Biotechnology, physiology and genetics of the yeastPichia anomala

Effects of Salinity on Physicochemical Properties, Flavor Compounds, and Bacterial Communities in Broad Bean Paste-Meju Fermentation

Broad bean paste (BBP) is a traditional fermented soy food, and its high salt content not only prolongs the fermentation time but also threatens human health. In this study, three BBP-meju with different salt concentrations were prepared, and the effects of varying salinity on fermentation were comprehensively compared. The results showed that salt-reduced fermentation contributed to the accumulation of amino acid nitrogen, reducing sugars, free amino acids, and organic acids. Alcohols, esters, aldehydes, and acids were the main volatile flavor compounds in BBP-meju, and the highest total volatile flavor compounds were found in medium-salt meju. Bacillus, Staphylococcus, Aspergillus, and Mortierella were the dominant microbial communities during fermentation, and there were also three opportunistic pathogens, Enterobacter, Pantoea, and Brevundimonas, respectively. According to Spearman correlation analysis, Wickerhamomyces, Bacillus, Staphylococcus, and Mortierella all showed highly significant positive correlations with ≥3 key flavor compounds, which may be the core functional flora. Furthermore, the dominant microbial genera worked synergistically to promote the formation of high-quality flavor compounds and inhibit the production of off-flavors during salt-reduced fermentation. This study provides a theoretical reference for the quality and safety control of low-salt fermented soy foods.

Fungal Community Succession and Volatile Compound Changes during Fermentation of Laobaigan Baijiu from Chinese Hengshui Region

To investigate the core fungal community succession and its effects of volatile compound production during different stages (D-1, D-2, D-3, E-4, E-5, and E-6) of Hengshui Laobaigan Baijiu, high-throughput sequencing (HTS) was carried out, accompanied by the identification and quantification of the volatile flavor compounds using headspace solid-phase coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS). HTS results demonstrated that the fungal community of stage D-1 was similar to that of E-4 after adding Daqu, while the richness and diversity of the fungal community were most prominent at stage E-6. Moreover, the addition of Daqu at the beginning of Ercha fermentation resulted in a significant increase in the relative abundances of the fungal community at the genus level, setting the stage for the production of volatile compounds. GC-MS analysis revealed the presence of a total of 45 volatile compounds. Combining the GC-MS result with the heat map and principal component analysis (PCA), the concentrations of volatile compounds were highest in stage E-5. Meanwhile, concentrations of esters, especially ethyl acetate, ethyl lactate, isoamyl acetate and ethyl hexanoate, were high in both stages E-5 and E-6. This indicated that stage E-5 was crucial to the fermentation process of Laobaigan Baijiu. Three fungal genera (Saccharomyces, Candida, and Pichia) were indicated as the core microbiota for the production of the main volatile flavor compounds of Laobaigan Baijiu through partial least square (PLS) analysis. The information provided in this study offered valuable insights into the fermentation mechanism of Laobaigan Baijiu, thereby serving as a theoretical framework for enhancing the quality of Baijiu and realizing cost-effective production.

The evolutionary ecology of fungal killer phenotypes

Ecological interactions influence evolutionary dynamics by selecting upon fitness variation within species. Antagonistic interactions often promote genetic and species diversity, despite the inherently suppressive effect they can have on the species experiencing them. A central aim of evolutionary ecology is to understand how diversity is maintained in systems experiencing antagonism. In this review, we address how certain single-celled and dimorphic fungi have evolved allelopathic killer phenotypes that engage in antagonistic interactions. We discuss the evolutionary pathways to the production of lethal toxins, the functions of killer phenotypes and the consequences of competition for toxin producers, their competitors and toxin-encoding endosymbionts. Killer phenotypes are powerful models because many appear to have evolved independently, enabling across-phylogeny comparisons of the origins, functions and consequences of allelopathic antagonism. Killer phenotypes can eliminate host competitors and influence evolutionary dynamics, yet the evolutionary ecology of killer phenotypes remains largely unknown. We discuss what is known and what remains to be ascertained about killer phenotype ecology and evolution, while bringing their model system properties to the reader's attention.

Microbiome of rehydrated corn and sorghum grain silages treated with microbial inoculants in different fermentation periods

Due to the co-evolved intricate relationships and mutual influence between changes in the microbiome and silage fermentation quality, we explored the effects of Lactobacillus plantarum and Propionibacterium acidipropionici (Inoc1) or Lactobacillus buchneri (Inoc2) inoculants on the diversity and bacterial and fungal community succession of rehydrated corn (CG) and sorghum (SG) grains and their silages using Illumina Miseq sequencing after 0, 3, 7, 21, 90, and 360 days of fermentation. The effects of inoculants on bacterial and fungal succession differed among the grains. Lactobacillus and Weissella species were the main bacteria involved in the fermentation of rehydrated corn and sorghum grain silage. Aspergillus spp. mold was predominant in rehydrated CG fermentation, while the yeast Wickerhamomyces anomalus was the major fungus in rehydrated SG silages. The Inoc1 was more efficient than CTRL and Inoc2 in promoting the sharp growth of Lactobacillus spp. and maintaining the stability of the bacterial community during long periods of storage in both grain silages. However, the bacterial and fungal communities of rehydrated corn and sorghum grain silages did not remain stable after 360 days of storage.

