Reduction of volatile acidity of wines by selected yeast strains

Insights into intraspecific diversity of central carbon metabolites in Saccharomyces cerevisiae during wine fermentation

Saccharomyces cerevisiae is a major actor in winemaking that converts sugars from the grape must into ethanol and CO2 with outstanding efficiency. Primary metabolites produced during fermentation have a great importance in wine. While ethanol content contributes to the overall profile, other metabolites like glycerol, succinate, acetate or lactate also have significant impacts, even when present in lower concentrations. S. cerevisiae is known for its great genetic diversity that is related to its natural or technological environment. However, the variation range of metabolic diversity which can be exploited to enhance wine quality depends on the pathway considered. Our experiment assessed the diversity of primary metabolites production in a set of 51 S. cerevisiae strains from various genetic backgrounds. Results pointed out great yield differences depending on the metabolite considered, with ethanol having the lowest variation. A negative correlation between ethanol and glycerol was observed, confirming glycerol synthesis as a suitable lever to reduce ethanol yield. Genetic groups were linked to specific yields, such as the wine group and high α-ketoglutarate and low acetate yields. This research highlights the potential of using natural yeast diversity in winemaking. It also provides a detailed data set on production of well known (ethanol, glycerol, acetate) or little-known (lactate) primary metabolites.

Emerging biotechnologies and non-thermal technologies for winemaking in a context of global warming

In the current situation, wine areas are affected by several problems in a context of global warming: asymmetric maturities, pH increasing, high alcohol degree and flat wines with low freshness and poor aroma profile. The use of emerging biotechnologies allows to control or manage such problems. Emerging non-Saccharomyces as Lachancea thermotolerans are very useful for controlling pH by the formation of stable lactic acid from sugars with a slight concomitant alcohol reduction. Lower pH improves freshness increasing simultaneously microbiological stability. The use of Hanseniaspora spp. (specially H. vineae and H. opuntiae) or Metschnikowia pulcherrima promotes a better aroma complexity and improves wine sensory profile by the expression of a more complex metabolic pattern and the release of extracellular enzymes. Some of them are also compatible or synergic with the acidification by L. thermotolerans, and M. pulcherrima is an interesting biotool for reductive winemaking and bioprotection. The use of bioprotection is a powerful tool in this context, allowing oxidation control by oxygen depletion, the inhibition of some wild microorganisms, improving the implantation of some starters and limiting SO2. This can be complemented with the use of reductive yeast derivatives with high contents of reducing peptides and relevant compounds such as glutathione that also are interesting to reduce SO2. Finally, the use of emerging non-thermal technologies as Ultra High-Pressure Homogenization (UHPH) and Pulsed Light (PL) increases wine stability by microbial control and inactivation of oxidative enzymes, improving the implantation of emerging non-Saccharomyces and lowering SO2 additions. GRAPHICAL ABSTRACT.

The Life of Saccharomyces and Non-Saccharomyces Yeasts in Drinking Wine

Drinking wine is a processed beverage that offers high nutritional and health benefits. It is produced from grape must, which undergoes fermentation by yeasts (and sometimes lactic acid bacteria) to create a product that is highly appreciated by consumers worldwide. However, if only one type of yeast, specifically Saccharomyces cerevisiae, was used in the fermentation process, the resulting wine would lack aroma and flavor and may be rejected by consumers. To produce wine with a desirable taste and aroma, non-Saccharomyces yeasts are necessary. These yeasts contribute volatile aromatic compounds that significantly impact the wine's final taste. They promote the release of primary aromatic compounds through a sequential hydrolysis mechanism involving several glycosidases unique to these yeasts. This review will discuss the unique characteristics of these yeasts (Schizosaccharomyces pombe, Pichia kluyveri, Torulaspora delbrueckii, Wickerhamomyces anomalus, Metschnikowia pulcherrima, Hanseniaspora vineae, Lachancea thermotolerans, Candida stellata, and others) and their impact on wine fermentations and co-fermentations. Their existence and the metabolites they produce enhance the complexity of wine flavor, resulting in a more enjoyable drinking experience.

Use of red grape pulp, marc and must in the production of beer

The aim of the paper was to determine the potential of using grape pulp, marc and must in the beer production process. Samples were fermented using non-Saccharomyces yeasts (Dekkera bruxellensis 3429, Metschnikowia pulcherrima MG970690), while Saccharomyces cerevisiae Safale US-05 was used as a control. Grape marc was obtained by pressing grape must. The grape marc, must and pulp were pasteurized and, together with wort, volumetrically introduced into fermentation flasks for fermentation. Mass changes taking place during the process were analyzed. Real extract, alcohol content, free amino nitrogen (FAN) content, titratable acidity, pH, color, organic acid profile and content of sugars were determined in obtained beers. The addition of grape marc, must and pulp increased the value of most of the tested parameters. It did not adversely affect the fermentation process. This offers the possibility of using grape marc, must and pulp in the brewing industry, even with the use of non-Saccharomyces yeast monocultures.

