Wine yeasts for the future

Selection of Native Non-Saccharomyces Yeasts with Biocontrol Activity against Spoilage Yeasts in Order to Produce Healthy Regional Wines

Two major spoilage yeasts in the wine industry, Brettanomyces bruxellensis and Zygosaccharomyces rouxii, produce off-flavors and gas, causing considerable economic losses. Traditionally, SO2 has been used in winemaking to prevent spoilage, but strict regulations are in place regarding its use due to its toxic and allergenic effects. To reduce its usage researchers have been searching for alternative techniques. One alternative is biocontrol, which can be used either independently or in a complementary way to chemical control (SO2). The present study analyzed 122 native non-Saccharomyces yeasts for their biocontrol activity and their ability to be employed under fermentation conditions, as well as certain enological traits. After the native non-Saccharomyces yeasts were assayed for their biocontrol activity, 10 biocontroller yeasts were selected and assayed for their ability to prevail in the fermentation medium, as well as with respect to their corresponding positive/negative contribution to the wine. Two yeasts that satisfy these characteristics were Wickerhamomyces anomalus BWa156 and Metschnikowia pulcherrima BMp29, which were selected for further research in application to mixed fermentations.

Influence of cell-cell contact between L. thermotolerans and S. cerevisiae on yeast interactions and the exo-metabolome

Sequential fermentation of grape must inoculated with L. thermotolerans and then S. cerevisiae 24 h later (typical wine-making practice) was conducted with or without cell-cell contact between the two yeast species. We monitored cell viability of the two species throughout fermentation by flow cytometry. The cell viability of S. cerevisiae decreased under both conditions, but the decrease was greater if there was cell-cell contact. An investigation of the nature of the interactions showed competition between the two species for nitrogen compounds, oxygen, and must sterols. Volatile-compound analysis showed differences between sequential and pure fermentation and that cell-cell contact modifies yeast metabolism, as the volatile-compound profile was significantly different from that of sequential fermentation without cell-cell contact. We further confirmed that cell-cell contact modifies yeast metabolism by analyzing the exo-metabolome of all fermentations by FT-ICR-MS analysis. These analyses show specific metabolite production and quantitative metabolite changes associated with each fermentation condition. This study shows that cell-cell contact not only affects cell viability, as already reported, but markedly affects yeast metabolism.

Apple bagasse as a substrate for the propagation of Patagonian wine yeast biomass

AIMS

A culture medium based on apple bagasse was designed and tested as a substrate for biomass production of conventional and unconventional native wine yeasts.

METHODS AND RESULTS

The physicochemical characterization of the apple bagasse was carried out and its potential utility as a constituent of a complete culture medium for the production of yeast biomass was analysed using the experimental statistical designs. Growth parameters of conventional and nonconventional Patagonian wine yeasts were analysed with Placket-Burman designs and response surface methodology, comparing in each assay the apple bagasse substrate with the commonly used substrate for biomass development, cane molasses. Culture media composition was optimized and models were validated.

CONCLUSIONS

This study demonstrates that, both from a nutritional and from an economic point of view, apple bagasse constitutes a more advantageous substrate than cane molasses for the propagation of native yeasts from Patagonia.

SIGNIFICANCE AND IMPACT OF THE STUDY

We used an alternate carbon-rich material, generously available in our region, originally generated as fruit industrial waste, to transform it into a source of sustainable, economically profitable and environmentally friendly energy resource.

Mixed alcoholic fermentation of Schizosaccharomyces pombe and Lachancea thermotolerans and its influence on mannose-containing polysaccharides wine Composition

This study researched the winemaking performance of new biotechnology involving the cooperation of Lachancea and Schizosaccharomyces genera in the production of wine. In all fermentations where Lachancea thermotolerans was involved, higher lactic acid concentrations appeared, while all fermentations where Schizosaccharomyces pombe was involved, lower levels in malic acid concentration took place. The sensorial properties of the final wines varied accordingly. Differences in mouthfeel properties and acidity occurred in the different fermentation trials. Fermentations with the highest concentration of hydrolyzed mannose showed the highest mouthfeel properties, but the lack of acidity reduced their overall impression. Wines made from a combination of L. thermotolerans and S. pombe showed the highest overall impression and were preferred by the tasters due to the balance between mouthfeel properties and acidity.

Analysis of the NCR Mechanisms in Hanseniaspora vineae and Saccharomyces cerevisiae During Winemaking

There is increasing interest in the use of non-Saccharomyces yeasts in winemaking due to their positive attributes. The non-Saccharomyces yeast Hanseniaspora vineae is an apiculate yeast that has been associated with the production of wine with good fermentation capacity and an increase in aromatic properties. However, this yeast represents a concern in mixed culture fermentation because of its nutrient consumption, especially nitrogen, as its mechanisms of regulation and consumption are still unknown. In this study, we analyzed the nitrogen consumption, as well as the nitrogen catabolism repression (NCR) mechanism, in two genome-sequenced H. vineae strains, using synthetic must fermentations. The use of synthetic must with an established nitrogen content allowed us to study the NCR mechanism in H. vineae, following the amino acid and ammonia consumption, and the expression of genes known to be regulated by the NCR mechanism in S. cerevisiae, AGP1, GAP1, MEP2, and PUT2. H. vineae exhibited a similar amino acid consumption and gene expression profile to S. cerevisiae. However, the wine strain of S. cerevisiae QA23 consumed ammonia and valine more quickly and, in contrast, tyrosine and tryptophan more slowly, than the H. vineae strains. Our results showed a similar behavior of nitrogen regulation in H. vineae and S. cerevisiae, indicating the presence of the NCR mechanism in this Hanseniaspora yeast differentiated before the whole genome duplication event of the Saccharomyces complex. Future study will elucidate if the NCR mechanism is the only strategy used by H. vineae to optimize nitrogen consumption.

