Zygosaccharomyces bailii — a profile of characteristics and spoilage activities

Resistance to preservatives and the viable but non-culturable state formation of Asaia lannensis in flavored syrups

Food security is a crucial issue that has caused extensive concern, and the use of food flavors has become prevalent over time. we used the molecular biological techniques, preservative susceptibility testing, viable but non-culturable (VBNC) state induction testing, and a transcriptome analysis to examine the bacterial contamination of favored syrup and identify the causes and develop effective control measures. The results showed that Asaia lannensis WLS1-1 is a microorganism that can spoil food and is a member of the acetic acid bacteria families. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) tests showed that WLS1-1 was susceptible to potassium sorbate (PS), sodium benzoate (SB), and sodium sulffte (SS) at pH 4.0. It revealed a progressive increase in resistance to these preservatives at increasing pH values. WLS1-1 was resistant to PS, SB and SS with an MIC of 4.0, 2.0 and 0.5  g/L at pH 5.0, respectively. The MIC values exceed the maximum permissible concentrations that can be added. The induction test of the VBNC state demonstrated that WLS1-1 lost its ability to grow after 321 days of PS induction, 229  days of SB induction and 52  days of SS induction combined with low temperature at 4°C. Additionally, laser confocal microscopy and a propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assay showed that WLS1-1 was still alive after VBNC formation. There were 7.192 ± 0.081 (PS), 5.416 ± 0.149 (SB) and 2.837 ± 0.134 (SS) log10(CFU/mL) of viable bacteria. An analysis of the transcriptome data suggests that Asaia lannensis can enter the VBNC state by regulating oxidative stress and decreasing protein synthesis and metabolic activity in response to low temperature and preservatives. The relative resistance of Asaia lannensis to preservatives and the induction of the VBNC state by preservatives are the primary factors that contribute to the contamination of favored syrup by this bacterium. To our knowledge, this study represents the first evidence of the ability of Asaia lannensis to enter the VBNC state and provides a theoretical foundation for the control of organisms with similar types of activity.

Hydrophobic diversification is the key to simultaneously increased antifungal activity and decreased cytotoxicity of two ab initio designed peptides

The fact that some antimicrobial peptides have been utilized clinically and as food preservatives stimulated the efforts in search of new candidates. In our previous studies, we succeeded in designing potent peptides against methicillin-resistant Staphylococcus aureus (MRSA), severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), and Ebola viruses based on the database filtering technology. The designed peptides were proved highly potent. However, this ab initio method has not been utilized to design antifungal peptides. This study report two novel antifungal peptides with 21 and 15 amino acids designed by more effectively extracting the most probable parameters from ∼1200 antifungal peptides in the antimicrobial peptide database (APD). Subsequent hydrophobic diversification led to two peptide variants with enhanced activity against four fungal strains but reduced cytotoxicity to four mammalian cell lines. DFTAFP-1A (KWSGAAAKKLKSLLSGLGKLL) and DFTAFP-2A (KWSGLLLKLGAASKL) retained activity against Zygosaccharomyces bailii at pH 5.6 and 6.3 or after autoclave. The peptides could permeabilize fungal membranes and adopted helical conformations in membrane mimetic micelles. Collectively, this study demonstrated not only the successful design of two novel antifungal peptides based on the APD database but also optimization of desired peptide properties. This improved database approach may be utilized to design useful peptides to combat other drug-resistant pathogens as well.

Kombucha: Production and Microbiological Research

Kombucha is a sparkling sugared tea commonly prepared using a sugared tea infusion and fermented at ambient temperature for several days using a cellulose pellicle also called tea fungus that is comprised of acetic acid bacteria and yeast. Consumption of Kombucha has been reported as early as 220 B.C. with various reported potential health benefits and appealing sensory properties. During Kombucha fermentation, sucrose is hydrolysed by yeast cells into fructose and glucose, which are then metabolised to ethanol. The ethanol is then oxidised by acetic acid bacteria (AAB) to produce acetic acid which is responsible for the reduction of the pH and also contributes to the sour taste of Kombucha. Characterisation of the AAB and yeast in the Kombucha starter culture can provide a better understanding of the fermentation process. This knowledge can potentially aid in the production of higher quality products as these microorganisms affect the production of metabolites such as organic acids which are associated with potential health benefits, as well as sensory properties. This review presents recent advances in the isolation, enumeration, biochemical characteristics, conventional phenotypic identification system, and modern genetic identification techniques of AAB and yeast present in Kombucha to gain a better understanding of the microbial diversity of the beverage.

The effect of organic acids and storage temperature on lite salad dressing rheology and Zygosaccharomyces parabailii growth

Zygosaccharomyces parabailii (Z. parabailii) causes spoilage in salad dressings due to its tolerance to osmotic pressure. The objective of this study was to determine the effect of organic acids and storage temperatures (4, 10, and 25 °C) on Z. parabailii growth and salad dressing mechanical properties. Acetic, lactic, and gluconic acids were used alone and in combination to acidify salad dressing. Z. parabailii-challenged formulations containing acetic acid alone tended to have lower counts of Z. parabailii when compared to Z. parabailii-challenged formulations containing other acid combinations. Overall, storage temperature had the most impact on Z. parabailii growth over a 45-day storage. Acidulant type and combination impacted salad dressing mechanical properties. During the 45-day storage period, all formulations showed increased viscosity, a Herschel–Bulkley viscosity profile, and elastic-dominant viscoelastic behavior. The degree of change in rheological behaviors over time was dependent on the type of acid used in the formulation.