Characteristics of beer brewed with unconventional yeasts and addition of grape must, pulp and marc

The aim of the paper was to determine potential of using grape pulp, marc and must in the beer production process. Samples were fermented using non-Saccharomyces yeasts (Dekkera bruxellensis 3429, Metschnikowia pulcherrima MG970690) and Saccharomyces cerevisiae Safale US-05 was used as a control. Grape marc was obtained by pressing grape must with a press. Subsequently, the grape marc, must and pulp were pasteurized and, together with wort, volumetrically introduced into fermentation flasks for fermentation. Mass changes taking place during the process were analyzed. Real extract, alcohol, free amino nitrogen (FAN) content, pH, color, sugars and organic acid profile were determined in obtained beers. The research has shown that the yeasts Dekkera bruxellensis 3429 fermented similarly to Saccharomyces cerevisiae Safale US-05. The yeast D. bruxellensis 3429 produced more alcohol in the finished beers in most cases and assimilated more FAN than M. pulcherrima MG970690. The D. bruxellensis 3429 strain most effectively used L-malic acid.

Effect of Saccharomyces cerevisiae and Saccharomyces pastorianus Co-Inoculation on Alcoholic Fermentation Behavior and Aromatic Profile of Sauvignon Blanc Wine

Enhancing the sensory profile of wines by exposing the aromas of the grape variety through the involvement of microorganisms has always been a challenge in winemaking. The aim of our work was to evaluate the impact of different fermentation schemes by using mixed and pure cultures of different Saccharomyces species to Sauvignon blanc wine chemical composition and sensory profile. The Sauvignon blanc must has been inoculated with mixed and pure cultures of S. pastorianus and S. cerevisiae strains. For the mixed fermentation schemes, one strain of S. pastorianus has been inoculated with different proportions of S. cerevisiae (S. pastorianus to S. cerevisiae: 99%–1%, 95%–5%, 90%–10%, 80%–20% and 70%–30% w/w) in co-inoculation with two commercial strains of S. cerevisiae. A total of 13 fermentations trials, three monocultures and 10 mixed cultures were performed in biological triplicate. The fermentation kinetics have been controlled by density measurement and classical oenological analyses were performed based on the International Organisation of Vine and Wine (OIV) analytical methods. The population dynamics were evaluated by the specific interdelta PCR reaction of the Saccharomyces species at the beginning and at the end of the fermentation process. The volatile compounds of the wine aroma, such as the esters, higher alcohols and thiols were analyzed by GC/MS. Sensory assessment by trained panel was carried out for all produced wines. Complete depletion of the sugars was achieved between 10 and 13 days for all the fermentation trials. The population dynamics analysis revealed that the S. cerevisiae strain was the most predominant at the end of the fermentation process in all inoculation ratios that were tested. The wines that were fermented with S. pastorianus, either in pure or mixed cultures, were characterized by significantly lower acetic acid production and higher malic acid degradation when compared to the wines that were fermented only with S. cerevisiae strains. The aroma profile of the produced wines was highly affected by both inoculation ratio and the S. cerevisiae strain that was used. The presence of S. pastorianus strain enhanced the production of the varietal thiols when compared to the samples that were fermented with the S. cerevisiae pure cultures. The mixed inoculation cultures of Saccharomyces species could lead to wines with unique character which can nicely express the varietal character of the grape variety.

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.

Formation, Losses, Preservation and Recovery of Aroma Compounds in the Winemaking Process

A wine’s aroma profile is an important part of the criteria affecting wine acceptability by consumers. Its characterisation is complex because volatile molecules usually belong to different classes such as alcohols, esters, aldehydes, acids, terpenes, phenols and lactones with a wide range of polarity, concentrations and undesirable off-aromas. This review focused on mechanisms and conditions of the formation of individual aroma compounds in wine such as esters and higher alcohols by yeast during fermentation. Additionally, aroma losses during fermentation are currently the subject of many studies because they can lead to a reduction in wine quality. Principles of aroma losses, their prevention and recovery techniques are described in this review.

Use of Non-Saccharomyces Yeasts in Berry Wine Production: Inspiration from Their Applications in Winemaking

Although berries (nongrape) are rich in health-promoting bioactive compounds, and their consumption is associated with a lower risk of diverse chronic diseases, only a fraction of the annual yield of berries is exploited and consumed. Development of berry wines presents an approach to increase the utilization of berries. Alcoholic fermentation is a complex process driven by yeasts, which influence key properties of wine diversification and quality. In winemaking, non-Saccharomyces yeasts were traditionally considered as undesired microorganisms because of their high production of metabolites with negative connotations. However, there has been a recent and growing interest in the application of non-Saccharomyces yeast in many innovative wineries. Numerous studies have demonstrated the potential of these yeasts to improve properties of wine as an alternative or complement to Saccharomyces cerevisiae. The broad use of non-Saccharomyces yeasts in winemaking provides a promising picture of these unconventional yeasts in berry wine production, which can be considered as a novel biotechnological approach for creating value-added berry products for the global market. This review provides an overview of the current use of non-Saccharomyces yeasts in winemaking and their applicative perspective in berry wine production.

