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

Gradient boosted regression as a tool to reveal key drivers of temporal dynamics in a synthetic yeast community

Microbial communities are vital to our lives, yet their ecological functioning and dynamics remain poorly understood. This understanding is crucial for assessing threats to these systems and leveraging their biotechnological applications. Given that temporal dynamics are linked to community functioning, this study investigated the drivers of community succession in the wine yeast community. We experimentally generated population dynamics data and used it to create an interpretable model with a gradient boosted regression tree approach. The model was trained on temporal data of viable species populations in various combinations, including pairs, triplets, and quadruplets, and was evaluated for predictive accuracy and input feature importance. Key findings revealed that the inoculation dosage of non-Saccharomyces species significantly influences their performance in mixed cultures, while Saccharomyces cerevisiae consistently dominates regardless of initial abundance. Additionally, we observed multispecies interactions where the dynamics of Wickerhamomyces anomalus were influenced by Torulaspora delbrueckii in pairwise cultures, but this interaction was altered by the inclusion of S. cerevisiae. This study provides insights into yeast community succession and offers valuable machine learning-based analysis techniques applicable to other microbial communities, opening new avenues for harnessing microbial communities.

Heterologous expression and characterization of salt-tolerant β-glucosidase from xerophilic Aspergillus chevalieri for hydrolysis of marine biomass

A salt-tolerant exo-β-1,3-glucosidase (BGL_MK86) was cloned from the xerophilic mold Aspergillus chevalieri MK86 and heterologously expressed in A. oryzae. Phylogenetic analysis suggests that BGL_MK86 belongs to glycoside hydrolase family 5 (aryl-phospho-β-D-glucosidase, BglC), and exhibits D-glucose tolerance. Recombinant BGL_MK86 (rBGL_MK86) exhibited 100-fold higher expression than native BGL_MK86. rBGL_MK86 was active over a wide range of NaCl concentrations [0%-18% (w/v)] and showed increased substrate affinity for p-nitrophenyl-β-D-glucopyranoside (pNPBG) and turnover number (kcat) in the presence of NaCl. The enzyme was stable over a broad pH range (5.5-9.5). The optimum reaction pH and temperature for hydrolysis of pNPBG were 5.5 and 45 °C, respectively. rBGL_MK86 acted on the β-1,3-linked glucose dimer laminaribiose, but not β-1,4-linked or β-1,6-linked glucose dimers (cellobiose or gentiobiose). It showed tenfold higher activity toward laminarin (a linear polymer of β-1,3 glucan) from Laminaria digitata than laminarin (β-1,3/β-1,6 glucan) from Eisenia bicyclis, likely due to its inability to act on β-1,6-linked glucose residues. The β-glucosidase retained hydrolytic activity toward crude laminarin preparations from marine biomass in moderately high salt concentrations. These properties indicate wide potential applications of this enzyme in saccharification of salt-bearing marine biomass.

Tripartite interactions comprising yeast-endobacteria systems in the gut of vector mosquitoes

It is shown that bacteria use yeast as a niche for survival in stressful conditions, therefore yeasts may act as temporary or permanent bacterial reservoirs. Endobacteria colonise the fungal vacuole of various osmotolerant yeasts which survive and multiply in sugar-rich sources such as plant nectars. Nectar-associated yeasts are present even in the digestive system of insects and often establish mutualistic symbioses with both hosts. Research on insect microbial symbioses is increasing but bacterial-fungal interactions are yet unexplored. Here, we have focused on the endobacteria of Wickerhamomyces anomalus (formerly Pichia anomala and Candida pelliculosa), an osmotolerant yeast associated with sugar sources and the insect gut. Symbiotic strains of W. anomalus influence larval development and contribute digestive processes in adults, in addition to exerting wide antimicrobial properties for host defence in diverse insects including mosquitoes. Antiplasmodial effects of W. anomalus have been shown in the gut of the female malaria vector mosquito Anopheles stephensi. This discovery highlights the potential of utilizing yeast as a promising tool for symbiotic control of mosquito-borne diseases. In the present study, we have carried out a large Next Generation Sequencing (NGS) metagenomics analysis including W. anomalus strains associated with vector mosquitoes Anopheles, Aedes and Culex, which has highlighted wide and heterogeneous EB communities in yeast. Furthermore, we have disclosed a Matryoshka-like association in the gut of A stephensi that comprises different EB in the strain of W. anomalus WaF17.12. Our investigations started with the localization of fast-moving bacteria-like bodies within the yeast vacuole of WaF17.12. Additional microscopy analyses have validated the presence of alive intravacuolar bacteria and 16S rDNA libraries from WaF17.12 have identified a few bacterial targets. Some of these EB have been isolated and tested for lytic properties and capability to re-infect the yeast cell. Moreover, a selective competence to enter yeast cell has been shown comparing different bacteria. We suggested possible tripartite interactions among EB, W. anomalus and the host, opening new knowledge on the vector biology.

