Oxygen is required to restore flor strain viability and lipid biosynthesis under fermentative conditions

Molecular characterization and expression profiling of two flavohemoglobin genes play essential roles in dissolved oxygen and NO stress in Saitozyma podzolica zwy2-3

Flavohemoglobins (Fhbs) are key enzymes involved in microbial nitrosative stress resistance and nitric oxide degradation. However, the roles of Fhbs in fungi remain largely unknown. In this study, SpFhb1 and SpFhb2, two flavohemoglobin-encoding genes in Saitozyma podzolica zwy2-3 were characterized. Protein structure analysis and molecular docking showed that SpFhbs were conserved in bacteria and fungi. Phylogenetic analysis revealed that SpFhb2 may be acquired through the transfer event of independent horizontal genes from bacteria. The expression levels of SpFhb1 and SpFhb2 showed opposite trend under high/low dissolved oxygen, implying that they may exhibited different functions. Through deletion and overexpression of SpFhbs, we confirmed that SpFhbs were conducive to lipid accumulation under high stress. The sensitivities of ΔFhb mutants to NO stress were significantly increased compared with that in the WT, indicating that they were required for NO detoxification and nitrosative stress resistance in S. podzolica zwy2-3. Furthermore, SpAsg1 was identified that simultaneously regulates SpFhbs, which functions in the lipid accumulation under high/low dissolved oxygen and NO stress in S. podzolica zwy2-3. Overall, two different SpFhbs were identified in this study, providing new insights into the mechanism of lipid accumulation in fungi under high/low dissolved oxygen and NO stress.

Analytical and Chemometric Characterization of Fino and Amontillado Sherries during Aging in Criaderas y Solera System

Fino and Amontillado are Sherry wines, produced in Marco de Jerez area (southern Spain), and aged in Criaderas y Solera system. Fino Sherry wine follows a biological aging process, under a veil of flor yeasts, while Amontillado Sherry wine shares the same biological aging firstly, followed by oxidative aging, which gives them special features. Organic acids, esters, higher alcohols, phenolic compounds and total dry extract of Sherries evolve during aging due to evaporation processes, physical-chemical reactions, wood contributions and microbiological activity. During aging, Sherry wines improve their organoleptic profile, as could be proved in the tasting sessions. Hierarchical Cluster Analysis and Factor Analysis with factor extraction using Principal Components of Sherry wines studied were carried out and natural groupings of the wines according to the type of aging and their age were observed. A strong correlation between the parameters analyzed and the aging of each wine has been seen in the Multiple Linear Regression studies, establishing two different models, one for each type of Sherry wine, that, with only four of all the variables studied estimated the wine age with more than 99% of confidence. This constitutes a useful tool to control the age of these Sherry wines in the winery.

Genetic and Phenotypic Characterisation of a Saccharomyces cerevisiae Population of 'Merwah' White Wine

The study of yeast biodiversity represents an important step in the preservation of the local heritage, and this work in particular has an innovative character since no further studies have investigated 'Merwah', one of the main grape varieties used in winemaking in Lebanon. To gain deeper knowledge of the genetic diversity and population structure of native Saccharomyces cerevisiae wine strains, 202 isolates were collected during spontaneous alcoholic fermentation of eight must/wine samples of cultivar 'Merwah', over two consecutive years (2016, 2017) in a traditional winery in Mount Lebanon (1400 m a.s.l.). The isolates were identified as S. cerevisiae on the basis of their morphology and preliminary sequence analysis of their internal transcribed spacer (ITS) PCR. They were then characterised at the strain level by interdelta PCR and genotyped using multiplex PCR reactions of 12 microsatellite markers. High genetic diversity was observed for the studied population. To select potential yeast starter strains from this population, micro-fermentations were carried out for 22 S. cerevisiae strains that were selected as representative of the 'Merwah' wine yeast population in order to determine their technological and oenological properties. Three indigenous yeast strains might represent candidates for pilot-scale fermentation in the winery, based on relevant features such as high fermentation vigour, low production of volatile acidity and H₂S and low residual sugar content at the end of alcoholic fermentation.