Impact of Non-Saccharomyces Wine Yeast Strains on Improving Healthy Characteristics and the Sensory Profile of Beer in Sequential Fermentation

The use of non-Saccharomyces yeasts in brewing is a useful tool for developing new products to meet the growing consumer demand for innovative products. Non-Saccharomyces yeasts can be used both in single and in mixed fermentations with Saccharomyces cerevisiae, as they are able to improve the sensory profile of beers, and they can be used to obtain functional beers (with a low ethanol content and melatonin production). The aim of this study was to evaluate this capacity in eight non-Saccharomyces strains isolated from Madrid agriculture. For this purpose, single fermentations were carried out with non-Saccharomyces strains and sequential fermentations with non-Saccharomyces and the commercial strain SafAle S-04. The Wickerhamomyces anomalus strain CLI 1028 was selected in pure culture for brewing beer with a low ethanol content (1.25% (v/v)) for its fruity and phenolic flavours and the absence of wort flavours. The best-evaluated strains in sequential fermentation were CLI 3 (Hanseniaspora vineae) and CLI 457 (Metschnikowia pulcherrima), due to their fruity notes as well as their superior bitterness, body, and balance. Volatile compounds and melatonin production were analysed by GC and HPLC, respectively. The beers were sensory-analysed by a trained panel. The results of the study show the potential of non-Saccharomyces strains in the production of low-alcohol beers, and as a flavour enhancement in sequential fermentation.

Yeasts Inhabiting Extreme Environments and Their Biotechnological Applications

Yeasts are microscopic fungi inhabiting all Earth environments, including those inhospitable for most life forms, considered extreme environments. According to their habitats, yeasts could be extremotolerant or extremophiles. Some are polyextremophiles, depending on their growth capacity, tolerance, and survival in the face of their habitat's physical and chemical constitution. The extreme yeasts are relevant for the industrial production of value-added compounds, such as biofuels, lipids, carotenoids, recombinant proteins, enzymes, among others. This review calls attention to the importance of yeasts inhabiting extreme environments, including metabolic and adaptive aspects to tolerate conditions of cold, heat, water availability, pH, salinity, osmolarity, UV radiation, and metal toxicity, which are relevant for biotechnological applications. We explore the habitats of extreme yeasts, highlighting key species, physiology, adaptations, and molecular identification. Finally, we summarize several findings related to the industrially-important extremophilic yeasts and describe current trends in biotechnological applications that will impact the bioeconomy.

The Flo Adhesin Family

The first step in the infection of fungal pathogens in humans is the adhesion of the pathogen to host tissue cells or abiotic surfaces such as catheters and implants. One of the main players involved in this are the expressed cell wall adhesins. Here, we review the Flo adhesin family and their involvement in the adhesion of these yeasts during human infections. Firstly, we redefined the Flo adhesin family based on the domain architectures that are present in the Flo adhesins and their functions, and set up a new classification of Flo adhesins. Next, the structure, function, and adhesion mechanisms of the Flo adhesins whose structure has been solved are discussed in detail. Finally, we identified from Pfam database datamining yeasts that could express Flo adhesins and are encountered in human infections and their adhesin architectures. These yeasts are discussed in relation to their adhesion characteristics and involvement in infections.

Wickerhamomyces Yeast Killer Toxins' Medical Applications

Possible implications and applications of the yeast killer phenomenon in the fight against infectious diseases are reviewed, with particular reference to some wide-spectrum killer toxins (KTs) produced by Wickerhamomyces anomalus and other related species. A perspective on the applications of these KTs in the medical field is provided considering (1) a direct use of killer strains, in particular in the symbiotic control of arthropod-borne diseases; (2) a direct use of KTs as experimental therapeutic agents; (3) the production, through the idiotypic network, of immunological derivatives of KTs and their use as potential anti-infective therapeutics. Studies on immunological derivatives of KTs in the context of vaccine development are also described.