Application of Bioactive Coatings with Killer Yeasts to Control Post-Harvest Apple Decay Caused by Botrytis cinerea and Penicillium italicum

A new method was proposed to produce alginate bio-films containing Pichia membranifaciens and Wickerhamomyces anomalus killer yeast to control the post-harvest fungal decay in organic apples caused by Botrytis cinerea and Penicillium italicum. Coatings with W. anomalus killer yeast effectively controlled the growth of P. italicum during storage at 22 °C. W. anomalus killer yeast incorporated in alginate reduced the P. italicum incidence from 90% (control) to 35% after 14 days of storage at 22 °C. Alginate biofilms with W. anomalus or P. membranifaciens also limited the incidence of the fungal decay of apples inoculated with B. cinerea compared with the control fruits, although the antagonistic capability against B. cinerea was lower than against P. italicum. The survival of W. anomalus cells in alginate coating was higher than P. membranifaciens. The incorporation of killer yeasts into alginate had no significant effect on the mechanical properties (tensile strength, percent elongation at break) of alginate coating, however, they increased the thickness of the biofilm. The bioactive coating reduced the fruit weight loss and had no significant effects on the fruit firmness during storage at 2 °C. As organic apples, produced without any synthetic fungicides, are especially prone to fungal decay during storage, the proposed alginate biofilms containing killer yeast seem to be a very promising solution by offering non-chemical, biological control of post-harvest pathogens.

Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding

We assessed fungal diversity in deep-sea sediments obtained from different depths in the Southern Ocean using the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA by metabarcoding through high-throughput sequencing (HTS). We detected 655,991 DNA reads representing 263 fungal amplicon sequence variants (ASVs), dominated by Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Chytridiomycota and Rozellomycota, confirming that deep-sea sediments can represent a hotspot of fungal diversity in Antarctica. The community diversity detected included 17 dominant fungal ASVs, 62 intermediate and 213 rare. The dominant fungi included taxa of Mortierella, Penicillium, Cladosporium, Pseudogymnoascus, Phaeosphaeria and Torula. Despite the extreme conditions of the Southern Ocean benthos, the total fungal community detected in these marine sediments displayed high indices of diversity and richness, and moderate dominance, which varied between the different depths sampled. The highest diversity indices were obtained in sediments from 550 m and 250 m depths. Only 49 ASVs (18.63%) were detected at all the depths sampled, while 16 ASVs were detected only in the deepest sediment sampled at 1463 m. Based on sequence identities, the fungal community included some globally distributed taxa, primarily recorded otherwise from terrestrial environments, suggesting transport from these to deep marine sediments. The assigned taxa included symbionts, decomposers and plant-, animal- and human-pathogenic fungi, suggesting that deep-sea sediments host a complex fungal diversity, although metabarcoding does not itself confirm that living or viable organisms are present.

Microbial-based Biocontrol Solutions for Fruits and Vegetables: Recent Insight, Patents, and Innovative Trends

BACKGROUND

Fruits and vegetables are susceptible to colonisation by undesired microflora, which, in pre- and post-harvest conditions, negatively impact the quality of these products, leading to a reduction of yield, shelf-life, and marketability. In the few last years, the use of microbial Biological Control Agents (BCAs) has assumed international relevance in order to control harmful microorganisms, as a promising alternative to chemical interventions.

OBJECTIVE

The purpose of this review is to discuss the microbial-based solutions applicable for the biocontrol of the main microbial spoilers, phytopathogens, and human food-borne pathogens affecting fruits and vegetables during their production and storage.

RESULTS

A comprehensive overview of the scientific literature investigating the effectiveness of BCA-based products available on the market is provided, as well as of the most recent patents protecting biotechnological applications in this field. Innovative trends are discussed, with a particular focus on the integration of BCAs to minimise spoilage phenomena and microbiological risks adopting combined approaches.