Influence of Microencapsulation on Fermentative Behavior of Hanseniaspora osmophila in Wine Mixed Starter Fermentation

In recent years, as a consequence of the re-evaluation of the role of non-Saccharomyces yeasts, several studies have been conducted on the use of controlled mixed fermentations with Saccharomyces and different non-Saccharomyces yeast species from the winemaking environment. To benefit from the metabolic particularities of some non-Saccharomyces yeasts, the management of a non-Saccharomyces strain in mixed fermentation is a crucial step, in particular the use of procedures addressed to increase the persistence of non-Saccharomyces strains during the fermentative process. The use of microencapsulation for cell immobilization might represent a strategy for enhancing the competitiveness of non-Saccharomyces yeasts during mixed fermentation. This study was aimed to assess the fermentative performance of a mixed starter culture, composed by a wild Hanseniaspora osmophila strain (ND1) and a commercial Saccharomyces cerevisiae strain (EC1118). For this purpose, free and microencapsulated cells of ND1 strain were tested in co-culture with EC1118 during mixed fermentations in order to evaluate the effect of the microencapsulation on fermentative behavior of mixed starter and final wine composition. The data have shown that H. osmophila cell formulation affects the persistence of both ND1 and EC1118 strains during fermentations and microencapsulation resulted in a suitable system to increase the fermentative efficiency of ND1 strain during mixed starter fermentation.

Effect of Grape Over-Ripening and Its Skin Presence on White Wine Alcoholic Fermentation in a Warm Climate Zone

The current trend of rising temperatures and sun irradiation associated to climate change is pushing traditional grape-producing areas with a warm climate towards a very accelerated ripening, leading to earlier harvesting dates and grape must with an unbalanced composition. However, this climatic trend could be exploited to produce other types of wine. In this sense, the increase in temperature could be used to produce wines with overripe grapes. In this regard, the aim of this research work is to evaluate the influence of different degrees and techniques of grape over-ripening to produce wines with the presence or absence of its skins during alcoholic fermentation. To this end, a physicochemical characterization of grape musts and wines obtained from overripe grapes and the monitoring of their fermentation has been performed. Over-ripening grapes by sun-drying has been established as a viable technique viability, producing musts and wines with unique physicochemical and sensory characteristics. In view of the above, it is considered that the production of wines from overripe grapes and in the presence or absence of grape skins is a viable approach to make new white wines taking advantage of the conditions imposed by climate change in a warm climate zone and meet the trends and expectations of current wine consumers.

The Use of Yeast Mixed Cultures for Deacidification and Improvement of the Composition of Cold Climate Grape Wines

Interest in the use of non-Saccharomyces yeast in mixed cultures is increasing due to the perceived improvement in the quality and complexity of the resulting wines. The aim of the study was to determine the ability of monocultures and mixed yeast cultures for deacidification and improvement of the composition of cold climate grape wines. Fermentation of grape musts with increased total acidity was carried out with the use of monocultures of Saccharomyces cerevisiae MH020215 (Sc), Zygosaccharomyces bailii 749 (Zb) and Metschnikowia pulcherrima MG970690 (Mp), and their mixed cultures, inoculated simultaneously and sequentially. Oenological parameters, organic acids and volatile compounds profiles of obtained wines were characterized. The fermentation kinetics and analytical profiles of the obtained wines showed that the use of mixed yeast cultures contributed to the reduction of volatile acidity and acetic acid content in the wines, as well as obtaining a favorable aromatic profile of the wines. The dominant higher alcohols in all wines were 2-methyl-1-propanol, 3-methyl-1-butanol and 2-methyl-1-butanol. Significantly higher amounts of the first two compounds were found in wines obtained with M. pulcherrima MG070690, both in monoculture and in mixed cultures. The monocultures of M. pulcherrima MG070690 (Mp) compared with Z. bailli 749 (Zb) synthesized higher levels of esters in wines, including ethyl acetate, ethyl propionate, isobutyl acetate, ethyl pyroracemate and isoamyl acetate.

Integrated transcriptomic and proteomic analysis of the acetic acid stress in Issatchenkia orientalis