Storage time and temperature affect microbial dynamics of yeasts and acetic acid bacteria in a kombucha beverage

Kombucha is a mildly sweet, slightly acidic fermented beverage, commercially available worldwide, that has attracted increasing consumers' interest due to its potential health benefits. Kombucha is commonly prepared using sugared black or green tea, but also other plant substrates are frequently utilised. Kombucha is obtained by fermentation using a symbiotic culture of bacteria and yeasts, whose composition varies depending on inoculum origin, plant substrates and environmental conditions. After fermentation, kombucha drinks are usually refrigerated at 4 °C, in order to maintain their biological and functional properties. There are no reports on the fate of microbial communities of kombucha in relation to long-term storage time and temperature. Here, for the first time, we monitored the diversity and dynamics of the microbial communities of a kombucha beverage fermented with different herbs during storage at 4 °C and at room temperature, for a period of 90 days, utilising culture-dependent and independent approaches. Moreover, cultivable yeasts and acetic acid bacteria (AAB) were isolated from the beverage, inoculated in pure culture, identified by molecular methods, and yeasts assessed for their functional properties. Total yeast counts were not affected by storage temperature and time, although their community composition changed, as Saccharomyces species significantly decreased after 45 days of storage at room temperature, completely disappearing after 90 days. On the other hand, Dekkera anomala (Brettanomyces anomalus), representing 52 % of the yeast isolates, remained viable up to 90 days at both storage temperatures, and was able to produce high levels of organic acids and exopolysaccharides. Data from DGGE (Denaturing Gradient Gel Electrophoresis) band sequencing confirmed that it was the dominant yeast species in all samples across storage. Other yeast isolates were represented by Saccharomyces and Zygosaccharomyces species. Among AAB, Gluconobacter oxydans, Novacetimonas hansenii and Komagataeibacter saccharivorans represented 46, 36 and 18 % of the isolates, whose occurrence remained unchanged across storage at 4 °C and did not vary up to 20 days of storage at room temperature. This work showed that the combination of culture-dependent and independent approaches is important for obtaining a complete picture of the distinctive core microbial community in kombucha beverages during storage, elucidating its diversity and composition, and preliminary characterizing yeast strains with putative functional activities.

Tobacco Plant Growth-Promoting and Antifungal Activities of Three Endophytic Yeast Strains

In this research, the biosynthetic and biocontrol potential of endophytic yeast to improve the growth and development of tobacco has been elucidated. Three yeast strains were enriched and isolated from different plant tissues. Partial sequence analysis of ITS5-5.8-ITS4 region of the nuclear ribosomal DNA with universal primers identified YD5, YE1, and YSW1 as Saccharomyces cerevisiae (S. cerevisiae), Zygosaccharomyces bailii (Z. bailii), and Saccharomyces kudriavzevii (S. kudriavzevii), respectively. When cultivated in a medium supplemented with 0.1% L-tryptophan, isolated yeast strains produced indole-3-acetic acid (IAA). The capacities of those strains to improve the mobility of phosphorus and synthesize siderophores has been proven. Their antimicrobial activities against several Solanaceae plant pathogenic fungi (Alternaria solani pathovar. tobacco, Rhizoctonia solani, and Fusarium solani pathovar. phaseoli) were determined. S. cerevisiae YD5, Z. bailii YE1, and S. kudriavzevii YSW1 inhibited the growth of all tested pathogens. Yeast strains were tested for endophytic colonization of tobacco by two different inoculation methods: soil drench (SD) and leaf spraying (LS). To establish colonization in the various tissues of tested tobacco (Nicotiana tabaccum L.) plants, samples were taken on the seventh, fourteenth, and twenty-first days after treatment (DAT), and explants were inoculated on yeast malt agar (YMA). Both techniques of inoculation showed a high frequency of colonization from 83.33% to 100%. To determine the effectiveness of the microbial endophytes, their effect on some physiological processes in the plant were analyzed, such as photosynthesis, stomatal conductivity, and transpiration intensity. The effect of single and double treatment with yeast inoculum on the development and biochemical parameters of tobacco was reported. Plants have the ability of structural and functional adaptation to stress effects of different natures. All treated plants had a higher content of photosynthetic pigments compared to the control. Photosynthesis is probably more intense, and growth stimulation has been observed. The chlorophyll a/b ratio remained similar, and the total chlorophyll/carotenoid ratio slightly increased as a result of elevated chlorophyll levels. The most significant stimulating effect was recorded in tobacco plants treated by foliar spraying with Z. bailii YE1 and S. cerevisiae YD5. In contrast, S. kudriavzevii YSW1 had a better effect when applied as a soil drench. Thus, S. cerevisiae YD5, Z. bailii YE1, and S. kudriavzevii YSW1 have a high potential to be used as a biocontrol agents in organic agriculture.

