Characterization of Osmotolerant Yeasts and Yeast-Like Molds from Apple Orchards and Apple Juice Processing Plants in China and Investigation of Their Spoilage Potential

Yeast Diversity in Honey and Pollen Samples from Stingless Bees in the State of Bahia, Brazil: Use of the MALDI-TOF MS/Genbank Proteomic Technique

(1) Background: The identification of microorganisms includes traditional biochemical methods, molecular biology methods evaluating the conserved regions of rRNA, and the molecular biology of proteins (proteomics), such as MALDI-TOF MS mass spectrometry. This work aimed to identify the biodiversity of yeasts associated with stingless bee species' honey and pollen, Melipona scutellaris, Nannotrigona testaceicornes, and Tetragonisca angustula, from the region of São Gonçalo dos Campos-Bahia (BA) state, Brazil. (2) Methods: Cellular proteins were extracted from 2837 microbial isolates (pollen and honey) and identified via MALDI-TOF MS. The identified yeast species were also compared to the mass spectra of taxonomically well-characterized reference strains, available from the National Center of Biotechnology Information (NCBI) database. (3) Results: Nine yeast species were identified: Candida maltosa, Candida norvegica, Kazachstania telluris, Schizosaccharomyces pombe, Scheffersomyces insectosus, Meyerozyma guilliermondii, Brettanomyces bruxellensis, Kazachstania exigua, and Starmerella lactis-condensi. Nannotrigona testaceicornes pollen had the highest number of yeast colonies. The yeasts Brettanomyces bruxellensis and Kazachstania telluris showed high populations in the samples of Nannotrigona testaceicornes and Melipona scutellaris, respectively. This work shows that there is some sharing of the same species of yeast between honey and pollen from the same beehive. (4) Conclusions: A total of 71.84% of the identified species present a high level of confidence at the species level. Eight yeast species (Candida maltosa, Candida norvegica, Kazachstania telluris, Schizosaccharomyces pombe, Scheffersomyces insectosus, Meyerozyma guilliermondii, Kazachstania exigua, and Starmerella lactis-condensi) were found for the first time in the samples that the authors inspected. This contributes to the construction of new knowledge about the diversity of yeasts associated with stingless bee products, as well as to the possibility of the biotechnological application of some yeast species.

Physiological and transcriptomic insights into sugar stress resistance in osmophilic yeast Zygosaccharomyces rouxii

The osmophilic yeast Zygosaccharomyces rouxii has attracted increasing attention for its ability to survive and grow in extremely high sugar environments. This trait determines its role in fermentation process and results in contamination in the food industry. However, the behavior of Z. rouxii in regulating cell metabolism to combat high sugar stress and the corresponding mechanism have not been completely elucidated. Here, the resistance strategies of Z. rouxii against high glucose stress were explored by physiological analysis at cell membrane level and transcriptomic analysis. Physiological analysis showed that under high glucose stress, colony transparency increased, cell volume decreased, which was accompanied by reduction in permeability and integrity of cell membrane and subsequent gradual recovering. Additionally, the proportion of ergosterol and unsaturated fatty acids in cell membrane significantly increased under high glucose stress. A comparison of transcriptome data showed that most of the obtained differentially expressed genes (DEGs) involved in ergosterol and linoleic acid synthesis pathways as well as cell wall integrity (CWI) and high osmolarity glycerol mitogen-activated protein kinase (HOG-MAPK) pathways, which was in line with the results of physiological data. Our results provided a theoretic basis to develop the process control for the production of high sugar foods.

Presence of Saccharomyces eubayanus in fermentative environments reveals a new adaptive scenario in Patagonia