Issatchenkia orientalis known as a multi-tolerant non-Saccharomyces yeast, which tolerant environmental stresses, exhibits potential in wine making and bioethanol production. It is essential for the growth of I. orientalis to tolerant acetic acid in the mixed cultures with Saccharomyces cerevisiae. In this work, RNA-sequence and TMT (Tandem Mass Tag) were used to examine the comprehensive transcriptomic and proteomic profiles of I. orientalis in response to acetic acid. The results showed that 876 genes were identified differentially transcribed in I. orientalis genome and 399 proteins expressed in proteome after 4 hr acetic acid (90 mM, pH 4.5). The comprehensive analysis showed a series of determinants of acetic acid tolerance: Glycolysis and TCA cycle provide enough nicotinamide adenine dinucleotide to effectively convert acetic acid. Genes associated with potassium, iron, zinc, and glutathione synthesis were upregulated. The same changes of differentially expressed genes and proteins were mainly concentrated in chaperones, coenzyme, energy production, and transformation. PRACTICAL APPLICATIONS: In addition to the main fermentation products, wine yeast also produces metabolite acetic acid in the fermentation process, and yeast cells are exposed to acetic acid stress, which restrains cell proliferation. Issatchenkia orientalis exhibits great potential in winemaking and bioethanol production. The yeast is known as a multi-tolerant non-Saccharomyces yeast that can tolerate a variety of environmental stresses. In this study, RNA-Seq and TMT were conducted to investigate the changes in transcriptional and proteomic profile of I. orientalis under acetic acid stress. The knowledge of the transcription and expression changes of the I. orientalis is expected to understand the tolerance mechanisms in I. orientalis and to guide traditional fermentation processes by Saccharomyces cerevisiae improving its high resistance to acetic acid stress.

Yeasts for low input winemaking: Microbial terroir and flavor differentiation

Vitis vinifera flowers and grape fruits are one of the most interesting ecosystem niches for native yeasts development. There are more than a 100 yeast species and millions of strains that participate and contribute to design the microbial terroir. The wine terroir concept is understood when grape and wine micro-regions were delimited by different quality characteristics after humans had been growing vines for more than 10,000 years. Environmental conditions, such as climate, soil composition, water management, winds and air quality, altitude, fauna and flora and microbes, are considered part of the "terroir" and contribute to a unique wine style. If "low input winemaking" strategies are applied, the terroir effect will be expected to be more authentic in terms of quality differentiation. Interestingly, the role of the microbial flora associated with vines was very little study until recently when new genetic technologies for massive species identification were developed. These biotechnologies allowed following their environmental changes and their effect in shaping the microbial profiles of different wine regions. In this chapter we explain the interesting positive effects on flavor diversity and wine quality obtained by using "friendly" native yeasts that allowed the microbial terroir flora to participate and contribute during fermentation.

Torulaspora delbrueckii produces high levels of C5 and C6 polyols during wine fermentations

Non-Saccharomyces yeasts impact wine fermentations and can diversify the flavor profiles of wines. However, little information is available on the metabolic networks of most of these species. Here we show that unlike the main wine yeast Saccharomyces cerevisiae, Torulaspora delbrueckii and to a lesser extent Lachancea thermotolerans produce significant concentrations of C5 and C6 polyols under wine fermentation conditions. In particular, D-arabitol, D-sorbitol and D-mannitol were produced at significant levels. Their release into the extracellular matrix started when that of glycerol ceased. The data also show that polyol production is influenced by initial sugar concentration, repressed by acetic acid and induced in ethanol supplemented media. Moreover, unlike glycerol and sorbitol, mannitol was partially re-assimilated when populations started to decline. The findings suggest that polyol synthesis is a physiological adaptation to stressful conditions characteristic of alcoholic fermentation and that these polyols may serve a similar purpose as glycerol production in S. cerevisiae, including osmoadaptation and redox balancing.

Use of Nonconventional Yeasts for Modulating Wine Acidity

In recent years, in line with consumer preferences and due to the effects of global climate change, new trends have emerged in wine fermentation and wine technology. Consumers are looking for wines with less ethanol and fruitier aromas, but also with a good balance in terms of acidity and mouthfeel. Nonconventional yeasts contain a wide range of different genera of non-Saccharomyces. If in the past they were considered spoilage yeasts, now they are used to enhance the aroma profile of wine or to modulate wine composition. Recent publications highlight the role of non-Saccharomyces as selected strains for controlling fermentations mostly in cofermentation with Saccharomyces. In this article, I have reviewed the ability of some bacteria and non-Saccharomyces strains to modulate wine acidity.

Lachancea thermotolerans, the Non-Saccharomyces Yeast that Reduces the Volatile Acidity of Wines

To improve the quality of fermented drinks, or more specifically, wine, some strains of yeast have been isolated, tested and studied, such as Saccharomyces and non-Saccharomyces. Some non-conventional yeasts present good fermentative capacities and are able to ferment in quite undesirable conditions, such as the case of must, or wines that have a high concentration of acetic acid. One of those yeasts is Lachancea thermotolerants (L. thermotolerans), which has been studied for its use in wine due to its ability to decrease pH through L-lactic acid production, giving the wines a pleasant acidity. This review focuses on the recent discovery of an interesting feature of L. thermotolerans—namely, its ability to decrease wines’ volatile acidity.

