Sugar- and salt-tolerant yeasts

Cellular Stress Impact on Yeast Activity in Biotechnological Processes-A Short Overview

The importance of Saccharomyces cerevisiae yeast cells is known worldwide, as they are the most used microorganisms in biotechnology for bioethanol and biofuel production. Also, they are analyzed and studied for their similar internal biochemical processes to human cells, for a better understanding of cell aging and response to cell stressors. The special ability of S. cerevisiae cells to develop in both aerobic and anaerobic conditions makes this microorganism a viable model to study the transformations and the way in which cellular metabolism is directed to face the stress conditions due to environmental changes. Thus, this review will emphasize the effects of oxidative, ethanol, and osmotic stress and also the physiological and genetic response of stress mitigation in yeast cells.

Screening of Yeasts Isolated from Baijiu Environments for Producing 3-Methylthio-1-propanol and Optimizing Production Conditions

3-Methylthio-1-propanol (3-Met) is widely used as a flavoring substance and an essential aroma ingredient in many foods. Producing 3-Met by microbial transformation is green and eco-friendly. In the present study, one strain, YHM-G, which produced a high level of 3-Met, was isolated from the Baijiu-producing environment. Strain YHM-G was identified as Hyphopichia burtonii according to its morphological properties, physiological and biochemical characteristics, and ribosomal large subunit 26S rRNA gene D1/D2 domain sequence analysis. The optimal conditions for 3-Met production by YHM-G were obtained by single factor design, Plackett-Burman design, steepest ascent path design and response surface methodology as follows: 42.7 g/L glucose, pH 6, 0.9 g/L yeast extract, 6 g/L L-methionine (L-Met), culture temperature 28 °C, shaking speed 210 rpm, loading volume 50 mL/250 mL, inoculum size 0.5% (v/v), culturing period 48 h and 2.5 g/L Tween-80. Under these optimal conditions, the 3-Met production by strain YHM-G was 3.16 g/L, a value 88.1% higher than that before optimization. Strain YHM-G can also produce a variety of flavor compounds that are important for many foods. This strain thus has the potential to increase the abundance of 3-Met in some fermented foods and enhance their aroma profiles.

The emerging threat antifungal-resistant Candida tropicalis in humans, animals, and environment

Antifungal resistance in humans, animals, and the environment is an emerging problem. Among the different fungal species that can develop resistance, Candida tropicalis is ubiquitous and causes infections in animals and humans. In Asia and some Latin American countries, C. tropicalis is among the most common species related to candidemia, and mortality rates are usually above 40%. Fluconazole resistance is especially reported in Asian countries and clonal spread in humans and the environment has been investigated in some studies. In Brazil, high rates of azole resistance have been found in animals and the environment. Multidrug resistance is still rare, but recent reports of clinical multidrug-resistant isolates are worrisome. The molecular apparatus of antifungal resistance has been majorly investigated in clinical C. tropicalis isolates, revealing that this species can develop resistance through the conjunction of different adaptative mechanisms. In this review article, we summarize the main findings regarding antifungal resistance and Candida tropicalis through an "One Health" approach.

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.

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).

Sugar-Rich Foods Carry Osmotolerant Yeasts with Intracellular Helicobacter Pylori and Staphylococcus spp

BACKGROUND

Sugar-rich foods are of the main components of daily human meals. These foods with high sugar and low water content kill bacteria. However, osmotolerant yeasts survive and multiply. The aim of this study was to examine the occurrence of intracellular Helicobacter pylori (H. pylori) and Staphylococcus spp. in yeast isolates from sugar-rich foods.

METHODS

Thirty-two yeast isolates from fresh fruits, dried fruits, commercial foods, and miscellaneous foods were identified by the sequencing of amplified products of 26S rDNA. Fluorescence microscopy and LIVE/DEAD bacterial viability kit were used to examine the occurrence of live bacteria inside the yeast’s vacuole. Immunofluorescence assay was used to confirm the identity of intracellular bacteria as H. pylori and Staphylococcus . Polymerase chain reaction (PCR) was used for the detection of 16S rDNA of H. pylori and Staphylococcus in the total DNA of yeasts.

RESULTS

Yeasts were identified as members of seven genera; Candida, Saccharomyces, Zygosaccharomyces, Pichia, Meyerozyma, Metschnikowia, and Wickerhamomyces. Intravacuolar bacteria were stained green with a bacterial viability kit, revealing that they were alive. Immunofluorescence assay confirmed the identity of intracellular H. pylori and Staphylococcus spp. PCR results revealed that among the 32 isolated yeasts, 53% were H. pylori -positive, 6% were Staphylococcus -positive, 18.7% were positive for both, and 21.8% were negative for both.

CONCLUSION

Detection of H. pylori - and Staphylococcus -16S rDNA in yeast isolates from dried fruits, and commercial foods showed the occurrence of more than one kind of endosymbiotic bacterium in yeasts’ vacuoles. While the establishment of H. pylori and Staphylococcus in yeast is a sophisticated survival strategy, yeast serves as a potent bacterial reservoir.