Linking the Diversity of Yeasts Inherent in Starter Cultures to Quorum Sensing Mechanism in Ethnic Fermented Alcoholic Beverages of Northeast India

In this review, the relevance of diversity of yeasts and their interactive association in household ethnic fermentation are discussed. The longstanding traditional household fermentation practice involves preparation of fermented product such as alcoholic beverages from various indigenous agricultural products with the help of microorganisms cultivated from local environment and perpetuated for hundreds of years through generations indoctrinating an indigenous knowledge system. Northeast India is known for its rich physiographic and geo-demographic diversity and is home to several ethnicities who follow unique practices of household traditional fermentation. The diversity of yeasts present within the microbial inoculum used for fermentation by different indigenous communities has been keenly studied and reported to be unique in spite of their common source for starter substrates. Saccharomyces yeasts are primarily involved in alcoholic fermentation, whereas non-Saccharomyces yeasts, which are reportedly confined to a particular geographical region, have been reported to contribute toward the final outcome of fermentation produce. During fermentation, interaction among these large microbial communities and their resulting physiological expression within the fermentation micro-environment is believed to affect the final quality of the product. Mechanism of quorum sensing plays an important role in these interactions in order to maintain proportionality of different yeast populations wherein the quorum sensing molecules not only regulate population density but also effectively aid in enhancement of alcoholic fermentation. Additionally, various secondary metabolites, which are secreted as a result of inter-species interactions, have been found to affect the quality of beverages produced. This review concludes that diverse species of yeasts and their interaction within the fermentation micro-environment influence the sustainability and productivity of household ethnic fermentation.

The killer yeast Wickerhamomyces anomalus Cf20 exerts a broad anti-Candida activity through the production of killer toxins and volatile compounds

Candidiasis is a group of opportunistic infections caused by yeast of the genus Candida. The appearance of drug resistance and the adverse effects of current antifungal therapies require the search for new, more efficient therapeutic alternatives. Killer yeasts have aroused as suitable candidates for mining new antifungal compounds. Killer strains secrete antimicrobial proteins named killer toxins, with promissory antifungal activity. Here we found that the killer yeast Wickerhamomyces anomalus Cf20 and its cell-free supernatant (CFS) inhibited six pathogenic strains and one collection strain of Candida spp. The inhibition is mainly mediated by secreted killer toxins and, to a lesser extent, by volatile compounds such as acetic acid and ethyl acetate. A new large killer toxin (>180 kDa) was purified, which exerted 70-74% of the total CFS anti-Candida activity, and the previously described glucanase KTCf20 was inhibitory in a lesser extent as well. In addition, we demonstrated that Cf20 possesses the genes encoding for the β-1,3-glucanases WaExg1 and WaExg2, proteins with extensively studied antifungal activity, particularly WaExg2. Finally, the 10-fold concentrated CFS exerted a high candidacidal effect at 37°C, completely inhibiting the fungal growth, although the nonconcentrated CFS (RCF 1) had very limited fungistatic activity at this temperature. In conclusion, W. anomalus Cf20 produces different low and high molecular weight compounds with anti-Candida activity that could be used to design new therapies for candidiasis and as a source for novel antimicrobial compounds as well.

Valorization of apple and grape wastes with malic acid-degrading yeasts

It is estimated that more than 20% of processed apples and grapes are discarded as waste, which is dominated by pomace rich in malic acid that could be converted to high-value organic acids or other chemicals. A total of 98 yeast strains isolated from apple, grape, and plum wastes were evaluated for their ability to degrade malic acid relative to known yeast strains. Most (94%) of the new isolates degraded malic acid efficiently (> 50%) in the presence and absence of exogenous glucose, whereas only 14% of the known strains could do so, thus confirming the value of exploring (and exploiting) natural biodiversity. The best candidates were evaluated in synthetic media for their ability to convert malic acid to other valuable products under aerobic and oxygen-limited conditions, with two strains that produced ethanol and acetic acid as potential biorefinery products during aerobic cultivations and oxygen-limited fermentations on sterilized apple and grape pomace. Noteworthy was the identification of a Saccharomyces cerevisiae strain that is more efficient in degrading malic acid than other members of the species. This natural strain could be of value in the wine-making industry that often requires pH corrections due to excess malic acid.

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

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

Effect of Saccharomyces and non-Saccharomyces native yeasts on beer aroma compounds

Recently, the increase in microbreweries and the consequent production of craft beers have reached exponential growth. The interest in non-conventional yeasts for innovation and a unique selling feature in beer fermentation is increasing. This work studied the autochthonous Saccharomyces and non-Saccharomyces yeasts, isolated from various food sources, with the ability to modify and improve the fermentative and aromatic profiles during alcoholic fermentation. The ability to ferment maltose and produce desirable aroma compounds were considered as the key characters for the screening selection. A synthetic beer wort was developed for this purpose, to simulate beer wort composition. A total of forty-seven yeast strains belonging to different genera were analysed according to their fermentation profile, volatile compounds production and sensory analysis. Three native strains of Saccharomyces cerevisiae, Zygoascus meyerae and Pichia anomala were selected to evaluate their aromatic profile in single and mixed fermentations. The strains produced 4-vinylguaiacol, β-phenylethyl alcohol, and isoamyl alcohol at levels significantly above the sensory threshold, making them interesting for wheat and blond craft beer styles. The native Hanseniaspora vineae was also included in a co-fermentation treatment, resulting in a promising yeast to produce fruity beers.

