Saccharomyces cerevisiae × Saccharomyces uvarum hybrids generated under different conditions share similar winemaking features

Nonconventional yeasts and hybrids for low temperature handcrafted sparkling ciders elaboration in Patagonia

Yeasts play a crucial role in transforming apple must into cider. While Saccharomyces cerevisiae (Sc) has been traditionally associated to cider fermentations worldwide, cryotolerant species such as Saccharomyces uvarum (Su) as well as natural S. cerevisiae × S. uvarum (Sc×Su) hybrids have also been detected in ciders fermented at low temperatures. This study aimed to evaluate the ability of two Patagonian cryotolerant yeast strains (Su and Se) and their interspecific hybrids with a Sc to conduct handcrafted apple must fermentations and a second fermentation process (champenoise method). The main chemical parameters and sensory quality of the resulting sparkling beverages was also analysed. Firstly, Sc×Se and Sc×Su hybrids were evaluated in their fermentative features at laboratory scale. Hybrids were compared with their respective parental species evidencing significant differences in the physicochemical and aromatic composition of the obtained base ciders. Both Su parental strain and the hybrid Sc×Se were selected for performing pilot scale fermentations (250 L) using natural (non-sterilized) apple juice at two different temperatures: 20 °C and 13 °C. Sc parental strain was also evaluated for comparative purposes. All base ciders obtained were then subjected to a second fermentation. A high implantation capacity of both Su and the hybrid was evidenced at the lowest evaluated temperature, while commercial Sc strain was not detected at the final fermentation stage, independently from the temperature. All sparkling ciders exhibited distinct physicochemical profiles. Ciders inoculated with commercial Sc (but effectively fermented with local Sc strains) allowed the development of malolactic fermentation (MLF) in processes carried out at both temperatures. Contrarily, no MLF was observed in ciders inoculated with either Su or the hybrid. Sparkling ciders fermented with Su displayed the highest concentrations of 2-phenylethanol and 2-phenylethyl acetate, regardless of the fermentation temperature. Conversely, ciders fermented with the hybrid at 20 °C exhibited the highest concentrations of ethyl octanoate and ethyl decanoate, contributing to floral and fruity notes in the beverage. Sensory analysis conducted with untrained individuals revealed a preference for sparkling ciders produced with the hybrid strain at both 20 °C and 13 °C. The cider fermented at 20 °C exhibited floral notes, sweetness, and a full body, while ciders fermented at 13 °C displayed moderate acidity and a well-balanced profile. Conversely, a trained panel described the cider fermented at 20 °C with Su as a fruity and acidic beverage, whereas the ciders fermented at 13 °C exhibited intense bitterness and acidity. This study highlights the potential of cryotolerant Saccharomyces species and hybrids in the development of new starter cultures for producing artisanal sparkling ciders with distinctive properties.

Beyond S. cerevisiae for winemaking: Fermentation-related trait diversity in the genus Saccharomyces

Saccharomyces cerevisiae is the yeast of choice for most inoculated wine fermentations worldwide. However, many other yeast species and genera display phenotypes of interest that may help address the environmental and commercial challenges the wine industry has been facing in recent years. This work aimed to provide, for the first time, a systematic phenotyping of all Saccharomyces species under winemaking conditions. For this purpose, we characterized the fermentative and metabolic properties of 92 Saccharomyces strains in synthetic grape must at two different temperatures. The fermentative potential of alternative yeasts was higher than expected, as nearly all strains were able to complete fermentation, in some cases more efficiently than commercial S. cerevisiae strains. Various species showed interesting metabolic traits, such as high glycerol, succinate and odour-active compound production, or low acetic acid production, compared to S. cerevisiae. Altogether, these results reveal that non-cerevisiae Saccharomyces yeasts are especially interesting for wine fermentation, as they may offer advantages over both S. cerevisiae and non-Saccharomyces strains. This study highlights the potential of alternative Saccharomyces species for winemaking, paving the way for further research and, potentially, for their industrial exploitation.