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.

Flocculation and Expression of FLO Genes of a Saccharomyces cerevisiae Mezcal Strain with High Stress Tolerance

Mezcal is a distillate produced by spontaneous fermentation of the must obtained from stalks of Agave spp. plants that are cooked and pressed. Agave must contains a high amount of fructose and phenolic compounds, and fermentation usually occurs under stressful (and uncontrolled) environmental conditions. Yeasts capable of growing under such conditions usually display advantageous biological and industrial traits for stress tolerance such as flocculation. In this study, seven Saccharomyces cerevisiae strains isolated from mezcal must were exposed to temperatures ranging between 10 and 40 °C, and to different sugar sources (fructose or glucose). Yeasts grown in fructose increased their stress tolerance, determined by colony count in a microdrop assay, under low temperature (10 °C) compared to the growth at 40 °C on solid cultures. The most stress-tolerant mezcal strain (Sc3Y8) and a commercial wine (Fermichamp) strain, used as control, were grown under fermentation conditions and exposed to long-term temperature stress to determine their performance and their potential for flocculation. Compared to glucose, fermentation on fructose increased the metabolite accumulation at the end of culture, particularly at 40 °C, with 2.3, 1.3 and 3.4 times more glycerol (8.6 g/L), ethanol (43.6 g/L) and acetic acid (7.3 g/L), respectively. Using confocal microscopy analysis, we detected morphological changes such as aggregation and wall recognition at the level of budding scars in yeast, particularly in the Sc3Y8 strain when it was exposed to 40 °C. The analysis confirmed that this mezcal strain was positive for flocculation in the presence of Ca²⁺ ions. Analysis of FLO1, FLO5 and FLO11 gene expression implicated in flocculation in both Saccharomyces strains showed a strong transcriptional induction, mainly of the FLO5 gene in the mezcal Sc3Y8 strain.

A simple and reliable method for the quantitative evaluation of anthocyanin adsorption by wine yeasts

Yeast pigments adsorption can modify wine color intensity and is considered an important trait in wine yeasts. The existing methods for the evaluation of yeast adsorption are laborious, time consuming, need confirmation experiments, or are difficult to apply for a large number of strains generated in breeding programs. In this study, a new test is proposed to measure yeast pigments adsorption and wine color in a single experiment. The optimized method included the microfermentation of grape musts obtained by thermal extraction, digital determination of yeast biomass color, and spectrophotometric wine intensity evaluation. Results showed significant negative correlation between yeast pigments adsorption and wine color intensity. Pigments adsorption occurs from the middle to the end of fermentation, indicating cell wall changes and/or anthocyanins modifications over the process. Significant differences were observed on anthocyanins adsorption and wine intensity among yeast strains independent of the grape variety, and yeasts could be grouped as low, medium and high adsorption strains. The proposed method showed high reproducibility and allows the concomitant screening of hundreds of yeast strains in a short period of time.

Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests

Agriculture is one of the main drivers of land conversion, and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carménère grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on vineyard phyllosphere. After conducting D2 and ITS2 amplicon sequencing, we found that fungal diversity indices did not change between conventional and organic vineyards, but community structure was sensitive to the agricultural management. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different in both habitats. Interestingly, the native forest had more unidentified species and unique OTUs than vineyards. Forest dominant species were Aureobasidium pullulans and Endoconidioma populi, whereas Davidiella tassiana, Didymella sp., and Alternaria eichhorniae were more abundant in vineyards. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.

Sequential inoculum of Hanseniaspora guilliermondii and Saccharomyces cerevisiae for winemaking Campanino on an industrial scale

In this study, the effect of sequential inoculation with non-Saccharomyces (Hanseniaspora guilliermondii) and Saccharomyces cerevisiae yeast on the distinctive characteristics of the Campanino white wine was investigated. For this purpose, three independent winemaking experiments were carried out on an industrial scale (batches A, B and C). In detail, the first one was carried out using the sequential inoculation technique while the other two, using a S. cerevisiae single-strain starter or no inoculation representing the control batches. Microbiological and chemical parameters and sensorial profiles of the wines were defined. Interestingly, the results showed that when sequential cultures (H. guilliermondii in a sequential mixture with S. cerevisiae) were used, a better wine aroma and quality was observed. More specifically, the wine obtained by sequential inoculation showed lower acetic acid values and enhanced volatile profiles than the wine from the control batches. Finally, sensorial analysis confirmed that the sequential cultures led to an improvement in wine flavour. Therefore, results suggest that the sequential inoculation using non-Saccharomyces and Saccharomyces yeast represents a biotechnological practice that can improve the quality features of traditional white wine. It has been shown for the first time that on an industrial scale H. guilliermondii could be used in sequential inoculum with S. cerevisiae in making white Campanino wine.