Molecular Tools for Leveraging the Potential of the Acid-Tolerant Yeast Zygosaccharomyces bailii as Cell Factory

Microorganisms offer a tremendous potential as cell factories, and they are indeed been used by humans since the previous centuries for biotransformations. Among them, yeasts combine the advantage of a unicellular state with a eukaryotic organization. Moreover, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycete budding yeast, is widely known for its peculiar tolerance to different stresses, among which are organic acids. Moreover, the recent reclassification of the species, including diverse hybrids, is further expanding both fundamental and applied interests. It is therefore reasonable that despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here we describe in detail the methods for determining chromosome number, size, and aneuploidy, transformation, classical target gene disruption or gene integration, and designing of episomal expression plasmids helpful for engineering the yeast Z. bailii .

The Use of Yeast Mixed Cultures for Deacidification and Improvement of the Composition of Cold Climate Grape Wines

Interest in the use of non-Saccharomyces yeast in mixed cultures is increasing due to the perceived improvement in the quality and complexity of the resulting wines. The aim of the study was to determine the ability of monocultures and mixed yeast cultures for deacidification and improvement of the composition of cold climate grape wines. Fermentation of grape musts with increased total acidity was carried out with the use of monocultures of Saccharomyces cerevisiae MH020215 (Sc), Zygosaccharomyces bailii 749 (Zb) and Metschnikowia pulcherrima MG970690 (Mp), and their mixed cultures, inoculated simultaneously and sequentially. Oenological parameters, organic acids and volatile compounds profiles of obtained wines were characterized. The fermentation kinetics and analytical profiles of the obtained wines showed that the use of mixed yeast cultures contributed to the reduction of volatile acidity and acetic acid content in the wines, as well as obtaining a favorable aromatic profile of the wines. The dominant higher alcohols in all wines were 2-methyl-1-propanol, 3-methyl-1-butanol and 2-methyl-1-butanol. Significantly higher amounts of the first two compounds were found in wines obtained with M. pulcherrima MG070690, both in monoculture and in mixed cultures. The monocultures of M. pulcherrima MG070690 (Mp) compared with Z. bailli 749 (Zb) synthesized higher levels of esters in wines, including ethyl acetate, ethyl propionate, isobutyl acetate, ethyl pyroracemate and isoamyl acetate.

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.

Physiological Genomics of the Highly Weak-Acid-Tolerant Food Spoilage Yeasts of Zygosaccharomyces bailii sensu lato

Zygosaccharomyces bailii and two closely related species, Z. parabailii and Z. pseudobailii ("Z. bailii species complex", "Z. bailii sensu lato" or simply "Z. bailii (s.l.)"), are frequently implicated in the spoilage of acidified preserved foods and beverages due to their tolerance to very high concentrations of weak acids used as food preservatives. The recent sequencing and annotation of these species' genomes have clarified their genomic organization and phylogenetic relationship, which includes events of interspecies hybridization. Mechanistic insights into their adaptation and tolerance to weak acids (e.g., acetic and lactic acids) are also being revealed. Moreover, the potential of Z. bailii (s.l.) to be used in industrial biotechnological processes as interesting cell factories for the production of organic acids, reduction of the ethanol content, increase of alcoholic beverages aroma complexity, as well as of genetic source for increasing weak acid resistance in yeast, is currently being considered. This chapter includes taxonomical, ecological, physiological, and biochemical aspects of Z. bailii (s.l.). The focus is on the exploitation of physiological genomics approaches that are providing the indispensable holistic knowledge to guide the effective design of strategies to overcome food spoilage or the rational exploitation of these yeasts as promising cell factories.

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.

Pathogenicity of Zygosaccharomyces bailii and Other Yeast Species to Mexican Fruit Fly (Diptera: Tephritidae) and Mass Rearing Implications

Yeasts from all immature life stages of Mexican fruit fly Anastrepha ludens (Loew) (Diptera: Tephritidae) from diet, insectary air, and rearing materials were isolated, identified and evaluated for pathogenicity. Fifteen species of yeasts with one to genus level were identified from 72 yeast cultures obtained. Zygosaccharomyces bailii was the only yeast found to be highly pathogenic to Mexican fruit fly. Seventy-two hours post inoculation, the diet in bioassay cups with Z. bailii consistently showed signs of fermentation with gas bubbling causing the migration of larvae to the walls and lids of bioassay cups. The spent diet from Z. balii-infested cups was crusty, cracked and had a pasty layer. Many larvae were small, moribund, and discolored, appearing caramel or blackish. Insect yield loss with Z. bailii in comparison to that of control ranged from 10 to 44% for larvae and 14 to 47% for pupae. Additionally, Z. bailii caused a reduction in mean pupal weight. The weakly pathogenic yeasts produced significantly less yield of larvae and pupae than the nonpathogenic ones included Trichosporon montevideense, Clavispora lucitaniae, Candida sp., C. rugosa, and Rhodotorula mucilaginosa. Yield loss of larvae caused by this group ranged from 12 (C. lusitaniae) to 18% (R. mucilaginosa). Yield losses for pupa were similar to that of larvae. The mean pupa weight for these species was above the minimum acceptable (16.50 mg) for the SIT program. The nonpathogenic yeast produced yields of larvae and pupae similar to the control included Cryptococcus diffluens, Pichia kudriavzevii, Meyerozyma guilliermondii, Wickerhamomyces anomalus, Trichosporon asahii, Debaryomyces hansenii, Candida tropicalis, Cryptococcus sp., Candida parapsilosis, and Hanseniaspora opuntiae. In conclusion, the identification and management of insect pathogenic yeasts, such as Z. balii in mass rearing systems of Mexican fruit fly must be considered to avoid their potential negative effects.