New malic acid producer strains of Saccharomyces cerevisiae for preserving wine acidity during alcoholic fermentation

In the context of climate change, the chemical composition of wines is characterized by a massive drop of malic acid concentration in grape berries. Then wine professionals have to find out physical and/or microbiological solutions to manage wine acidity. The aim of this study is to develop wine Saccharomyces cerevisiae strains able to produce significant amount of malic acid during the alcoholic fermentation. By applying a large phenotypic survey in small scale fermentations, the production level of malic acid in seven grape juices confirmed the importance of the grape juice in the production of malic acid during the alcoholic fermentation. Beside the grape juice effect, our results demonstrated that extreme individuals able to produce up to 3 g/L of malic acid can be selected by crossing together appropriate parental strains. A multivariate analysis of the dataset generated illustrate that the initial the amount of malic acid produced by yeast is a determining exogenous factor for controlling the final pH of wine. Interestingly most of the acidifying strains selected are particularly enriched in alleles that have been previously reported for increasing the level of malic acid at the end of the alcoholic fermentation. A small set of acidifying strains were compared with strains able to consume a large amount of malic acid previously selected. The total acidity of resulting wines was statistically different and a panelist of 28 judges was able to discriminate the two groups of strains during a free sorting task analysis.

Characterization of Saccharomyces Strains Isolated from “Kéknyelű” Grape Must and Their Potential for Wine Production

Novel wine yeast strains have the potential to satisfy customer demand for new sensorial experiences and to ensure that wine producers have strains that can produce wine as efficiently as possible. In this respect, hybrid yeast strains have recently been the subject of intense research, as they are able to combine the favourable characteristics of both parental strains. In this study, two Saccharomyces “Kéknyelű” grape juice isolates were identified by species-specific PCR and PCR-RFLP methods and investigated with respect to their wine fermentation potential. Physiological characterization of the isolated strains was performed and included assessment of ethanol, sulphur dioxide, temperature and glucose (osmotic stress) tolerance, killer-toxin production, glucose fermentation ability at 16 °C and 24 °C, and laboratory-scale fermentation using sterile “Kéknyelű” must. Volatile components of the final product were studied by gas chromatography (GC) and mass spectrometry (MS). One isolate was identified as a S. cerevisiae × S. kudriavzevii hybrid and the other was S. cerevisiae. Both strains were characterized by high ethanol, sulphur dioxide and glucose tolerance, and the S. cerevisiae strain exhibited the killer phenotype. The hybrid isolate showed good glucose fermentation ability and achieved the lowest residual sugar content in wine. The ester production of the hybrid strain was high compared to the control S. cerevisiae starter strain, and this contributed to the fruity aroma of the wine. Both strains have good oenological characteristics, but only the hybrid yeast has the potential for use in wine fermentation.

Hybridization of Saccharomyces cerevisiae Sourdough Strains with Cryotolerant Saccharomyces bayanus NBRC1948 as a Strategy to Increase Diversity of Strains Available for Lager Beer Fermentation

The search for novel brewing strains from non-brewing environments represents an emerging trend to increase genetic and phenotypic diversities in brewing yeast culture collections. Another valuable tool is hybridization, where beneficial traits of individual strains are combined in a single organism. This has been used successfully to create de novo hybrids from parental brewing strains by mimicking natural Saccharomycescerevisiae ale × Saccharomyceseubayanus lager yeast hybrids. Here, we integrated both these approaches to create synthetic hybrids for lager fermentation using parental strains from niches other than beer. Using a phenotype-centered strategy, S. cerevisiae sourdough strains and the S. eubayanus × Saccharomyces uvarum strain NBRC1948 (also referred to as Saccharomyces bayanus) were chosen for their brewing aptitudes. We demonstrated that, in contrast to S. cerevisiae × S. uvarum crosses, hybridization yield was positively affected by time of exposure to starvation, but not by staggered mating. In laboratory-scale fermentation trials at 20 °C, one triple S. cerevisiae × S. eubayanus × S. uvarum hybrid showed a heterotic phenotype compared with the parents. In 2 L wort fermentation trials at 12 °C, this hybrid inherited the ability to consume efficiently maltotriose from NBRC1948 and, like the sourdough S. cerevisiae parent, produced appreciable levels of the positive aroma compounds 3-methylbutyl acetate (banana/pear), ethyl acetate (general fruit aroma) and ethyl hexanoate (green apple, aniseed, and cherry aroma). Based on these evidences, the phenotype-centered approach appears promising for designing de novo lager beer hybrids and may help to diversify aroma profiles in lager beer.