Oenological Impact of the Hanseniaspora/Kloeckera Yeast Genus on Wines—A Review

Apiculate yeasts of the genus Hanseniaspora/Kloeckera are the main species present on mature grapes and play a significant role at the beginning of fermentation, producing enzymes and aroma compounds that expand the diversity of wine color and flavor. Ten species of the genus Hanseniaspora have been recovered from grapes and are associated in two groups: H. valbyensis, H. guilliermondii, H. uvarum, H. opuntiae, H. thailandica, H. meyeri, and H. clermontiae; and H. vineae, H. osmophila, and H. occidentalis. This review focuses on the application of some strains belonging to this genus in co-fermentation with Saccharomyces cerevisiae that demonstrates their positive contribution to winemaking. Some consistent results have shown more intense flavors and complex, full-bodied wines, compared with wines produced by the use of S. cerevisiae alone. Recent genetic and physiologic studies have improved the knowledge of the Hanseniaspora/Kloeckera species. Significant increases in acetyl esters, benzenoids, and sesquiterpene flavor compounds, and relative decreases in alcohols and acids have been reported, due to different fermentation pathways compared to conventional wine yeasts.

Challenges of the Non-Conventional Yeast Wickerhamomyces anomalus in Winemaking

Nowadays it is widely accepted that non-Saccharomyces yeasts, which prevail during the early stages of alcoholic fermentation, contribute significantly to the character and quality of the final wine. Among these yeasts, Wickerhamomyces anomalus (formerly Pichia anomala, Hansenula anomala, Candida pelliculosa) has gained considerable importance for the wine industry since it exhibits interesting and potentially exploitable physiological and metabolic characteristics, although its growth along fermentation can still be seen as an uncontrollable risk. This species is widespread in nature and has been isolated from different environments including grapes and wines. Its use together with Saccharomyces cerevisiae in mixed culture fermentations has been proposed to increase wine particular characteristics. Here, we review the ability of W. anomalus to produce enzymes and metabolites of oenological relevance and we discuss its potential as a biocontrol agent in winemaking. Finally, biotechnological applications of W. anomalus beyond wine fermentation are briefly described.

Specific Phenotypic Traits of Starmerella bacillaris Related to Nitrogen Source Consumption and Central Carbon Metabolite Production during Wine Fermentation

Mixed fermentations using a controlled inoculation of Starmerella bacillaris and Saccharomyces cerevisiae starter cultures represent a feasible way to modulate wine composition that takes advantage of both the phenotypic specificities of the non-Saccharomyces strain and the ability of S. cerevisiae to complete wine fermentation. However, according to the composition of grape juices, the consumption by Starm. bacillaris of nutrients, in particular of nitrogen sources, during the first stages of the process may result in depletions that further limit the growth of S. cerevisiae and lead to stuck or sluggish fermentations. Consequently, understanding the preferences of non-Saccharomyces yeasts for the nitrogen sources available in grape must together with their phenotypic specificities is essential for an efficient implementation of sequential wine fermentations with Starm. bacillaris and S. cerevisiae species. The results of our study demonstrate a clear preference for ammonium compared to amino acids for the non-Saccharomyces species. This finding underlines the importance of nitrogen sources, which modulate the functional characteristics of inoculated yeast strains to better control the fermentation process and product quality.

Over the last few years, the potential of non-Saccharomyces yeasts to improve the sensory quality of wine has been well recognized. In particular, the use of Starmerella bacillaris in mixed fermentations with Saccharomyces cerevisiae was reported as an appropriate way to enhance glycerol formation and reduce ethanol production. However, during sequential fermentation, many factors, such as the inoculation timing, strain combination, and physical and biochemical interactions, can affect yeast growth, the fermentation process, and/or metabolite synthesis. Among them, the availability of yeast-assimilable nitrogen (YAN), due to its role in the control of growth and fermentation, has been identified as a key parameter. Consequently, a comprehensive understanding of the metabolic specificities and the nitrogen requirements would be valuable to better exploit the potential of Starm. bacillaris during wine fermentation. In this study, marked differences in the consumption of the total and individual nitrogen sources were registered between the two species, while the two Starm. bacillaris strains generally behaved uniformly. Starm. bacillaris strains are differentiated by their preferential uptake of ammonium compared with amino acids that are poorly assimilated or even produced (alanine). Otherwise, the non-Saccharomyces yeast exhibits low activity through the acetaldehyde pathway, which triggers an important redistribution of fluxes through the central carbon metabolic network. In particular, the formation of metabolites deriving from the two glycolytic intermediates glyceraldehyde-3-phosphate and pyruvate is substantially increased during fermentations by Starm. bacillaris. This knowledge will be useful to better control the fermentation process in mixed fermentation with Starm. bacillaris and S. cerevisiae.

IMPORTANCE Mixed fermentations using a controlled inoculation of Starmerella bacillaris and Saccharomyces cerevisiae starter cultures represent a feasible way to modulate wine composition that takes advantage of both the phenotypic specificities of the non-Saccharomyces strain and the ability of S. cerevisiae to complete wine fermentation. However, according to the composition of grape juices, the consumption by Starm. bacillaris of nutrients, in particular of nitrogen sources, during the first stages of the process may result in depletions that further limit the growth of S. cerevisiae and lead to stuck or sluggish fermentations. Consequently, understanding the preferences of non-Saccharomyces yeasts for the nitrogen sources available in grape must together with their phenotypic specificities is essential for an efficient implementation of sequential wine fermentations with Starm. bacillaris and S. cerevisiae species. The results of our study demonstrate a clear preference for ammonium compared to amino acids for the non-Saccharomyces species. This finding underlines the importance of nitrogen sources, which modulate the functional characteristics of inoculated yeast strains to better control the fermentation process and product quality.

