Diversity and evolution of non-Saccharomycesyeast populations during wine fermentation: effect of grape ripeness and cold maceration

Contributions of Hanseniaspora species to Pinot Noir microbial terroir in Oregon's Willamette Valley wine region

The apiculate yeast genus Hanseniaspora has appeared frequently in enological research for more than 100 years, mostly focused upon the species H. uvarum due to its notable capacity to cause spoilage. Recently, there has been increased research into the potential benefits of other Hanseniaspora species, such as H. vineae, in producing more complex wines. Furthermore, large-scale DNA sequencing-based (metabarcoding) vineyard ecology studies have suggested that Hanseniaspora species may not be evenly distributed. To address potential differences across geographical areas in Oregon, we sampled extensively from 12 vineyards within the Willamette Valley American Viticultural Area (AVA), across 2 sub-AVAs (Eola-Amity Hills and Yamhill-Carlton). Metabarcoding was then used to assess the contribution of Hanseniaspora to the grape berry fungal community and the impact of wine processing on diversity. While 6 of the 23 recognized Hanseniaspora species were present on Pinot Noir grapes in the Willamette Valley AVA, differences between vineyards were driven by the abundance of H. uvarum. Significant positive correlations between the amount of H. uvarum present in must and at cold soak, and then cold soak to early ferment were observed. While intuitive, it is worth noting that no prior studies have observed this across such a large number of grape samples from different vineyards. Our results provide clear evidence that the abundance of H. uvarum on grapes may be an important predictor of potential impacts on wine quality, particularly if performing cold soak, which acts as an enrichment step.

IMPORTANCE

Hanseniaspora yeasts are frequently found in uninoculated wine fermentations, and depending upon the species present, their contributions to the wine may be positive or negative. We found that in Oregon's Willamette Valley, the most common species of Hanseniaspora in Pinot Noir vineyards was the known spoilage organism, H. uvarum. This species was one of the strongest contributors to differences in fungal communities between different vineyards and was enriched during typical Pinot Noir processing. These results support Hanseniaspora as an integral and functional component of vineyard "microbial terroir" within Oregon.

Comparison of DNA purification methods for high-throughput sequencing of fungal communities from wine fermentation

High-throughput sequencing approaches, which target a taxonomically discriminant locus, allow for in-depth insight into microbial communities' compositions. Although microorganisms are historically investigated by cultivation on artificial culture media, this method presents strong limitations, since only a limited proportion of microorganisms can be grown in vitro. This pitfall appears even more limiting in enological and winemaking processes, during which a wide range of molds, yeasts, and bacteria are observed at the different stages of the fermentation course. Such an understanding of those dynamic communities and how they impact wine quality therefore stands as a major challenge for the future of enology. As of now, although high-throughput sequencing has already allowed for the investigation of fungal communities, there is no available comparative study focusing on the performance of microbial deoxyribonucleic acid (DNA) extraction in enological matrixes. This study aims to provide a comparison of five selected extraction methods, assayed on both must and fermenting must, as well as on finished wine. These procedures were evaluated according to their extraction yields, the purity of their extracted DNA, and the robustness of downstream molecular analyses, including polymerase chain reaction and high-throughput sequencing of fungal communities. Altogether, two out of the five assessed microbial DNA extraction methods (DNeasy PowerSoil Pro Kit and E.Z.N.A.® Food DNA Kit) appeared suitable for robust evaluations of the microbial communities in wine samples. Consequently, this study provides robust tools for facilitated upcoming studies to further investigate microbial communities during winemaking using high-throughput sequencing.

Insights into the ecology of Schizosaccharomyces species in natural and artificial habitats

The fission yeast genus Schizosaccharomyces contains important model organisms for biological research. In particular, S. pombe is a widely used model eukaryote. So far little is known about the natural and artificial habitats of species in this genus. Finding out where S. pombe and other fission yeast species occur and how they live in their habitats can promote better understanding of their biology. Here we investigate in which substrates S. pombe, S. octosporus, S. osmophilus and S. japonicus are present. To this end about 2100 samples consisting of soil, tree sap fluxes, fresh fruit, dried fruit, honey, cacao beans, molasses and other substrates were analyzed. Effective isolation methods that allow efficient isolation of the above mentioned species were developed. Based on the frequency of isolating different fission yeast species in various substrates and on extensive literature survey, conclusions are drawn on their ecology. The results suggest that the primary habitat of S. pombe and S. octosporus is honeybee honey. Both species were also frequently detected on certain dried fruit like raisins, mango or pineapple to which they could be brought by the honey bees during ripening or during drying. While S. pombe was regularly isolated from grape mash and from fermented raw cacao beans S. octosporus was never isolated from fresh fruit. The main habitat of S. osmophilus seems to be solitary bee beebread. It was rarely isolated from raisins. S. japonicus was mainly found in forest substrates although it occurs on fruit and in fruit fermentations, too.