Homologous Recombination: A GRAS Yeast Genome Editing Tool

The fermentation industry is known to be very conservative, relying on traditional yeast management. Yet, in the modern fast-paced world, change comes about in facets such as climate change altering the quality and quantity of harvests, changes due to government regulations e.g., the use of pesticides or SO2, the need to become more sustainable, and of course by changes in consumer preferences. As a silent companion of the fermentation industry, the wine yeast Saccharomyces cerevisiae has followed mankind through millennia, changing from a Kulturfolger, into a domesticated species for the production of bread, beer, and wine and further on into a platform strain for the production of biofuels, enzymes, flavors, or pharmaceuticals. This success story is based on the ‘awesome power of yeast genetics’. Central to this is the very efficient homologous recombination (HR) machinery of S. cerevisiae that allows highly-specific genome edits. This microsurgery tool is so reliable that yeast has put a generally recognized as safe (GRAS) label onto itself and entrusted to itself the life-changing decision of mating type-switching. Later, yeast became its own genome editor, interpreted as domestication events, to adapt to harsh fermentation conditions. In biotechnology, yeast HR has been used with tremendous success over the last 40 years. Here we discuss several types of yeast genome edits then focus on HR and its inherent potential for evolving novel wine yeast strains and styles relevant for changing markets.

Diversity and Postzygotic Evolution of the Mitochondrial Genome in Hybrids of Saccharomyces Species Isolated by Double Sterility Barrier

Eukaryotic species are reproductively isolated by sterility barriers that prevent interspecies fertilization (prezygotic sterility barrier) or the fertilization results in infertile offspring (postzygotic sterility barrier). The Saccharomyces species are isolated by postzygotic sterility barriers. Their allodiploid hybrids form no viable gametes (ascospores) and the viable ascospores of the allotetraploids cannot fertilize (conjugate). Our previous work revealed that this mechanism of reproductive isolation differs from those operating in plants and animals and we designated it double sterility barrier (the failure of homeologous chromosomes to pair and the repression of mating by mating-type heterozygosity). Other studies implicated nucleo-mitochondrial incompatibilities in the sterility of the Saccharomyces hybrids, a mechanism assumed to play a central role in the reproductive isolation of animal species. In this project the mitochondrial genomes of 50 cevarum (S. cerevisiae × S. uvarum) hybrids were analyzed. 62% had S. cerevisiae mitotypes, 4% had S. uvarum mitotypes, and 34% had recombinant mitotypes. All but one hybrid formed viable spores indicating that they had genomes larger than allodiploid. Most of these spores were sterile (no sporulation in the clone of vegetative descendants; a feature characteristic of allodiploids). But regardless of their mitotypes, most hybrids could also form fertile alloaneuploid spore clones at low frequencies upon the loss of the MAT-carrying chromosome of the S. uvarum subgenome during meiosis. Hence, the cevarum alloploid nuclear genome is compatible with both parental mitochondrial genomes as well as with their recombinants, and the sterility of the hybrids is maintained by the double sterility barrier (determined in the nuclear genome) rather than by nucleo-mitochondrial incompatibilities. During allotetraploid sporulation both the nuclear and the mitochondrial genomes of the hybrids could segregate but no correlation was observed between the sterility or the fertility of the spore clones and their mitotypes. Nucleo-mitochondrial incompatibility was manifested as respiration deficiency in certain meiotic segregants. As respiration is required for meiosis-sporulation but not for fertilization (conjugation), these segregants were deficient only in sporulation. Thus, the nucleo-mitochondrial incompatibility affects the sexual processes only indirectly through the inactivation of respiration and causes only partial sterility in certain segregant spore clones.