Differences Between Indigenous Yeast Populations in Spontaneously Fermenting Musts From V. vinifera L. and V. labrusca L. Grapes Harvested in the Same Geographic Location

Yeast communities associated with Vitis vinifera L. ecosystems have been widely characterized. Less is known, however, about yeast communities present in grapes and fermenting musts from Vitis non-vinifera ecosystems. Moreover, there are no comparative studies concerning yeast communities in grapes from V. vinifera L. and non-vinifera Vitis species in vineyards from a shared terroir. In this work, we have used a culture-dependent strategy, phenotypic analyses, and molecular genotyping, to study the most representative yeast species present in spontaneously fermenting musts of grapes harvested from neighboring V. vinifera L. (cv. Malbec) and V. labrusca L. (cv. Isabella) vineyards. Phenotypic analyses of H₂S production, ethanol tolerance and carbon utilization, on randomly selected strains of each Hanseniaspora uvarum, Starmerella bacillaris and Saccharomyces cerevisiae strains, as well as microsatellite genotyping of S. cerevisiae isolates from each the Malbec and Isabella grape musts, suggest that V. vinifera L. and V. labrusca L. ecosystems could harbor different yeast strain populations. Thus, microbial communities in exotic Vitis species may offer opportunities to look for unique yeast strains that could not be present in conventional V. vinifera L. ecosystems.

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation

Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. Commercially, there is now a growing trend away from using wine yeast (Saccharomyces) starter cultures, toward the historic practice of uninoculated or “wild” fermentation, where the yeasts and bacteria associated with the grapes and/or winery perform the fermentation. It is the varied metabolic contributions of these numerous non-Saccharomyces species that are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts. To map the microflora of spontaneous fermentation, metagenomic techniques were employed to characterize and monitor the progression of fungal species in 5 different wild fermentations. Both amplicon-based ribosomal DNA internal transcribed spacer (ITS) phylotyping and shotgun metagenomics were used to assess community structure across different stages of fermentation. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant overabundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia. By identifying biases such as that observed for Metschnikowia, abundance measurements from future ITS phylotyping datasets can be corrected to provide more accurate species representation. Ultimately, as more shotgun metagenomic and single-strain de novo assemblies for key wine species become available, the accuracy of both ITS-amplicon and shotgun studies will greatly increase, providing a powerful methodology for deciphering the influence of the microbial community on the wine flavor and aroma.

The use of indigenous Saccharomyces cerevisiae and Starmerella bacillaris strains as a tool to create chemical complexity in local wines

The performance of two vineyard strains, Saccharomyces cerevisiae SacPK7 and Starmerella bacillaris StbPK9, was evaluated in laboratory and pilot scale fermentations of Cretan grape must under the following inoculation schemes: single inoculation of SacPK7 (IS), simultaneous inoculation of StbPK9 and SacPK7 (SM), and sequential inoculation of StbPK9 followed by SacPK7 (SQ). Un-inoculated (spontaneous) fermentations (SP) and fermentations inoculated with control S. cerevisiae strains (CS) were also conducted as reference. Star. bacillaris not only did not restrict but also slightly promoted the growth of S. cerevisiae when the two strains were co-inoculated at equal quantities. On the contrary, the SQ inoculation scheme conferred a competitive advantage to Star. bacillaris over S. cerevisiae, which maximum population was reduced, while increased levels of Star. bacillaris were recorded. The fermentation kinetics were also affected, accordingly. The completion of fermentation was faster in SM, IS and CS ferments than in SQ and SP. Ethanol accumulation had a predominant role in the early death of Star. bacillaris, since its growth was similarly arrested irrespective of the dominating yeast species, the magnitude of yeast population or the availability of energy sources. Interestingly, the inoculation scheme applied significantly affected the chemical profiles of the resulting wines. SQ produced the most divergent chemical profile in sterile must, with glycerol, acetic acid, acetaldehyde, residual glucose, malic acid, ethyl acetate and higher alcohols being the key compounds affected by the prolonged activity of StbPK9. In pilot scale ferments, the indigenous S. cerevisiae produced twice as high levels of esters and higher alcohols compared to the commercial starter. Star. bacillaris further increased the levels of ethyl esters in the respective ferments. The use of a mixed S. cerevisiae/Star. bacillaris starter culture instead of S. cerevisiae alone enhanced the chemical complexity of Cretan local wine. The magnitude of differentiation was even higher when the addition of Star. bacillaris preceded that of S. cerevisiae. The highest divergence in analytical profiles was recorded between wines produced by native strain combinations and commercial S. cerevisiae. Present results show that the use of indigenous yeast formulations provides significant diversification to local wines, in line with the microbial terroir concept and recent observations that indigenous yeast strains may confer regional characters to wines.

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.