Oenological Characterization of Native Hanseniaspora uvarum Strains

The utilization of native yeast strains associated with a distinct terroir for autochthonous grape types represents a novel trend in winemaking, contributing to the production of unique wines with regional character. Hence, this study aimed to isolate native strains of the yeast H. uvarum from the surface of various fruits and to characterize its fermentation capability in Prokupac grape must. Out of 31 yeasts, 8 isolates were identified as H. uvarum. The isolates were able to grow at low (4 °C) temperatures, SO2 concentrations up to 300 ppm and ethanol concentrations up to 5%. Additionally, they provided a good profile of organic acids during the microvinification of sterile grape must. Although the content of acetic acid (0.54–0.63 g/L) was relatively high, the sniffing test proved that the yeast isolates developed a pleasant aroma characterized as fruity. All H. uvarum isolates produced twice the concentration of glycerol compared to commercial wine yeast Saccharomyces cerevisiae, contributing to the fullness and sweetness of the wine. The results for pure and sequential fermentation protocols confirmed that the selected S-2 isolate has good oenological characteristics, the capability to reduce the ethanol content (up to 1% v/v) and a potential to give a distinctive note to Prokupac-grape wines.

Diversity of non-Saccharomyces yeasts of grape berry surfaces from representative Cabernet Sauvignon vineyards in Henan Province, China

Non-Saccharomyces yeasts are important players during winemaking and may come from grapes grown in vineyards. To study the diversity of non-Saccharomyces yeasts on surface grape berries, 433 strains were isolated from different Cabernet Sauvignon vineyards grown in Henan Province. Our results demonstrated that these strains were classified into 16 morphotypes according to their growth morphology on Wallerstein Laboratory agar medium, and were identified as seven species from four genera: Hanseniaspora opuntiae, Hanseniaspora vineae, Hanseniaspora uvarum, Pichia occidentalis, Pichia kluyveri, Issatchenkia terricola and Saturnispora diversa based on a series of molecular biological experiments. Hanseniaspora opuntiae was obtained from all sampling sites except Changyuan County, while Pichia kluyveri and Saturnispora diversa were only found in sites of Zhengzhou Grape Resource Garden and Minquan County, respectively. The site Minquan was home of the greatest species richness while only one single species (Hanseniaspora opuntiae) was detected at NAPA winery from Zhengzhou or at Anyang County. Finally, this study suggested that the geographic distribution and diversity of non-Saccharomyces yeast populations on Cabernet Sauvignon grape berries were likely to be determined by a combination of grape varieties and environmental factors.

Biodiversity of yeasts isolated during spontaneous fermentation of cool climate grape musts

Biodiversity of native yeasts, especially in winemaking, has hidden potential. In order to use the value of non-Saccharomyces strains in wine production and to minimise the possibility of its deterioration, it is necessary to thoroughly study the yeast cultures present on grape fruits and in grape must, as well as their metabolic properties. The aim of the study was to characterise the yeast microbiota found during spontaneous fermentation of grape musts obtained from grape varieties ‘Rondo’, ‘Regent’ and ‘Johanniter’. Grapes from two vineyards (Srebrna Góra and Zadora) located in southern Poland were used for the research. Succession of subsequent groups of yeasts was observed during the process. Metschnikowia pulcherrima yeasts were identified both at the beginning and the end of the process. Hanseniaspora uvarum, Wickerhamomyces onychis and Torulaspora delbrueckii strains were also identified during the fermentation. Torulaspora delbrueckii and Wickerhamomyces onychis strains were identified only in grape musts obtained from grapes of the Zadora vineyard. These strains may be characteristic of this vineyard and shape the identity of wines formed in it. Our research has provided specific knowledge on the biodiversity of yeast cultures on grapes and during their spontaneous fermentation. The research results presented indicate the possibility of using native strains for fermentation of grape musts, allowing to obtain a product with favourable chemical composition and sensory profile.

Determination of the oenological properties of yeast strains isolated from spontaneously fermented grape musts obtained from cool climate grape varieties

The international competitiveness of the wine sector and consumer demands for the unique wine styles pose challenges in improving the fermentation process. The basis of proper alcoholic fermentation is knowledge about how individual yeast strains interact with the aroma, taste and color of wine, what results in possibility to select species used as starter cultures. To use the value of non-Saccharomyces yeast strains in wine production and to minimize the possibility of wine deterioration, it is necessary to precisely recognize the yeast cultures present on the fruit of the vine and in grape must, as well as their metabolic properties. The aim of the study was to determine the oenological properties of yeasts isolated from spontaneously fermented grape musts obtained from cool climate grapes. For this purpose, Zweigelt grape must was fermented with yeast monocultures. Alcohol, extract, sugars, glycerol, total acidity and free amine nitrogen were analyzed in the obtained wines. Poor fermentation properties of yeast strains results in obtaining wines with relatively large amounts of residual sugars and low alcohol. A decrease in overall acidity was noted in sets with the participation of M. pulcherrima MG971264, while in other tests the opposite trend was observed. Although some microorganisms have the ability to assimilate organic acids found in wine, they are not able to carry out fermentation or they do it inefficiently. Solution to this problem may, therefore, be use of mixed cultures of noble and non-Saccharomyces yeast, what effectively reduce the concentration of organic acids, while not adversely affecting the organoleptic characteristics of the drink.