Patagonia (Argentina and Chile) harbors the highest Saccharomyces eubayanus genomic diversity and its widest predominance in natural environments. In this work, S. eubayanus was isolated for the first time from a fermentative environment. This species was found dominating both a traditional apple chicha fermentation as well as feral apple trees in the Andean region of Aluminé (Argentina). S. eubayanus was the only Saccharomyces species found in the isolation substrates, although it coexisted with other non-Saccharomyces species. The absence of strong fermentative competitors of the Saccharomyces genus (like Saccharomyces uvarum or Saccharomyces cerevisiae) in the feral apples could promote the development and implantation of S. eubayanus in a spontaneous apple must fermentation. Phylogeographic analyses revealed a high intraspecific diversity in S. eubayanus, enabling the characterization of strains belonging to the genomic subpopulations PA1, PA2, and PB1 according to the sequences obtained for the intFR gene region. This result evidence that the studied sampling area represents a natural habitat for the species. Being a novel finding, studying the causes that allowed this species to prosper in a fermentative environment becomes essential. Hence, the physiological profile of the new isolates, including their ability to grow at different temperature, nitrogen, and ethanol concentrations was evaluated in comparison with a set of S. eubayanus strains previously isolated from natural environment and representing different genomic subpopulations. Greater physiological diversity was evidenced when strains isolated from both natural and fermentative environments were analyzed overall. Furthermore, no direct relationship between genomic population and physiological behavior was observed; on the opposite, strains appeared to exhibit similar behavior, primarily grouped by isolation origin.

Starmerella lactis-condensi, a yeast that has adapted to the conditions in the oenological environment

The yeast Starmerella (Candida) lactis-condensi is considered a food contaminant microorganism. The aim of our research was to determine why St. lactis-condensi could become the dominant species of Essences, the top sweet wine speciality of Tokaj wine region in Hungary. We investigated the physiological properties of these yeasts based on parameters that may influence their ability to selectively proliferate and persist during maturation in wines with very high sugar content. These include glucose and fructose, alcohol, and sulphur tolerance. Our studies have shown that St. lactis-condensi is a fructophilic yeast that is able to adapt quickly to very high sugar concentrations (up to 500 g/L) in the Essences. The high glucose concentration inhibits its growth, as well as that of the St. bacillaris (Candida zemplinina) strains tested. The type and amount of sugars in the Essences, together with the sulphur and alcohol content, influence the composition of the dominant yeast biota. Analysis of (GTG)₅ microsatellite in the nuclear genome and mtDNA-RFLP studies demonstrate that a diverse population of St. lactis-condensi occurs in the Tokaj wine region, in the Essences. This yeast species is characterised by both physiological and genetic biodiversity. GC-MS analysis of Essences colonised exclusively with these yeasts showed no deterioration in quality.

Non-conventional yeast strains: Unexploited resources for effective commercialization of second generation bioethanol

The conventional yeast (Saccharomyces cerevisiae) is the most studied yeast and has been used in many important industrial productions, especially in bioethanol production from first generation feedstock (sugar and starchy biomass). However, for reduced cost and to avoid competition with food, second generation bioethanol, which is produced from lignocellulosic feedstock, is now being investigated. Production of second generation bioethanol involves pre-treatment and hydrolysis of lignocellulosic biomass to sugar monomers containing, amongst others, d-glucose and D-xylose. Intrinsically, S. cerevisiae strains lack the ability to ferment pentose sugars and genetic engineering of S. cerevisiae to inculcate the ability to ferment pentose sugars is ongoing to develop recombinant strains with the required stability and robustness for commercial second generation bioethanol production. Furthermore, pre-treatment of these lignocellulosic wastes leads to the release of inhibitory compounds which adversely affect the growth and fermentation by S. cerevisae. S. cerevisiae also lacks the ability to grow at high temperatures which favour Simultaneous Saccharification and Fermentation of substrates to bioethanol. There is, therefore, a need for robust yeast species which can co-ferment hexose and pentose sugars and can tolerate high temperatures and the inhibitory substances produced during pre-treatment and hydrolysis of lignocellulosic materials. Non-conventional yeast strains are potential solutions to these problems due to their abilities to ferment both hexose and pentose sugars, and tolerate high temperature and stress conditions encountered during ethanol production from lignocellulosic hydrolysate. This review highlights the limitations of the conventional yeast species and the potentials of non-conventional yeast strains in commercialization of second generation bioethanol.

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).