MALDI-TOF MS Supplementary database for species identification employing the yeast diversity encountered on southern Brazil grapes

The study of grape microflora is of interest when autochthonous yeasts, which are related to typical wine characteristics, are intended to be used in winemaking. The election of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) as the first method for yeast identification was based on its accuracy and rapidity compared to alternative laboratory protocols for identification. The aims of this study are to consolidate the MALDI-TOF MS Supplementary database for environmental yeasts already constructed, to expand it through the addition of standard spectra of not included yeast species, and to discuss the grape microflora encountered in Southern Brazil. A total of 358 strains, isolated from grape berries, were submitted to protein profiling employing Biotyper and Supplementary database. Molecular biology techniques were used as alternatives to identify 6.4% of strains not promptly designated by protein profiling. These strains corresponded to the species Candida californica, Zygoascus meyerae, Candida akabanensis, Candida azyma, and Hanseniaspora vineae. The MALDI-TOF MS spectra of the identified species were added to Supplementary database. The presented results strengthen the need for further expansion of the mass spectra database to broaden its microbiological application.

Volatile profiles and chromatic characteristics of red wines produced with Starmerella bacillaris and Saccharomyces cerevisiae

The use of mixed fermentations with Starmerella bacillaris and Saccharomyces cerevisiae is gaining attention in recent years due to their ability to modulate the metabolites production of enological interest. In the present study, four of the most popular planted red grape varieties (Cabernet sauvignon, Merlot, Pinot noir and Shiraz) were fermented using the aforementioned species and two different inoculation protocols (inoculation of S. cerevisiae after 24 and 48 h from the Starm. bacillaris inoculation), in order to evaluate their impact on the volatile composition and chromatic characteristics of wines. Analysis from chemical composition showed that titratable acidity and glycerol content exhibited marked differences among wines after fermentation. For volatile compounds, mixed fermented wines using an inoculation delay of 48 h led to reduction of volatile compounds (mainly esters). A shorter 24 h delay produced wines with higher values of color intensity than pure fermented wines. The differences observed between the inoculation protocols can be explained by the growth dynamics of both species during fermentation. These findings suggest that mixed fermentations posed a great potential in reducing metabolites which are considered negative for wine quality (mainly ethyl acetate and volatile fatty acids) and with an improvement of the chromatic profile of the wines.

Analysis of ribosomal RNA stability in dead cells of wine yeast by quantitative PCR

During wine production, some yeasts enter a Viable But Not Culturable (VBNC) state, which may influence the quality and stability of the final wine through remnant metabolic activity or by resuscitation. Culture-independent techniques are used for obtaining an accurate estimation of the number of live cells, and quantitative PCR could be the most accurate technique. As a marker of cell viability, rRNA was evaluated by analyzing its stability in dead cells. The species-specific stability of rRNA was tested in Saccharomyces cerevisiae, as well as in three species of non-Saccharomyces yeast (Hanseniaspora uvarum, Torulaspora delbrueckii and Starmerella bacillaris). High temperature and antimicrobial dimethyl dicarbonate (DMDC) treatments were efficient in lysing the yeast cells. rRNA gene and rRNA (as cDNA) were analyzed over 48 h after cell lysis by quantitative PCR. The results confirmed the stability of rRNA for 48 h after the cell lysis treatments. To sum up, rRNA may not be a good marker of cell viability in the wine yeasts that were tested.

Non-Saccharomyces in Wine: Effect Upon Oenococcus oeni and Malolactic Fermentation

This work is a short review of the interactions between oenological yeasts and lactic acid bacteria (LAB), especially Oenococcus oeni, the main species carrying out the malolactic fermentation (MLF). The emphasis has been placed on non-Saccharomyces effects due to their recent increased interest in winemaking. Those interactions are variable, ranging from inhibitory, to neutral and stimulatory and are mediated by some known compounds, which will be discussed. One phenomena responsible of inhibitory interactions is the media exhaustion by yeasts, and particularly a decrease in L-malic acid by some non-Saccharomyces. Clearly ethanol is the main inhibitory compound of LAB produced by S. cerevisiae, but non-Saccharomyces can be used to decrease it. Sulfur dioxide and medium chain fatty acids (MCFAs) produced by yeasts can exhibit inhibitory effect upon LAB or even result lethal. Interestingly mixed fermentations with non-Saccharomyces present less MCFA concentration. Among organic acids derived as result of yeast metabolism, succinic acid seems to be the most related with MLF inhibition. Several protein factors produced by S. cerevisiae inhibiting O. oeni have been described, but they have not been studied in non-Saccharomyces. According to the stimulatory effects, the use of non-Saccharomyces can increase the concentration of favorable mediators such as citric acid, pyruvic acid, or other compounds derived of yeast autolysis such as peptides, glucans, or mannoproteins. The emergence of non-Saccharomyces in winemaking present a new scenario in which MLF has to take place. For this reason, new tools and approaches should be explored to better understand this new winemaking context.