Alterations in Yeast Species Composition of Uninoculated Wine Ferments by the Addition of Sulphur Dioxide

Uninoculated wine fermentations are conducted by a consortium of wine yeast and bacteria that establish themselves either from the grape surface or from the winery environment. Of the additives that are commonly used by winemakers, sulphur dioxide (SO2) represents the main antimicrobial preservative and its use can have drastic effects on the microbial composition of the fermentation. To investigate the effect of SO2 on the resident yeast community of uninoculated ferments, Chardonnay grape juice from 2018 and 2019 was treated with a variety of SO2 concentrations ranging up to 100 mg/L and was then allowed to undergo fermentation, with the yeast community structure being assessed via high-throughput meta-barcoding (phylotyping). While the addition of SO2 was shown to select against the presence of many species of non-Saccharomyces yeasts, there was a clear and increasing selection for the species Hanseniaspora osmophila as concentrations of SO2 rose above 40 mg/L in fermentations from both vintages. Chemical analysis of the wines resulting from these treatments showed significant increases in acetate esters, and specifically the desirable aroma compound 2-phenylethyl acetate, that accompanied the increase in abundance of H. osmophila. The ability to modulate the yeast community structure of an uninoculated ferment and the resulting chemical composition of the final wine, as demonstrated in this study, represents an important tool for winemakers to begin to be able to influence the organoleptic profile of uninoculated wines.

Evaluation of Saccharomyces cerevisiae Wine Yeast Competitive Fitness in Enologically Relevant Environments by Barcode Sequencing

When a wine yeast is inoculated into grape juice the potential variation in juice composition that confronts it is huge. Assessing the performance characteristics of the many commercially available wine yeasts in the many possible grape juice compositions is a daunting task. To this end we have developed a barcoded Saccharomyces cerevisiae wine yeast collection to facilitate the task of performance assessment that will contribute to a broader understanding of genotype-phenotype relations. Barcode sequencing of mixed populations is used to monitor strain abundance in different grape juices and grape juice-like environments. Choice of DNA extraction method is shown to affect strain-specific barcode count in this highly related set of S. cerevisiae strains; however, the analytical approach is shown to be robust toward strain dependent variation in DNA extraction efficiency. Of the 38 unique compositional variables assessed, resistance to copper and SO₂ are found to be dominant discriminatory factors in wine yeast performance. Finally, a comparison of competitive fitness profile with performance in single inoculum fermentations reveal strain dependent correspondence of yeast performance using these two different approaches.

The Influence of Non-Saccharomyces Species on Wine Fermentation Quality Parameters

In the past, some microbiological studies have considered most non-Saccharomyces species to be undesirable spoilage microorganisms. For several decades, that belief made the Saccharomyces genus the only option considered by winemakers for achieving the best possible wine quality. Nevertheless, in recent decades, some strains of non-Saccharomyces species have been proven to improve the quality of wine. Non-Saccharomyces species can positively influence quality parameters such as aroma, acidity, color, and food safety. These quality improvements allow winemakers to produce innovative and differentiated wines. For that reason, the yeast strains Torulaspora delbrueckii, Lachancea thermotolerans, Metschnikowia pulcherrima, Schizosaccharomyces pombe, and Pichia kluyveri are now available on the market. Other interesting species, such as Starmerella bacillaris, Meyerozyma guilliermondii, Hanseniospora spp., and others, will probably be available in the near future.

Quantitative and qualitative composition of yeast microbiota in spontaneously fermented grape musts obtained from cool climate grape varieties 'Rondo' and 'Regent'

The aim of the study was to characterise, quantitatively and qualitatively, the yeast microbiota found during spontaneous fermentation of grape musts obtained from the red grape varieties 'Rondo' and 'Regent'. For the research, grapes originating from two vineyards (Srebrna Góra and Spotkaniówka) located in southern Poland were used. Musts of the studied grape varieties provided a favourable environment for the growth of microorganisms. Musts obtained from fruits from the Spotkaniówka vineyard were characterised by a higher overall number of yeasts. A maximum number of cells were recorded from the fourth to the ninth day of the process, in all of the analysed musts. The growing season of 2013 proved to be the least favourable for the growth of microorganisms on grapes, which resulted in their smaller number in the batches during spontaneous fermentation. During the process, succession of different groups of yeasts was observed. It was initiated by Hanseniaspora uvarum and Candida railenensis strains, which, with the progress of spontaneous fermentation, were replaced by Saccharomyces cerevisiae strains. Metschnikowia pulcherrima and Pichia membranifaciens yeasts were identified at both the beginning and the end of the process. During fermentation, Zygoascus meyerae, Kluyveromyces lactis and Nakazawaea ishiwadae strains were also identified.