Use of Saccharomyces cerevisiae var. boulardii in co-fermentations with S. cerevisiae for the production of craft beers with potential healthy value-added

In recent years, the awareness of consumers about the impact of food on health is constantly increasing. A high amount of dietary antioxidant intake can be supplied by beverages widely consumed, such as wine, coffee, beer. Recently, an increase in the consumer interest was observed for beer, in consequence of the high phenolic antioxidants and low ethanol content present in this beverage. Among all beer types, in recent years, consumption of craft beers has gained popularity. Being an unpasteurized and unfiltered, craft beer is potentially a new vehicle for delivering health effects. While health benefits of lactic acid bacteria as probiotics are well known, few data are available on probiotic yeasts in fermented food. Therefore, this study was aimed to analyse the effect of integrating the well-known probiotic yeast strain of S. cerevisiae var. boulardii (S.b) in mixed cultures with S. cerevisiae strains for production of beers with increased healthy benefits. The probiotic strain of S.b was tested in mixed cultures with selected S. cerevisiae strains, during wort fermentation. As the viability during processing operations is one of the criteria for selecting suitable strains of probiotic microorganisms, the survival of probiotic yeast during the fermentation and the presence of highly viable cells at the end of fermentations were evaluated. In almost all the mixed fermentations, at the end of the process the probiotic yeast was predominant on S. cerevisiae strain, and the experimental beers contained a high number of viable cells of S.b strain (ranging between 8 × 10⁶ and 7.0 × 10⁷/mL). The analysis of experimental beers for the content of main volatile compounds showed that the inclusion of S.b strain in mixed starter did not affect negatively beer aroma. Moreover, the inclusion of S.b strain in mixed starters determined an increase in the antioxidant activity and polyphenols content, in comparison to beers from single starter fermentations, indicating the influence of S.b strain on these parameters. Some mixed starter cultures tested in this study resulted a very promising tool to increase the healthy quality of the product, such as the improve the antioxidant activity and polyphenols content of beer.

Improving truffle mycelium flavour through strain selection targeting volatiles of the Ehrlich pathway

Truffles (Tuber spp.) are the fruiting bodies of symbiotic fungi, which are prized food delicacies. The marked aroma variability observed among truffles of the same species has been attributed to a series of factors that are still debated. This is because factors (i.e. genetics, maturation, geographical location and the microbial community colonizing truffles) often co-vary in truffle orchards. Here, we removed the co-variance effect by investigating truffle flavour in axenic cultures of nine strains of the white truffle Tuber borchii. This allowed us to investigate the influence of genetics on truffle aroma. Specifically, we quantified aroma variability and explored whether strain selection could be used to improve human-sensed truffle flavour. Our results illustrate that aroma variability among strains is predominantly linked to amino acid catabolism through the Ehrlich pathway, as confirmed by 13C labelling experiments. We furthermore exemplified through sensory analysis that the human nose is able to distinguish among strains and that sulfur volatiles derived from the catabolism of methionine have the strongest influence on aroma characteristics. Overall, our results demonstrate that genetics influences truffle aroma much more deeply than previously thought and illustrate the usefulness of strain selection for improving truffle flavour.

Comparative metabolomics profiling of engineered Saccharomyces cerevisiae lead to a strategy that improving β-carotene production by acetate supplementation

A comparative metabolomic analysis was conducted on recombinant Saccharomyces cerevisiae strain producing β-carotene and the parent strain cultivated with glucose as carbon source using gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography-mass spectrometry (HPLC-MS) and ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) based approach. The results showed that most of the central intermediates associated with amino acids, carbohydrates, glycolysis and TCA cycle intermediates (acetic acid, glycerol, citric acid, pyruvic acid and succinic acid), fatty acids, ergosterol and energy metabolites were produced in a lower amount in recombinant strain, as compared to the parent strain. To increase β-carotene production in recombinant strain, a strategy that exogenous addition of acetate (10 g/l) in exponential phase was developed, which could enhance most intracellular metabolites levels and result in 39.3% and 14.2% improvement of β-carotene concentration and production, respectively, which was accompanied by the enhancement of acetyl-CoA, fatty acids, ergosterol and ATP contents in cells. These results indicated that the amounts of intracellular metabolites in engineered strain are largely consumed by carotenoid formation. Therefore, maintaining intracellular metabolites pool at normal levels is essential for carotenoid biosynthesis. To relieve this limitation, rational supplementation of acetate could be a potential way because it can partially restore the levels of intracellular metabolites and improve the production of carotenoid compounds in recombinant S. cerevisiae.

Acetic Acid Causes Endoplasmic Reticulum Stress and Induces the Unfolded Protein Response in Saccharomyces cerevisiae

Since acetic acid inhibits the growth and fermentation ability of Saccharomyces cerevisiae, it is one of the practical hindrances to the efficient production of bioethanol from a lignocellulosic biomass. Although extensive information is available on yeast response to acetic acid stress, the involvement of endoplasmic reticulum (ER) and unfolded protein response (UPR) has not been addressed. We herein demonstrated that acetic acid causes ER stress and induces the UPR. The accumulation of misfolded proteins in the ER and activation of Ire1p and Hac1p, an ER-stress sensor and ER stress-responsive transcription factor, respectively, were induced by a treatment with acetic acid stress (>0.2% v/v). Other monocarboxylic acids such as propionic acid and sorbic acid, but not lactic acid, also induced the UPR. Additionally, ire1Δ and hac1Δ cells were more sensitive to acetic acid than wild-type cells, indicating that activation of the Ire1p-Hac1p pathway is required for maximum tolerance to acetic acid. Furthermore, the combination of mild acetic acid stress (0.1% acetic acid) and mild ethanol stress (5% ethanol) induced the UPR, whereas neither mild ethanol stress nor mild acetic acid stress individually activated Ire1p, suggesting that ER stress is easily induced in yeast cells during the fermentation process of lignocellulosic hydrolysates. It was possible to avoid the induction of ER stress caused by acetic acid and the combined stress by adjusting extracellular pH.

Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains

Due to the importance of Saccharomyces cerevisiae in wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences of S. cerevisiae wine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ∼4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance (CUP), flocculation (FLO), and glucose metabolism (HXT), as well as the SNO gene family whose members are expressed before or during the diauxic shift, showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains, and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation.

Omics analysis of acetic acid tolerance in Saccharomyces cerevisiae

Acetic acid is an inhibitor in industrial processes such as wine making and bioethanol production from cellulosic hydrolysate. It causes energy depletion, inhibition of metabolic enzyme activity, growth arrest and ethanol productivity losses in Saccharomyces cerevisiae. Therefore, understanding the mechanisms of the yeast responses to acetic acid stress is essential for improving acetic acid tolerance and ethanol production. Although 329 genes associated with acetic acid tolerance have been identified in the Saccharomyces genome and included in the database ( http://www.yeastgenome.org/observable/resistance_to_acetic_acid/overview ), the cellular mechanistic responses to acetic acid remain unclear in this organism. Post-genomic approaches such as transcriptomics, proteomics, metabolomics and chemogenomics are being applied to yeast and are providing insight into the mechanisms and interactions of genes, proteins and other components that together determine complex quantitative phenotypic traits such as acetic acid tolerance. This review focuses on these omics approaches in the response to acetic acid in S. cerevisiae. Additionally, several novel strains with improved acetic acid tolerance have been engineered by modifying key genes, and the application of these strains and recently acquired knowledge to industrial processes is also discussed.

Looking beyond Saccharomyces: the potential of non-conventional yeast species for desirable traits in bioethanol fermentation

Saccharomyces cerevisiae has been used for millennia in the production of food and beverages and is by far the most studied yeast species. Currently, it is also the most used microorganism in the production of first-generation bioethanol from sugar or starch crops. Second-generation bioethanol, on the other hand, is produced from lignocellulosic feedstocks that are pretreated and hydrolyzed to obtain monomeric sugars, mainly D-glucose, D-xylose and L-arabinose. Recently, S. cerevisiae recombinant strains capable of fermenting pentose sugars have been generated. However, the pretreatment of the biomass results in hydrolysates with high osmolarity and high concentrations of inhibitors. These compounds negatively influence the fermentation process. Therefore, robust strains with high stress tolerance are required. Up to now, more than 2000 yeast species have been described and some of these could provide a solution to these limitations because of their high tolerance to the most predominant stress conditions present in a second-generation bioethanol reactor. In this review, we will summarize what is known about the non-conventional yeast species showing unusual tolerance to these stresses, namely Zygosaccharomyces rouxii (osmotolerance), Kluyveromyces marxianus and Ogataea (Hansenula) polymorpha (thermotolerance), Dekkera bruxellensis (ethanol tolerance), Pichia kudriavzevii (furan derivatives tolerance) and Z. bailii (acetic acid tolerance).

Hybridization within Saccharomyces Genus Results in Homoeostasis and Phenotypic Novelty in Winemaking Conditions

Despite its biotechnological interest, hybridization, which can result in hybrid vigor, has not commonly been studied or exploited in the yeast genus. From a diallel design including 55 intra- and interspecific hybrids between Saccharomyces cerevisiae and S. uvarum grown at two temperatures in enological conditions, we analyzed as many as 35 fermentation traits with original statistical and modeling tools. We first showed that, depending on the types of trait--kinetics parameters, life-history traits, enological parameters and aromas -, the sources of variation (strain, temperature and strain * temperature effects) differed in a large extent. Then we compared globally three groups of hybrids and their parents at two growth temperatures: intraspecific hybrids S. cerevisiae * S. cerevisiae, intraspecific hybrids S. uvarum * S. uvarum and interspecific hybrids S. cerevisiae * S. uvarum. We found that hybridization could generate multi-trait phenotypes with improved oenological performances and better homeostasis with respect to temperature. These results could explain why interspecific hybridization is so common in natural and domesticated yeast, and open the way to applications for wine-making.