Yeast population dynamics on air exposure in total mixed ration silage with sweet potato residue

To investigate the yeast population dynamics during air exposure in total mixed ration (TMR) silage containing sweet potato residue. TMR were ensiled in laboratory silos (1 kg) with or without two lactic acid bacteria strains, Lactobacillus plantarum (LP), and Lactobacillus amylovorus (LA). Fermentation characteristics were measured and yeast population was investigated by ITS1 region gene sequencing using Illumina MiSeq platform. All treatments were well ensiled, and L. amylovorus improved aerobic stability. During aerobic exposure, Pichia kudriavzevii was detected with increased relative abundance in all treatments and more relative abundant in LP. Pichia fermentans was more relative abundant in control. Higher relative abundance of Pichia anomala was detected in deteriorating LP. The relative abundance of Pichia ohmeri increased during later aerobic exposure in the control and LA, with a significant increase in the count of yeast population. Despite Cryptococcus was detected more relative abundant during early stage of aerobic exposure, the yeast population was below the detection limit. Aerobic deterioration was characterized by an increase in operational taxonomic units of Pichia. High relative abundance of P. anomala and P. kudriavzevii made aerobic deterioration easier. Inhibition of P. fermentans might be an effective strategy for improving the aerobic stability to some instance.

Draft genome sequence of Wickerhamomyces anomalus LBCM1105, isolated from cachaça fermentation

Wickerhamomyces anomalus LBCM1105 is a yeast isolated from cachaça distillery fermentation vats, notable for exceptional glycerol consumption ability. We report its draft genome with 20.5x in-depth coverage and around 90% extension and completeness. It harbors the sequences of proteins involved in glycerol transport and metabolism.

The establishment of a fungal consortium in a new winery

The biodiversity and evolution of fungal communities were monitored over a period of 3 vintages in a new winery. Samples were collected before grape receipt and 3 months after fermentation from 3 different wine related environments (WRE): floor, walls and equipment and analyzed using Illumina Mi-Seq. Genera of mold and filamentous fungi (294), non-enological (10) and wine-associated yeasts (25) were detected on all WREs before the arrival of the first harvest. Among them, genera like Alternaria and Aureobasidium persisted during two vintages. Therefore, these genera are not specific to winery environment and appear to be adapted to natural or anthropic environments due to their ubiquitous character. Some genera like Candida were also detected before the first harvest but only on one WREs, whereas, on the other WREs they were found after the harvest. The ubiquitous character and phenotypic traits of these fungal genera can explain their dynamics. After the first harvest and during 3 vintages the initial consortium was enriched by oenological genera like Starmerella introduced either by harvest or by potential transfers between the different WREs. However, these establishing genera, including Saccharomyces, do not appear to persist due to their low adaptation to the stressful conditions of winery environment.

Contribution of Non-Saccharomyces Yeasts to Wine Freshness. A Review

Freshness, although it is a concept difficult to define in wines, can be understood as a combination of different circumstances. Organolepticwise, bluish red, floral and fruity, more acidic and full-bodied wines, are perceived as younger and fresher by consumers. In traditional winemaking processes, these attributes are hard to boost if no other technology or biotechnology is involved. In this regard, the right selection of yeast strains plays an important role in meeting these parameters and obtaining wines with fresher profiles. Another approach in getting fresh wines is through the use of novel non-thermal technologies during winemaking. Herein, the contributions of non-Saccharomyces yeasts and emerging technologies to these parameters are reviewed and discussed.

Enhancement of glycerol production by UV-mutagenesis of the marine yeast Wickerhamomyces anomalus HH16: kinetics and optimization of the fermentation process

The current study aims to enhance glycerol production using UV-mutagenesis of the marine yeast Wickerhamomyces anomalus HH16 isolated from marine sediment collected from South Sinai Governorate, Egypt. Besides optimization of the culture conditions and analyzing the kinetic parameters of growth and glycerol biosynthesis by the mutant strain were studied. The marine yeast isolate HH16 was selected as the front runner glycerol-producer among all tested isolates, with glycerol yield recorded as 66.55 gl^-1. The isolate was identified based on the phenotypic and genotypic characteristics of W. anomalus. The genotypic characterization based on the internal transcribed spacer (ITS) sequence was deposited in the GenBank database with the accession number MK182824. UV-mutagenesis of W. anomalus HH16 by its exposure to UV radiation (254 nm, 200 mW cm^-2) for 5 min; increased its capability in the glycerol production rate with 16.97% (80.15 g l^-1). Based on the kinetic and Monod equations, the maximum specific growth rate (μ _max) and maximum specific glycerol production rate (v _max) by the mutant strain W. anomalus HH16MU5 were 0.21 h^-1 and 0.103 g g^-1, respectively. Optimization of the fermentation parameters such as nitrogen source, salinity and pH has been achieved. The maximum glycerol production 86.55 g l^-1 has been attained in a fermentation medium composed of 200 g l^-1 glucose, 1 g l^-1 peptone, 3 g l^-1 yeast extract, and 58.44 g l^-1 NaCl, this medium was adjusted at pH 8 and incubated for 3 days at 30° C. Moreover, results indicated the ability of this yeast to produce glycerol (73.33 g l^-1) using a seawater based medium. These findings suggest the applicability of using the yeast isolate W. anomalus HH16MU5 as a potential producer of glycerol for industrial purposes.

