Advances in the control of wine spoilage by Zygosaccharomyces and Dekkera/Brettanomyces

Reviewing the Source, Physiological Characteristics, and Aroma Production Mechanisms of Aroma-Producing Yeasts

Flavor is an essential element of food quality. Flavor can be improved by adding flavoring substances or via microbial fermentation to impart aroma. Aroma-producing yeasts are a group of microorganisms that can produce aroma compounds, providing a strong aroma to foods and thus playing a great role in the modern fermentation industry. The physiological characteristics of aroma-producing yeast, including alcohol tolerance, acid tolerance, and salt tolerance, are introduced in this article, beginning with their origins and biological properties. The main mechanism of aroma-producing yeast is then analyzed based on its physiological roles in the fermentation process. Functional enzymes such as proteases, lipases, and glycosidase are released by yeast during the fermentation process. Sugars, fats, and proteins in the environment can be degraded by these enzymes via pathways such as glycolysis, methoxylation, the Ehrlich pathway, and esterification, resulting in the production of various aromatic esters (such as ethyl acetate and ethyl caproate), alcohols (such as phenethyl alcohol), and terpenes (such as monoterpenes, sesquiterpenes, and squalene). Furthermore, yeast cells can serve as cell synthesis factories, wherein specific synthesis pathways can be introduced into cells using synthetic biology techniques to achieve high-throughput production. In addition, the applications of aroma yeast in the food, pharmaceutical, and cosmetic industries are summarized, and the future development trends of aroma yeasts are discussed to provide a theoretical basis for their application in the food fermentation industry.

Survey of the yeast ecology of dehydrated grapes and strain selection for wine fermentation

In this study we investigated the yeast population present on partially dehydrated Nebbiolo grapes destined for 'Sforzato di Valtellina', with the aim to select indigenous starters suitable for the production of this wine. Yeasts were enumerated, isolated, and identified by molecular methods (5.8S-ITS-RFLP and D1/D2 domain sequencing). A genetic, physiological (ethanol and sulphur dioxide tolerance, potentially useful enzymatic activities, hydrogen sulphide production, adhesive properties, and killer activity) and oenological (laboratory pure micro-fermentations) characterization was also carried out. Based on relevant physiological features, seven non-Saccharomyces strains were chosen for laboratory-scale fermentations, either in pure or in mixed-culture (simultaneous and sequential inoculum) with a commercial Saccharomyces cerevisiae strain. Finally, the best couples and inoculation strategy were further tested in mixed fermentations in winery. In both laboratory and winery, microbiological and chemical analyses were conducted during fermentation. The most abundant species on grapes were Hanseniaspora uvarum (27.4 % of the isolates), followed by Metschnikowia spp. (21.0 %) and Starmerella bacillaris (12.9 %). Technological characterization highlighted several inter- and intra-species differences. The best oenological aptitude was highlighted for species Starm. bacillaris, Metschnikowia spp., Pichia kluyveri and Zygosaccharomyces bailli. The best fermentation performances in laboratory-scale fermentations were found for Starm. bacillaris and P. kluyveri, due to their ability to reduce ethanol (-0.34 % v/v) and enhance glycerol production (+0.46 g/L). This behavior was further confirmed in winery. Results of this study contribute to the knowledge of yeast communities associated with a specific environment, like those of Valtellina wine region.

A Genome-Wide Phenotypic Analysis of Saccharomyces cerevisiae’s Adaptive Response and Tolerance to Chitosan in Conditions Relevant for Winemaking