Performance of a Newly Isolated Salt-Tolerant Yeast Strain Sterigmatomyces halophilus SSA-1575 for Azo Dye Decolorization and Detoxification

The effective degradation of hazardous contaminants remains an intractable challenge in wastewater processing, especially for the high concentration of salty azo dye wastewater. However, some unique yeast symbionts identified from the termite gut system present an impressive function to deconstruct some aromatic compounds, which imply that they may be valued to work on the dye degradation for various textile effluents. In this investigation, a newly isolated and unique yeast strain, Sterigmatomyces halophilus SSA-1575, was identified from the gut system of a wood-feeding termite (WFT), Reticulitermes chinensis. Under the optimized ambient conditions, the yeast strain SSA-1575 showed a complete decolorization efficiency on Reactive Black 5 (RB5) within 24 h, where this azo dye solution had a concentration of a 50 mg/L RB5. NADH-dichlorophenol indophenol (NADH-DCIP) reductase and lignin peroxidase (LiP) were determined as the key reductase and oxidase of S. halophilus SSA-1575. Enhanced decolorization was recorded when the medium was supplemented with carbon and energy sources, including glucose, ammonium sulfate, and yeast extract. To understand a possible degradation pathway well, UV-Vis spectroscopy, FTIR and Mass Spectrometry analyses were employed to analyze the possible decolorization pathway by SSA-1575. Determination of relatively high NADH-DCIP reductase suggested that the asymmetric cleavage of RB5 azo bond was mainly catalyzed by NADH-DCIP reductase, and finally resulting in the formation of colorless aromatic amines devoid of any chromophores. The ecotoxicology assessment of RB5 after a decolorization processing by SSA-1575, was finally conducted to evaluate the safety of its metabolic intermediates from RB5. The results of Microtox assay indicate a capability of S. halophilus SSA-1575, in the detoxification of the toxic RB5 pollutant. This study revealed the effectiveness of halotolerant yeasts in the eco-friendly remediation of hazardous pollutants and dye wastewater processing for the textile industry.

Draft Genome Sequence of Zygosaccharomyces mellis CA-7, Isolated from Honey

In this study, we report the draft genome sequence of Zygosaccharomyces mellis CA-7, isolated from purchased honey imported from Canada. The 10.19-Mb genome contains 4,963 gene models. To our knowledge, this annotated genome sequence is the first from the species Z. mellis and will contribute to a better understanding of the osmotolerance of microorganisms in high-sugar products.

In this study, we report the draft genome sequence of Zygosaccharomyces mellis CA-7, isolated from purchased honey imported from Canada. The 10.19-Mb genome contains 4,963 gene models. To our knowledge, this annotated genome sequence is the first from the species Z. mellis and will contribute to a better understanding of the osmotolerance of microorganisms in high-sugar products.

Extreme Osmotolerance and Halotolerance in Food-Relevant Yeasts and the Role of Glycerol-Dependent Cell Individuality

Osmotolerance or halotolerance are used to describe resistance to sugars and salt, or only salt, respectively. Here, a comprehensive screen of more than 600 different yeast isolates revealed that osmosensitive species were equally affected by NaCl and glucose. However, the relative toxicity of salt became increasingly prominent in more osmoresistant species. We confirmed that growth inhibition by glucose in a laboratory strain of Saccharomyces cerevisiae occurred at a lower water activity (A_w) than by salt (NaCl), and pre-growth in high levels of glucose or salt gave enhanced cross-resistance to either. Salt toxicity was largely due to osmotic stress but with an additive enhancement due to effects of the relevant cation. Almost all of the yeast isolates from the screen were also noted to exhibit hetero-resistance to both salt and sugar, whereby high concentrations restricted growth to a small minority of cells within the clonal populations. Rare resistant colonies required growth for up to 28 days to become visible. This cell individuality was more marked with salt than sugar, a possible further reflection of the ion toxicity effect. In both cases, heteroresistance in S. cerevisiae was strikingly dependent on the GPD1 gene product, important for glycerol synthesis. In contrast, a tps1Δ deletant impaired for trehalose showed altered MIC but no change in heteroresistance. Effects on heteroresistance were evident in chronic (but not acute) salt or glucose stress, particularly relevant to growth on low A_w foods. The study reports diverse osmotolerance and halotolerance phenotypes and heteroresistance across an extensive panel of yeast isolates, and indicates that Gpd1-dependent glycerol synthesis is a key determinant enabling growth of rare yeast subpopulations at low A_w, brought about by glucose and in particular salt.

An Update on Candida tropicalis Based on Basic and Clinical Approaches

Candida tropicalis has emerged as one of the most important Candida species. It has been widely considered the second most virulent Candida species, only preceded by C. albicans. Besides, this species has been recognized as a very strong biofilm producer, surpassing C. albicans in most of the studies. In addition, it produces a wide range of other virulence factors, including: adhesion to buccal epithelial and endothelial cells; the secretion of lytic enzymes, such as proteinases, phospholipases, and hemolysins, bud-to-hyphae transition (also called morphogenesis) and the phenomenon called phenotypic switching. This is a species very closely related to C. albicans and has been easily identified with both phenotypic and molecular methods. In addition, no cryptic sibling species were yet described in the literature, what is contradictory to some other medically important Candida species. C. tropicalis is a clinically relevant species and may be the second or third etiological agent of candidemia, specifically in Latin American countries and Asia. Antifungal resistance to the azoles, polyenes, and echinocandins has already been described. Apart from all these characteristics, C. tropicalis has been considered an osmotolerant microorganism and this ability to survive to high salt concentration may be important for fungal persistence in saline environments. This physiological characteristic makes this species suitable for use in biotechnology processes. Here we describe an update of C. tropicalis, focusing on all these previously mentioned subjects.