Microbiota of different wine grape berries

The wine grape berries share a complex microbial ecology including filamentous fungi, yeasts and bacteria. The microbiota reveals different physiological characteristics and depends on the grape ripening stage and the availability of nutrients with different effect on wine production. The microbiota of grape berries (n = 12) was isolated and identified in the present study. The samples were collected in September 2018. Grape berries were obtained from Vrbovo vineyard located in Slovakia. The grape berries investigated belonged to Blue Frankish, Cabernet Sauvignon, Chardonnay, Dornfelder, Feteasca regala, Green Veltliner, Irsai Oliver, Mūller Thurgau, Pálava, Pinot Blanc, Rhinriesling and Welschriesling varieties. The microorganisms were cultivated on Malt extract agar (MEA) at 25 °C for five days in aerobically for microscopic filamentous fungi and Tryptone Soya agar (TSA) at 37 °C for 24 – 48 h aerobically for bacteria and yeasts. Total bacterial counts on different wine grape berries ranged from 2.57 ±0.09 in Chardonnay to 4.39 ±0.21 log CFU.g-1 in Pálava. Microscopic filamentous fungi count ranged from 1.18 ±0.03 in Blue Frankish to 2.60 ±0.17 log CFU.g-1 in Welschriesling. MALDI-TOF MS Biotyper mass spectrometry was used for identification of microorganisms (bacteria and yeasts) and microscopic filamentous fungi with manuals. The most identified microscopic fungal species was Alternaria sp., for yeasts Issatchenkia orientalis and Leuconostoc mesenteroides subsp. mesenteroides for bacteria.

Advances in the Study of Candida stellata

Candida stellata is an imperfect yeast of the genus Candida that belongs to the order Saccharomycetales, while phylum Ascomycota. C. stellata was isolated originally from a must overripe in Germany but is widespread in natural and artificial habitats. C. stellata is a yeast with a taxonomic history characterized by numerous changes; it is either a heterogeneous species or easily confused with other yeast species that colonize the same substrates. The strain DBVPG 3827, frequently used to investigate the oenological properties of C. stellata, was recently renamed as Starmerella bombicola, which can be easily confused with C. zemplinina or related species like C. lactis-condensi. Strains of C. stellata have been used in the processing of foods and feeds for thousands of years. This species, which is commonly isolated from grape must, has been found to be competitive and persistent in fermentation in both white and red wine in various wine regions of the world and tolerates a concentration of at least 9% (v/v) ethanol. Although these yeasts can produce spoilage, several studies have been conducted to characterize C. stellata for their ability to produce desirable metabolites for wine flavor, such as acetate esters, or for the presence of enzymatic activities that enhance wine aroma, such as β-glucosidase. This microorganism could also possess many interesting technological properties that could be applied in food processing. Exo and endoglucosidases and polygalactosidase of C. stellata are important in the degradation of β-glucans produced by Botrytis cinerea. In traditional balsamic vinegar production, C. stellata shapes the aromatic profile of traditional vinegar, producing ethanol from fructose and high concentrations of glycerol, succinic acid, ethyl acetate, and acetoin. Chemical characterization of exocellular polysaccharides produced by non-Saccharomyces yeasts revealed them to essentially be mannoproteins with high mannose contents, ranging from 73–74% for Starmerella bombicola. Numerous studies have clearly proven that these macromolecules make multiple positive contributions to wine quality. Recent studies on C. stellata strains in wines made by co-fermentation with Saccharomyces cerevisiae have found that the aroma attributes of the individual strains were apparent when the inoculation protocol permitted the growth and activity of both yeasts. The exploitation of the diversity of biochemical and sensory properties of non-Saccharomyces yeast could be of interest for obtaining new products.

The Impact of Saccharomyces cerevisiae on a Wine Yeast Consortium in Natural and Inoculated Fermentations

Natural, also referred to as spontaneous wine fermentations, are carried out by the native microbiota of the grape juice, without inoculation of selected, industrially produced yeast or bacterial strains. Such fermentations are commonly initiated by non-Saccharomyces yeast species that numerically dominate the must. Community composition and numerical dominance of species vary significantly between individual musts, but Saccharomyces cerevisiae will in most cases dominate the late stages of the fermentation and complete the process. Nevertheless, non-Saccharomyces species contribute significantly, positively or negatively, to the character and quality of the final product. The contribution is species and strain dependent and will depend on each species or strain's absolute and relative contribution to total metabolically active biomass, and will therefore, be a function of its relative fitness within the microbial ecosystem. However, the population dynamics of multispecies fermentations are not well understood. Consequently, the oenological potential of the microbiome in any given grape must, can currently not be evaluated or predicted. To better characterize the rules that govern the complex wine microbial ecosystem, a model yeast consortium comprising eight species commonly encountered in South African grape musts and an ARISA based method to monitor their dynamics were developed and validated. The dynamics of these species were evaluated in synthetic must in the presence or absence of S. cerevisiae using direct viable counts and ARISA. The data show that S. cerevisiae specifically suppresses certain species while appearing to favor the persistence of other species. Growth dynamics in Chenin blanc grape must fermentation was monitored only through viable counts. The interactions observed in the synthetic must, were upheld in the natural must fermentations, suggesting the broad applicability of the observed ecosystem dynamics. Importantly, the presence of indigenous yeast populations did not appear to affect the broad interaction patterns between the consortium species. The data show that the wine ecosystem is characterized by both mutually supportive and inhibitory species. The current study presents a first step in the development of a model to predict the oenological potential of any given wine mycobiome.

Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection

The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties.

Isolation and Identification of the Indigenous Yeast Population during Spontaneous Fermentation of Isabella (Vitis labrusca L.) Grape Must

Grape must harbors a complex community of yeast species responsible for spontaneous alcoholic fermentation. Although there are detailed studies on the microbiota of Vitis vinifera L. grapes, less is known about the diversity and behavior of yeast communities present on fermenting grape must from other species of Vitis. In this work, we used a culture-dependent method to study the identity and dynamics of the indigenous yeast population present during the spontaneous fermentation of Isabella (Vitis labrusca L.) grape must. Alcoholic fermentation was conducted using standard enological practices, and the associated non-Saccharomyces and S. cerevisiae yeast community was analyzed using selective growth media and 5.8-ITS DNA sequencing. Candida californica, Candida hellenica, Starmerella bacillaris (synonym Candida zemplinina), Hanseniaspora uvarum, and Hanseniaspora vineae were the main non-Saccharomyces species identified on Isabella fermenting must. Issatchenkia hanoiensis, a yeast species rarely found on Vitis vinifera L. grapes, was also recognized on Isabella grape must. Candida azymoides, Candida californica and Pichia cecembensis, identified in this work on Isabella fermenting must, have not previously been found on Vitis vinifera L. grape must. Interestingly, C. azymoides, I. hanoiensis and P. cecembensis have recently been isolated from the surface of Vitis labrusca L. grapes from vineyards in the Azores archipelago, suggesting that specific Vitis-yeast species associations are formed independently of geographic origin. We suggest that C. azymoides, C. californica, and P. cecembensis are yeast species preferentially associated with Vitis labrusca L. grapes. Specific biological interactions between grapevines and yeast species may underlie the assembly of differential Vitis-microbial communities.

The Antarctic yeast Candida sake: Understanding cold metabolism impact on wine

Current winemaking trends include low-temperature fermentations and using non-Saccharomyces yeasts as the most promising tools to produce lower alcohol and increased aromatic complexity wines. Here we explored the oenological attributes of a C. sake strain, H14Cs, isolated in the sub-Antarctic region. As expected, the cold sea water yeast strain showed greater cold growth, Na⁺-toxicity resistance and freeze tolerance than the S. cerevisiae QA23 strain, which we used as a commercial wine yeast control. C. sake H14Cs was found to be more sensitive to ethanol. The fermentation trials of low-sugar content must demonstrated that C. sake H14Cs allowed the cold-induced lag phase of growth to be eliminated and also notably reduced the ethanol (-30%) and glycerol (-50%) content in wine. Instead C. sake produced sorbitol as a compatible osmolyte. Finally, the inspection of the main wine volatile compounds revealed that C. sake produced more higher alcohols than S. cerevisiae. In conclusion, our work evidences that using the Antarctic C. sake H14Cs yeast improves low-temperature must fermentations and has the potential to provide a wine with less ethanol and also particular attributes.

Wine microbiology is driven by vineyard and winery anthropogenic factors

The effects of different anthropic activities (vineyard: phytosanitary protection; winery: pressing and sulfiting) on the fungal populations of grape berries were studied. The global diversity of fungal populations (moulds and yeasts) was performed by pyrosequencing. The anthropic activities studied modified fungal diversity. Thus, a decrease in biodiversity was measured for three successive vintages for the grapes of the plot cultivated with Organic protection compared to plots treated with Conventional and Ecophyto protections. The fungal populations were then considerably modified by the pressing‐clarification step. The addition of sulfur dioxide also modified population dynamics and favoured the domination of the species Saccharomyces cerevisiae during fermentation. The non‐targeted chemical analysis of musts and wines by FT‐ICR‐MS showed that the wines could be discriminated at the end of alcoholic fermentation as a function of adding SO₂ or not, but also and above all as a function of phytosanitary protection, regardless of whether these fermentations took place in the presence of SO₂ or not. Thus, the existence of signatures in wines of chemical diversity and microbiology linked to vineyard protection has been highlighted.

Culture-dependent and independent techniques to monitor yeast species during cold soak carried out at different temperatures in winemaking

Transformation of grape must into wine is a process that may vary according to the consumers' requirements. Application of cold soak prior to alcoholic fermentation is a common practice in cellars in order to enhance flavor complexity and extraction of phenolic compounds. However, the effect of this step on wine yeast microbiota is not well-known. The current study simultaneously analyzed the effect of different cold soak temperatures on the microbiological population throughout the process and the use of culture-dependent and independent techniques to study this yeast ecology. The temperatures assayed were those normally applied in wineries: 2.5, 8 and 12°C. PCR-DGGE allowed detection of the most representative species such as Hanseniaspora uvarum, Starmerella bacillaris and Saccharomyces cerevisiae. As could be expected, highest diversity indices were obtained at the beginning of each process, and survival of H. uvarum or S. bacillaris depended on the temperature. Our results are in agreement with those obtained with culture independent methods, but qPCR showed higher precision and a different behavior was observed for each yeast species and at each temperature assayed. Comparison of both culture-independent techniques can provide a general overview of the whole process, although DGGE does not reveal the diversity expected due to the reported problems with the sensitivity of this technique.