Non-Conventional Yeasts as Alternatives in Modern Baking for Improved Performance and Aroma Enhancement

Saccharomyces cerevisiae remains the baker’s yeast of choice in the baking industry. However, its ability to ferment cereal flour sugars and accumulate CO2 as a principal role of yeast in baking is not as unique as previously thought decades ago. The widely conserved fermentative lifestyle among the Saccharomycotina has increased our interest in the search for non-conventional yeast strains to either augment conventional baker’s yeast or develop robust strains to cater for the now diverse consumer-driven markets. A decade of research on alternative baker’s yeasts has shown that non-conventional yeasts are increasingly becoming important due to their wide carbon fermentation ranges, their novel aromatic flavour generation, and their robust stress tolerance. This review presents the credentials of non-conventional yeasts as attractive yeasts for modern baking. The evolution of the fermentative trait and tolerance to baking-associated stresses as two important attributes of baker’s yeast are discussed besides their contribution to aroma enhancement. The review further discusses the approaches to obtain new strains suitable for baking applications.

Vinification without Saccharomyces: Interacting Osmotolerant and "Spoilage" Yeast Communities in Fermenting and Ageing Botrytised High-Sugar Wines (Tokaj Essence)

The conversion of grape juice to wine starts with complex yeast communities consisting of strains that have colonised the harvested grape and/or reside in the winery environment. As the conditions in the fermenting juice gradually become inhibitory for most species, they are rapidly overgrown by the more adaptable Saccharomyces strains, which then complete the fermentation. However, there are environmental factors that even Saccharomyces cannot cope with. We show that when the sugar content is extremely high, osmotolerant yeasts, usually considered as “spoilage yeasts“, ferment the must. The examination of the yeast biota of 22 botrytised Tokaj Essence wines of sugar concentrations ranging from 365 to 752 g∙L⁻¹ identified the osmotolerant Zygosaccharomyces rouxii, Candida (Starmerella) lactis-condensi and Candida zemplinina (Starmerella bacillaris) as the dominating species. Ten additional species, mostly known as osmotolerant spoilage yeasts or biofilm-producing yeasts, were detected as minor components of the populations. The high phenotypical and molecular (karyotype, mtDNA restriction fragment length polymorphism (RFLP) and microsatellite-primed PCR (MSP-PCR)) diversity of the conspecific strains indicated that diverse clones of the species coexisted in the wines. Genetic segregation of certain clones and interactions (antagonism and crossfeeding) of the species also appeared to shape the fermenting yeast biota.

Assessment of different antimicrobials to inhibit the growth of Zygosaccharomyces rouxii cocktail in concentrated apple juice

Zygosaccharomyces rouxii represents the main spoilage cause of concentrated apple juice, leading to waste of products or recalls. Essential oils components derived from plants have been found to present antimicrobial activities against various microbes. However, few work has been reported about their antimicrobial activities against Z. rouxii in concentrated apple juice. In this work, reparameterized Gompertz equation was used to evaluate the antimicrobial activities of different antimicrobials to inhibit the growth of a Z. rouxii cocktail (6.3 lg colony forming units/mL) composed of six strains isolated from concentrated apple juice and two strains from honey and grape must. The obtained mathematical models presented that thymol, carvacrol and trans-cinnamaldehyde were the promising options to inhibit Z. rouxii in 30 ^oBrix apple juice, reaching a maximal decrease on yeast growth of around 99.65 ± 0.61%. Whereas other antimicrobials showed lower antimicrobial activities with a maximal growth decrease of ranging from 67.13 ± 3.62% to 13.38 ± 1.16%. Additionally, the sensorial characteristics were not affected when the antimicrobials assayed were applied at the effective concentrations in commercial apple juice product. This work provided a theoretical feasibility that thymol, carvacrol and trans-cinnamaldehyde could be applied as natural preservatives for the control of Z. rouxii-related spoilage in fruit juice industry.

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.

Potential use of electronic tongue coupled with chemometrics analysis for early detection of the spoilage of Zygosaccharomyces rouxii in apple juice

Apple juice spoilage by Zygosaccharomyces rouxii could scarcely be identified at early stage. It is crucial to recognize the spoilage at early stage to prevent waste of products. In present study, electronic tongue was applied to detect the spoilage of Z. rouxii in apple juice, using taste evaluation by panelists as reference. Combined with linear discriminant analysis, identification of the contaminated juice was fulfilled after 12 h, equivalent to yeast population of less than 2.0 lg colony forming units/mL. At the level, panelists were not capable of discerning the spoilage. Sensors HA, ZZ, BB and BA were relatively more sensitive to the changes in overall taste of apple juice. Moreover, cell number of Z. rouxii could be properly quantified by partial least squares regression models with high determination coefficient of 0.98-0.99. Electronic tongue appears to be a powerful approach to realize early detection of contamination of Z. rouxii.