Analysis of the correlation between bacteria and fungi in sugarcane tops silage prior to and after aerobic exposure

The correlation between bacteria and fungi in sugarcane tops silage prior to and after aerobic exposure was analyzed. The results showed that the abundance of Lactobacillus increased from 0.03% to 27.84% from d 0-60. Additionally, the abundance of Pichia also increased from 0.003% to 15.46% from d 0-60. Following aerobic exposure, the abundance of Lactobacillus increased by 42.39% at d 3. Moreover, Pichia was the dominant fungal genus after aerobic exposure. Spearman's correlation analysis showed that Pichia was positively correlated with the genera Lactobacillus and Pediococcus, but negatively correlated with the genera Acinetobacter, Citrobacter, and Serratia. Aspergillus, Cladosporium, and Fusarium were positively correlated with the genera Clostridium, Lactobacillus, and Pediococcus, but negatively correlated with the genera Acinetobacter, Citrobacter, and Serratia. Spearman's correlation also suggested that Aspergillus, Cladosporium, and Fusarium could be inhibited by screening Serratia, thereby reducing mycotoxins in silage.

Biocontrol of Aspergillus flavus in Ensiled Sorghum by Water Kefir Microorganisms

The capacity of microorganisms from water kefir (WK) to control Aspergillus flavus growth during the aerobic phase of ensiled sorghum grains was determined. Sorghum inoculated with A. flavus was treated with filter-sterilized and non-sterilized water kefir, ensiled, and incubated 7 days at 25 °C. A. flavus growth was quantified by qPCR after incubation. Mold growth was inhibited in the presence of water kefir while no inhibition was observed when filter-sterilized water kefir was applied, demonstrating the relevant role of the microorganisms in the kefir water in the biocontrol process. Fungal and bacterial diversity in treated sorghum mini-silos was analyzed by high-throughput sequencing. Firmicutes was the predominant bacterial phyla and Lactobacillus represented the most abundant genus, while Ascomycota was the predominant fungal phyla with Saccharomyces and Pichia as the major genera. Bacterial and yeast counts before and after incubation indicated that the microbial community obtained from WK was able to grow in the sorghum mini-silos in the presence of A. flavus. Results of the present work indicate that the use of a mixed inoculum of microorganisms present in WK may represent an alternative management practice to avoid the growth of A. flavus in ensiled sorghum grains and the concomitant contamination with aflatoxins.

Role of biocontrol yeasts Debaryomyces hansenii and Wickerhamomyces anomalus in plants' defence mechanisms against Monilinia fructicola in apple fruits

The role of killer yeasts of the species Debaryomyces hansenii and Wickerhamomyces anomalus in biocontrol of Monilinia fructicola, and their involvement in plant defence mechanisms against brown rot in apple fruits, were investigated. D. hansenii KI2a and W. anomalus BS91 strains showed the highest in vitro biocontrol activity, inhibiting mycelium growth by 69.53% and 66.08% respectively, as compared to control fungal cultures. Brown rot on apple fruits was significantly reduced by BS91 and two strains of D. hansenii KI2a and AII4b by 92.46%, 85.10% and 70.02%, respectively, in comparison to infected fruits, which did not receive any pre-treatment. In enzymatic tests, the most significant changes in peroxidase (POD) and catalase (CAT) activities were observed in fruits inoculated either with BS91 followed by M. fructicola infection or with AII4b yeast strain alone, where POD activities were significantly higher by 67% and 54%, respectively, and CAT activities were significantly lower by 65% and 68%, respectively, than in untreated control fruits. These results confirmed the ability of killer yeasts to influence host-defence related enzyme activities in apple fruit tissue and may suggest that AII4b killer strain has a potential as biocontrol agent prior to infection by triggering immune response mechanisms in plant tissue, whereas BS91 strain is the most effective during pathogen infection and could be used as biocontrol agent in postharvest disease onset. Accordingly, the antagonistic strains of W. anomalus BS91 and D. hansenii KI2a and AII4b could be proposed as active ingredients for the development of biofungicide against M. fructicola.