Persistence of Two Non-Saccharomyces Yeasts (Hanseniaspora and Starmerella) in the Cellar

Different genera and/or species of yeasts present on grape berries, in musts and wines are widely described. Nevertheless, the community of non-Saccharomyces yeasts present in the cellar is still given little attention. Thus it is not known if the cellar is a real ecological niche for these yeasts or if it is merely a transient habitat for populations brought in by grape berries during the winemaking period. This study focused on three species of non-Saccharomyces yeasts commonly encountered during vinification: Starmerella bacillaris (synonymy with Candida zemplinina), Hanseniaspora guilliermondii and Hanseniaspora uvarum. More than 1200 isolates were identified at the strain level by FT-IR spectroscopy (207 different FTIR strain pattern). Only a small proportion of non-Saccharomyces yeasts present in musts came directly from grape berries for the three species studied. Some strains were found in the must in two consecutive years and some of them were also found in the cellar environment before the arrival of the harvest of second vintage. This study demonstrates for the first time the persistence of non-Saccharomyces yeast strains from year to year in the cellar. Sulfur dioxide can affect yeast populations in the must and therefore their persistence in the cellar environment.

Hanseniaspora uvarum from Winemaking Environments Show Spatial and Temporal Genetic Clustering

Hanseniaspora uvarum is one of the most abundant yeast species found on grapes and in grape must, at least before the onset of alcoholic fermentation (AF) which is usually performed by Saccharomyces species. The aim of this study was to characterize the genetic and phenotypic variability within the H. uvarum species. One hundred and fifteen strains isolated from winemaking environments in different geographical origins were analyzed using 11 microsatellite markers and a subset of 47 strains were analyzed by AFLP. H. uvarum isolates clustered mainly on the basis of their geographical localization as revealed by microsatellites. In addition, a strong clustering based on year of isolation was evidenced, indicating that the genetic diversity of H. uvarum isolates was related to both spatial and temporal variations. Conversely, clustering analysis based on AFLP data provided a different picture with groups showing no particular characteristics, but provided higher strain discrimination. This result indicated that AFLP approaches are inadequate to establish the genetic relationship between individuals, but allowed good strain discrimination. At the phenotypic level, several extracellular enzymatic activities of enological relevance (pectinase, chitinase, protease, β-glucosidase) were measured but showed low diversity. The impact of environmental factors of enological interest (temperature, anaerobia, and copper addition) on growth was also assessed and showed poor variation. Altogether, this work provided both new analytical tool (microsatellites) and new insights into the genetic and phenotypic diversity of H. uvarum, a yeast species that has previously been identified as a potential candidate for co-inoculation in grape must, but whose intraspecific variability had never been fully assessed.

Yeast population dynamics during prefermentative cold soak of Cabernet Sauvignon and Malbec wines

Prefermentative cold soak is a widely used technique in red wine production, but the impact on the development of native yeast species is hardly described. The aim of this work was to analyse the dynamics and diversity of yeast populations during prefermentative cold soak in red wines. Three different temperatures (14 ± 1 °C; 8 ± 1 °C and 2.5 ± 1 °C) were used for prefermentative cold soak in Cabernet Sauvignon and Malbec grape musts. Saccharomyces and non-Saccharomyces populations during cold soak and alcoholic fermentation were analysed. In addition, the impact on chemical and sensory properties of the wines was examined. Yeast dynamics during prefermentative cold soak were temperature dependent. At 14 ± 1 °C, the total yeast population progressively increased throughout the cold soak period. Conversely, at 2.5 ± 1 °C, the yeast populations maintained stable during the same period. Prefermentative cold soak conducted at 14±1°C favoured development of Hanseniospora uvarum and Candida zemplinina, whereas cold soak conducted at 8 ± 1 °C favoured growth of Saccharomyces cerevisiae. At 2.5 ± 1 °C, no changes in yeast species were recorded. Acidity and bitterness, two sensory descriptors, appear to be related to wines produced with prefermentative cold soak carried out at 14 ± 1 °C. This fact could be associated with the increase in non-Saccharomyces during the prefermentation stage. Our results emphasise the importance of the temperature as a determinant factor to allow an increase in non-Saccharomyces population during prefermentative cold soak and consequently to modify sensorial attributes of wines as well as their sensorial impact.

Selection and characterization of a Patagonian Pichia kudriavzevii for wine deacidification

AIMS

The purpose of this study was to select autochthonous yeasts with metabolic ability to degrade L-malic acid for its potential use in young wine deacidification.