Biocontrol activity of Starmerella bacillaris yeast against blue mold disease on apple fruit and its effect on cider fermentation

The reduction of chemical fungicides in agriculture has led to the use of microorganisms as biocontrol agents. Starmerella bacillaris is a non-Saccharomyces yeast associated with overripe and botrytized grape berries microbiota. Its use has been proposed for wine fermentation because of yeast fructophilic character and high glycerol production. Recently, S. bacillaris has been demonstrated to possess antifungal activity against Botrytis cinerea on the grape. Penicillium expansum is the pathogen responsible for the blue mold rot, the most important postharvest disease of apples. These fruits are the raw material of the cider, an alcoholic beverage commonly produced using S. cerevisiae starter cultures. In this study 14 S. bacillaris strains have been studied to evaluate their postharvest antifungal activity against P. expansum on apples. Moreover, the fermentation performances in apple juice of these non-Saccharomyces strains were tested, both in single-strain fermentation and in sequential fermentation, together with S. cerevisiae. Four S. bacillaris strains, able to significantly decrease blue mold rot symptoms and to increase glycerol content during fermentation have been selected to improve apple and cider quality.

Fourier Transform Near-Infrared Spectroscopy and Chemometrics To Predict Zygosacchromyces rouxii in Apple and Kiwi Fruit Juices

This study investigated the capability of near-infrared spectroscopy (NIRS) to predict the concentration of Zygosaccharomyces rouxii in apple and kiwi fruit juices. The yeast was inoculated in fresh kiwi fruit juice ( n = 68), reconstituted kiwi juice ( n = 85), and reconstituted apple juice ( n = 64), followed by NIR spectra collection and plate counting. A principal component analysis indicated direct orthogonal signal correction preprocessing was suitable to separate spectral samples. Parameter optimization algorithms increased the performance of support vector machine regression models developed in a single variety juice system and a multiple variety juice system. Single variety juice models achieved accurate prediction of Z. rouxii concentrations, with the limit of quantification at 3 to 15 CFU/mL ( R² = 0.997 to 0.999), and the method was also feasible for Hanseniaspora uvarum and Candida tropicalis. The best multiple variety juice model obtained had a limit of quantification of 237 CFU/mL ( R² = 0.961) for Z. rouxii. A Bland-Altman analysis indicated good agreement between the support vector machine regression model and the plate counting method. It suggests that NIRS can be a high-throughput method for prediction of Z. rouxii counts in kiwi fruit and apple juices.

Spoilage yeasts: What are the sources of contamination of foods and beverages?

Foods and beverages are nutrient-rich ecosystems in which most microorganisms are able to grow. Moreover, several factors, such as physicochemical characteristics, storage temperature, culinary practices, and application of technologies for storage, also define the microbial population of foods and beverages. The yeast population has been well-characterised in fresh and processed fruit and vegetables, dairy products, dry-cured meat products, and beverages, among others. Some species are agents of alteration in different foods and beverages. Since the most comprehensive studies of spoilage yeasts have been performed in the winemaking process, hence, these studies form the thread of the discussion in this review. The natural yeast populations in raw ingredients and environmental contamination in the manufacturing facilities are the main modes by which food contamination occurs. After contamination, yeasts play a significant role in food and beverage spoilage, particularly in the alteration of fermented foods. Several mechanisms contribute to spoilage by yeasts, such as the production of lytic enzymes (lipases, proteases, and cellulases) and gas, utilisation of organic acids, discolouration, and off-flavours. This review addresses the role of yeasts in foods and beverages degradation by considering the modes of contamination and colonisation by yeasts, the yeast population diversity, mechanisms involved, and the analytical techniques for their identification, primarily molecular methods.