Adaptive Response and Tolerance to Acetic Acid in Saccharomyces cerevisiae and Zygosaccharomyces bailii: A Physiological Genomics Perspective

Acetic acid is an important microbial growth inhibitor in the food industry; it is used as a preservative in foods and beverages and is produced during normal yeast metabolism in biotechnological processes. Acetic acid is also a major inhibitory compound present in lignocellulosic hydrolysates affecting the use of this promising carbon source for sustainable bioprocesses. Although the molecular mechanisms underlying Saccharomyces cerevisiae response and adaptation to acetic acid have been studied for years, only recently they have been examined in more detail in Zygosaccharomyces bailii. However, due to its remarkable tolerance to acetic acid and other weak acids this yeast species is a major threat in the spoilage of acidic foods and beverages and considered as an interesting alternative cell factory in Biotechnology. This review paper emphasizes genome-wide strategies that are providing global insights into the molecular targets, signaling pathways and mechanisms behind S. cerevisiae and Z. bailii tolerance to acetic acid, and extends this information to other weak acids whenever relevant. Such comprehensive perspective and the knowledge gathered in these two yeast species allowed the identification of candidate molecular targets, either for the design of effective strategies to overcome yeast spoilage in acidic foods and beverages, or for the rational genome engineering to construct more robust industrial strains. Examples of successful applications are provided.

Genome sequence of the highly weak-acid-tolerant Zygosaccharomyces bailii IST302, amenable to genetic manipulations and physiological studies

Zygosaccharomyces bailii is one of the most problematic spoilage yeast species found in the food and beverage industry particularly in acidic products, due to its exceptional resistance to weak acid stress. This article describes the annotation of the genome sequence of Z. bailii IST302, a strain recently proven to be amenable to genetic manipulations and physiological studies. The work was based on the annotated genomes of strain ISA1307, an interspecies hybrid between Z. bailii and a closely related species, and the Z. bailii reference strain CLIB 213T. The resulting genome sequence of Z. bailii IST302 is distributed through 105 scaffolds, comprising a total of 5142 genes and a size of 10.8 Mb. Contrasting with CLIB 213T, strain IST302 does not form cell aggregates, allowing its manipulation in the laboratory for genetic and physiological studies. Comparative cell cycle analysis with the haploid and diploid Saccharomyces cerevisiae strains BY4741 and BY4743, respectively, suggests that Z. bailii IST302 is haploid. This is an additional trait that makes this strain attractive for the functional analysis of non-essential genes envisaging the elucidation of mechanisms underlying its high tolerance to weak acid food preservatives, or the investigation and exploitation of the potential of this resilient yeast species as cell factory.

Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch

Many interspecies hybrids have been discovered in yeasts, but most of these hybrids are asexual and can replicate only mitotically. Whole-genome duplication has been proposed as a mechanism by which interspecies hybrids can regain fertility, restoring their ability to perform meiosis and sporulate. Here, we show that this process occurred naturally during the evolution of Zygosaccharomyces parabailii, an interspecies hybrid that was formed by mating between 2 parents that differed by 7% in genome sequence and by many interchromosomal rearrangements. Surprisingly, Z. parabailii has a full sexual cycle and is genetically haploid. It goes through mating-type switching and autodiploidization, followed by immediate sporulation. We identified the key evolutionary event that enabled Z. parabailii to regain fertility, which was breakage of 1 of the 2 homeologous copies of the mating-type (MAT) locus in the hybrid, resulting in a chromosomal rearrangement and irreparable damage to 1 MAT locus. This rearrangement was caused by HO endonuclease, which normally functions in mating-type switching. With 1 copy of MAT inactivated, the interspecies hybrid now behaves as a haploid. Our results provide the first demonstration that MAT locus damage is a naturally occurring evolutionary mechanism for whole-genome duplication and restoration of fertility to interspecies hybrids. The events that occurred in Z. parabailii strongly resemble those postulated to have caused ancient whole-genome duplication in an ancestor of Saccharomyces cerevisiae.