METHODS AND RESULTS

Fifty seven Patagonian nonSaccharomyces yeast of oenological origin were identified by conventional molecular methods and tested in their capability to grow at the expense of L-malic acid. Only four isolates belonging to Pichia kudriavzevii species showed this property, and one of them was selected to continue with the study. This isolate, named as P. kudriavzevii ÑNI15, was able to degrade L-malic acid in microvinifications, increasing the pH 0·2-0·3 units with a minimal effect on the acid structure of wine. Additionally, this isolate produced low levels of ethanol, important levels of glycerol (10·41 ± 0·48 g l(-1) ) and acceptable amounts of acetic acid (0·86 ± 0·13 g l(-1) ). In addition, it improved the sensorial attributes of wine increasing its fruity aroma.

CONCLUSIONS

The selection of yeasts for oenological use among nonSaccharomyces species led to the finding of a yeast strain with novel and interesting oenological characteristics which could have significant implications in the production of well-balanced and more physicochemical and microbiological stable young wines.

SIGNIFICANCE AND IMPACT OF THE STUDY

The use of P. kudriavzevii ÑNI15 as mixed starter with S. cerevisiae would eliminate the cultural and cellar operations undertaken to adjust the musts acidity, therefore improving wine quality and reducing production costs.

Evaluation of MALDI-TOF mass spectrometry for identification of environmental yeasts and development of supplementary database

Yeast identification using traditional methods which employ morphological, physiological, and biochemical characteristics can be considered a hard task as it requires experienced microbiologists and a rigorous control in culture conditions that could implicate in different outcomes. Considering clinical or industrial applications, the fast and accurate identification of microorganisms is a crescent demand. Hence, molecular biology approaches has been extensively used and, more recently, protein profiling using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has proved to be an even more efficient tool for taxonomic purposes. Nonetheless, concerning to mass spectrometry, data available for the differentiation of yeast species for industrial purpose is limited and reference databases commercially available comprise almost exclusively clinical microorganisms. In this context, studies focusing on environmental isolates are required to extend the existing databases. The development of a supplementary database and the assessment of a commercial database for taxonomic identifications of environmental yeast are the aims of this study. We challenge MALDI-TOF MS to create protein profiles for 845 yeast strains isolated from grape must and 67.7 % of the strains were successfully identified according to previously available manufacturer database. The remaining 32.3 % strains were not identified due to the absence of a reference spectrum. After matching the correct taxon for these strains by using molecular biology approaches, the spectra concerning the missing species were added in a supplementary database. This new library was able to accurately predict unidentified species at first instance by MALDI-TOF MS, proving it is a powerful tool for the identification of environmental yeasts.

Characterisation of commercial and natural Torulaspora delbrueckii wine yeast strains

Forty-three South African Torulaspora delbrueckii yeast isolates from the ARC Infruitec-Nietvoorbij yeast culture collection, the T. delbrueckii type strain (CBS 1146), one reference T. delbrueckii strain (CBS 4663), two T. delbrueckii strains isolated from commercial yeast blends (Viniflora® Harmony.nsac and Viniflora® Melody.nsac), and a commercial Saccharomyces cerevisiae yeast (VIN 13) had their identities confirmed and were characterised using conventional and molecular microbiological techniques. These included a selection of growth media as well as CHEF electrophoretic karyotyping and PCR-RFLP analyses. Based on the biochemical and physiological results the strains were divided into 13 groups. The performances of the yeasts were also monitored by means of laboratory-scale fermentations in grape must at 15 °C and 22 °C. The fermentation kinetic data showed that at 22 °C, the yeasts were divided into two distinct groups, a faster and a slower fermenting group. The fermentation curves of the laboratory-scale study at 15 °C showed that, at this lower temperature, the yeasts also fermented at different speeds, but the fermentation curves showed greater separation. The biochemical and physiological grouping did not coincide with the fermentation abilities and good fermenters could be found in more than one group. Chemical analyses of the resultant wines (alcohol, volatile acidity, glycerol, total SO2, residual sugar) were used in Principle Component Analyses. The yeasts that grouped close to the S. cerevisiae reference strain (VIN 13) showed more acceptable wine chemical profiles, while those further away displayed less acceptable profiles. Three locally isolated strains and one commercial T. delbrueckii yeast strain, Viniflora® Harmony.nsac. produced wines with acceptable chemical profiles at both temperatures. These strains also had comparable fermentation kinetics to the S. cerevisiae reference. Therefore, depending on the fermentation temperature, different T. delbrueckii strains will be suitable for specific wine styles and some may even be considered for single inoculations without S. cerevisiae in industrial fermentations.