The Microbial Diversity of Sherry Wines

The principal role of wine yeast is to transform efficiently the grape-berries’ sugars to ethanol, carbon dioxide, and other metabolites, without the production of off-flavors. Wine yeast strains are able to ferment musts, while other commercial or laboratory strains fail to do so. The genetic differences that characterize wine yeast strains in contrast to the biological ageing of the veil-forming yeasts in Sherry wines are poorly understood. Saccharomyces cerevisiae strains frequently exhibit rather specific phenotypic features needed for adaptation to a special environment, like fortified wines with ethanol up to 15% (v/v), known as Sherry wines. Factors that affect the correct development of the veil of flor during ageing are also reviewed, along with the related aspects of wine composition, biofilm formation processes, and yeast autolysis. This review highlights the importance of yeast ecology and yeast metabolic reactions in determining Sherry wine quality and the wealth of untapped indigenous microorganisms co-existing with the veil-forming yeast strains. It covers the complexity of the veil forming wine yeasts’ genetic features, and the genetic techniques often used in strain selection and monitoring during fermentation or biological ageing. Finally, the outlook for new insights to protect and to maintain the microbiota of the Sherry wines will be discussed.

Volatile profile of white wines fermented with sequential inoculation of Starmerella bacillaris and Saccharomyces cerevisiae

Mixed fermentations with Starmerella bacillaris and Saccharomyces cerevisiae affect the chemical composition of wines, by modulating various metabolites of oenological interest. The current study was carried out to elucidate the effect of sequential inoculation of the above mentioned species on the production of white wines, especially on the chemical and aromatic characteristics of Chardonnay, Muscat, Riesling and Sauvignon blanc wines. Titratable acidity and glycerol content exhibited evident differences among the wines after fermentation. For volatile compounds, mixed fermentations led to a reduction of the total esters, including ethyl acetate, which is a compound responsible for wine deterioration. However, Sauvignon blanc wines fermented by mixed cultures contained significantly higher levels of esters and thiols, both associated with positive sensory attributes. These findings suggest that sequential inoculations possess great potential in affecting and modulating the chemical and aromatic profile of white wines, especially those produced from Sauvignon blanc grapes.

Altered Fermentation Performances, Growth, and Metabolic Footprints Reveal Competition for Nutrients between Yeast Species Inoculated in Synthetic Grape Juice-Like Medium

The sequential inoculation of non-Saccharomyces yeasts and Saccharomyces cerevisiae in grape juice is becoming an increasingly popular practice to diversify wine styles and/or to obtain more complex wines with a peculiar microbial footprint. One of the main interactions is competition for nutrients, especially nitrogen sources, that directly impacts not only fermentation performance but also the production of aroma compounds. In order to better understand the interactions taking place between non-Saccharomyces yeasts and S. cerevisiae during alcoholic fermentation, sequential inoculations of three yeast species (Pichia burtonii, Kluyveromyces marxianus, Zygoascus meyerae) with S. cerevisiae were performed individually in a synthetic medium. Different species-dependent interactions were evidenced. Indeed, the three sequential inoculations resulted in three different behaviors in terms of growth. P. burtonii and Z. meyerae declined after the inoculation of S. cerevisiae which promptly outcompeted the other two species. However, while the presence of P. burtonii did not impact the fermentation kinetics of S. cerevisiae, that of Z. meyerae rendered the overall kinetics very slow and with no clear exponential phase. K. marxianus and S. cerevisiae both declined and became undetectable before fermentation completion. The results also demonstrated that yeasts differed in their preference for nitrogen sources. Unlike Z. meyerae and P. burtonii, K. marxianus appeared to be a competitor for S. cerevisiae (as evidenced by the uptake of ammonium and amino acids), thereby explaining the resulting stuck fermentation. Nevertheless, the results suggested that competition for other nutrients (probably vitamins) occurred during the sequential inoculation of Z. meyerae with S. cerevisiae. The metabolic footprint of the non-Saccharomyces yeasts determined after 48 h of fermentation remained until the end of fermentation and combined with that of S. cerevisiae. For instance, fermentations performed with K. marxianus were characterized by the formation of phenylethanol and phenylethyl acetate, while those performed with P. burtonii or Z. meyerae displayed higher production of isoamyl alcohol and ethyl esters. When considering sequential inoculation of yeasts, the nutritional requirements of the yeasts used should be carefully considered and adjusted accordingly. Finally, our chemical data suggests that the organoleptic properties of the wine are altered in a species specific manner.

The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems

The yeast Lachancea thermotolerans (formerly Kluyveromyces thermotolerans) is a species with remarkable, yet underexplored, biotechnological potential. This ubiquist occupies a range of natural and anthropic habitats covering a wide geographic span. To gain an insight into L. thermotolerans population diversity and structure, 172 isolates sourced from diverse habitats worldwide were analysed using a set of 14 microsatellite markers. The resultant clustering revealed that the evolution of L. thermotolerans has been driven by the geography and ecological niche of the isolation sources. Isolates originating from anthropic environments, in particular grapes and wine, were genetically close, thus suggesting domestication events within the species. The observed clustering was further validated by several means including, population structure analysis, F-statistics, Mantel’s test and the analysis of molecular variance (AMOVA). Phenotypic performance of isolates was tested using several growth substrates and physicochemical conditions, providing added support for the clustering. Altogether, this study sheds light on the genotypic and phenotypic diversity of L. thermotolerans, contributing to a better understanding of the population structure, ecology and evolution of this non-Saccharomyces yeast.