It has recently been proposed that the whole-genome duplication (WGD) event that occurred during evolution of an ancestor of the yeast S. cerevisiae was the result of a hybridization between 2 parental yeast species that were significantly divergent in DNA sequence, followed by a doubling of the genome content to restore the hybrid’s ability to make viable spores. However, the molecular details of how genome doubling could occur in a hybrid were unclear because most known interspecies hybrid yeasts have no sexual cycle. We show here that Z. parabailii provides an almost exact precedent for the steps proposed to have occurred during the S. cerevisiae WGD. Two divergent haploid parental species, each with 8 chromosomes, mated to form a hybrid that was initially sterile but regained fertility when 1 copy of its mating-type locus became damaged by the mating-type switching apparatus. As a result of this damage, the Z. parabailii life cycle now consists of a 16-chromosome haploid phase and a transient 32-chromosome diploid phase. Each pair of homeologous genes behaves as 2 independent Mendelian loci during meiosis.

Antimicrobial efficacy of emulsified essential oil components against weak acid-adapted spoilage yeasts in clear and cloudy apple juice

The antimicrobial activity of oil-in-water emulsions containing dual combinations of the essential oil components cinnamaldehyde, perillaldehyde, and citral was examined against two acid-resistant yeast strains (Zygosaccharomyces bailii) in beverage systems composed of diluted clear or cloudy apple juice and in a Sabouraud dextrose broth model. Antimicrobial properties of an encapsulated oil-in-water emulsion and of essential oil components dissolved in 10% dimethyl sulfoxide were compared using plate counts and turbidity measurements. Growth curves were modulated to qualitatively assess differences in antimicrobial efficacy. The impact of the presence of a beverage emulsion without essential oils (unloaded; 5% oil and 1% modified starch, pH 3.0) on the antimicrobial efficacy also was investigated. Dual combinations of essential oil components were sufficient to completely inhibit and/or kill yeast cells in diluted apple juice and Sabouraud dextrose broth systems at very low concentrations (100 to 200 μg/ml). However, the combination of perillaldehyde and citral had the weakest antimicrobial effect; a concentration of 400 μg/ml was necessary to prevent yeast growth in beverages, and up to 800 μg/ml was required in systems to which an unloaded emulsion had been added. The antimicrobial activity of essential oil components did not differ in diluted clear and cloudy apple juices and was not affected by being added in emulsified form or dissolved in dimethyl sulfoxide as long as there was no unloaded emulsion also present. These results indicate that formulations of essential oil combinations encapsulated together in emulsions are highly effective for inhibiting and/or killing microorganisms in real beverage systems.

Population heterogeneity and dynamics in starter culture and lag phase adaptation of the spoilage yeast Zygosaccharomyces bailii to weak acid preservatives

The food spoilage yeast Zygosaccharomyces bailii shows great resistance to weak-acid preservatives, including sorbic acid (2, 4-hexadienoic acid). That extreme resistance was shown to be due to population heterogeneity, with a small sub-population of cells resistant to a variety of weak acids, probably caused by a lower internal pH reducing the uptake of all weak acids. In the present paper, it was found that resistant cells were extremely rare in exponential cultures, but increased by up to 8000-fold in stationary phase. Inoculation of media containing sorbic acid with a population of Z. bailii cells gave rise to what appeared to be a prolonged lag phase, suggesting adaptation to the conditions before the cells entered the period of exponential growth. However, the apparent lag phase caused by sorbic acid was largely due to the time required for the resistant sub-population to grow to detectable levels. The slow growth rate of the sub-population was identical to that of the final total population. The non-resistant bulk population remained viable for 3 days but had lost viability by 6 days and, during that time, there was no indication of any development of resistance in the bulk population. The sub-population growing in sorbic acid showed very high population diversity in colony size and internal pH. After removal of sorbic acid, the population rapidly reverted back to the normal, largely non-resistant, population distribution. The data presented suggest that a reevaluation of the lag phase in microbial batch culture is required, at least for the resistance of Z. bailii to sorbic acid. Furthermore, the significance of phenotypic diversity and heterogeneity in microbial populations is discussed more broadly with potential relevance to bacterial “persisters”, natural selection and evolution.

•

Extreme Z. bailii resistance to sorbic acid was due to population heterogeneity.

•

There was a massive rise in resistant cells after exponential growth.

•

Extended lag phase caused by weak acids was not an adaptive response.

•

Prolonged lag phase was due to population replacement.

•

Stress, starvation or weak acid, caused a rise in population diversity.

Molecular tools and protocols for engineering the acid-tolerant yeast Zygosaccharomyces bailii as a potential cell factory

Microorganisms offer a tremendous potential as cell factories, and they are indeed used by humans for centuries for biotransformations. Among them, yeasts combine the advantage of unicellular state with a eukaryotic organization, and, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycetales budding yeast, is widely known for its peculiar tolerance to various stresses, among which are organic acids. Despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here, we describe in detail protocols for transformation, for target gene disruption or gene integration, and for designing episomal expression plasmids helpful for developing and further studying the yeast Z. bailii.