In the wine industry, the use of chitosan, a non-toxic biodegradable polysaccharide with antimicrobial properties, has been gaining interest with respect to envisaging the reduction in the use of sulfur dioxide (SO2). Although the mechanisms of toxicity of chitosan against fungal cells have been addressed before, most of the studies undertaken used other sources of chitosan and/or used conditions to solubilize the polymer that were not compatible with winemaking. Herein, the effect of a commercial formulation of chitosan approved for use in winemaking over the growth of the spoilage yeast species Dekkera anomala, Saccharomycodes ludwigii, Zygosaccharomyces bailii, and Pichia anomala was assessed. At the legally allowed concentration of 0.1 g/L, chitosan inhibited the growth of all spoilage yeasts, except for the tested Pichia anomala strains. Interestingly, the highly SO2-tolerant yeasts S. ludwigii and Z. bailii were highly susceptible to chitosan. The growth of commercial Saccharomyces cerevisiae was also impacted by chitosan, in a strain-dependent manner, albeit at higher concentrations. To dissect this differential inhibitory potential and gain further insight into the interaction of chitosan over fungal cells, we explored a chemogenomic analysis to identify all of the S. cerevisiae genes conferring protection against or increasing susceptibility to the commercial formulation of chitosan. Among the genes found to confer protection against chitosan, a high proportion was found to encode proteins required for the assembly and structuring of the cell wall, enzymes involved in the synthesis of plasma membrane lipids, and components of signaling pathways that respond to damages in the plasma membrane (e.g., the Rim101 pathway). The data obtained also suggest that the fungal ribosome and the vacuolar V-ATPase could be directly targeted by chitosan, since the deletion of genes encoding proteins required for the structure and function of these organelles was found to increase tolerance to chitosan. We also demonstrated, for the first time, that the deletion of ITR1, AGP2 and FPS1, encoding plasma membrane transporters, prominently increased the tolerance of S. cerevisiae to chitosan, suggesting that they can serve as carriers for chitosan. Besides providing new insights into the mode of action of chitosan against wine yeasts, this study adds relevant information for its rational use as a substitute/complementary preservative to SO2.

Zygosaccharomyces rouxii is the predominant species responsible for the spoilage of the mix base for ice cream and ethanol is the best inhibitor tested

A mix base for ice cream (MBIC) is used to produce artisanal or industrial ice creams and desserts and consists of a mixture of different ingredients, including sugar, egg yolk, natural flavors, starch and milk proteins. MBICs, which have chemical-physical characteristics that include a pH of 5.61 and an activity water (A_w) less than or equal to 0.822, are packaged in tin boxes and stored at ambient temperature. Despite the low A_w, MBIC can support osmotolerant and osmophilic yeast growth. The aim of our work was to study the behavior of Zygosaccharomyces rouxii, the main microorganisms responsible of MBIC spoilage, either in the vivo or in a model system in order to inhibit its growth by the selection of antimicrobial agents. Different osmotolerant yeasts belonging to the genus Zygosaccharomyces were isolated and identified from spoiled and unspoiled lots of MBICs. In particular, Z. rouxii was the predominant species responsible for the spoilage, which depended on the high temperature of storage (>20 °C) and was highlighted by the presence of alcohol, esters, acids and gas (CO₂), which blew open the tin boxes. To stop spoilage, different antimicrobial compounds were tested: sulfur dioxide, sorbic and benzoic acids and ethanol. However, only 2% v/v ethanol was required to achieve the total inhibition of the Z. rouxii cocktails tested in this work. The use of other antimicrobials cannot be recommended because they were not able to stop yeast spoilage and changed the color and flavor of the products. Conversely, the use of ethanol is suggested because of its extreme effectiveness against osmotolerant yeasts, and the added amount was less than or equal to the taste threshold limit. The MBICs, treated with ethanol, were stable till the end of their shelf-life (6 months).

Effects of ultrasound treatments on wine microorganisms

Ultrasound is one of the most promising non-thermal an emerging technique in food technology. The objective of the present work was to evaluate the effect of different ultrasonic treatments on the most important wine microbiota (Saccharomyces and non-Saccharomyces yeasts and lactic acid bacteria). Two stages were carried out: the assessment step, where six different ultrasonic treatments (with varying power, time, and pulses) were used on Saccharomyces cerevisiae, Brettanomyces spp., and Lactiplantibacillus plantarum; and the validation step, where two chosen ultrasonic treatments were used on Zigosaccharomyces bailli, Brettanomyces spp., Saccharomyces cerevisiae, Saccharomyces bayanus, Pichia membranifaciens, Schizosaccharomyces pombe, and Hanseniaspora osmophila. The most sensitive microorganism was Brettanomyces spp., and the most resistant was Lactiplantibacillus plantarum. Ultrasonic treatments had varying effects on vitality (delay of growth or maximum OD reduction) and on viability (reduction of microbial growth).

Antimicrobial Activity of Nanoencapsulated Essential Oils of Tasmannia lanceolata, Backhousia citriodora and Syzygium anisatum against Weak-Acid Resistant Zygosaccharomyces bailii in Clear Apple Juice