Lipidomic profiling of Saccharomyces cerevisiae and Zygosaccharomyces bailii reveals critical changes in lipid composition in response to acetic acid stress

When using microorganisms as cell factories in the production of bio-based fuels or chemicals from lignocellulosic hydrolysate, inhibitory concentrations of acetic acid, released from the biomass, reduce the production rate. The undissociated form of acetic acid enters the cell by passive diffusion across the lipid bilayer, mediating toxic effects inside the cell. In order to elucidate a possible link between lipid composition and acetic acid stress, the present study presents detailed lipidomic profiling of the major lipid species found in the plasma membrane, including glycerophospholipids, sphingolipids and sterols, in Saccharomyces cerevisiae (CEN.PK 113_7D) and Zygosaccharomyces bailii (CBS7555) cultured with acetic acid. Detailed physiological characterization of the response of the two yeasts to acetic acid has also been performed in aerobic batch cultivations using bioreactors. Physiological characterization revealed, as expected, that Z. bailii is more tolerant to acetic acid than S. cerevisiae. Z. bailii grew at acetic acid concentrations above 24 g L⁻¹, while limited growth of S. cerevisiae was observed after 11 h when cultured with only 12 g L⁻¹ acetic acid. Detailed lipidomic profiling using electrospray ionization, multiple-reaction-monitoring mass spectrometry (ESI-MRM-MS) showed remarkable changes in the glycerophospholipid composition of Z. bailii, including an increase in saturated glycerophospholipids and considerable increases in complex sphingolipids in both S. cerevisiae (IPC 6.2×, MIPC 9.1×, M(IP)₂C 2.2×) and Z. bailii (IPC 4.9×, MIPC 2.7×, M(IP)₂C 2.7×), when cultured with acetic acid. In addition, the basal level of complex sphingolipids was significantly higher in Z. bailii than in S. cerevisiae, further emphasizing the proposed link between lipid saturation, high sphingolipid levels and acetic acid tolerance. The results also suggest that acetic acid tolerance is associated with the ability of a given strain to generate large rearrangements in its lipid profile.

Functional improvement of Saccharomyces cerevisiae to reduce volatile acidity in wine

Control of volatile acidity (VA) is a major issue for wine quality. In this study, we investigated the production of VA by a deletion mutant of the fermentation stress response gene AAF1 in the budding yeast Saccharomyces cerevisiae. Fermentations were carried out in commercial Chardonnay grape must to mimic industrial wine-making conditions. We demonstrated that a wine yeast strain deleted for AAF1 reduced acetic acid levels in wine by up to 39.2% without increasing the acetaldehyde levels, revealing a potential for industrial application. Deletion of the cytosolic aldehyde dehydrogenase gene ALD6 also reduced acetic acid levels dramatically, but increased the acetaldehyde levels by 41.4%, which is not desired by the wine industry. By comparison, ALD4 and the AAF1 paralog RSF2 had no effects on acetic acid production in wine. Deletion of AAF1 was detrimental to the growth of ald6Δ and ald4Δald6Δ mutants, but had no effect on acetic acid production. Overexpression of AAF1 dramatically increased acetic acid levels in wine in an Ald6p-dependent manner, indicating that Aaf1p regulates acetic acid production mainly via Ald6p. Overexpression of AAF1 in an ald4Δald6Δ strain produced significantly more acetic acid in wine than the ald4Δald6Δ mutant, suggesting that Aaf1p may also regulate acetic acid synthesis independently of Ald4p and Ald6p.

Molecular mechanisms of Saccharomyces cerevisiae stress adaptation and programmed cell death in response to acetic acid

Beyond its classical biotechnological applications such as food and beverage production or as a cell factory, the yeast Saccharomyces cerevisiae is a valuable model organism to study fundamental mechanisms of cell response to stressful environmental changes. Acetic acid is a physiological product of yeast fermentation and it is a well-known food preservative due to its antimicrobial action. Acetic acid has recently been shown to cause yeast cell death and aging. Here we shall focus on the molecular mechanisms of S. cerevisiae stress adaptation and programmed cell death in response to acetic acid. We shall elaborate on the intracellular signaling pathways involved in the cross-talk of pro-survival and pro-death pathways underlying the importance of understanding fundamental aspects of yeast cell homeostasis to improve the performance of a given yeast strain in biotechnological applications.

The fate of acetic acid during glucose co-metabolism by the spoilage yeast Zygosaccharomyces bailii

Zygosaccharomyces bailii is one of the most widely represented spoilage yeast species, being able to metabolise acetic acid in the presence of glucose. To clarify whether simultaneous utilisation of the two substrates affects growth efficiency, we examined growth in single- and mixed-substrate cultures with glucose and acetic acid. Our findings indicate that the biomass yield in the first phase of growth is the result of the weighted sum of the respective biomass yields on single-substrate medium, supporting the conclusion that biomass yield on each substrate is not affected by the presence of the other at pH 3.0 and 5.0, at least for the substrate concentrations examined. In vivo(13)C-NMR spectroscopy studies showed that the gluconeogenic pathway is not operational and that [2-(13)C]acetate is metabolised via the Krebs cycle leading to the production of glutamate labelled on C(2), C(3) and C(4). The incorporation of [U-(14)C]acetate in the cellular constituents resulted mainly in the labelling of the protein and lipid pools 51.5% and 31.5%, respectively. Overall, our data establish that glucose is metabolised primarily through the glycolytic pathway, and acetic acid is used as an additional source of acetyl-CoA both for lipid synthesis and the Krebs cycle. This study provides useful clues for the design of new strategies aimed at overcoming yeast spoilage in acidic, sugar-containing food environments. Moreover, the elucidation of the molecular basis underlying the resistance phenotype of Z. bailii to acetic acid will have a potential impact on the improvement of the performance of S. cerevisiae industrial strains often exposed to acetic acid stress conditions, such as in wine and bioethanol production.