High-affinity transport, cyanide-resistant respiration, and ethanol production under aerobiosis underlying efficient high glycerol consumption by Wickerhamomyces anomalus

Wickerhamomyces anomalus strain LBCM1105 was originally isolated from the wort of cachaça (the Brazilian fermented sugarcane juice-derived Brazilian spirit) and has been shown to grow exceptionally well at high amounts of glycerol. This paramount residue from the biodiesel industry is a promising cheap carbon source for yeast biotechnology. The assessment of the physiological traits underlying the W. anomalus glycerol consumption ability in opposition to Saccharomyces cerevisiae is presented. A new WaStl1 concentrative glycerol-H⁺ symporter with twice the affinity of S. cerevisiae was identified. As in this yeast, WaSTL1 is repressed by glucose and derepressed/induced by glycerol but much more highly expressed. Moreover, LBCM1105 aerobically growing on glycerol was found to produce ethanol, providing a redox escape to compensate the redox imbalance at the level of cyanide-resistant respiration (CRR) and glycerol 3P shuttle. This work is critical for understanding the utilization of glycerol by non-Saccharomyces yeasts being indispensable to consider their industrial application feeding on biodiesel residue.

Challenges of the Non-Conventional Yeast Wickerhamomyces anomalus in Winemaking

Nowadays it is widely accepted that non-Saccharomyces yeasts, which prevail during the early stages of alcoholic fermentation, contribute significantly to the character and quality of the final wine. Among these yeasts, Wickerhamomyces anomalus (formerly Pichia anomala, Hansenula anomala, Candida pelliculosa) has gained considerable importance for the wine industry since it exhibits interesting and potentially exploitable physiological and metabolic characteristics, although its growth along fermentation can still be seen as an uncontrollable risk. This species is widespread in nature and has been isolated from different environments including grapes and wines. Its use together with Saccharomyces cerevisiae in mixed culture fermentations has been proposed to increase wine particular characteristics. Here, we review the ability of W. anomalus to produce enzymes and metabolites of oenological relevance and we discuss its potential as a biocontrol agent in winemaking. Finally, biotechnological applications of W. anomalus beyond wine fermentation are briefly described.

Genome dynamics and evolution in yeasts: A long-term yeast-bacteria competition experiment

There is an enormous genetic diversity evident in modern yeasts, but our understanding of the ecological basis of such diversifications in nature remains at best fragmented so far. Here we report a long-term experiment mimicking a primordial competitive environment, in which yeast and bacteria co-exist and compete against each other. Eighteen yeasts covering a wide phylogenetic background spanning approximately 250 million years of evolutionary history were used to establish independent evolution lines for at most 130 passages. Our collection of hundreds of modified strains generated through such a rare two-species cross-kingdom competition experiment re-created the appearance of large-scale genomic rearrangements and altered phenotypes important in the diversification history of yeasts. At the same time, the methodology employed in this evolutionary study would also be a non-gene-technological method of reprogramming yeast genomes and then selecting yeast strains with desired traits. Cross-kingdom competition may therefore be a method of significant value to generate industrially useful yeast strains with new metabolic traits.

Characterization of bacteria and yeasts isolated from traditional fermentation starter (Fen-Daqu) through a 1H NMR-based metabolomics approach

Daqu is a traditional fermentation starter for the production of baijiu and vinegar. It is an important saccharifying and fermenting agent associated with alcoholic fermentation and also a determining factor for the flavour development of these products. Bacterial and yeast isolates from a traditional fermentation starter (Fen-Daqu) were examined for their amylolytic activity, ethanol tolerance and metabolite production during sorghum-based laboratory-scale alcoholic fermentation. The selected strains (Bacillus licheniformis, Pediococcus pentosaceus, Lactobacillus plantarum, Pichia kudriavzevii, Wickerhamomyces anomalus, Saccharomyces cerevisiae, and Saccharomycopsis fibuligera) were blended in different combinations, omitting one particular strain in each mixture. ¹H nuclear magnetic resonance (NMR) spectroscopy coupled with multivariate statistical analysis was used to investigate the influence of the selected strains on the metabolic changes observed under the different laboratory-controlled fermentation conditions. Principal component analysis showed differences in the metabolites produced by different mixtures of pure cultures. S. cerevisiae was found to be superior to other species with respect to ethanol production. S. fibuligera and B. licheniformis converted starch or polysaccharides to soluble sugars. Lactic acid bacteria had high amylolytic and proteolytic activities, thereby contributing to increased saccharification and protein degradation. W. anomalus was found to have a positive effect on the flavour of the Daqu-derived product. This study highlights the specific functions of S. cerevisiae, S. fibuligera, B. licheniformis, W. anomalus and lactic acid bacteria in the production of light-flavour baijiu (fen-jiu). Our results show that all investigated species deliver an important contribution to the functionality of the fermentation starter Daqu.

Candidacidal Activity of a Novel Killer Toxin from Wickerhamomyces anomalus against Fluconazole-Susceptible and -Resistant Strains

The isolation and characterization from the sand fly Phlebotomus perniciosus of a Wickerhamomyces anomalus yeast strain (Wa1F1) displaying the killer phenotype was recently reported. In the present work, the killer toxin (KT) produced by Wa1F1 was purified and characterized, and its antimicrobial activity in vitro was investigated against fluconazole- susceptible and -resistant clinical isolates and laboratory strains of Candida albicans and C. glabrata displaying known mutations. Wa1F1-KT showed a differential killing ability against different mutant strains of the same species. The results may be useful for the design of therapeutic molecules based on Wa1F1-KT and the study of yeast resistance mechanisms.