Phenotypic landscape of non-conventional yeast species for different stress tolerance traits desirable in bioethanol fermentation

BACKGROUND

Non-conventional yeasts present a huge, yet barely exploited, resource of yeast biodiversity for industrial applications. This presents a great opportunity to explore alternative ethanol-fermenting yeasts that are more adapted to some of the stress factors present in the harsh environmental conditions in second-generation (2G) bioethanol fermentation. Extremely tolerant yeast species are interesting candidates to investigate the underlying tolerance mechanisms and to identify genes that when transferred to existing industrial strains could help to design more stress-tolerant cell factories. For this purpose, we performed a high-throughput phenotypic evaluation of a large collection of non-conventional yeast species to identify the tolerance limits of the different yeast species for desirable stress tolerance traits in 2G bioethanol production. Next, 12 multi-tolerant strains were selected and used in fermentations under different stressful conditions. Five strains out of which, showing desirable fermentation characteristics, were then evaluated in small-scale, semi-anaerobic fermentations with lignocellulose hydrolysates.

RESULTS

Our results revealed the phenotypic landscape of many non-conventional yeast species which have not been previously characterized for tolerance to stress conditions relevant for bioethanol production. This has identified for each stress condition evaluated several extremely tolerant non-Saccharomyces yeasts. It also revealed multi-tolerance in several yeast species, which makes those species good candidates to investigate the molecular basis of a robust general stress tolerance. The results showed that some non-conventional yeast species have similar or even better fermentation efficiency compared to S. cerevisiae in the presence of certain stressful conditions.

CONCLUSION

Prior to this study, our knowledge on extreme stress-tolerant phenotypes in non-conventional yeasts was limited to only few species. Our work has now revealed in a systematic way the potential of non-Saccharomyces species to emerge either as alternative host species or as a source of valuable genetic information for construction of more robust industrial S. serevisiae bioethanol production yeasts. Striking examples include yeast species like Pichia kudriavzevii and Wickerhamomyces anomalus that show very high tolerance to diverse stress factors. This large-scale phenotypic analysis has yielded a detailed database useful as a resource for future studies to understand and benefit from the molecular mechanisms underlying the extreme phenotypes of non-conventional yeast species.

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

Yeasts and yeast-like fungal isolates were recovered from apple orchards and apple juice processing plants located in the Shaanxi province of China. The strains were evaluated for osmotolerance by growing them in 50% (w/v) glucose. Of the strains tested, 66 were positive for osmotolerance and were subsequently identified by 26S or 5.8S-ITS ribosomal RNA (rRNA) gene sequencing. Physiological tests and RAPD-PCR analysis were performed to reveal the polymorphism of isolates belonging to the same species. Further, the spoilage potential of the 66 isolates was determining by evaluating their growth in 50% to 70% (w/v) glucose and measuring gas generation in 50% (w/v) glucose. Thirteen osmotolerant isolates representing 9 species were obtained from 10 apple orchards and 53 target isolates representing 19 species were recovered from 2 apple juice processing plants. In total, members of 14 genera and 23 species of osmotolerant isolates including yeast-like molds were recovered from all sources. The commonly recovered osmotolerant isolates belonged to Kluyveromyces marxianus, Hanseniaspora uvarum, Saccharomyces cerevisiae, Zygosaccharomyces rouxii, Candida tropicalis, and Pichia kudriavzevii. The polymorphism of isolates belonging to the same species was limited to 1 to 3 biotypes. The majority of species were capable of growing within a range of glucose concentration, similar to sugar concentrations found in apple juice products with a lag phase from 96 to 192 h. Overall, Z. rouxii was particularly the most tolerant to high glucose concentration with the shortest lag phase of 48 h in 70% (w/v) glucose and the fastest gas generation rate in 50% (w/v) glucose.

Advances in yeast systematics and phylogeny and their use as predictors of biotechnologically important metabolic pathways

Detection, identification and classification of yeasts have undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of the nuclear large subunit rRNA gene and from ITS now permits many laboratories to identify species quickly and accurately, thus replacing the laborious and often inaccurate phenotypic tests previously used. Phylogenetic analysis of gene sequences is leading to a major revision of yeast systematics that will result in redefinition of nearly all genera. This new understanding of species relationships has prompted a change of rules for naming and classifying yeasts and other fungi, and these new rules are presented in the recently implemented International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). The use of molecular methods for species identification and the impact of Code changes on classification will be discussed, as will use of phylogeny for prediction of biotechnological applications.