CONCLUSION

This study underlines the growing interest about biocontrol strategies to counteract the growth of spoilage and/or pathogenic microorganisms indicating that in the next years a considerable increase of commercial products and patents will be developed worldwide to exploit innovative biotechnological solutions in the sector.

Expression of the Thermobifida fusca β-1,3-Glucanase in Yarrowia lipolytica and Its Application in Hydrolysis of β-1,3-Glucan from Four Kinds of Polyporaceae

The gene encoding a thermostable β-1,3-glucanase was cloned from Thermobifida fusca and expressed constitutively by Yarrowia lipolytica using plasmid pYLSC1. The expression level of the recombinant β-1,3-glucanase reached up to 270 U/mL in the culture medium. After a treatment with endo-β-N-acetyl-glucosaminidase H, the recombinant protein appeared as a single protein band, with a molecular size of approximately 66 kDa on the SDS-polyacrylamide gel. The molecular weight was consistent with the size predicted from the nucleotide sequence. The optimum temperature and pH of the transformant β-1,3-glucanase were 60 °C and pH 8.0, respectively. This β-1,3-glucanase was tolerant to 10% methanol, ethanol, and DMSO, retaining 70% activity. The enzyme markedly hydrolyzed Wolfiporia cocos and Pycnoporus sanguineus glucans. The DPPH and ABTS scavenging potential, reducing power and total phenolic contents of these two Polyporaceae hydrolysates, were significantly increased after 18 h of the enzymatic reaction. The present results indicate that T. fusca β-1,3-glucanase from Y. lipolytica transformant (pYLSC1-13g) hydrolyzes W. cocos and P. sanguineus glucans and improves the antioxidant potential of the hydrolysates.

Non-Saccharomyces in Winemaking: Source of Mannoproteins, Nitrogen, Enzymes, and Antimicrobial Compounds

Traditionally, non-Saccharomyces yeasts have been considered contaminants because of their high production of metabolites with negative connotations in wine. This aspect has been changing in recent years due to an increased interest in the use of these yeasts in the winemaking process. The majority of these yeasts have a low fermentation power, being used in mixed fermentations with Saccharomyces cerevisiae due to their ability to produce metabolites of enological interest, such as glycerol, fatty acids, organic acids, esters, higher alcohols, stable pigments, among others. Additionally, existing literature reports various compounds derived from the cellular structure of non-Saccharomyces yeasts with benefits in the winemaking process, such as polysaccharides, proteins, enzymes, peptides, amino acids, or antimicrobial compounds, some of which, besides contributing to improving the quality of the wine, can be used as a source of nitrogen for the fermentation yeasts. These compounds can be produced exogenously, and later incorporated into the winemaking process, or be uptake directly by S. cerevisiae from the fermentation medium after their release via lysis of non-Saccharomyces yeasts in sequential fermentations.

The production and application of enzymes related to the quality of fruit wine

Grape wine is the most widely consumed fruit wine in the world. With the increasing diversification of consumers' needs, the variety of fruit wines in the market is becoming more and more abundant. Whether it is the production of grape wine or other fruit wines these processes are inseparable from the participation of enzymes. The quality of these wines is closely related to the application of enzymes in the winemaking process. Enzymes are involved in pretreatment, fermentation, filtration, flavoring, aging and storage of fruit wines. This review systematically illustrated the role of pectinase, β-glucanase, β-glucosidase, glucose oxidase, lysozyme, protease, tannase and urease in the production of wines and their current production status and also provided a theoretical basis for better application of various enzymes in the production of various fruit wines. This knowledge could be great significance to improve the quality of fruit wines and reduce the production costs in the fruit wine industry.

Yeast Mycocins: a great potential for application in health

Mycocins have demonstrated inhibition of fungi, bacteria, parasites and viruses, in addition to being studied as epidemiological markers and in the development of vaccines. They are defined as extracellular proteins or glycoproteins with different activities, the main mechanism of action being the inhibition of β-glucan synthesis in the cell wall of sensitive strains. Given the resistance problems created by several microorganisms to agents commonly used in clinical practice, the discovery of new substances with this purpose becomes essential. Mycocins have potential as anti-microbials because they show minimal toxicity and do not present resistance.

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.