The anti-yeast activity of oil-in-water encapsulated nanoemulsion containing individual or a combination of the three essential oils of Tasmanian pepper leaf (Tasmannia lanceolata), lemon myrtle (Backhousia citriodora), and anise myrtle (Syzygium anisatum) against weak-acid resistant Zygosaccharomyces bailii in clear apple juice was investigated. The effectiveness of the shelf-life extension of Z. bailii-spiked (1 × 103 CFU/mL) clear apple juice was evaluated and compared between natural (essential oils) and synthetic (sodium benzoate) antimicrobial agents. Essential oils showed an immediate reduction in the Z. bailii cell population at day-0 and exerted a fungicidal activity at day-4 of storage, with no further noticeable growth at the end of the experiment (day-28). At lower concentrations, Tasmanian pepper leaf oil of 0.0025% had >6 log CFU/mL at day-12 of storage. For lemon myrtle essential oils, the yeast population reached >6 log CFU/mL at day-24 and day-20 for concentrations of 0.02% and 0.01%, respectively. The fungicidal activity of Tasmanian pepper leaf oil reduced from 0.005% to 0.0025% v/v when mixed at a ratio of 1:1 with anise myrtle oil. The results of the present study suggest that these three native Australian herbs have the potential to be used in the beverage industry by controlling Zygosaccharomyces bailii in clear apple juice products.

Emerging Non-Thermal Technologies as Alternative to SO2 for the Production of Wine

SO₂ is an antioxidant and selective antimicrobial additive, inhibiting the growth of molds in the must during the early stages of wine production, as well as undesirable bacteria and yeasts during fermentation, thus avoiding microbial spoilage during wine production and storage. The addition of SO₂ is regulated to a maximum of 150–350 ppm, as this chemical preservative can cause adverse effects in consumers such as allergic reactions. Therefore, the wine industry is interested in finding alternative strategies to reduce SO₂ levels, while maintaining wine quality. The use of non-thermal or cold pasteurization technologies for wine preservation was reviewed. The effect of pulsed electric fields (PEF), high pressure processing (HPP), power ultrasound (US), ultraviolet irradiation (UV), high pressure homogenization (HPH), filtration and low electric current (LEC) on wine quality and microbial inactivation was explored and the technologies were compared. PEF and HPP proved to be effective wine pasteurization technologies as they inactivate key wine spoilage yeasts, including Brettanomyces, and bacteria in short periods of time, while retaining the characteristic flavor and aroma of the wine produced. PEF is a promising technology for the beverage industry as it is a continuous process, requiring only microseconds of processing time for the inactivation of undesirable microbes in wines, with commercial scale, higher throughput production potential.

Changes of microorganism composition in fresh and stored bee pollen from Southern Germany

Analysis of plant pollen can provide valuable insights into the existing spectrum of microorganisms in the environment. When harvesting bee-collected pollen as a dietary supplement for human consumption, timely preservation of the freshly collected pollen is fundamental for product quality. Environmental microorganisms contained in freshly collected pollen can lead to spoilage by degradation of pollen components. In this study, freshly collected bee pollen was sampled at different locations and stored under various storage conditions to examine the hypothesis that storage conditions may have an effect on the composition of microorganisms in pollen samples. The samples were analyzed using 16S and 18S amplicon sequencing and characterized by palynological analysis. Interestingly, the bacterial communities between pollen samples from different locations varied only slightly, whereas for fungal community compositions, this effect was substantially increased. Further, we noticed that fungal communities in pollen are particularly sensitive to storage conditions. The fungal genera proportion Cladosporium and Mycosphaerella decreased, while Zygosaccharomyces and Aspergillus increased during storage. Aspergillus and Zygosaccharomyces fractions increased during storage at 30 °C, which could negatively impact the pollen quality if it is used as a dietary supplement.

Enumeration of Brettanomyces in Wine Using Impedance

Brettanomyces bruxellensis is a wine spoilage concern in wineries around the world. In order to maintain wine quality during storage and ageing, it is imperative to control and monitor this yeast. Being a fastidious slow growing yeast, which requires 5 to 14 days of incubation for visible growth in agar plates, it is difficult to detect growth (colonies) by conventional agar plate count method. Yeast enumeration by impedance was investigated because previous research using other microorganisms has shown that it is potentially faster than plate counting. The relationship between plate counting and impedance detection times was investigated for Brettanomyces inoculated in red wine samples. A linear relationship between log plate count concentrations and impedance detection times was found. Incubation time was reduced from 120 h down to 0.9 and 57.7 h for samples with 6.7 × 107 and 1.8 × 102 cfu/mL, respectively, using the ‘indirect’ impedance method. The ‘direct’ method also reduced the incubation times to 9.5 and 81.9 h, for the same concentrations. The ‘indirect’ impedance method has the potential to be used by the wine industry to control and monitor the Brettanomyces numbers in wines.