Yeast diversity in relation to the production of fuels and chemicals

In addition to ethanol, yeasts have the potential to produce many other industrially-relevant chemicals from numerous different carbon sources. However there remains a paucity of information about overall capability across the yeast family tree. Here, 11 diverse species of yeasts with genetic backgrounds representative of different branches of the family tree were investigated. They were compared for their abilities to grow on a range of sugar carbon sources, to produce potential platform chemicals from such substrates and to ferment hydrothermally pretreated rice straw under simultaneous saccharification and fermentation conditions. The yeasts differed considerably in their metabolic capabilities and production of ethanol. A number could produce significant amounts of ethyl acetate, arabinitol, glycerol and acetate in addition to ethanol, including from hitherto unreported carbon sources. They also demonstrated widely differing efficiencies in the fermentation of sugars derived from pre-treated rice straw biomass and differential sensitivities to fermentation inhibitors. A new catabolic property of Rhodotorula mucilaginosa (NCYC 65) was discovered in which sugar substrate is cleaved but the products are not metabolised. We propose that engineering this and some of the other properties discovered in this study and transferring such properties to conventional industrial yeast strains could greatly expand their biotechnological utility.

Microbial dynamics during production of lesser mealworms (Alphitobius diaperinus) for human consumption at industrial scale

In this study, the microbial dynamics during an industrial production cyle of lesser mealworms (Alphitobius diaperinus), sold for human consumption, were characterised. The microbial numbers as well as the microbial diversity were generally higher for the substrate, existing of remaining feed, faeces and exuviae, than for the larvae. Most of the species-level operational taxonomic units, identified using Illumina MiSeq sequencing, that were present in the feed were also detected in the larvae and vice versa. However, bacterial diversity decreased in the larvae during rearing. These results suggested that the feed is an important determinant of the insect bacterial community, but that some bacterial species show a competitive advantage inside the insect gut and become dominant. A blanching treatment of the larvae after harvest reduced most microbial counts, but the number of aerobic endospores remained at 4.0 log cfu/g. Whereas food pathogens Salmonella spp., Listeria monocytogenes, Bacillus cereus or coagulase-positive staphylococci were not detected in our study, fungal isolates corresponding to the genera Aspergillus and Fusarium were recovered. Therefore, it cannot be excluded that mycotoxins were present. The results of this study contribute to a better understanding of the microbial dynamics and food safety aspects during the production of edible insects.

A sustainable use of low-cost raw substrates for biodiesel production by the oleaginous yeast Wickerhamomyces anomalus

Over the past decade, the increasing demand of vegetable oils for biodiesel production has highlighted the need for alternative oil feedstocks that do not compete with food production. In this context, the combined use of agro-industrial wastes and oleaginous microorganisms could be a promising strategy for sustainable biodiesel production. The present investigation involves the performance of the oleaginous yeast Wickerhamomyces anomalus strain EC28 to produce lipids from different agro-industrial wastewaters (i.e., deproteinized cheese whey, olive mill wastewater, and wastewaters from confectionary industries) and waste frying oils (i.e., waste oil from frying fish, waste oil from frying potato and waste oil from frying meat). Results indicated that this strain can adequately grow on agro-industrial wastewater-based media and produce substantial amounts of lipids [up to 24%, wt/wt in deproteinized cheese whey-based medium and olive mill wastewater-based medium (75%, v/v in water)] of similar fatty acid composition to that of the most commonly used vegetable oils in the biodiesel industry. However, the addition of frying oils to the culture media resulted in a significant decrease in total lipid content, probably due to excess of available nitrogen released from meat, fish, and potato into the frying oil. The estimated properties of the resulting biodiesels, such as SV (190.69-203.13), IV (61.77-88.32), CN (53.45-59.32), and CFPP (-0.54 to 10.4), are reported, for the first time, for W. anomalus and correlate well with specified standards. In conclusion, W. anomalus strain EC28, for which there is very limited amount of available information, might be regarded as a promising candidate for biodiesel production and additional efforts for process improvement should be envisaged.

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.

Summer temperature can predict the distribution of wild yeast populations

The wine yeast, Saccharomyces cerevisiae, is the best understood microbial eukaryote at the molecular and cellular level, yet its natural geographic distribution is unknown. Here we report the results of a field survey for S. cerevisiae,S. paradoxus and other budding yeast on oak trees in Europe. We show that yeast species differ in their geographic distributions, and investigated which ecological variables can predict the isolation rate of S. paradoxus, the most abundant species. We find a positive association between trunk girth and S. paradoxus abundance suggesting that older trees harbor more yeast. S. paradoxus isolation frequency is also associated with summer temperature, showing highest isolation rates at intermediate temperatures. Using our statistical model, we estimated a range of summer temperatures at which we expect high S. paradoxus isolation rates, and show that the geographic distribution predicted by this optimum temperature range is consistent with the worldwide distribution of sites where S. paradoxus has been isolated. Using laboratory estimates of optimal growth temperatures for S. cerevisiae relative to S. paradoxus, we also estimated an optimum range of summer temperatures for S. cerevisiae. The geographic distribution of these optimum temperatures is consistent with the locations where wild S. cerevisiae have been reported, and can explain why only human-associated S. cerevisiae strains are isolated at northernmost latitudes. Our results provide a starting point for targeted isolation of S. cerevisiae from natural habitats, which could lead to a better understanding of climate associations and natural history in this important model microbe.