A Future Place for Saccharomyces Mixtures and Hybrids in Wine Making

Each year, winemakers can face sluggish or stuck fermentations during wine making, especially when a spontaneous fermentation is performed, even if strains of the classical wine yeast Saccharomyces cerevisiae are applied. Problems are inevitable when low ammonium concentrations (<160 mg L−1 grape must) or an excess of fructose compared to glucose are observed during grape must fermentation. S. cerevisiae strains cannot use all kinds of amino acids as the sole nitrogen source but usually need free ammonium (optimal concentration: 600 mg L−1 grape must). It preferably consumes glucose, leading often to an excess of fructose in the fermenting must, which contains glucose and fructose in an equal ratio at the beginning of fermentation. Yeast hybrids have been isolated from wines several times and different strains are already commercially available. The united properties of the parent strains can provide advantages under sophisticated fermentation conditions. However, the involvement of a hybrid yeast for the rectification of fermentation disorders in spontaneous fermentations has only been described recently in the literature. Recent investigations have provided convincing evidence that fermentation problems can be overcome when must fermentations are successively performed with Saccharomyces bayanus strain HL 77 and the triple hybrid S. cerevisiae × Saccharomyces kudriavzevii × S. bayanus strain HL 78. The triple hybrid strain HL 78 uses amino acids as a nitrogen source in the absence of ammonium and it also exhibits a fructophilic character with an enhanced uptake of fructose in comparison to glucose. The application of genetically modified yeast strains is not allowed for starter cultures in wine making, but the usage of yeast mixtures and hybrid strains could be a promising tool for winemakers to solve fermentation problems during spontaneous fermentation or for the creation of novel wine types with desired sensory characteristics under more challenging conditions, especially when the composition of the must components is not optimal because of, e.g., critical climatic or soil conditions.

Wine Phenolic Compounds: Antimicrobial Properties against Yeasts, Lactic Acid and Acetic Acid Bacteria

Microorganisms play an important role in the conversion of grape juice into wine. Yeasts belonging the genus Saccharomyces are mainly responsible for the production of ethanol, but members of other genera are known as producers of off-flavors, e.g., volatile phenols. Lactic acid and acetic acid bacteria also occur regularly in must and wine. They are mostly undesirable due to their capacity to produce wine-spoiling compounds (acetic acid, biogenic amines, N-heterocycles, diacetyl, etc.). In conventional winemaking, additions of sulfite or lysozyme are used to inhibit growth of spoilage microorganisms. However, there is increasing concern about the health risks connected with these enological additives and high interest in finding alternatives. Phenols are naturally occurring compounds in grapes and wine and are well known for their antimicrobial and health-promoting activities. In this study, we tested a selection of phenolic compounds for their effect on growth and viability of wine-associated yeasts and bacteria. Our investigations confirmed the antimicrobial activities of ferulic acid and resveratrol described in previous studies. In addition, we found syringaldehyde highly efficient against wine-spoiling bacteria at concentrations of 250–1000 µg/mL. The promising bioactive activities of this aromatic aldehyde and its potential for winemaking deserves further research.

Past and Future of Non-Saccharomyces Yeasts: From Spoilage Microorganisms to Biotechnological Tools for Improving Wine Aroma Complexity

It is well established that non-Saccharomyces wine yeasts, considered in the past as undesired or spoilage yeasts, can enhance the analytical composition, and aroma profile of the wine. The contribution of non-Saccharomyces yeasts, including the ability to secret enzymes and produce secondary metabolites, glycerol and ethanol, release of mannoproteins or contributions to color stability, is species- and strain-specific, pointing out the key importance of a clever strain selection. The use of mixed starters of selected non-Saccharomyces yeasts with strains of Saccharomyces cerevisiae represents an alternative to both spontaneous and inoculated wine fermentations, taking advantage of the potential positive role that non-Saccharomyces wine yeast species play in the organoleptic characteristics of wine. In this context mixed starters can meet the growing demand for new and improved wine yeast strains adapted to different types and styles of wine. With the aim of presenting old and new evidences on the potential of non-Saccharomyces yeasts to address this market trend, we mainly review the studies focused on non-Saccharomyces strain selection and design of mixed starters directed to improve primary and secondary aroma of wines. The ability of non-Saccharomyces wine yeasts to produce enzymes and metabolites of oenological relevance is also discussed.