Wine yeast species show strong inter- and intra-specific variability in their sensitivity to ultraviolet radiation

While the trend in winemaking is toward reducing the inputs and especially sulphites utilization, emerging technologies for the preservation of wine is a relevant topic for the industry. Amongst yeast spoilage in wine, Brettanomyces bruxellensis is undoubtedly the most feared. In this study, UV-C treatment is investigated. This non-thermal technique is widely used for food preservation. A first approach was conducted using a drop-platted system to compare the sensitivity of various strains to UV-C surface treatment. 147 strains distributed amongst fourteen yeast species related to wine environment were assessed for six UV-C doses. An important variability in UV-C response was observed at the interspecific level. Interestingly, cellar resident species, which are mainly associated with wine spoilage, shows higher sensitivity to UV-C than vineyard-resident species. A focus on B. bruxellensis species with 104 screened strains highlighted an important effect of the UV-C, with intra-specific variation. This intra-specific variation was confirmed on 6 strains in liquid red wine by using a home-made pilot. 6624 J.L^-1 was enough for a reduction of 5 log₁₀ of magnitude for 5 upon 6 strains. These results highlight the potential of UV-C utilization against wine yeast spoiler at cellar scale.

Wine phenolic profile altered by yeast: Mechanisms and influences

Grape phenolic compounds undergo various types of transformations during winemaking under the influences of yeasts, which further impacts the sensory attributes, thus the quality of wine. Understanding the roles of yeasts in phenolics transformation is important for controlling wine quality through fermentation culture selection. This literature review discusses the mechanisms of how yeasts alter the phenolic compounds during winemaking, summarizes the effects of Saccharomyces cerevisiae and non-Saccharomyces yeasts on the content and composition of phenolics in wine, and highlights the influences of mixed cultural fermentation on the phenolic profile of wine. Collectively, this paper aims to provide a deeper understanding on yeast-phenolics interactions and to identify the current literature gaps for future research.

Zygosaccharomyces rouxii, an Aromatic Yeast Isolated From Chili Sauce, Is Able to Biosynthesize 2-Phenylethanol via the Shikimate or Ehrlich Pathways

We isolated an aromatic strain of yeast (M2013310) from chili sauce. Assembly, annotation, and phylogenetic analysis based on genome sequencing, identified M2013310 as an allodiploid yeast that was closely related to Zygosaccharomyces rouxii. During fermentation, M2013310, produced an aromatic alcohol with a rose-honey scent; gas chromatography tandem mass spectrometry identified this alcohol as 2-phenylethanol. The concentration of 2-phenylethanol reached 3.8 mg/L, 1.79 g/L, and 3.58 g/L, in M3 (NH₄⁺), M3 (NH₄⁺ + Phe), and M3 (Phe) culture media, after 72 h of fermentation, respectively. The mRNA expression levels of ARO8 encoding aromatic aminotransferases I and ARO10 encoding phenylpyruvate decarboxylase by M2013310 in M3 (Phe) were the lowest of the three different forms of media tested. These results indicated that M2013310 can synthesize 2-phenylethanol via the Shikimate or Ehrlich pathways and the production of 2-phenylethanol may be significantly improved by the over-expression of these two genes. Our research identified a promising strain of yeast (M2013310) that could be used to improve the production of 2-phenylethanol.

Microbial Resources as a Tool for Enhancing Sustainability in Winemaking

In agriculture, the wine sector is one of the industries most affected by the sustainability issue. It is responsible for about 0.3% of annual global greenhouse gas emissions from anthropogenic activities. Sustainability in vitiviniculture was firstly linked to vineyard management, where the use of fertilizers, pesticides and heavy metals is a major concern. More recently, the contribution of winemaking, from grape harvest to bottling, has also been considered. Several cellar processes could be improved for reducing the environmental impact of the whole chain, including microbe-driven transformations. This paper reviews the potential of microorganisms and interactions thereof as a natural, environmentally friendly tool to improve the sustainability aspects of winemaking, all along the production chain. The main phases identified as potentially interesting for exploiting microbial activities to lower inputs are: (i) pre-fermentative stages, (ii) alcoholic fermentation, (iii) stage between alcoholic and malolactic fermentation, (iv) malolactic fermentation, (v) stabilization and spoilage risk management, and (vi) by-products and wastewater treatment. The presence of proper yeast or bacterial strains, the management and timing of inoculation of starter cultures, and some appropriate technological modifications that favor selected microbial activities can lead to several positive effects, including (among other) energy savings, reduction of chemical additives such as sulfites, and reuse of certain residues.