Extreme resistance to weak-acid preservatives in the spoilage yeast Zygosaccharomyces bailii

Weak-acid preservatives, such as sorbic acid and acetic acid, are used in many low pH foods to prevent spoilage by fungi. The spoilage yeast Zygosaccharomyces bailii is notorious for its extreme resistance to preservatives and ability to grow in excess of legally-permitted concentrations of preservatives. Extreme resistance was confirmed in 38 strains of Z. bailii to several weak-acid preservatives. Using the brewing yeast Saccharomyces cerevisiae as a control, tests showed that Z. bailii was ~3-fold more resistant to a variety of weak-acids but was not more resistant to alcohols, aldehydes, esters, ethers, ketones, or hydrophilic chelating acids. The weak acids were chemically very diverse in structure, making it improbable that the universal resistance was caused by degradation or metabolism. Examination of Z. bailii cell populations showed that extreme resistance to sorbic acid, benzoic acid and acetic acid was limited to a few cells within the population, numbers decreasing with concentration of weak acid to <1 in 1000. Re-inoculation of resistant sub-populations into weak-acid-containing media showed that all cells now possessed extreme resistance. Resistant sub-populations grown in any weak-acid preservative also showed ~100% cross-resistance to other weak-acid preservatives. Tests using (14)C-acetic acid showed that weak-acid accumulation was much lower in the resistant sub-populations. Acid accumulation is caused by acid dissociation in the higher pH of the cytoplasm. Tests on intracellular pH (pHi) in the resistant sub-population showed that the pH was much lower, ~ pH5.6, than in the sensitive bulk population. The hypothesis is proposed that extreme resistance to weak-acid preservatives in Z. bailii is due to population heterogeneity, with a small proportion of cells having a lower intracellular pH. This reduces the level of accumulation of any weak acid in the cytoplasm, thus conferring resistance to all weak acids, but not to other inhibitors.

Proposal of Zygosaccharomyces parabailii sp. nov. and Zygosaccharomyces pseudobailii sp. nov., novel species closely related to Zygosaccharomyces bailii

Twenty-three yeast strains traditionally identified as Zygosaccharomyces bailii were studied in order to clarify their taxonomy and phylogenetic relationships. The molecular phylogeny from rRNA gene sequences showed that these yeasts were well divided into three major groups, and two of the groups could be clearly distinguished from the type strain of Z. bailii at the species level. Therefore, we propose Zygosaccharomyces parabailii sp. nov. (type strain ATCC 56075(T)  = NBRC 1047(T)  = NCYC 128(T)  = CBS 12809(T)) and Zygosaccharomyces pseudobailii sp. nov. (type strain ATCC 56074(T)  = NBRC 0488(T)  = CBS 2856(T)) to accommodate the yeasts belonging to the two groups. By conventional physiological tests, Z. bailii and the two novel species are not clearly distinguished from one another, as variations exist more frequently between individual strains and are not species-specific. However, the conclusions from rRNA gene sequence analyses are well supported by genome fingerprinting patterns as well as other protein-coding gene sequence comparisons.

Olive fermentation brine: biotechnological potentialities and valorization

Olive fermentation brine causes an important local environmental problem in Mediterranean countries. Valorization is a relatively new concept in the field of industrial residue management, promoting the principle of sustainable development. One of the valorization objectives regarding food processing by-products is the recovery of fine chemicals and the production of value metabolites via chemical and biotechnological processes. In this article, recent research studies for the valorization of olive fermentation brine performed by several authors were reviewed. Special attention was paid to the metabolic products produced during table olive preparation. The selection of the corresponding valorization process will depend on the agricultural or industrial environment of the olive fermentation brine. Although some methods are strongly consolidated in this sector, other options, more respectful to the environment, should also be considered.

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

Understanding the characteristics of yeast spoilage, as well as the available control technologies, is vital to producing consistent, high-quality wine. Zygosaccharomyces bailii contamination may result in refermentation and CO2 production in sweet wines or grape juice concentrate, whereas Brettanomyces bruxellensis spoilage often contributes off-odors and flavors to red wines. Early detection of these yeasts by selective/differential media or genetic methods is important to minimize potential spoilage. More established methods of microbial control include sulfur dioxide, dimethyl dicarbonate, and filtration. Current research is focused on the use of chitosan, pulsed electric fields, low electric current, and ultrasonics as means to protect wine quality.

Surviving in the presence of sulphur dioxide: strategies developed by wine yeasts

Sulphur dioxide has been used as a common preservative in wine since at least the nineteenth century. Its use has even become essential to the making of quality wines because of its antioxidant, antioxidasic and antiseptic properties. The chemistry of SO₂ in wine is fairly complex due to its dissociation into different species and its binding to other compounds produced by yeasts and bacteria during fermentation. The only antiseptic species is the minute part remaining as molecular SO₂. The latter concentration is both dependent on pH and concentration of free bisulphite. However, certain yeast species have developed cellular and molecular mechanisms as a response to SO₂ exposure. Some of these mechanisms are fairly complex and have only been investigated recently, at least for the molecular mechanisms. They include sulphite reduction, sulphite oxidation, acetaldehyde production, sulphite efflux and the entry into viable but not culturable state, as the ultimate response. In this review, the chemistry of SO₂ in wine is explained together with the impact of SO₂ on yeast cells. The different defence mechanisms are described and discussed, mostly based on current knowledge available for Saccharomyces cerevisiae.