Yeast-Yeast Interactions: Mechanisms, Methodologies and Impact on Composition

During the winemaking process, alcoholic fermentation is carried out by a consortium of yeasts in which interactions occurs. The consequences of these interactions on the wine matrix have been widely described for several years with the aim of controlling the winemaking process as well as possible. In this review, we highlight the wide diversity of methodologies used to study these interactions, and their underlying mechanisms and consequences on the final wine composition and characteristics. The wide variety of matrix parameters, yeast couples, and culture conditions have led to contradictions between the results of the different studies considered. More recent aspects of modifications in the composition of the matrix are addressed through different approaches that have not been synthesized recently. Non-volatile and volatile metabolomics, as well as sensory analysis approaches are developed in this paper. The description of the matrix composition modification does not appear sufficient to explain interaction mechanisms, making it vital to take an integrated approach to draw definite conclusions on them.

Differential Contribution of the Parental Genomes to a S. cerevisiae × S. uvarum Hybrid, Inferred by Phenomic, Genomic, and Transcriptomic Analyses, at Different Industrial Stress Conditions

In European regions of cold climate, S. uvarum can replace S. cerevisiae in wine fermentations performed at low temperatures. S. uvarum is a cryotolerant yeast that produces more glycerol, less acetic acid and exhibits a better aroma profile. However, this species exhibits a poor ethanol tolerance compared with S. cerevisiae. In the present study, we obtained by rare mating (non-GMO strategy), and a subsequent sporulation, an interspecific S. cerevisiae × S. uvarum spore-derivative hybrid that improves or maintains a combination of parental traits of interest for the wine industry, such as good fermentation performance, increased ethanol tolerance, and high glycerol and aroma productions. Genomic sequencing analysis showed that the artificial spore-derivative hybrid is an allotriploid, which is very common among natural hybrids. Its genome contains one genome copy from the S. uvarum parental genome and two heterozygous copies of the S. cerevisiae parental genome, with the exception of a monosomic S. cerevisiae chromosome III, where the sex-determining MAT locus is located. This genome constitution supports that the original hybrid from which the spore was obtained likely originated by a rare-mating event between a mating-competent S. cerevisiae diploid cell and either a diploid or a haploid S. uvarum cell of the opposite mating type. Moreover, a comparative transcriptomic analysis reveals that each spore-derivative hybrid subgenome is regulating different processes during the fermentation, in which each parental species has demonstrated to be more efficient. Therefore, interactions between the two subgenomes in the spore-derivative hybrid improve those differential species-specific adaptations to the wine fermentation environments, already present in the parental species.

Inheritance of winemaking stress factors tolerance in Saccharomyces uvarum/S. eubayanus × S. cerevisiae artificial hybrids

Stress has been defined as any environmental factor that impairs the growth of a living organism. High concentrations of ethanol, sugars and SO₂ as well as temperature variations occurring during winemaking processes are some recognized stress factors that yeasts must overcome in order to avoid stuck or sluggish fermentations. At least two of these factors -sugar and ethanol concentrations- are strongly influenced by the global warming, which become them a worry for the future years in the winemaking industry. One of the most interesting strategies to face this complex situation is the generation of hybrids possessing, in a single yeast strain, a broader range of stress factors tolerance than their parents. In the present study, we evaluated four artificial hybrids generated with S. cerevisiae, S. uvarum and S. eubayanus using a non-GMO-generating method, in their tolerance to a set of winemaking stress factors. Their capacity to overcome specific artificial winemaking situations associated with global warming was also analyzed. All four hybrids were able to grow in a wider temperature range (8-37 °C) than their parents. Hybrids showed intermediate tolerance to higher ethanol, sugar and sulphite concentrations than their parents. Additionally, the hybrids showed an excellent fermentative behaviour in musts containing high fructose concentrations at low temperature as well as under a condition mimicking a stuck fermentation.