Genomic Insights Into Sugar Adaptation in an Extremophile Yeast Zygosaccharomyces rouxii

The osmotolerant Zygosaccharomyces rouxii is known for its trait to survive in extreme high sugar environments. This ability determines its role in the fermentation process and leads to yeast spoilage in the food industry. However, our knowledge of the gene expression in response to high sugar stress remains limited. Here, we conducted RNA-sequencing (RNA-seq) under different sugar concentrations of the spoilage yeast, Z. rouxii, which exhibit extremely high tolerance to sugar stress. The obtained differentially expressed genes (DEGs) are significantly different to that of the Saccharomyces cerevisiae, which is sensitive to extreme high sugar stress. Most of the DEGs participated in the “glucan synthesis,” “transmembrane transport,” “ribosome,” etc. In this work, we also demonstrated that the gene ZYRO0B03476g (ZrKAR2) encoding Kar2p can significantly affect the growth of Z. rouxii under high sugar stress. In addition, we combined with a previous study on the genome sequence of Z. rouxii, indicating that several gene families contain significantly more gene copies in the Z. rouxii lineage, which involved in tolerance to sugar stress. Our results provide a gene insight for understanding the high sugar tolerance trait, which may impact food and biotechnological industries and improve the osmotolerance in other organisms.

The Use of Candida pyralidae and Pichia kluyveri to Control Spoilage Microorganisms of Raw Fruits Used for Beverage Production

Undesired fermentation of fruit-derived beverages by fungal, yeast and bacterial spoilage organisms are among the major contributors of product losses in the food industry. As an alternative to chemical preservatives, the use of Candida pyralidae and Pichia kluyveri was assessed for antimicrobial activity against several yeasts (Dekkera bruxellensis, Dekkera anomala, Zygosaccharomyces bailii) and fungi (Botrytis cinerea, Colletotrichum acutatum and Rhizopus stolonifer) associated with spoilage of fruit and fruit-derived beverages. The antagonistic properties of C. pyralidae and P. kluyveri were evaluated on cheap solidified medium (grape pomace extract) as well as on fruits (grapes and apples). Volatile organic compounds (VOCs) from C. pyralidae and P. kluyveri deemed to have antimicrobial activity were identified by gas chromatography-mass spectrometry (GC-MS). A cell suspension of C. pyralidae and P. kluyveri showed growth inhibition activity against all spoilage microorganisms studied. Direct contact and extracellular VOCs were two of the mechanisms of inhibition. Twenty-five VOCs belonging to the categories of alcohols, organic acids and esters were identified as potential sources for the biocontrol activity observed in this study. This study reports, for the first time, the ability of C. pyralidae to inhibit fungal growth and also for P. kluyveri to show growth inhibition activity against spoilage organisms (n = 6) in a single study.

Established and Upcoming Yeast Expression Systems

Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.

Optimizing concentrations and contact times of cleaning and sanitizing agents for inactivating winery spoilage microorganisms

Microbial management is one of the most critical aspects of winery operations and is normally achieved via chemical control. This study sought to optimize winery cleaning and sanitation protocols for the management of winery spoilage microorganisms by applying multiple techniques commonly found in clinical health settings to winery-relevant conditions. The minimum inhibitory concentration and minimum biocidal concentration assay and a modified minimum biofilm inactivation assay were performed for three common winery spoilage yeast (S. cerevisiae, B. bruxellensis, Z. baili). Results indicate that inhibitory and biocidal concentrations vary dramatically between organisms but are largely in line with established application rates for inactivation of all cells in planktonic and biofilm physiologies. Dual-channel fluorescence staining was employed to determine minimum inactivation time for S. cerevisiae using two peracetic acid concentrations. Propidium Iodide and SYBR Green 1 stains were validated as a live/dead proxy (R2 = 0.99) and used to determine the contact time required to inactivate cell suspensions. Peracetic acid treatment trials indicate that S. cerevisiaepopulations are inactivated in five minutes or less at concentrations of 1−1.5 mg/L. In conjunction, these experiments provide insight for winemakers to critically think about cleaning and sanitation protocols and how to optimize these processes.