Looking beyond Saccharomyces: the potential of non-conventional yeast species for desirable traits in bioethanol fermentation

Saccharomyces cerevisiae has been used for millennia in the production of food and beverages and is by far the most studied yeast species. Currently, it is also the most used microorganism in the production of first-generation bioethanol from sugar or starch crops. Second-generation bioethanol, on the other hand, is produced from lignocellulosic feedstocks that are pretreated and hydrolyzed to obtain monomeric sugars, mainly D-glucose, D-xylose and L-arabinose. Recently, S. cerevisiae recombinant strains capable of fermenting pentose sugars have been generated. However, the pretreatment of the biomass results in hydrolysates with high osmolarity and high concentrations of inhibitors. These compounds negatively influence the fermentation process. Therefore, robust strains with high stress tolerance are required. Up to now, more than 2000 yeast species have been described and some of these could provide a solution to these limitations because of their high tolerance to the most predominant stress conditions present in a second-generation bioethanol reactor. In this review, we will summarize what is known about the non-conventional yeast species showing unusual tolerance to these stresses, namely Zygosaccharomyces rouxii (osmotolerance), Kluyveromyces marxianus and Ogataea (Hansenula) polymorpha (thermotolerance), Dekkera bruxellensis (ethanol tolerance), Pichia kudriavzevii (furan derivatives tolerance) and Z. bailii (acetic acid tolerance).

Phenotypic evaluation of natural and industrial Saccharomyces yeasts for different traits desirable in industrial bioethanol production

Saccharomyces cerevisiae is the organism of choice for many food and beverage fermentations because it thrives in high-sugar and high-ethanol conditions. However, the conditions encountered in bioethanol fermentation pose specific challenges, including extremely high sugar and ethanol concentrations, high temperature, and the presence of specific toxic compounds. It is generally considered that exploring the natural biodiversity of Saccharomyces strains may be an interesting route to find superior bioethanol strains and may also improve our understanding of the challenges faced by yeast cells during bioethanol fermentation. In this study, we phenotypically evaluated a large collection of diverse Saccharomyces strains on six selective traits relevant for bioethanol production with increasing stress intensity. Our results demonstrate a remarkably large phenotypic diversity among different Saccharomyces species and among S. cerevisiae strains from different origins. Currently applied bioethanol strains showed a high tolerance to many of these relevant traits, but several other natural and industrial S. cerevisiae strains outcompeted the bioethanol strains for specific traits. These multitolerant strains performed well in fermentation experiments mimicking industrial bioethanol production. Together, our results illustrate the potential of phenotyping the natural biodiversity of yeasts to find superior industrial strains that may be used in bioethanol production or can be used as a basis for further strain improvement through genetic engineering, experimental evolution, or breeding. Additionally, our study provides a basis for new insights into the relationships between tolerance to different stressors.

Growth/no growth models for Zygosaccharomyces rouxii associated with acidic, sweet intermediate moisture food products

The most notorious spoilage organism of sweet intermediate moisture foods (IMFs) is Zygosaccharomyces rouxii, which can grow at low water activity, low pH and in the presence of organic acids. Together with an increased consumer demand for preservative free and healthier food products with less sugar and fat and a traditionally long self-life of sweet IMFs, the presence of Z. rouxii in the raw materials for IMFs has made assessment of the microbiological stability a significant hurdle in product development. Therefore, knowledge on growth/no growth boundaries of Z. rouxii in sweet IMFs is important to ensure microbiological stability and aid product development. Several models have been developed for fat based, sweet IMFs. However, fruit/sugar based IMFs, such as fruit based chocolate fillings and jams, have lower pH and aw than what is accounted for in previously developed models. In the present study growth/no growth models for acidified sweet IMFs were developed with the variables aw (0.65-0.80), pH (2.5-4.0), ethanol (0-14.5% (w/w) in water phase) and time (0-90 days). Two different strains of Z. rouxii previously found to show pronounced resistance to the investigated variables were included in model development, to account for strain differences. For both strains data sets with and without the presence of sorbic acid (250 ppm on product basis) were built. Incorporation of time as an exploratory variable in the models gave the possibility to predict the growth/no growth boundaries at each time between 0 and 90 days without decreasing the predictive power of the models. The influence of ethanol and aw on the growth/no growth boundary of Z. rouxii was most pronounced in the first 30 days and 60 days of incubation, respectively. The effect of pH was almost negligible in the range of 2.5-4.0. The presence of low levels of sorbic acid (250 ppm) eliminated growth of both strains at all conditions tested. The two strains tested have previously been shown to have similar tolerance towards the single stress factors included in the study, but when the stress factors were combined the two strains showed difference in their ability to grow illustrating the importance of including more strains when developing growth/no growth models. The developed models can be useful tools for development of new acidic sweet IMFs.

