chromosomal translocations generate an overexpression of the SSU1 gene and confer increased sulfite resistance. This study highlights the relevance of chromosomal rearrangements to promote the adaptation of yeast to anthropic environments.

Background: The cider industry is becoming an increasingly important segment of the apple fruit sector in Argentina. This study evaluated different inoculation strategies using two Patagonian strains to produce ciders with reduced malic acid and enhanced quality from acidic apple musts. Methods: Fermentations were performed using Pichia kudriavzevii NPCC1651 (isolated from cider) and Saccharomyces cerevisiae ÑIF8 (isolated from wine) in pure, simultaneous, and sequential inoculations. Viable cell counts, glucose and fructose consumption kinetics, and malic acid depletion were measured during fermentation, while physicochemical and aromatic profiles of the ciders were also analyzed in the final products. Results: P. kudriavzevii was capable of coexisting with S. cerevisiae until the final stages of fermentation, independently from the inoculation strategy employed. The simultaneous inoculation at a 1:1 ratio and the sequential inoculation initiated with S. cerevisiae showed the best performance. Both strategies produced ciders with high fermentative efficiency and elevated levels of lactic and succinic acids, isoamyl alcohol, 2-phenylethanol, isoamyl acetate, and 2-phenylethyl acetate while reducing acetic acid and ethyl acetate levels. These fermentations also achieved higher malic acid consumption compared to pure cultures. Conclusions: The simultaneous inoculation at a 1:1 ratio is proposed for further pilot-scale testing in natural acidic musts due to its operational practicality and its potential to produce ciders with reduced malic acid and improved sensory quality.

Honey possesses unique properties, characterized by its high sugar concentration and the synergistic interaction among nectar, pollen, bees, and yeasts. These features render it an exceptional substrate for exploring microbial diversity for bioprospecting purposes. In this study, we characterized fermentative yeast populations from 19 honey samples collected in Northern Patagonia, Argentina. A total of 380 yeast isolates were obtained, identifying eight yeast species. Starmerella magnoliae emerged as the dominant species, found in 76% of samples and representing 63% of total isolates. Intraspecific diversity analysis, using mtDNA-RFLP and sequencing of nuclear genes (FSY1 and FFZ1), revealed the presence of two distinct phylogeographic populations. Phenotypic assays indicated that most S. magnoliae strains tolerate high sulfite and ethanol concentrations, alongside exhibiting broad temperature tolerance, with some strains thriving even at 37 °C. Despite the fact that none of the strains completed the fermentation, microfermentation trials confirmed the fructophilic nature of this species and highlighted intraspecific variability in glycerol and acetic acid production. These findings underscore S. magnoliae as a promising non-Saccharomyces yeast for the fermented beverage industry.

Background: The cider industry is becoming an increasingly important segment of the apple fruit sector in Argentina. This study evaluated different inoculation strategies using two Patagonian strains to produce ciders with reduced malic acid and enhanced quality from acidic apple musts. Methods: Fermentations were performed using Pichia kudriavzevii NPCC1651 (isolated from cider) and Saccharomyces cerevisiae ÑIF8 (isolated from wine) in pure, simultaneous, and sequential inoculations. Viable cell counts, glucose and fructose consumption kinetics, and malic acid depletion were measured during fermentation, while physicochemical and aromatic profiles of the ciders were also analyzed in the final products. Results: P. kudriavzevii was capable to coexist with S. cerevisiae until the final stages of fermentation, independently from the inoculation strategy employed. The simultaneous inoculation at a 1:1 ratio and the sequential inoculation initiated with S. cerevisiae showed the best performance. Both strategies produced ciders with high fermentative efficiency, elevated levels of lactic and succinic acids, isoamyl alcohol, 2-phenylethanol, isoamyl acetate and 2-phenylethyl acetate, while reducing acetic acid and ethyl acetate levels. These fermentations also achieved higher malic acid consumption compared to pure cultures. Conclusion: The simultaneous inoculation at a 1:1 ratio is proposed for further pilot-scale testing in natural acidic musts due to its operational practicality and its potential to produce ciders with reduced malic acid and improved sensory quality.