Improving the Cryotolerance of Wine Yeast by Interspecific Hybridization in the Genus Saccharomyces

Fermentations carried out at low temperatures (10–15°C) enhance the production and retention of flavor volatiles, but also increase the chances of slowing or arresting the process. Notwithstanding, as Saccharomyces cerevisiae is the main species responsible for alcoholic fermentation, other species of the genus Saccharomyces, such as cryophilic species Saccharomyces eubayanus, Saccharomyces kudriavzevii and Saccharomyces uvarum, are better adapted to low-temperature fermentations during winemaking. In this work, a Saccharomyces cerevisiae × S. uvarum hybrid was constructed to improve the enological features of a wine S. cerevisiae strain at low temperature. Fermentations of white grape musts were performed, and the phenotypic differences between parental and hybrid strains under different temperature conditions were examined. This work demonstrates that hybridization constitutes an effective approach to obtain yeast strains with desirable physiological features, like low-temperature fermentation capacity, which genetically depend on the expression of numerous genes (polygenic character). As this interspecific hybridization approach is not considered a GMO, the genetically improved strains can be quickly transferred to the wine industry.

Mechanisms of Yeast Adaptation to Wine Fermentations

Cells face genetic and/or environmental changes in order to outlast and proliferate. Characterization of changes after stress at different "omics" levels is crucial to understand the adaptation of yeast to changing conditions. Wine fermentation is a stressful situation which yeast cells have to cope with. Genome-wide analyses extend our cellular physiology knowledge by pointing out the mechanisms that contribute to sense the stress caused by these perturbations (temperature, ethanol, sulfites, nitrogen, etc.) and related signaling pathways. The model organism, Saccharomyces cerevisiae, was studied in response to industrial stresses and changes at different cellular levels (transcriptomic, proteomic, and metabolomics), which were followed statically and/or dynamically in the short and long terms. This chapter focuses on the response of yeast cells to the diverse stress situations that occur during wine fermentations, which induce perturbations, including nutritional changes, ethanol stress, temperature stress, oxidative stress, etc.

Interspecies Hybridisation and Genome Chimerisation in Saccharomyces: Combining of Gene Pools of Species and Its Biotechnological Perspectives

Over the last one and a half decade, interspecies hybridisation has gained continuously increasing attention as a breeding technique suitable for transferring of genetic information between Saccharomyces species and mixing of their gene pools without genetic engineering. The hybrids frequently show positive transgressive phenotypes. Segregation of the hybrid genome results in mosaic (chimeric) strains that can outperform both the parents and the hybrids or exhibit novel positive phenotypic properties. Mitotic segregation can take place during the vegetative propagation of the sterile allodiploid hybrid cells. Meiotic segregation becomes possible after genome duplication (tetraploidisation) if it is followed by break-down of sterility. The allotetraploid cells are seemingly fertile because they form viable spores. But because of the autodiploidisation of the meiosis, sterile allodiploid spores are produced and thus the hybrid genome does not segregate (the second sterility barrier). However, malsegregation of MAT-carrying chromosomes in one of the subgenomes during allotetraploid meiosis (loss of MAT heterozygosity) results in fertile alloaneuploid spores. The breakdown of (the second) sterility barrier is followed by the loss of additional chromosomes in rapid succession and recombination between the subgenomes. The process (genome autoreduction in meiosis or GARMe) chimerises the genome and generates strains with chimeric (mosaic) genomes composed of various combinations of the genes of the parental strains. Since one of the subgenomes is preferentially reduced, the outcome is usually a strain having an (almost) complete genome from one parent and only a few genes or mosaics from the genome of the other parent. The fertility of the spores produced during GARMe provides possibilities also for introgressive backcrossing with one or the other parental strain, but genome chimerisation and gene transfer through series of backcrosses always with the same parent is likely to be less efficient than through meiotic or mitotic genome autoreduction. Hybridisation and the evolution of the hybrid genome (resizing and chimerisation) have been exploited in the improvement of industrial strains and applied to the breeding of new strains for specific purposes. Lists of successful projects are shown and certain major trends are discussed.