Pichia anomala, a new species of yeast-like endosymbionts and its variation in small brown planthopper (Laodelphax striatellus)

Yeast-like symbionts (YLS) are endosymbionts that promote the growth of delphacid planthoppers (Hemiptera: Delphacidae), some of which are pests on cultivated rice. Identification and characterization of YLS growth can be helpful for pest control, because it has been demonstrated that there is a variety of YLS in rice planthopper and they affected the planthopper's growth and virulence to plant hosts. So, elucidation of the species of YLS in planthopper is crucial for exploiting a new way to control planthopper. In this study, a new isolated of YLS was obtained from the small brown planthopper, Laodelphax striatellus, which was cultured in vitro, simultaneously identified as Pichia anomala based on its phylogenetic analysis. In order to confirm the existence of P. anomala in the L. striatellus body, we used the denaturing gradient gel electrophoresis (DGGE) to identify the YLS and obtain the specific bands for P. anomala. The quantification and localization of P. anomala in L. striatellus samples were determined by fluorescent in situ hybridization (FISH) using genus-specific 18S rDNA targeted probe. The result confirmed that a certain number of P. anomala exist in L. striatellus's abdomen. Subsequently, the variation and copy number of P. anomala in different L. striatellus instars was measured by using absolute quantitative real-time PCR (qPCR), the results indicated that the new isolated strain was closely related to the developmental process of L. striatellus.

Assessing the potential of wild yeasts for bioethanol production

Bioethanol fermentations expose yeasts to a new, complex and challenging fermentation medium with specific inhibitors and sugar mixtures depending on the type of carbon source. It is, therefore, suggested that the natural diversity of yeasts should be further exploited in order to find yeasts with good ethanol yield in stressed fermentation media. In this study, we screened more than 50 yeast isolates of which we selected five isolates with promising features. The species Candida bombi, Wickerhamomyces anomalus and Torulaspora delbrueckii showed better osmo- and hydroxymethylfurfural tolerance than Saccharomyces cerevisiae. However, S. cerevisiae isolates had the highest ethanol yield in fermentation experiments mimicking high gravity fermentations (25 % glucose) and artificial lignocellulose hydrolysates (with a myriad of inhibitors). Interestingly, among two tested S. cerevisiae strains, a wild strain isolated from an oak tree performed better than Ethanol Red, a S. cerevisiae strain which is currently commonly used in industrial bioethanol fermentations. Additionally, a W. anomalus strain isolated from sugar beet thick juice was found to have a comparable ethanol yield, but needed longer fermentation time. Other non-Saccharomyces yeasts yielded lower ethanol amounts.

The yeast Wickerhamomyces anomalus AS1 secretes a multifunctional exo-β-1,3-glucanase with implications for winemaking

A multifunctional exo-β-1,3-glucanase (WaExg2) was purified from the culture supernatant of the yeast Wickerhamomyces anomalus AS1. The enzyme was identified by mass spectroscopic analysis of tryptic peptide fragments and the encoding gene WaEXG2 was sequenced. The latter codes for a protein of 427 amino acids, beginning with a probable signal peptide (17 aa) for secretion. The mature protein has a molecular mass of 47 456 Da with a calculated pI of 4.84. The somewhat higher mass of the protein in SDS-PAGE might be due to bound carbohydrates. Presumptive disulphide bridges confer a high compactness to the molecule. This explains the apparent smaller molecular mass (35 kDa) of the native enzyme determined by electrophoresis, whereas the unfolded form is consistent with the theoretical mass. Enzymatic hydrolysis of selected glycosides and glycans by WaExg2 was proved by TLC analysis of cleavage products. Glucose was detected as the sole hydrolysis product from laminarin, underlining that the enzyme acts as an exoglucanase. In addition, the enzyme efficiently hydrolysed small β-linked glycosides (arbutin, esculin, polydatin, salicin) and disaccharides (cellobiose, gentiobiose). WaExg2 was active under typical wine-related conditions, such as low pH (3.5-4.0), high sugar concentrations (up to 20% w/v), high ethanol concentrations (10-15% v/v), presence of sulphites (up to 2 mm) and various cations. Therefore, the characterized enzyme might have multiple uses in winemaking, to increase concentrations of sensory and bioactive compounds by splitting glycosylated precursors or to reduce viscosity by hydrolysis of glycan slimes.