Novel wine yeast with mutations in YAP1 that produce less acetic acid during fermentation

Acetic acid, a byproduct formed during yeast alcoholic fermentation, is the main component of volatile acidity (VA). When present in high concentrations in wine, acetic acid imparts an undesirable 'vinegary' character that results in a significant reduction in quality and sales. Previously, it has been shown that saké yeast strains resistant to the antifungal cerulenin produce significantly lower levels of VA. In this study, we used a classical mutagenesis method to isolate a series of cerulenin-resistant strains, derived from a commercial diploid wine yeast. Four of the selected strains showed a consistent low-VA production phenotype after small-scale fermentation of different white and red grape musts. Specific mutations in YAP1, a gene encoding a transcription factor required for oxidative stress tolerance, were found in three of the four low-VA strains. When integrated into the genome of a haploid wine strain, the mutated YAP1 alleles partially reproduced the low-VA production phenotype of the diploid cerulenin-resistant strains, suggesting that YAP1 might play a role in (regulating) acetic acid production during fermentation. This study offers prospects for the development of low-VA wine yeast starter strains that could assist winemakers in their effort to consistently produce wine to definable quality specifications.

Effects of acetic acid, ethanol, and SO(2) on the removal of volatile acidity from acidic wines by two Saccharomyces cerevisiae commercial strains

Herein, we report the influence of different combinations of initial concentration of acetic acid and ethanol on the removal of acetic acid from acidic wines by two commercial Saccharomyces cerevisiae strains S26 and S29. Both strains reduced the volatile acidity of an acidic wine (1.0 gl(-1) acetic acid and 11% (v/v) ethanol) by 78% and 48%, respectively. Acetic acid removal by strains S26 and S29 was associated with a decrease in ethanol concentration of 0.7 and 1.2% (v/v), respectively. Strain S26 revealed better removal efficiency due to its higher tolerance to stress factors imposed by acidic wines. Sulfur dioxide (SO(2)) in the concentration range 95-170 mg l(-1)inhibits the ability of both strains to reduce the volatile acidity of the acidic wine used under our experimental conditions. Therefore, deacidification should be carried out either in wines stabilized by filtration or in wines with SO(2)concentrations up to 70 mg l(-1). Deacidification of wines with the better performing strain S26 was associated with changes in the concentration of volatile compounds. The most pronounced increase was observed for isoamyl acetate (banana) and ethyl hexanoate (apple, pineapple), with an 18- and 25-fold increment, respectively, to values above the detection threshold. The acetaldehyde concentration of the deacidified wine was 2.3 times higher, and may have a detrimental effect on the wine aroma. Moreover, deacidification led to increased fatty acids concentration, but still within the range of values described for spontaneous fermentations, and with apparently no negative impact on the organoleptical properties.

Biological diversity of Saccharomyces yeasts of spontaneously fermenting wines in four wine regions: comparative genotypic and phenotypic analysis

Combination of molecular genetic analysis (karyotyping, PCR-RFLP of MET2, the ITS1-ITS2 region and the NTS region) and physiological examination (melibiose and mannitol utilization, sugar-, ethanol- and copper tolerance, killer activity, fermentation vigor and production of metabolites) of yeasts isolated from spontaneously fermenting wines in four wine regions revealed very high diversity in the Saccharomyces cerevisiae populations. Practically each S. cerevisiae isolate showed a unique pattern of properties. Although the strains originating from the same wine were quite similar in certain traits, they showed diversity in other properties. These results indicate that alcoholic fermentation in grape wines is performed by highly diverse yeast consortia rather than by one or two dominating strains. The less frequent Saccharomyces uvarum strains were less diverse, showed lower karyotype variability, were Mel(+), Man(+), more sensitive to 60% sugar, and ethanol or copper in the medium. They produced less acetic acid and fermented better at 14 degrees C than most of the S. cerevisiae isolates, but certain S. cerevisiae strains showed comparably high fermentation rates at this temperature, indicating that it is not a general rule that S. uvarum ferments better than S. cerevisiae at low temperatures. The segregation of certain traits (melibiose utilization, mannitol utilization and copper resistance) in both species indicates that the genomes can easily change during vegetative propagation. The higher diversity among the S. cerevisiae isolates suggests that the S. cerevisiae genome may be more flexible than the S. uvarum genome and may allow more efficient adaptation to the continuously changing environment in the fermenting wine.

Comparative genomics of protoploid Saccharomycetaceae

Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.