Fungal Spoilage in Food Processing

Food processing, packaging, and formulation strategies are often specifically designed to inhibit or control microbial growth to prevent spoilage. Some of the most restrictive strategies rely solely or on combinations of pH reduction, preservatives, water activity limitation, control of oxygen tension, thermal processing, and hermetic packaging. In concert, these strategies are used to inactivate potential spoilage microorganisms or inhibit their growth. However, for select microbes that can overcome these controls, the lack of competition from additional background microbiota helps facilitate their propagation.

Wash-free colorimetric homogeneous immunoassay for Zygosaccharomyces rouxii

A rapid and convenient AuNP-based method for detecting large microbes was developed.

Incidence of osmophilic yeasts and Zygosaccharomyces rouxii during the production of concentrate grape juices

Zygosaccharomyces rouxii is the main spoilage yeast of grape juice concentrates. Detection and identification of Z. rouxii during the production of grape juice concentrate is critical to prevent spoilage in the final product. In this work, three grape juice concentrate processing plants were assessed by identifying osmophilic yeasts in juices and surfaces during different stages of a complete production line. Subsequently, molecular typing of Z. rouxii isolates was done to determine the strain distribution of this spoilage yeast. Osmotolerant yeast species, other than Z. rouxii, were mainly recovered from processing plant environments. Z. rouxii was only isolated from surface samples with grape juice remains. Z. rouxii was largely isolated from grape juice samples with some degree of concentration. Storage of grape juice pre-concentrate and concentrate allowed an increase in the Z. rouxii population. A widely distributed dominant molecular Z. rouxii pattern was found in samples from all three processing plants, suggesting resident microbes inside the plant.

Protein abundance changes of Zygosaccharomyces rouxii in different sugar concentrations

Zygosaccharomyces rouxii is a yeast which can cause spoilage in the concentrated juice industries. It exhibits resistance to high sugar concentrations but genome- and proteome-wide studies on Z. rouxii in response to high sugar concentrations have been poorly investigated. Herein, by using a 2-D electrophoresis based workflow, the proteome of a wild strain of Z. rouxii under different sugar concentrations has been analyzed. Proteins were extracted, quantified, and subjected to 2-DE analysis in the pH range 4-7. Differences in growth (lag phase), protein content (13.97-19.23mg/g cell dry weight) and number of resolved spots (196-296) were found between sugar concentrations. ANOVA test showed that 168 spots were different, and 47 spots, corresponding to 40 unique gene products have been identified. These protein species are involved in carbohydrate and energy metabolism, amino acid metabolism, response to stimulus, protein transport and vesicle organization, cell morphogenesis regulation, transcription and translation, nucleotide metabolism, amino-sugar nucleotide-sugar pathways, oxidoreductases balancing, and ribosome biogenesis. The present study provides important information about how Z. rouxii acts to cope with high sugar concentration at molecular levels, which might enhance our global understanding of Z. rouxii's high sugar-tolerance trait.

Early detection of Zygosaccharomyces rouxii--spawned spoilage in apple juice by electronic nose combined with chemometrics

Spoilage spawned by Zygosaccharomyces rouxii can cause sensory defect in apple juice, which could hardly be perceived in the early stage and therefore would lead to the serious economic loss. Thus, it is essential to detect the contamination in early stage to avoid costly waste of products or recalls. In this work the performance of an electronic nose (e-nose) coupled with chemometric analysis was evaluated for diagnosis of the contamination in apple juice, using test panel evaluation as reference. The feasibility of using e-nose responses to predict the spoilage level of apple juice was also evaluated. Coupled with linear discriminant analysis (LDA), detection of the contamination was achieved after 12h, corresponding to the cell concentration of less than 2.0 log 10 CFU/mL, the level at which the test panelists could not yet identify the contamination, indicating that the signals of e-nose could be utilized as early indicators for the onset of contamination. Loading analysis indicated that sensors 2, 6, 7 and 8 were the most important in the detection of Z. rouxii-contaminated apple juice. Moreover, Z. rouxii counts in unknown samples could be well predicted by the established models using partial least squares (PLS) algorithm with high correlation coefficient (R) of 0.98 (Z. rouxii strain ATCC 2623 and ATCC 8383) and 0.97 (Z. rouxii strain B-WHX-12-53). Based on these results, e-nose appears to be promising for rapid analysis of the odor in apple juice during processing or on the shelf to realize the early detection of potential contamination caused by Z. rouxii strains.