Transcriptomic Response of Saccharomyces cerevisiae during Fermentation under Oleic Acid and Ergosterol Depletion

Under anaerobic/hypoxic conditions, Saccharomyces cerevisiae relies on external lipid supplements to modulate membrane lipid fraction in response to different stresses. Here, transcriptomic responses of two S. cerevisiae wine strains were evaluated during hypoxic fermentation of a synthetic must with/without ergosterol and oleic acid supplementation. In the absence of lipids, the two strains, namely EC1118 and M25, showed different behaviour, with M25 significantly decreasing its fermentation rate from the 72 h after inoculum. At this time point, the whole genome transcriptomic analysis revealed common and strain-specific responses to the lack of lipid supplementation. Common responses included the upregulation of the genes involved in ergosterol biosynthesis, as well as the seripauperin and the heat shock protein multigene families. In addition, the upregulation of the aerobic isoforms of genes involved in mitochondrial electron transport is compatible with the previously observed accumulation of reactive oxygen species in the two strains during growth in absence of lipids. Considering the strain-specific responses, M25 downregulated the transcription of genes involved in glucose transport, methionine biosynthesis and of those encoding mannoproteins required for adaptation to low temperatures and hypoxia. The identification of these pathways, which are presumably involved in yeast resistance to stresses, will assist industrial strain selection.

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.

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.

Flor Yeast: New Perspectives Beyond Wine Aging

The most important dogma in white-wine production is the preservation of the wine aroma and the limitation of the oxidative action of oxygen. In contrast, the aging of Sherry and Sherry-like wines is an aerobic process that depends on the oxidative activity of flor strains of Saccharomyces cerevisiae. Under depletion of nitrogen and fermentable carbon sources, these yeast produce aggregates of floating cells and form an air–liquid biofilm on the wine surface, which is also known as velum or flor. This behavior is due to genetic and metabolic peculiarities that differentiate flor yeast from other wine yeast. This review will focus first on the most updated data obtained through the analysis of flor yeast with -omic tools. Comparative genomics, proteomics, and metabolomics of flor and wine yeast strains are shedding new light on several features of these special yeast, and in particular, they have revealed the extent of proteome remodeling imposed by the biofilm life-style. Finally, new insights in terms of promotion and inhibition of biofilm formation through small molecules, amino acids, and di/tri-peptides, and novel possibilities for the exploitation of biofilm immobilization within a fungal hyphae framework, will be discussed.

Impact of nutrient imbalance on wine alcoholic fermentations: nitrogen excess enhances yeast cell death in lipid-limited must

We evaluated the consequences of nutritional imbalances, particularly lipid/nitrogen imbalances, on wine yeast survival during alcoholic fermentation. We report that lipid limitation (ergosterol limitation in our model) led to a rapid loss of viability during the stationary phase of fermentation and that the cell death rate is strongly modulated by nitrogen availability and nature. Yeast survival was reduced in the presence of excess nitrogen in lipid-limited fermentations. The rapidly dying yeast cells in fermentations in high nitrogen and lipid-limited conditions displayed a lower storage of the carbohydrates trehalose and glycogen than observed in nitrogen-limited cells. We studied the cell stress response using HSP12 promoter-driven GFP expression as a marker, and found that lipid limitation triggered a weaker stress response than nitrogen limitation. We used a SCH9-deleted strain to assess the involvement of nitrogen signalling pathways in the triggering of cell death. Deletion of SCH9 increased yeast viability in the presence of excess nitrogen, indicating that a signalling pathway acting through Sch9p is involved in this nitrogen-triggered cell death. We also show that various nitrogen sources, but not histidine or proline, provoked cell death. Our various findings indicate that lipid limitation does not elicit a transcriptional programme that leads to a stress response protecting yeast cells and that nitrogen excess triggers cell death by modulating this stress response, but not through HSP12. These results reveal a possibly negative role of nitrogen in fermentation, with reported effects referring to ergosterol limitation conditions. These effects should be taken into account in the management of alcoholic fermentations.

Production of bioethanol from effluents of the dairy industry by Kluyveromyces marxianus