Starter cultures as biocontrol strategy to prevent Brettanomyces bruxellensis proliferation in wine

Brettanomyces bruxellensis is a common and significant wine spoilage microorganism. B. bruxellensis strains generally detain the molecular basis to produce compounds that are detrimental for the organoleptic quality of the wine, including some classes of volatile phenols that derive from the sequential bioconversion of specific hydroxycinnamic acids such as ferulate and p-coumarate. Although B. bruxellensis can be detected at any stage of the winemaking process, it is typically isolated at the end of the alcoholic fermentation (AF), before the staring of the spontaneous malolactic fermentation (MLF) or during barrel aging. For this reason, the endemic diffusion of B. bruxellensis leads to consistent economic losses in the wine industry. Considering the interest in reducing sulfur dioxide use during winemaking, in recent years, biological alternatives, such as the use of tailored selected yeast and bacterial strains inoculated to promote AF and MLF, are actively sought as biocontrol agents to avoid the “Bretta” character in wines. Here, we review the importance of dedicated characterization and selection of starter cultures for AF and MLF in wine, in order to reduce or prevent both growth of B. bruxellensis and its production of volatile phenols in the matrix.

Antibody biosensors for spoilage yeast detection based on impedance spectroscopy

Brettanomyces is a yeast species responsible for wine and cider spoilage, producing volatile phenols that result in off-odors and loss of fruity sensorial qualities. Current commercial detection methods for these spoilage species are liable to frequent false positives, long culture times and fungal contamination. In this work, an interdigitated (IDE) biosensor was created to detect Brettanomyces using immunological reactions and impedance spectroscopy analysis. To promote efficient antibody immobilization on the electrodes' surface and to decrease non-specific adsorption, a Self-Assembled Monolayer (SAM) was developed. An impedance spectroscopy analysis, over four yeast strains, confirmed our device's increased efficacy. Compared to label-free sensors, antibody biosensors showed a higher relative impedance. The results also suggested that these biosensors could be a promising method to monitor some spoilage yeasts, offering an efficient alternative to the laborious and expensive traditional methods.

Physiology, ecology and industrial applications of aroma formation in yeast

Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation. Additionally, we discuss the different physiological and ecological roles of aroma-active metabolites, including recent findings that point at their role as signaling molecules and attractants for insect vectors.

Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480

Wine production is an important commercial issue for the liquor industry. The global production was estimated at 275.7 million hectoliters in 2015. The loss of wine production due to Brettanomyces bruxellensis contamination is currently a problem. This yeast causes a "horse sweat" flavor in wine, which is an undesired organoleptic attribute. To date, 6 B. bruxellensis annotated genome sequences are available (LAMAP2480, AWRI1499, AWRI1608, AWRI1613, ST05.12/22, and CBS2499), and whole genome comparisons between strains are limited. In this article, we reassembled and reannotated the genome of B. bruxellensis LAMAP2480, obtaining a 27-Mb assembly with 5.5 kb of N50. In addition, the genome of B. bruxellensis LAMAP2480 was analyzed in the context of spoilage yeast and potential as a biotechnological tool. In addition, we carried out an exploratory transcriptomic analysis of this strain grown in synthetic wine. Several genes related to stress tolerance, micronutrient acquisition, ethanol production, and lignocellulose assimilation were found. In conclusion, the analysis of the genome of B. bruxellensis LAMAP2480 reaffirms the biotechnological potential of this strain. This research represents an interesting platform for the study of the spoilage yeast B. bruxellensis.

South Brazilian wines: culturable yeasts associated to bottled wines produced in Rio Grande do Sul and Santa Catarina

A comprehensive understanding of the presence and role of yeasts in bottled wines helps to know and control the organoleptic quality of the final product. The South Region of Brazil is an important wine producer, and the state of "Rio Grande do Sul" (RS) accounts for 90% of Brazilian wines. The state of "Santa Catarina" (SC) started the production in 1975, and is currently the fifth Brazilian producer. As there is little information about yeasts present in Brazilian wines, our main objective was to assess the composition of culturable yeasts associated to bottled wines produced in RS and SC, South of Brazil. We sampled 20 RS and 29 SC bottled wines produced between 2003 and 2011, and we isolated culturable yeasts in non-selective agar plates. We identified all isolates by sequencing of the D1/D2 domain of LSU rDNA or ITS1-5.8 S-ITS2 region, and comparison with type strain sequences deposited in GenBank database. Six yeast species were shared in the final product in both regions. We obtained two spoilage yeast profiles: RS with Zygosaccharomyces bailii and Pichia membranifaciens (Dekkera bruxellensis was found only in specific table wines); and SC with Dekkera bruxellensis and Pichia manshurica. Knowledge concerning the different spoilage profiles is important for winemaking practices in both regions.