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production

Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments. Results suggested that microbiomes of berries collected at four different localities share a core composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales typical of manure (i.e. Lysinibacillus, Bacillus, and Sporosarcina), whereas in the Santadi locality, berries showed soil bacteria such as Pasteurellales and Bacteroidales as well as Rhodospirillales and Lactobacillales which are commonly involved in wine fermentation. In the case of fungi, the most abundant taxa were Dothioraceae, Pleosporaceae, and Saccharomycodaceae, and although the proportion of these families varied among localities, they occurred ubiquitously in all vineyards. During vinification processes performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature, even if Saccharomyces cerevisiae represented the most abundant fungal species. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropologic conditions (e.g., farming management), and the fruits’ microorganisms persist during the fermentation process. For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality.

Saccharomyces cerevisiae vineyard strains have different nitrogen requirements that affect their fermentation performances

In this work the fermentation performances of seven vineyard strains, together with the industrial strain EC1118, have been investigated at three differing yeast assimilable nitrogen (YAN) concentrations (300 mg N l^-1 , 150 mg N l^-1 and 70 mg N l^-1 ) in synthetic musts. The results indicated that the response to different nitrogen levels is strain dependent. Most of the strains showed a dramatic decrease of the fermentation at 70 mg N l^-1 but no significant differences in CO₂ production were found when fermentations at 300 mg N l^-1 and 150 mg N l^-1 were compared. Only one among the vineyard strains showed a decrease of the fermentation when 150 mg N l^-1 were present in the must. These results contribute to shed light on strain nitrogen requirements and offer new perspectives to manage the fermentation process during winemaking.

SIGNIFICANCE AND IMPACT OF THE STUDY

Selected vineyard Saccharomyces cerevisiae strains can improve the quality and the complexity of local wines. Wine quality is also influenced by nitrogen availability that modulates yeast fermentation activity. In this work, yeast nitrogen assimilation was evaluated to clarify the nitrogen requirements of vineyard strains. Most of the strains needed high nitrogen levels to express the best fermentation performances. The results obtained indicate the critical nitrogen levels. When the nitrogen concentration was above the critical level, the fermentation process increased, but if the level of nitrogen was further increased no effect on the fermentation was found.

Oxygen availability and strain combination modulate yeast growth dynamics in mixed culture fermentations of grape must with Starmerella bacillaris and Saccharomyces cerevisiae

Starmerella bacillaris (synonym Candida zemplinina) is a non-Saccharomyces yeast that has been proposed as a co-inoculant of selected Saccharomyces cerevisiae strains in mixed culture fermentations to enhance the analytical composition of the wines. In order to acquire further knowledge on the metabolic interactions between these two species, in this study we investigated the impact of oxygen addition and combination of Starm. bacillaris with S. cerevisiae strains on the microbial growth and metabolite production. Fermentations were carried out under two different conditions of oxygen availability. Oxygen availability and strain combination clearly influenced the population dynamics throughout the fermentation. Oxygen concentration increased the survival time of Starm. bacillaris and decreased the growth rate of S. cerevisiae strains in mixed culture fermentations, whereas it did not affect the growth of the latter in pure culture fermentations. This study reveals new knowledge about the influence of oxygen availability on the successional evolution of yeast species during wine fermentation.

Selection of non-Saccharomyces yeasts to be used in grape musts with high alcoholic potential: a strategy to obtain wines with reduced ethanol content

Ethanol content of wine has increased over the last decades as consequence of searching phenolic maturity, requiring increased grape maturity. This may result in the production of wines with excessive alcohol levels (sometimes more than 15% (v/v)), sluggish and stuck fermentations and excessive volatile acidity. Many strategies to reduce ethanol in wines are being studied, and microbial methods have some additional advantages. However, because of the broad intra- and interspecies variability, new selection criteria should be included. Therefore, the goal of the present work was to design and evaluate a simple and integral procedure for non-Saccharomyces yeast selection. This strategy allowed selection of yeasts that presented successful implantation in grape must with high alcohol potential and their use in co-cultures could reduce the ethanol in wines. A total of 114 native non-Saccharomyces yeasts were assayed to determine their respiratory, fermentative and physiological characteristics of enological interest. Hanseniaspora uvarum BHu9 and BHu11, H. osmophila BHo51, Starmerella bacillaris BSb55 and Candida membranaefaciens BCm71 were selected as candidates to design co-culture starters.

Schizosaccharomyces pombe and Saccharomyces cerevisiae yeasts in sequential fermentations: Effect on phenolic acids of fermented Kei-apple (Dovyalis caffra L.) juice

Kei-apple (Dovyalis caffra) is an evergreen tree indigenous to Southern Africa. The fruit contains high concentrations of l-malic acid, ascorbic acid, and phenolic acids. Kei-apple juice was sequentially inoculated with Schizosaccharomyces pombe and Saccharomyces cerevisiae yeasts. A reference fermentation using only S. cerevisiae was included. The fermentation was monitored by recording mass loss. At the end of fermentation, twelve untrained judges conducted free choice aroma profiling on the fruit wines. The Kei-apple juice and wines were analysed for total titratable acidity, total soluble solids, pH, alcohol, l-malic acid, and phenolic acids. Total titratable acidity was ca. 70% lower in Kei-apple wines produced with S. pombe+S. cerevisiae than in Kei-apple juice. Kei-apple wines produced with S. pombe+S. cerevisiae showed substantially lower concentrations of l-malic acid than Kei-apple wines produced with S. cerevisiae only. Wines produced with S. cerevisiae only proved higher in phenolic acid concentrations than wines produced with S. pombe+S. cerevisiae. Chlorogenic acid was the most abundant phenolic acid measured in the Kei-apple wines, followed by protocatechuic acid. Judges described the Kei-apple wines produced with S. pombe+S. cerevisiae as having noticeable off-odours, while wines produced with S. cerevisiae were described as fresh and fruity. Kei-apple wines (S. pombe+S. cerevisiae and S. cerevisiae) were of comparable vegetative and organic character. Saccharomyces cerevisiae produced Kei-apple wine with increased caffeic, chlorogenic, protocatechuic, and sinapic acids, whereas S. pombe+S. cerevisiae produced Kei-apple wines with increased ferulic, and p-coumaric acids and low l-malic acid.