Fermentative behaviour and competition capacity of cryotolerant Saccharomyces species in different nitrogen conditions

The selection of yeasts with low nitrogen requirement is a current need in winemaking. In this work, we analysed nitrogen requirements of strains belonging to the cryotolerant species S. uvarum, S. eubayanus and S. kudriavzevii, in order to evaluate their potential for conducting the fermentation of low nitrogen content grape musts. Our result demonstrated that S. eubayanus is the species less influenced by the increasing nitrogen concentrations in both growth and fermentation conditions. Strains showing the best behaviours, S. eubayanus NPCC 1285 and S. uvarum NPCC 1317, were selected to be tested in mixed cultures with S. cerevisiae T73 at different temperatures (12 °C, 20 °C and 28 °C) in synthetic grape must with different nitrogen concentrations (60, 140 and 300 mg/L YAN). The cryotolerant strains dominated the fermentations carried out at 12 °C while S. cerevisiae prevailed at 28 °C independently from the nitrogen concentration. At intermediate temperature, 20 °C, S. eubayanus mono and mixed cultures showed the best fermentative behaviour especially with low and intermediate nitrogen concentration. In summary, cryotolerant Saccharomyces species, particularly S. eubayanus, could be interesting tools to avoid fermentations stucks caused by low nitrogen content in grape musts.

A Unique Saccharomyces cerevisiae × Saccharomyces uvarum Hybrid Isolated From Norwegian Farmhouse Beer: Characterization and Reconstruction

An unknown interspecies Saccharomyces hybrid, "Muri," was recently isolated from a "kveik" culture, a traditional Norwegian farmhouse brewing yeast culture (Preiss et al., 2018). Here we used whole genome sequencing to reveal the strain as an allodiploid Saccharomyces cerevisiae × Saccharomyces uvarum hybrid. Phylogenetic analysis of its sub-genomes revealed that the S. cerevisiae and S. uvarum parent strains of Muri appear to be most closely related to English ale and Central European cider and wine strains, respectively. We then performed phenotypic analysis on a number of brewing-relevant traits in a range of S. cerevisiae, S. uvarum and hybrid strains closely related to the Muri hybrid. The Muri strain possesses a range of industrially desirable phenotypic properties, including broad temperature tolerance, good ethanol tolerance, and efficient carbohydrate use, therefore making it an interesting candidate for not only brewing applications, but potentially various other industrial fermentations, such as biofuel production and distilling. We identified the two S. cerevisiae and S. uvarum strains that were genetically and phenotypically most similar to the Muri hybrid, and then attempted to reconstruct the Muri hybrid by generating de novo interspecific hybrids between these two strains. The de novo hybrids were compared with the original Muri hybrid, and many appeared phenotypically more similar to Muri than either of the parent strains. This study introduces a novel approach to studying hybrid strains and strain development by combining genomic and phenotypic analysis to identify closely related parent strains for construction of de novo hybrids.

New Trends in the Uses of Yeasts in Oenology

The most important factor in winemaking is the quality of the final product and the new trends in oenology are dictated by wine consumers and producers. Traditionally the red wine is the most consumed and more popular; however, in the last times, the wine companies try to attract other groups of populations, especially young people and women that prefer sweet, whites or rosé wines, very fruity and with low alcohol content. Besides the new trends in consumer preferences, there are also increased concerns on the effects of alcohol consumption on health and the effects of global climate change on grape ripening and wine composition producing wines with high alcohol content. Although S. cerevisiae is the most frequent species in wines, and the subject of most studies, S. uvarum and hybrids between Saccharomyces species such as S. cerevisiae×S. kudriavzevii and S. cerevisiae×S. uvarum are also involved in wine fermentations and can be preponderant in certain wine regions. New yeast starters of non-cerevisiae strains (S. uvarum) or hybrids (S. cerevisiae×S. uvarum and S. cerevisiae×S. kudriavzevii) can contribute to solve some problems of the wineries. They exhibit good fermentative capabilities at low temperatures, producing wines with lower alcohol and higher glycerol amounts, while fulfilling the requirements of the commercial yeasts, such as a good fermentative performance and aromatic profiles that are of great interest for the wine industry. In this review, we will analyze different applications of nonconventional yeasts to solve the current winemaking demands.