Effect of pretreatments on microbial growth and sensory properties of dry-salted olives

The effect of various washing solutions (acetic acid, lactic acid, and chlorine dioxide) and NaCl concentrations (2.5, 5.0, and 10.0%) on the stability of dry-salted olives (cultivars Gemlik and Edincik) during storage was studied. Vacuum-packed olives were stored at 4°C for 7 months and monitored for microbiological changes that occurred in the dry-salted olives during the dry-salting process and for their stability during storage. Microbial populations were enumerated using pour plating (for aerobic plate counts) and spread plating (for counts of lactic acid bacteria and yeasts and molds). Aerobic plate counts were <2.5 log CFU/g for olive samples washed in chlorine dioxide at all NaCl concentrations. At 4°C, the population of yeasts and molds increased steadily during the shelf life in Gemlik olive samples washed with all of the solutions, except chlorine dioxide, whereas yeast and mold counts in Edincik olives decreased depending on the increase in salt concentration. Therefore, different combinations of organic acids, NaCl, and vacuum packaging can be successfully used to control the growth of yeasts and molds in these olives. The combination of vacuum sealing (with a 10-ppm chlorine dioxide wash) and storage at 4°C was the most effective approach for controlling the growth of lactic acid bacteria and yeasts and molds. Members of the sensory panel considered saltiness to be appropriate at 2.5 and 5.0% NaCl. Softness and bitterness scores increased with reduced NaCl concentrations, but rancidity and hardness scores increased as NaCl concentration increased.

Strategies to increase the stability of intermediate moisture foods towards Zygosaccharomyces rouxii: the effect of temperature, ethanol, pH and water activity, with or without the influence of organic acids

Intermediate moisture foods (IMF) are in general microbiologically stable products. However, due to health concerns consumer demands are increasingly forcing producers to lower the fat, sugar and preservatives content, which impede the stability of the IMF products. One of the strategies to counteract these problems is the storage of IMF products at lower temperatures. Thorough knowledge on growth/no growth boundaries of Zygosaccharomyces rouxii in IMF products, also at different storage temperatures is an important tool for ensuring microbiologically stability. In this study, growth/no growth models for Z. rouxii, developed by Vermeulen et al. (2012) were further extended by incorporating the factor temperature. Three different data sets were build: (i) without organic acids, (ii) with acetic acid (10,000 ppm on product basis) and (iii) with sorbic acid (1500 ppm on product basis). For each of these data sets three different growth/no growth models were developed after 30, 60 and 90 days. The results show that the influence of temperature is only significant in the lower temperature range (8-15 °C). Also, the effect of pH is negligible (pH 5.0-6.2) unless organic acids are present. More specific, acetic acid had only an additive effect to ethanol and aw at low pH, whereas sorbic acid had also an additive effect at the higher pH values. For incubation periods longer than 30 days the growth/no growth boundary remained stable but enlarged gradually between day 60 and 90, except for the lower temperature range (<12 °C) where the boundary shifts to more stringent environmental conditions.

Effects of pH and sugar concentration in Zygosaccharomyces rouxii growth and time for spoilage in concentrated grape juice at isothermal and non-isothermal conditions

The effect of pH (1.7-3.2) and sugar concentration (64-68 °Brix) on the growth of Zygosaccharomyces rouxii MC9 using response surface methodology was studied. Experiments were carried out in concentrated grape juice inoculated with Z. rouxii at isothermal conditions (23 °C) for 60 days. pH was the variable with the highest effect on growth parameters (potential maximum growth rate and lag phase duration), although the effect of sugar concentration were also significant. In a second experiment, the time for spoilage by this microorganism in concentrated grape juice was evaluated at isothermal (23 °C) and non-isothermal conditions, in an effort to reproduce standard storage and overseas shipping temperature conditions, respectively. Results show that pH was again the environmental factor with the highest impact on delaying the spoilage of the product. Thereby, a pH value below 2.0 was enough to increase the shelf life of the product for more than 60 days in both isothermal and non-isothermal conditions. The information obtained in the present work could be used by producers and buyers to predict the growth and time for spoilage of Z. rouxii in concentrated grape juice.

Comparative analysis of salt-tolerant gene HOG1 in a Zygosaccharomyces rouxii mutant strain and its parent strain

BACKGROUND

A higher-salt-tolerant mutant strain Zygosaccharomyces rouxii 3-2 (strain S3-2) that could be used for improving the flavour of high-salt liquid state soy sauce was previously constructed from parent strain Z. rouxii (strain S) by genome shuffling. However, whether the mutations in this strain affect HOG1 encoding MAPK Hog1p and improve intracellular glycerol production remains to be elucidated.

RESULTS

Although two mutations in the ORF and one in the promoter of the HOG1 gene sequence of strain S3-2 occurred compared with that of strain S, there was no significant difference in secondary and tertiary structures between S3-2Hog1p and SHog1p. It was found that the expression level of S3-2HOG1 was higher than that of SHOG1 in YPDN medium with high salt concentration. Furthermore, overexpression of S3-2HOG1 in Saccharomyces cerevisiae W303-1A could improve the salt tolerance and osmotolerance of engineered yeast compared with that of SHOG1.

CONCLUSION

Enhancement of the transcription level of HOG1 induced by mutation in the promoter region may be one of the main reasons for the improved salt tolerance of strain S3-2 compared with that of strain S. Considering food security, the conservation of S3-2HOG1 would be beneficial for application of strain S3-2 in the fermentation of soy sauce.

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.