The impact of different barrel sanitation approaches on the spoilage microflora and phenols composition of wine

Careful control of spoilage microflora inside wine containers is a key issue during winemaking. To date, attention has been paid to the development of an effective protocol for the eradication of spoilage agents, especially Brettanomyces, from barrels. Few studies have taken into account the modifications caused by sanitation treatments in wine and wood barrels. In the present study the effects of two sanitation treatments (ozone and sodium hydroxide) on barrel spoilage microflora and the composition of the wine stored inside them were evaluated. The phenols of wine (38 compounds) were characterised using a UHPLC-MS during the first 3 months of wine ageing, to see possible alterations in composition due to the chemical exchange from wood to wine in presence of sanitising agents. With the same scope, a panel of 13 judges carried out sensorial analysis of wines. The results showed that the tested treatments had little effect on the organoleptic characteristics of wines, but underline the different performance of the sanitation treatments in terms of eradicating microorganisms.

Impedance technology reduces the enumeration time of Brettanomyces yeast during beer fermentation

Brettanomyces yeasts are increasingly being used to produce lambic style beers and craft beers with unique flavors. Currently, the industry monitors Brettanomyces bruxellensis using time consuming plate counting. B. bruxellensis is a fastidious slow growing organism, requiring five days of incubation at 30°C for visible growth on agar plates. Thus, a need exists to develop a quicker, feasible method to enumerate this yeast. The aim of this study was therefore to determine the feasibility of using the 'direct' and 'indirect' impedance methods for the enumeration of B. bruxellensis in beer and to monitor the growth of the yeast during fermentation. The impedance methods were able to decrease the incubation time of beer samples containing Brettanomyces from 120 h down to 2 and 84 h for samples containing 10⁷ and 10³ cfu/mL, respectively. The 'indirect' method was more successful than the 'direct' method, presenting a smaller error and wider detection range. Overall, the 'indirect' impedance method is a viable alternative to plate counting for the enumeration of yeasts in the brewing industry because it decreases preparation and incubation times, thereby increasing throughput and decreasing the chance of contamination.

Effects of Oxygen Availability on Acetic Acid Tolerance and Intracellular pH in Dekkera bruxellensis

The yeast Dekkera bruxellensis, associated with wine and beer production, has recently received attention, because its high ethanol and acid tolerance enables it to compete with Saccharomyces cerevisiae in distilleries that produce fuel ethanol. We investigated how different cultivation conditions affect the acetic acid tolerance of D. bruxellensis We analyzed the ability of two strains (CBS 98 and CBS 4482) exhibiting different degrees of tolerance to grow in the presence of acetic acid under aerobic and oxygen-limited conditions. We found that the concomitant presence of acetic acid and oxygen had a negative effect on D. bruxellensis growth. In contrast, incubation under oxygen-limited conditions resulted in reproducible growth kinetics that exhibited a shorter adaptive phase and higher growth rates than those with cultivation under aerobic conditions. This positive effect was more pronounced in CBS 98, the more-sensitive strain. Cultivation of CBS 98 cells under oxygen-limited conditions improved their ability to restore their intracellular pH upon acetic acid exposure and to reduce the oxidative damage to intracellular macromolecules caused by the presence of acetic acid. This study reveals an important role of oxidative stress in acetic acid tolerance in D. bruxellensis, indicating that reduced oxygen availability can protect against the damage caused by the presence of acetic acid. This aspect is important for optimizing industrial processes performed in the presence of acetic acid.

IMPORTANCE

This study reveals an important role of oxidative stress in acetic acid tolerance in D. bruxellensis, indicating that reduced oxygen availability can have a protective role against the damage caused by the presence of acetic acid. This aspect is important for the optimization of industrial processes performed in the presence of acetic acid.

Sphingolipids contribute to acetic acid resistance in Zygosaccharomyces bailii

Lignocellulosic raw material plays a crucial role in the development of sustainable processes for the production of fuels and chemicals. Weak acids such as acetic acid and formic acid are troublesome inhibitors restricting efficient microbial conversion of the biomass to desired products. To improve our understanding of weak acid inhibition and to identify engineering strategies to reduce acetic acid toxicity, the highly acetic‐acid‐tolerant yeast Zygosaccharomyces bailii was studied. The impact of acetic acid membrane permeability on acetic acid tolerance in Z. bailii was investigated with particular focus on how the previously demonstrated high sphingolipid content in the plasma membrane influences acetic acid tolerance and membrane permeability. Through molecular dynamics simulations, we concluded that membranes with a high content of sphingolipids are thicker and more dense, increasing the free energy barrier for the permeation of acetic acid through the membrane. Z. bailii cultured with the drug myriocin, known to decrease cellular sphingo­lipid levels, exhibited significant growth inhibition in the presence of acetic acid, while growth in medium without acetic acid was unaffected by the myriocin addition. Furthermore, following an acetic acid pulse, the intracellular pH decreased more in myriocin‐treated cells than in control cells. This indicates a higher inflow rate of acetic acid and confirms that the reduction in growth of cells cultured with myriocin in the medium with acetic acid was due to an increase in membrane permeability, thereby demonstrating the importance of a high fraction of sphingolipids in the membrane of Z. bailii to facilitate acetic acid resistance; a property potentially transferable to desired production organisms suffering from weak acid stress. Biotechnol. Bioeng. 2016;113: 744–753. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