Use of Native Yeast Strains for In-Bottle Fermentation to Face the Uniformity in Sparkling Wine Production

The in-bottle fermentation of sparkling wines is currently triggered by few commercialized Saccharomyces cerevisiae strains. This lack of diversity in tirage yeast cultures leads to a prevalent uniformity in sensory profiles of the end products. The aim of this study has been to exploit the natural multiplicity of yeast populations in order to introduce variability in sparkling wines throughout the re-fermentation step. A collection of 133 S. cerevisiae strains were screened on the basis of technological criteria (fermenting power and vigor, SO₂ tolerance, alcohol tolerance, flocculence) and qualitative features (acetic acid, glycerol and H₂S productions). These activities allowed the selection of yeasts capable of dominating the in-bottle fermentation in actual cellar conditions: in particular, the performances of FX and FY strains (isolated in Franciacorta area), and OX and OY strains (isolated in Oltrepò Pavese area), were compared to those of habitually used starter cultures (IOC18-2007, EC1118, Lalvin DV10), by involving nine wineries belonging to the two Consortia of Appellation of Origin. The microbiological analyses of samples have revealed that the indigenous strains showed an increased latency period and a higher cultivability along the aging time than the commercial starter cultures do. Results of chemical analyses and sensory evaluation of the samples after 18 months sur lies have shown that significant differences (p < 0.05) were present among the strains for alcoholic strength, carbon dioxide overpressure and pleasantness, whereas they were not observed for residual sugars content, titratable acidity or volatile acidity. Indigenous S. cerevisiae exhibited comparable values respect to the commercial starter cultures. The ANOVA has also proven that the base wine formulation is a key factor, by significantly affecting (p < 0.01) some oenological parameters of wine, like alcoholic strength, volatile acidity, carbon dioxide overpressure, titratable acidity and dry extract. The use of native yeast strains for the re-fermentation step can be considered a convenient way for introducing differentiation to the final product without modifying the traditional technology. In a perspective of "precision enology," where the wine is designed on specific vine cultivars and microorganisms, this work underlines that exploring yeast biodiversity is a strategic activity to improve the production.

Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics.

The Combined Use of Schizosaccharomyces pombe and Lachancea thermotolerans-Effect on the Anthocyanin Wine Composition

The most popular methodology to make red wine is through the combined use of Saccharomyces cerevisiae yeast and lactic acid bacteria, for alcoholic fermentation and malolactic fermentation respectively. This classic winemaking practice produces stable red wines from a microbiological point of view. This study aims to investigate a recent red winemaking biotechnology, which through the combined use of Lachancea thermotolerans and Schizosaccharomyces pombe is used as an alternative to the classic malolactic fermentation. In this new methodology, Schizosaccharomycespombe totally consumes malic acid, while Lachancea thermotolerans produces lactic acid, avoiding excessive deacidification of musts with low acidity in warm viticulture areas such as Spain. This new methodology has been reported to be a positive alternative to malolactic fermentation in low acidity wines, since it has the advantage to produce wines with a more fruity flavor, less acetic acid, less ethyl carbamate originators and less biogenic amines than the traditional wines produced via conventional fermentation techniques. The study focuses on unexplored facts related to this novel biotechnology such as color and anthocyanin profile.

Biomanufacturing: history and perspective

Biomanufacturing is a type of manufacturing that utilizes biological systems (e.g., living microorganisms, resting cells, animal cells, plant cells, tissues, enzymes, or in vitro synthetic (enzymatic) systems) to produce commercially important biomolecules for use in the agricultural, food, material, energy, and pharmaceutical industries. History of biomanufacturing could be classified into the three revolutions in terms of respective product types (mainly), production platforms, and research technologies. Biomanufacturing 1.0 focuses on the production of primary metabolites (e.g., butanol, acetone, ethanol, citric acid) by using mono-culture fermentation; biomanufacturing 2.0 focuses on the production of secondary metabolites (e.g., penicillin, streptomycin) by using a dedicated mutant and aerobic submerged liquid fermentation; and biomanufacturing 3.0 focuses on the production of large-size biomolecules—proteins and enzymes (e.g., erythropoietin, insulin, growth hormone, amylase, DNA polymerase) by using recombinant DNA technology and advanced cell culture. Biomanufacturing 4.0 could focus on new products, for example, human tissues or cells made by regenerative medicine, artificial starch made by in vitro synthetic biosystems, isobutanol fermented by metabolic engineering, and synthetic biology-driven microorganisms, as well as exiting products produced by far better approaches. Biomanufacturing 4.0 would help address some of the most important challenges of humankind, such as food security, energy security and sustainability, water crisis, climate change, health issues, and conflict related to the energy, food, and water nexus.