Morphological responses to high sugar concentrations differ from adaptation to high salt concentrations in the xerophilic fungi Wallemia spp

Fungi from the food-borne basidiomycetous genus Wallemia, which comprises Wallemia ichthyophaga, Wallemia muriae and Wallemia sebi, are among the most xerophilic organisms described. Their morphological adaptations to life at high NaCl concentrations are reflected in increased cell-wall thickness and size of cellular aggregates. The objectives of this study were to examine their growth and to define cell morphology and any ultrastructural cell-wall changes when these fungi are grown in low and high glucose and honey concentrations, as environmental osmolytes. We analysed their growth parameters and morphological characteristics by light microscopy and transmission and scanning electron microscopy. Wallemia ichthyophaga grew slowly in all of the sugar-based media, while W. muriae and W. sebi demonstrated better growth. Wallemia ichthyophaga adapted to the high glucose and honey concentrations with formation of larger cellular aggregates, while cell-wall thickness was increased only at the high glucose concentration. Wallemia muriae and W. sebi demonstrated particularly smaller sizes of hyphal aggregates at the high glucose concentration, and different and less explicit changes in cell-wall thickness. Adaptive responses show that the phylogenetically more distant W. ichthyophaga is better adapted to high salt conditions, whereas W. muriae and W. sebi cope better with a high sugar environment.

Antimicrobial impact of the components of essential oil of Litsea cubeba from Taiwan and antimicrobial activity of the oil in food systems

Using natural additives to preserve foods has become popular due to consumer demands for nature and safety. Antimicrobial activity is one of the most important properties in many plant essential oils (EOs). The antimicrobial activity of the essential oil of Litsea cubeba (LC-EO) from Taiwan and the antimicrobial impact of individual volatile components in the oil on pathogens or spoilage microorganisms: Vibrio parahaemolyticus, Listeria monocytogenes, Lactobacillus plantarum, and Hansenula anomala in vitro, and the antimicrobial activity of the LC-EO against these organisms in food systems were studied. The "antimicrobial impact" (AI) is a new term that combines the effects of minimal microbicidal concentration (MMC) and quantity of an antimicrobial substance. The AI can quantitatively reflect the relative importance of individual components of the EO on the entire antimicrobial activity of the EO. The MMCs of the LC-EO against V. parahaemolyticus, L. monocytogenes, L. plantarum, and H. anomala were determined as 750, 750, 1500, and 375 μg/g, respectively in vitro. The MMCs of the LC-EO were 3000, 6000, and 12,000 μg/g for L. monocytogenes in tofu stored at 4 °C, 25 °C, and 37 °C, respectively. The temperature affected the bacterial growth which consequently influenced the MMCs of the LC-EO. The MMCs of the LC-EO were 3000, 6000, and 375 μg/g for Vibrio spp. in oysters, L. plantarum in orange-milk beverage, and H. anomala in soy sauce, respectively. Except for soy sauce, the food systems exhibited marked matrix effects on diminishing the antimicrobial activity of the LC-EO. Averagely, citral accounted for ca 70% of the total AI value for all the tested organisms, and the rest of the AI value of the LC-EO was determined by all the tested compounds (ca 4%) and the unidentified compounds (ca 26%).

Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast

In addition to genetic differences between individuals as a result of nucleotide sequence variation, epigenetic changes that occur as a result of DNA methylation may also contribute to population niche width by enhancing phenotypic plasticity, although this intriguing possibility remains essentially untested. Using the nectar-living yeast Metschnikowia reukaufii as study subject, we examine the hypothesis that changes in genome-wide DNA methylation patterns underlie the ability of this fugitive species to exploit a broad resource range in its heterogeneous and patchy environment. Data on floral nectar characteristics and their use by M. reukaufii in the wild were combined with laboratory experiments and methylation-sensitive amplified polymorphism (MSAP) analyses designed to detect epigenetic responses of single genotypes to variations in sugar environment that mimicked those occurring naturally in nectar. M. reukaufii exploited a broad range of resources, occurring in nectar of 48% of species and 52% of families surveyed, and its host plants exhibited broad intra- and interspecific variation in sugar-related nectar features. Under experimental conditions, sugar composition, sugar concentration and their interaction significantly influenced the mean probability of MSAP markers experiencing a transition from unmethylated to methylated state. Alterations in methylation status were not random but predictably associated with certain markers. The methylation inhibitor 5-azacytidine (5-AzaC) had strong inhibitory effects on M. reukaufii proliferation in sugar-containing media, and a direct relationship existed across sugar × concentration experimental levels linking inhibitory effect of 5-AzaC and mean per-marker probability of genome-wide methylation. Environmentally induced DNA methylation polymorphisms allowed genotypes to grow successfully in extreme sugar environments, and the broad population niche width of M. reukaufii was largely made possible by epigenetic changes enabling genotype plasticity in resource use.