Analysis of Growth Inhibition and Metabolism of Hydroxycinnamic Acids by Brewing and Spoilage Strains of Brettanomyces Yeast

Brettanomyces yeasts are well-known as spoilage organisms in both the wine and beer industries, but also contribute important desirable characters to certain beer styles. These properties are mediated in large part by Brettanomyces' metabolism of hydroxycinnamic acids (HCAs) present in beverage raw materials. Here we compare growth inhibition by, and metabolism of, HCAs among commercial brewing strains and spoilage strains of B. bruxellensis and B. anomalus. These properties vary widely among the different strains tested and between the HCAs analyzed. Brewing strains showed more efficient metabolism of ferulic acid over p-coumaric acid, a trait not shared among the spoilage strains.

Dielectrophoresis chips improve PCR detection of the food-spoiling yeast Zygosaccharomyces rouxii in apple juice

Dielectrophoretic (DEP) manipulation of cells present in real samples is challenging. We show in this work that an interdigitated DEP chip can be used to trap and wash a population of the food-spoiling yeast Zygosaccharomyces rouxii that contaminates a sample of apple juice. By previously calibrating the chip, the yeast population loaded is efficiently trapped, washed, and recovered in a small-volume fraction that, in turn, can be used for efficient PCR detection of this yeast. DEP washing of yeast cells gets rid of PCR inhibitors present in apple juice and facilitates PCR analysis. This and previous works on the use of DEP chips to improve PCR analysis show that a potential use of DEP is to be used as a treatment of real samples prior to PCR.

The genome sequence of the highly acetic acid-tolerant Zygosaccharomyces bailii-derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant

In this work, it is described the sequencing and annotation of the genome of the yeast strain ISA1307, isolated from a sparkling wine continuous production plant. This strain, formerly considered of the Zygosaccharomyces bailii species, has been used to study Z. bailii physiology, in particular, its extreme tolerance to acetic acid stress at low pH. The analysis of the genome sequence described in this work indicates that strain ISA1307 is an interspecies hybrid between Z. bailii and a closely related species. The genome sequence of ISA1307 is distributed through 154 scaffolds and has a size of around 21.2 Mb, corresponding to 96% of the genome size estimated by flow cytometry. Annotation of ISA1307 genome includes 4385 duplicated genes (∼90% of the total number of predicted genes) and 1155 predicted single-copy genes. The functional categories including a higher number of genes are ‘Metabolism and generation of energy’, ‘Protein folding, modification and targeting’ and ‘Biogenesis of cellular components’. The knowledge of the genome sequence of the ISA1307 strain is expected to contribute to accelerate systems-level understanding of stress resistance mechanisms in Z. bailii and to inspire and guide novel biotechnological applications of this yeast species/strain in fermentation processes, given its high resilience to acidic stress. The availability of the ISA1307 genome sequence also paves the way to a better understanding of the genetic mechanisms underlying the generation and selection of more robust hybrid yeast strains in the stressful environment of wine fermentations.

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.

Raman spectroscopy and chemometrics for identification and strain discrimination of the wine spoilage yeasts Saccharomyces cerevisiae, Zygosaccharomyces bailii, and Brettanomyces bruxellensis

The yeasts Zygosaccharomyces bailii, Dekkera bruxellensis (anamorph, Brettanomyces bruxellensis), and Saccharomyces cerevisiae are the major spoilage agents of finished wine. A novel method using Raman spectroscopy in combination with a chemometric classification tool has been developed for the identification of these yeast species and for strain discrimination of these yeasts. Raman spectra were collected for six strains of each of the yeasts Z. bailii, B. bruxellensis, and S. cerevisiae. The yeasts were classified with high sensitivity at the species level: 93.8% for Z. bailii, 92.3% for B. bruxellensis, and 98.6% for S. cerevisiae. Furthermore, we have demonstrated that it is possible to discriminate between strains of these species. These yeasts were classified at the strain level with an overall accuracy of 81.8%.