Sulfometuron resistance as a genetic marker for yeast populations in wine fermentations

Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast

Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer's strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer's) yeast strains leading to diversification of the product portfolio.

Wine yeast selection in the Iberian Peninsula: Saccharomyces and non-Saccharomyces as drivers of innovation in Spanish and Portuguese wine industries

Yeast selection for the wine industry in Spain started in 1950 for the understanding of the microbial ecology, and for the selection of optimal strains to improve the performance of alcoholic fermentation and the overall wine quality. This process has been strongly developed over the last 30 years, firstly on Saccharomyces cerevisiae, and, lately, with intense activity on non-Saccharomyces. Several thousand yeast strains have been isolated, identified and tested to select those with better performance and/or specific technological properties. The present review proposes a global survey of this massive ex-situ preservation of eukaryotic microorganisms, a reservoir of biotechnological solutions for the wine sector, overviewing relevant screenings that led to the selection of strains from 12 genera and 22 species of oenological significance. In the first part, the attention goes to the selection programmes related to relevant wine-producing areas (i.e. Douro, Extremadura, Galicia, La Mancha and Uclés, Ribera del Duero, Rioja, Sherry area, and Valencia). In the second part, the focus shifted on specific non-Saccharomyces genera/species selected from different Spanish and Portuguese regions, exploited to enhance particular attributes of the wines. A fil rouge of the dissertation is the design of tailored biotechnological solutions for wines typical of given geographic areas.

Using mixed inocula of Saccharomyces cerevisiae killer strains to improve the quality of traditional sparkling-wine

The quality of traditional sparkling-wine depends on the aging process in the presence of dead yeast cells. These cells undergo a slow autolysis process thereby releasing some compounds, mostly colloidal polymers such as polysaccharides and mannoproteins, which influence the wine's foam properties and mouthfeel. Saccharomyces cerevisiae killer yeasts were tested to increase cell death and autolysis during mixed-yeast-inoculated second fermentation and aging. These yeasts killed sensitive strains in killer plate assays done under conditions of low pH and temperature similar to those used in sparkling-wine making, although some strains showed a different killer behaviour during the second fermentation. The fast killer effect improved the foam quality and mouthfeel of the mixed-inoculated wines, while the slow killer effect gave small improvements over single-inoculated wines. The effect was faster under high-pressure than under low-pressure conditions. Wine quality improvement did not correlate with the polysaccharide, protein, mannan, or aromatic compound concentrations, suggesting that the mouthfeel and foaming quality of sparkling wine are very complex properties influenced by other wine compounds and their interactions, as well as probably by the specific chemical composition of a given wine.

Effects of new Torulaspora delbrueckii killer yeasts on the must fermentation kinetics and aroma compounds of white table wine

Torulaspora delbrueckii is becoming widely recommended for improving some specific characteristics of wines. However, its impact on wine quality is still far from satisfactory at the winery level, mostly because it is easily replaced by Saccharomyces cerevisiae-like yeasts during must fermentation. New T. delbrueckii killer strains were here isolated and selected for winemaking. They killed S. cerevisiae yeasts and were able to dominate and complete the fermentation of sterile grape must. Sequential yeast inoculation of non-sterile white must with T. delbrueckii followed by S. cerevisiae did not ensure T. delbrueckii dominance or wine quality improvement. Only a single initial must inoculation at high cell concentrations allowed the T. delbrueckii killer strains to dominate and complete the must fermentation to reach above 11% ethanol, but not the non-killer strains. None of the wines underwent malolactic fermentation as long as the must had low turbidity and pH. Although no statistically significant differences were found in the wine quality score, the S. cerevisiae-dominated wines were preferred over the T. delbrueckii-dominated ones because the former had high-intensity fresh fruit aromas while the latter had lower intensity, but nevertheless nice and unusual dried fruit/pastry aromas. Except for ethyl propanoate and 3-ethoxy-1-propanol, which were more abundant in the T. delbrueckii–dominated wines, most of the compounds with fresh fruit odor descriptors, including those with the greatest odor activity values (isoamyl acetate, ethyl hexanoate, and ethyl octanoate), were more abundant in the S. cerevisiae–dominated wines. The low relative concentrations of these fruity compounds made it possible to detect in the T. delbrueckii–dominated wines the low-relative-concentration compounds with dried fruit and pastry odors. An example was γ-ethoxy-butyrolactone which was significantly more abundant in these wines than in those dominated by S. cerevisiae.