Production of arabitol from glycerol: strain screening and study of factors affecting production yield

Glycerol is a major by-product from biodiesel production, and developing new uses for glycerol is imperative to overall economics and sustainability of the biodiesel industry. With the aim of producing xylitol and/or arabitol as the value-added products from glycerol, 214 yeast strains, many osmotolerant, were first screened in this study. No strains were found to produce large amounts of xylitol as the dominant metabolite. Some produced polyol mixtures that might present difficulties to downstream separation and purification. Several Debaryomyces hansenii strains produced arabitol as the predominant metabolite with high yields, and D. hansenii strain SBP-1 (NRRL Y-7483) was chosen for further study on the effects of several growth conditions. The optimal temperature was found to be 30°C. Very low dissolved oxygen concentrations or anaerobic conditions inhibited polyol yields. Arabitol yield improved with increasing initial glycerol concentrations, reaching approximately 50% (w/w) with 150 g/L initial glycerol. However, the osmotic stress created by high salt concentrations (≥50 g/L) negatively affected arabitol production. Addition of glucose and xylose improved arabitol production while addition of sorbitol reduced production. Results from this work show that arabitol is a promising value-added product from glycerol using D. hansenii SBP-1 as the producing strain.

Macromolecular and elemental composition analysis and extracellular metabolite balances of Pichia pastoris growing at different oxygen levels

BACKGROUND

Analysis of the cell operation at the metabolic level requires collecting data of different types and to determine their confidence level. In addition, the acquired information has to be combined in order to obtain a consistent operational view. In the case of Pichia pastoris, information of its biomass composition at macromolecular and elemental level is scarce particularly when different environmental conditions, such as oxygen availability or, genetic backgrounds (e.g. recombinant protein production vs. non production conditions) are compared.

RESULTS

P. pastoris cells growing in carbon-limited chemostat cultures under different oxygenation conditions (% O2 in the bioreactor inlet gas: 21%, 11% and 8%, corresponding to normoxic, oxygen-limiting and hypoxic conditions, respectively), as well as under recombinant protein (antibody fragment, Fab) producing and non-producing conditions, were analyzed from different points of view. On the one hand, the macromolecular and elemental composition of the biomass was measured using different techniques at the different experimental conditions and proper reconciliation techniques were applied for gross error detection of the measured substrates and products conversion rates. On the other hand, fermentation data was analyzed applying elemental mass balances. This allowed detecting a previously missed by-product secreted under hypoxic conditions, identified as arabinitol (aka. arabitol). After identification of this C5 sugar alcohol as a fermentation by-product, the mass balances of the fermentation experiments were validated.

CONCLUSIONS

After application of a range of analytical and statistical techniques, a consistent view of growth parameters and compositional data of P. pastoris cells growing under different oxygenation conditions was obtained. The obtained data provides a first view of the effects of oxygen limitation on the physiology of this microorganism, while recombinant Fab production seems to have little or no impact at this level of analysis. Furthermore, the results will be highly useful in other complementary quantitative studies of P. pastoris physiology, such as metabolic flux analysis.

Inhospitable sweetness: nectar filtering of pollinator-borne inocula leads to impoverished, phylogenetically clustered yeast communities

Identifying the rules and mechanisms that determine the composition and diversity of naturally co-occurring species assemblages is a central topic in community ecology. Although micro-organisms represent the 'unseen majority' of species, individuals and biomass in many ecosystems and play pivotal roles in community development and function, the study of the factors influencing the assembly of microbial communities has lagged behind that of plant and animal communities. In this paper, we investigate experimentally the mechanisms accounting for the low species richness of yeast communities inhabiting the nectar of the bumble-bee-pollinated Helleborus foetidus (Ranunculaceae), and explore the relationships between community assembly rules and phylogenetic relatedness. By comparing yeast communities on the glossae of foraging bumble-bees (the potential species pool) with those eventually establishing in virgin nectar probed with bee glossae (the realized community), we address the questions: (i) does nectar filter yeast inocula, so that the communities eventually established there are not random subsamples of species on bumble-bee glossae? and (ii) do yeast communities establishing in H. foetidus nectar exhibit some phylogenetic bias relative to the species pool on bumble-bee glossae? Results show that nectar filtering leads to species-poor, phylogenetically clustered yeast communities that are a predictable subset of pollinator-borne inocula. Such strong habitat filtering is probably due to H. foetidus nectar representing a harsh environment for most yeasts, where only a few phylogenetically related nectar specialists physiologically endowed to tolerate a combination of high osmotic pressure and fungicidal compounds are able to develop.

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.

Effect of Salts on Growth and Pectinase Production by Halotolerant Yeast, Debaryomyces nepalensis NCYC 3413

In this study, Debaryomyces nepalensis NCYC 3413 isolated from rotten apple was studied for its halotolerance and its growth was compared with that of Saccharomyces cerevisiae in high salt medium. The specific growth rate of D. nepalensis was not affected by KCl even up to a concentration of 1 M: , whereas NaCl and LiCl affected the growth of D. nepalensis. Among all tested salts, LiCl showed maximum inhibition on growth. At all conditions, halotolerance of D. nepalensis was much higher than that of S. cerevisiae. D. nepalensis showed maximum viability (80-100%) when grown in KCl, which was higher than with NaCl and LiCl. Pectinase production by D. nepalensis was noted at all high salt concentrations, namely, 2 M NaCl, 2 M KCl, and 0.5 M LiCl, and the maximum specific activity was observed when the strain was grown in 2 M NaCl.