Cationic antimicrobial (ε-polylysine)-anionic polysaccharide (pectin) interactions: influence of polymer charge on physical stability and antimicrobial efficacy

The cationic biopolymer ε-polylysine (ε-PL) is a potent food-grade antimicrobial that is highly effective against a range of food pathogens and spoilage organisms. In compositionally complex systems such as foods and beverages, cationic ε-PL molecules may associate with anionic substances, leading to increased turbidity, sediment formation, and reduced antimicrobial activity. This study therefore characterized the interactions between cationic ε-PL and anionic pectins with different degrees of esterification (DE) and then investigated the influence of these interactions on the antimicrobial efficacy of ε-PL. The nature of the interactions was characterized using isothermal titration calorimetry (ITC), microelectrophoresis (ME), and turbidity measurements. High (DE 61%), medium (DE 51%), and low (DE 42%) methoxyl pectins interacted with ε-PL molecules through electrostatic forces, forming either soluble or insoluble complexes with various electrical charges, depending on the relative mass ratio of pectin and ε-PL. The interaction of pectin with ε-PL increased as the negative charge density on the pectin molecules increased, that is, with decreasing DE. The antimicrobial efficacy of ε-PL against two acid-resistant spoilage yeasts (Zygosaccharomyces bailii and Saccharomyces cerevisiae) decreased progressively in the presence of increasing levels of all three pectins. Nevertheless, the low DE pectin decreased the antimicrobial efficacy of ε-PL much more dramatically, likely due to strong electrostatic binding of ε-PL onto low DE pectin molecules reducing its interaction with anionic microbe surfaces. This study provides knowledge that will facilitate the rational application of ε-PL as an antimicrobial in complex food systems.

Physicochemical properties and antimicrobial efficacy of electrostatic complexes based on cationic ε-polylysine and anionic pectin

ε-Polylysine (ε-PL) is a food-grade cationic antimicrobial that is highly effective against a wide range of food pathogens and spoilage organisms. However, its application within foods and beverages is currently limited because of its tendency to associate with anionic substances, thereby increasing product turbidity or forming sediments. In this study, we examined a potential means of overcoming these problems by forming electrostatic complexes between cationic ε-PL and anionic pectin. The nature of the complexes formed depended on the mass ratio of pectin to ε-PL (R(P-PL)), since this determined their electrical characteristics, aggregation stability, and antimicrobial efficacy. The electrical charge on the complexes went from positive to negative with increasing R(P-PL), with the point of zero charge being around R(P-PL) ∼ 8. Soluble complexes or stable colloidal dispersions were formed at low and high R(P-PL) levels, but insoluble complexes were formed at intermediate levels (i.e., 4 ≤ R(P-PL) ≤ 16). The complexes maintained good antimicrobial activity (minimum inhibitory concentration of ε-PL < 10 μg/mL) at R(P-PL) ≤ 20 against two acid resistant spoilage yeasts: Zygosaccharomyces bailli and Saccharomyces cerevisiae. Finally, we showed that certain ε-PL-pectin complexes (10 μg/mL ε-PL; R(P-PL) ≥ 2) could be incorporated into green tea beverages without adversely affecting their appearance or physical stability. This work has shown that the function of a cationic antimicrobial agent (ε-polylysine) can be improved by incorporating it within electrostatic complexes using a food-grade anionic biopolymer (pectin).

Effects of acetic acid, ethanol, and SO(2) on the removal of volatile acidity from acidic wines by two Saccharomyces cerevisiae commercial strains

Herein, we report the influence of different combinations of initial concentration of acetic acid and ethanol on the removal of acetic acid from acidic wines by two commercial Saccharomyces cerevisiae strains S26 and S29. Both strains reduced the volatile acidity of an acidic wine (1.0 gl(-1) acetic acid and 11% (v/v) ethanol) by 78% and 48%, respectively. Acetic acid removal by strains S26 and S29 was associated with a decrease in ethanol concentration of 0.7 and 1.2% (v/v), respectively. Strain S26 revealed better removal efficiency due to its higher tolerance to stress factors imposed by acidic wines. Sulfur dioxide (SO(2)) in the concentration range 95-170 mg l(-1)inhibits the ability of both strains to reduce the volatile acidity of the acidic wine used under our experimental conditions. Therefore, deacidification should be carried out either in wines stabilized by filtration or in wines with SO(2)concentrations up to 70 mg l(-1). Deacidification of wines with the better performing strain S26 was associated with changes in the concentration of volatile compounds. The most pronounced increase was observed for isoamyl acetate (banana) and ethyl hexanoate (apple, pineapple), with an 18- and 25-fold increment, respectively, to values above the detection threshold. The acetaldehyde concentration of the deacidified wine was 2.3 times higher, and may have a detrimental effect on the wine aroma. Moreover, deacidification led to increased fatty acids concentration, but still within the range of values described for spontaneous fermentations, and with apparently no negative impact on the organoleptical properties.