A low-cost procedure for production of fresh autochthonous wine yeast

A low-cost procedure was designed for easy and rapid response-on-demand production of fresh wine yeast for local wine-making. The pilot plant produced fresh yeast culture concentrate with good microbial quality and excellent oenological properties from four selected wine yeasts. The best production yields were obtained using 2% sugar beet molasses and a working culture volume of less than 60% of the fermenter capacity. The yeast yield using 2% sugar grape juice was low and had poor cell viability after freeze storage, although the resulting yeast would be directly available for use in the winery. The performance of these yeasts in commercial wineries was excellent; they dominated must fermentation and improved its kinetics, as well as improving the physicochemical parameters and the organoleptic quality of red and white wines.

Wine yeast molecular typing using a simplified method for simultaneously extracting mtDNA, nuclear DNA and virus dsRNA

Quick and accurate methods are required for the identification of industrial, environmental, and clinical yeast strains. We propose a rapid method for the simultaneous extraction of yeast mtDNA, nuclear DNA, and virus dsRNA. It is simpler, cheaper, and faster than the previously reported methods. It allows one to choose among a broad range of molecular analysis approaches for yeast typing, avoiding the need to use of several different methods for the separate extraction of each nucleic acid type. The application of this method followed by the combined analysis of mtDNA and dsRNA (ScV-M and W) is a highly attractive option for fast and efficient wine yeast typing.

Construction of sterile ime1Delta-transgenic Saccharomyces cerevisiae wine yeasts unable to disseminate in nature

The use of new transgenic yeasts in industry carries a potential environmental risk because their dispersal, introducing new artificial genetic combinations into nature, could have unpredictable consequences. This risk could be avoided by using sterile transgenic yeasts that are unable to sporulate and mate with wild yeasts. These sterile yeasts would not survive the annual cyclic harvesting periods, being condemned to disappear in the wineries and vineyards in less than a year. We have constructed new ime1Delta wine yeasts that are unable to sporulate and mate, bear easy-to-detect genetic markers, and quickly disappear in grape must fermentation immediately after sporulation of the yeast population. These sterile yeasts maintained the same biotechnological properties as their parent yeasts without any detectable deleterious effect of the ime1Delta mutation. These yeasts are therefore interesting biotechnologically for food industry applications and for genetically modified microorganism environmental monitoring studies.

Analysis of homothallic Saccharomyces cerevisiae strain mating during must fermentation

Genetic instability and genome renewal may cause loss of heterozygosity (LOH) in homothallic wine yeasts (Saccharomyces cerevisiae), leading to the elimination of the recessive lethal or deleterious alleles that decrease yeast fitness. LOH was not detected in genetically stable wine yeasts during must fermentation. However, after sporulation, the heterozygosity of the new yeast population decreased during must fermentation. The frequency of mating between just-germinated haploid cells from different tetrads was very low, and the mating of haploid cells from the same ascus was favored because of the physical proximity. Also, mating restriction between haploid cells from the same ascus was found, leading to a very low frequency of self spore clone mating. This mating restriction slowed down the LOH process of the yeast population, maintaining the heterozygote frequency higher than would be expected assuming a fully random mating of the haploid yeasts or according to the Mortimer genome renewal proposal. The observed LOH occurs because of the linkage of the locus MAT to the chromosome III centromere, without the necessity for self spore clone mating or the high frequency of gene conversion and rapid asymmetric LOH observed in genetically unstable yeasts. This phenomenon is enough in itself to explain the high level of homozygosis found in natural populations of wine yeasts. The LOH process for centromere-linked markers would be slower than that for the nonlinked markers, because the linkage decreases the frequency of newly originated heterozygous yeasts after each round of sporulation and mating. This phenomenon is interesting in yeast evolution and may cause important sudden phenotype changes in genetically stable wine yeasts.

Rhodamine-pink as a genetic marker for yeast populations in wine fermentation

Winemaking with selected yeasts requires simple techniques to monitor the inoculated yeast. New high-concentration rhodamine-resistant mutants and low-concentration rhodamine-pink mutants, easy to detect by replica-plate assay, were obtained from selected wine yeasts. The rhodamine-pink mutations were dominant and were located at the pdr5 locus that encodes for the Pdr5 ATP-binding cassette multidrug resistance transporter. The mutants were genetically stable but had lost the killer phenotype of the parent yeast strain. They were genetically improved by elimination of recessive growth-retarding alleles followed by crossing with selected killer wine yeasts. Several spore-clones were selected according to their must fermentation kinetics and the organoleptic quality of the wine. Some spore-clones were tested in industrial winemaking, and they were easily monitored during must fermentation using a simple color-plate assay. They accounted for >96% of the total yeasts in the must, and the resulting wine had as good a quality as those made with standard commercial wine yeasts. The rhodamine-pink yeasts may also be detected by direct seeding onto rhodamine agar or by observation under fluorescence microscopy. These possibilities greatly reduce the time of analysis and make the monitoring procedure for rhodamine-pink yeasts faster, easier, and cheaper than for the genetically marked wine yeasts obtained previously.