Characterization of the yeast flora present in some Turkish high-sugar products

In this study, 129 Turkish high-sugar products were examined in terms of their yeast flora and 73 representative strains were isolated. Yeast isolates were identified at species level by using Apilab Plus (bioMérieux, France), a specific computer program developed for ID 32C strips (bioMérieux, France). While one of the isolates could be identified at genus level as Aureobasidium, 66 of them were identified as 21 species belonging to 8 different genera. The distribution of these isolates were as follows: Candida (38), Rhodotorula (8), Zygosaccharomyces (7), Cryptococcus (6), Saccharomyces (3), Debaryomyces (2), Pichia (1) and Torulaspora (1). Approximately 70% of the isolates were found to have the ability to grow on media with 50% (w/w) glucose. Hence, they were characterized as xerotolerant strains. Although Zygosaccharomyces rouxii is known as the most xerotolerant yeast species, only two strains of Z. rouxii could be isolated from Turkish high-sugar foods. During identification studies, it was observed that ID 32C test strips should certainly be supported by morphological and physiological tests for obtaining more reliable identification results. If not, closely related yeast species such as anamorph and telemorph forms can not be distinguished.

Outlines for the definition of halotolerance/halophily in yeasts: Candida versatilis (halophila) CBS4019 as the archetype?

Candida versatilis (halophila) CBS4019 was chosen to study the physiological reactions of long-term exposure to extremely high salt concentrations. In general, our results show a significant increase in enzyme expression during growth under stress conditions. Although glycerol and mannitol pathways are not under glucose repression, they were found to be metabolically regulated. Glycerol-3P-dehydrogenase used either of its cofactors NADPH or NADH, being in favor of NADPH during growth with high salt concentrations. This ability of interchanging cofactors, an increased fermentation rate, and the observed mannitol pathway activity are suggested to contribute to the yeasts' redox stability. Enzymes per se were not salt-tolerant in vitro. Consistently, intracellular sodium was low and intracellular potassium, a requirement for growth, was high. The concept of halophily and its applicability to yeasts is discussed.

Cloning and expression of two genes coding for sodium pumps in the salt-tolerant yeast Debaryomyces hansenii

Two genes encoding Na(+)-ATPases from Debaryomyces hansenii were cloned and sequenced. The genes, designated ENA1 from D. hansenii (DhENA1) and DhENA2, exhibited high homology with the corresponding genes from Schwanniomyces occidentalis. DhENA1 was expressed in the presence of high Na(+) concentrations, while the expression of DhENA2 also required high pH. A mutant of Saccharomyces cerevisiae lacking the Na(+) efflux systems and sensitive to Na(+), when transformed with DhENA1 or DhENA2, recovered Na(+) tolerance and also the ability to extrude Na(+).

Effects of salts on Debaryomyces hansenii and Saccharomyces cerevisiae under stress conditions

The effect of Na+ and K+ on growth and thermal death of Debaryomyces hansenii and Saccharomyces cerevisiae were compared under stress conditions as those commonly found in food environments. At the supraoptimal temperature of 34 degrees C both cations at concentrations of 0.5 M stimulated growth of D. hansenii, while K+ had no effect and Na+ inhibited growth of S. cerevisiae. At 8 degrees C, close to the minimum temperature for growth in both species, both cations inhibited both yeasts, this effect being more pronounced with Na+ in S. cerevisiae. At extreme pH values (7.8 and 3.5) both cations at concentrations of 0.25 M stimulated D. hansenii while Na+ inhibited S. cerevisiae. K+ inhibited this yeast at pH 3.5. Thermal inactivation rates, measured at 38 degrees C in D. hansenii and at 48 degrees C in S. cerevisiae, decreased in the presence of both cations. This protective effect could be observed in a wider range of concentrations in D. hansenii. These results call the attention to the fact that not all yeasts have the same behaviour on what concerns synergy or antagonism of salt together with other stress factors and should be taken into consideration in the establishment of food preservation procedures.

Combined effects of pH and sugar on growth rate of Zygosaccharomyces rouxii, a bakery product spoilage yeast

The effects of citric acid-modified pH (pH 2.5, 2.75, 3, 3.5, 4, 4.5, 5, and 5.5) and a 30% glucose-70% sucrose mixture (300, 400, 500, 600, 700, 800, 875, and 900 g/liter) on an osmophilic yeast, Zygosaccharomyces rouxii, were determined by using synthetic medium. One hundred experiments were carried out; 50-ml culture flasks were inoculated with 10(3) CFU ml(-1) by using a collection strain and a wild-type strain cocktail. The biomass was measured by counting cell colonies, and growth curves were fitted by using a Baranyi equation. The growth rate decreased linearly with sugar concentration, while the effect of pH was nonlinear. Indeed, the optimal pH range was found to be pH 3.5 to 5, and pH 2.5 resulted in a 30% reduction in the growth rate. Finally, we evaluated the performance of two nonlinear predictive models developed previously to describe bacterial contamination. Equations derived from the Rosso and Ratkowsky models gave similar results; however, the model that included dimensionless terms based on the Ratkowsky equation was preferred because it contained fewer estimated parameters and also because biological interpretation of the results was easier.