Whey and scotta are effluents coming from cheese and ricotta processing respectively. Whey contains minerals, lipids, lactose and proteins; scotta contains mainly lactose. Whey can be reused in several ways, such as protein extraction or animal feeding, while nowadays scotta is just considered as a waste; moreover, due to very high volumes of whey produced in the world, it poses serious environmental and disposal problems. Alternative destinations of these effluents, such as biotechnological transformations, can be a way to reach both goals of improving the added value of the agroindustrial processes and reducing their environmental impact. In this work we investigated the way to produce bioethanol from lactose of whey and scotta and to optimize the fermentation yields. Kluyveromyces marxianus var. marxianus was chosen as lactose-fermenting yeast. Batch, aerobic and anaerobic, fermentations and semicontinuous fermentations in dispersed phase and in packed bed reactor were carried out of row whey, scotta and mix 1:1 whey:scotta at a laboratory scale. Different temperatures (28-40°C) were also tested to check whether the thermotolerance of the chosen yeast could be useful to improve the ethanol yield. The best performances were reached at low temperatures (28°C); high temperatures are also compatible with good ethanol yields in whey fermentations, but not in scotta fermentations. Semicontinuous fermentations in dispersed phase gave the best fermentation performances, particularly with scotta. Then both effluents can be considered suitable for ethanol production. The good yields obtained from scotta allow us to transform this waste in a source.

Effect of oxygen and lipid supplementation on the volatile composition of chemically defined medium and Chardonnay wine fermented with Saccharomyces cerevisiae

Oxygen or lipids are required to complete stressful alcoholic fermentation. Lack of these nutrients can inhibit sugar uptake and growth, which leads to incomplete or 'stuck' fermentation. Oxygen or lipids supplementation not only restores yeast fermentative activity and also affects formation of yeast volatile metabolites. To clarify the effect of oxygen and lipid supplementation on the formation of flavour active metabolites during wine fermentation, we evaluated the addition of these two nutrients to chemically defined grape juice and filter clarified Chardonnay must. Lipid addition increased the concentration of esters, higher alcohols and volatile acids, whereas oxygen increased the concentration of higher alcohols and altered the proportion of acetate to ethyl esters and the proportion of branch-chain acids to medium-chain fatty acids. Combined addition of lipids and oxygen showed an additive effect on concentration of higher alcohols whereas oxygen suppressed the enhancing effect of lipids on formation of esters and volatile acids. Our results demonstrate the potential of lipid and oxygen supplementation for the manipulation of wine aroma in white wine fermentation.

The effect of scale on gene expression: commercial versus laboratory wine fermentations

Molecular and cellular processes that are responsible for industrially relevant phenotypes of fermenting microorganisms are a central focus of biotechnological research. Such research intends to generate insights and solutions for fermentation-based industries with regards to issues such as improving product yield or the quality of the final fermentation product. For logistical reasons, and to ensure data reproducibility, such research is mostly carried out in defined or synthetic media and in small-scale fermentation vessels. Two questions are frequently raised regarding the applicability of this approach to solve problems experienced in industrial fermentations: (1) Is synthetic medium a sufficiently accurate approximation of the generally more complex natural (and frequently highly variable) substrates that are employed in most fermentation-based industries, and (2) can results obtained in small-scale laboratory fermentations be extrapolated to large-scale industrial environments? Here, we address the second question through a comparative transcriptomic approach by assessing the response of an industrial wine yeast strain fermenting a natural grape juice in small-scale laboratory and large-scale industrial conditions. In yeast, transcriptome analysis is arguably the best available tool to holistically assess the physiological state of a population and its response to changing environmental conditions. The data suggest that scale does indeed impact on some environmental parameters such as oxygen availability. However, the data show that small-scale fermentations nevertheless accurately reflect general molecular processes and adaptations during large-scale fermentation and that extrapolation of laboratory datasets to real industrial processes can be justified.

The impact of co-inoculation with Oenococcus oeni on the trancriptome of Saccharomyces cerevisiae and on the flavour-active metabolite profiles during fermentation in synthetic must

Co-inoculation of commercial yeast strains with a bacterial starter culture at the beginning of fermentation of certain varietal grape juices is rapidly becoming a preferred option in the global wine industry, and frequently replaces the previously dominant sequential inoculation strategy where bacterial strains, responsible for malolactic fermentation, are inoculated after alcoholic fermentation has been completed. However, while several studies have highlighted potential advantages of co-inoculation, such studies have mainly focused on broad fermentation properties of the mixed cultures, and no data exist regarding the impact of this strategy on many oenologically relevant attributes of specific wine yeast strains such as aroma production. Here we investigate the impact of co-inoculation on a commercial yeast strain during alcoholic fermentation by comparing the transcriptome of this strain in yeast-only and in co-inoculated fermentations of synthetic must. The data show that a significant number of genes are differentially expressed in this strain in these two conditions. Some of the differentially expressed genes appear to respond to chemical changes in the fermenting must that are linked to bacterial metabolic activities, whereas others might represent a direct response of the yeast to the presence of a competing organism.