Cloning of the Zygosaccharomyces bailii GAS1 homologue and effect of cell wall engineering on protein secretory phenotype

Background

Zygosaccharomyces bailii is a diploid budding yeast still poorly characterized, but widely recognised as tolerant to several stresses, most of which related to industrial processes of production. Because of that, it would be very interesting to develop its ability as a cell factory. Gas1p is a β-1,3-glucanosyltransglycosylase which plays an important role in cell wall construction and in determining its permeability. Cell wall defective mutants of Saccharomyces cerevisiae and Pichia pastoris, deleted in the GAS1 gene, were reported as super-secretive. The aim of this study was the cloning and deletion of the GAS1 homologue of Z. bailii and the evaluation of its deletion on recombinant protein secretion.

Results

The GAS1 homologue of Z. bailii was cloned by PCR, and when expressed in a S. cerevisiae GAS1 null mutant was able to restore the parental phenotype. The respective Z. bailii Δgas1 deleted strain was obtained by targeted deletion of both alleles of the ZbGAS1 gene with deletion cassettes having flanking regions of ~400 bp. The morphological and physiological characterization of the Z. bailii null mutant resulted very similar to that of the corresponding S. cerevisiae mutant. As for S. cerevisiae, in the Z. bailii Δgas1 the total amount of protein released in the medium was significantly higher. Moreover, three different heterologous proteins were expressed and secreted in said mutant. The amount of enzymatic activity found in the medium was almost doubled in the case of the Candida rugosa lipase CRL1 and of the Yarrowia lipolytica protease XPR2, while for human IL-1β secretion disruption had no relevant effect.

Conclusions

The data presented confirm that the engineering of the cell wall is an effective way to improve protein secretion in yeast. They also confirmed that Z. bailii is an interesting candidate, despite the knowledge of its genome and the tools for its manipulation still need to be improved. However, as already widely reported in literature, our data confirmed that an "always working" solution to the problems related to recombinant protein production can be hardly, if never, found; instead, manipulations have to be finely tuned for each specific product and/or combination of host cell and product.

Yeasts associated to Traditional Balsamic Vinegar: Ecological and technological features

Traditional Balsamic Vinegar (TBV) is an Italian homemade vinegar made with cooked grape must through a three-step process: conversion of sugars to ethanol by naturally occurring yeasts; oxidation of ethanol to acetic acid by acetic acid bacteria (AAB); and, finally, at least 12-years ageing. The cooked must is a selective and stressful medium for yeasts growth, due to its high sugar content and low pH values. Recent studies have shown that a large number of yeast species are involved in the fermentation, among them there are Zygosaccharomyces bailii, Zygosaccharomyces rouxii, Zygosaccharomyces pseudorouxii, Zygosaccharomyces mellis, Zygosaccharomyces bisporus, Zygosaccharomyces lentus, Hanseniaspora valbyensis, Hanseniaspora osmophila, Candida lactis-condensi, Candida stellata, Saccharomycodes ludwigii and Saccharomyces cerevisiae. Nevertheless, the TBV-associated yeast population could be even more complex and many other slow-growing or poorly cultivable species might contribute to cooked must fermentation. In this review the main TBV yeast species are described, pointing out their role in TBV production and their influence on final product quality. Finally, both future developments in TBV yeast community studies (culture-independent and metagenomic techniques) and technological advances in TBV making (use of starter culture) are discussed.

Decarboxylation of sorbic acid by spoilage yeasts is associated with the PAD1 gene

The spoilage yeast Saccharomyces cerevisiae degraded the food preservative sorbic acid (2,4-hexadienoic acid) to a volatile hydrocarbon, identified by gas chromatography mass spectrometry as 1,3-pentadiene. The gene responsible was identified as PAD1, previously associated with the decarboxylation of the aromatic carboxylic acids cinnamic acid, ferulic acid, and coumaric acid to styrene, 4-vinylguaiacol, and 4-vinylphenol, respectively. The loss of PAD1 resulted in the simultaneous loss of decarboxylation activity against both sorbic and cinnamic acids. Pad1p is therefore an unusual decarboxylase capable of accepting both aromatic and aliphatic carboxylic acids as substrates. All members of the Saccharomyces genus (sensu stricto) were found to decarboxylate both sorbic and cinnamic acids. PAD1 homologues and decarboxylation activity were found also in Candida albicans, Candida dubliniensis, Debaryomyces hansenii, and Pichia anomala. The decarboxylation of sorbic acid was assessed as a possible mechanism of resistance in spoilage yeasts. The decarboxylation of either sorbic or cinnamic acid was not detected for Zygosaccharomyces, Kazachstania (Saccharomyces sensu lato), Zygotorulaspora, or Torulaspora, the genera containing the most notorious spoilage yeasts. Scatter plots showed no correlation between the extent of sorbic acid decarboxylation and resistance to sorbic acid in spoilage yeasts. Inhibitory concentrations of sorbic acid were almost identical for S. cerevisiae wild-type and Deltapad1 strains. We concluded that Pad1p-mediated sorbic acid decarboxylation did not constitute a significant mechanism of resistance to weak-acid preservatives by spoilage yeasts, even if the decarboxylation contributed to spoilage through the generation of unpleasant odors.