An innovative tool reveals interaction mechanisms among yeast populations under oenological conditions

Alcoholic fermentation of grape must is a complex process, involving several yeast genera and species. The early stages in fermentation are dominated by non-Saccharomyces yeasts that are gradually replaced by the Saccharomyces cerevisiae species, which takes over the fermentation. Quantitative studies have reported the influence of non-Saccharomyces yeast species on wine quality and evaluated their biotechnological interest. The industrial yeast market, which, until recently, exclusively focused on S. cerevisiae, now offers S. cerevisiae/non-Saccharomyces (including Torulaspora delbrueckii) multi-starters. The development of these new mixed industrial starters requires a better understanding of the interaction mechanisms between yeast populations in order to optimize the aromatic impact of the non-Saccharomyces yeast while ensuring complete alcoholic fermentation thanks to S. cerevisiae. For this purpose, a new double-compartment fermentor was designed with the following characteristics: (1) physical separation of two yeast populations, (2) homogeneity of the culture medium in both compartments, (3) fermentation kinetics monitored by weight loss due to CO2 release, and (4) independent monitoring of growth kinetics in the two compartments. This tool was used to compare mixed inoculations of S. cerevisiae/T. delbrueckii with and without physical separation. Our results revealed that physical contact/proximity between S. cerevisiae and T. delbrueckii induced rapid death of T. delbrueckii, a phenomenon previously described and attributed to a cell-cell contact mechanism. In contrast, when physically separated from S. cerevisiae, T. delbrueckii maintained its viability and its metabolic activity had a marked impact on S. cerevisiae growth and viability. The double fermentor is thus a powerful tool for studying yeast interactions. Our findings shed new light on interaction mechanisms described in microorganism populations.

Effect of inoculation on strawberry fermentation and acetification processes using native strains of yeast and acetic acid bacteria

The aim of this work was to analyze the microbiota involved in the traditional vinegar elaboration of strawberry fruit during a spontaneous and inoculated process. In the spontaneous processes, low biodiversity was detected in both alcoholic fermentation (AF) and acetification. Nevertheless, a strain of Saccharomyces cerevisiae and of Acetobacter malorum were selected and tested as starter cultures in the inoculation study. The inoculated processes with these strains were compared with another spontaneous process, yielding a significant reduction in time for AF with a total imposition of the S. cerevisiae strain. The resulting strawberry wine was acetified in different containers (glass and wood) yielding an initial imposition of the A. malorum inoculated strain, although displacement by Gluconacetobacter species was observed in the wood barrels.

Yeasts and yeast-like organisms associated with fruits and blossoms of different fruit trees

Yeasts are common inhabitants of the phyllosphere, but our knowledge of their diversity in various plant organs is still limited. This study focused on the diversity of yeasts and yeast-like organisms associated with matured fruits and fully open blossoms of apple, plum, and pear trees, during 2 consecutive years at 3 localities in southwest Slovakia. The occurrence of yeasts and yeast-like organisms in fruit samples was 2½ times higher and the yeast community more diverse than that in blossom samples. Only 2 species (Aureobasidium pullulans and Metschnikowia pulcherrima) occurred regularly in the blossom samples, whereas Galactomyces candidus, Hanseniaspora guilliermondii, Hanseniaspora uvarum, M. pulcherrima, Pichia kluyveri, Pichia kudriavzevii, and Saccharomyces cerevisiae were the most frequently isolated species from the fruit samples. The ratio of the number of samples where only individual species were present to the number of samples where 2 or more species were found (consortium) was counted. The occurrence of individual species in comparison with consortia was much higher in blossom samples than in fruit samples. In the latter, consortia predominated. Aureobasidium pullulans, M. pulcherrima, and S. cerevisiae, isolated from both the fruits and blossoms, can be considered as resident yeast species of various fruit tree species cultivated in southwest Slovakia localities.

Use of denaturing gradient gel electrophoresis for the identification of mixed oral yeasts in human saliva

A PCR-denaturing gradient gel electrophoresis (DGGE) method was established for the simultaneous presumptive identification of multiple yeast species commonly present in the oral cavity. Published primer sets targeting different regions of the Saccharomyces cerevisiae 26-28S rRNA gene (denoted primer sets N and U) and the 18S rRNA gene (primer set E) were evaluated with ten Candida and four non-Candida yeast species, and twenty Candida albicans isolates. Optimized PCR-DGGE conditions using primer set N were applied to presumptively identify, by band matching, yeasts in the saliva of 25 individuals. Identities were confirmed by DNA sequencing and compared with those using CHROMagar Candida culture. All primer sets yielded detectable DGGE bands for all species tested. Primer set N yielded mainly single bands and could distinguish all species examined, including differentiating Candida dubliniensis from C. albicans. Primer set U was less discriminatory among species but yielded multiple bands that distinguished subspecies groups within C. albicans. Primer set E gave poor yeast discrimination. DGGE analysis identified yeasts in 17 of the 25 saliva samples. Six saliva samples contained two yeast species: three contained C. albicans and three C. dubliniensis. C. dubliniensis was present alone in one saliva sample (total prevalence 16 %). CHROMagar culture detected yeasts in 16 of the yeast-containing saliva samples and did not enable identification of 7 yeast species identified by DGGE. In conclusion, DGGE identification of oral yeast species with primer set N is a relatively fast and reliable method for the simultaneous presumptive identification of mixed yeasts in oral saliva samples.