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Scientific Reports Apr 2020As a complex microbial ecosystem, wine is a particularly interesting model for studying interactions between microorganisms as fermentation can be done by microbial...
As a complex microbial ecosystem, wine is a particularly interesting model for studying interactions between microorganisms as fermentation can be done by microbial consortia, a unique strain or mixed culture. The effect of a specific yeast strain on its environments is unique and characterized by its metabolites and their concentration. With its great resolution and excellent mass accuracy, ultrahigh resolution mass spectrometry (uHRMS) is the perfect tool to analyze the yeast metabolome at the end of alcoholic fermentation. This work reports the change in wine chemical composition from pure and mixed culture fermentation with Lachancea thermotolerans, Starmerella bacillaris, Metschnikowia pulcherrima and S. cerevisiae. We could clearly differentiate wines according to the yeast strain used in single cultures and markers, which reflect important differences between the yeast species, were extracted and annotated. Moreover, uHRMS revealed underlining intra species metabolomics differences, showing differences at the strain level between the two Starmerella bacillaris. Non volatile metabolomics analysis of single and sequential fermentations confirmed that mixed fermentations lead to a different composition. Distinct metabolites appeared in wines from sequential fermentation compared to single fermentation. This suggests that interactions between yeasts are not neutral.
Topics: Alcohols; Fermentation; Metabolome; Microbiota; Saccharomycetales; Volatile Organic Compounds; Wine
PubMed: 32269331
DOI: 10.1038/s41598-020-63182-6 -
BioRxiv : the Preprint Server For... Jul 2023Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The...
Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast , but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera and trended larger, while several species in the order Saccharomycetales, which includes , exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.
PubMed: 37577532
DOI: 10.1101/2023.07.28.551029 -
Frontiers in Microbiology 2023Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The...
INTRODUCTION
Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast , but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available.
METHODS
By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades.
RESULTS
Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera and trended larger, while several species in the order Saccharomycetales, which includes , exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements.
DISCUSSION
As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.
PubMed: 38075892
DOI: 10.3389/fmicb.2023.1268944 -
Journal of Fungi (Basel, Switzerland) Oct 2022The aim of this study was to investigate the effects of purified β-glucosidases from SLY-4, F2-24, and HX-13 (named as SLY-4E, F2-24E, and HX-13E, respectively) on...
The aim of this study was to investigate the effects of purified β-glucosidases from SLY-4, F2-24, and HX-13 (named as SLY-4E, F2-24E, and HX-13E, respectively) on the flavor complexity and typicality of wines. Cabernet Sauvignon wines were fermented by with the addition of SLY-4E, F2-24E, and HX-13E; the fermentation process and characteristics of wines were analyzed. The addition of SLY-4E, F2-24E, and HX-13E into must improved the contents of terpenes, higher alcohols, and esters, and decreased the contents of C compounds and fatty acids, which enhanced the fruity, floral, and taste aspects, reducing the unpleasant green of wines with no significant difference in their appearance. β-glucosidases from different yeast species produced different aroma compound profiles which presented different flavor and quality. F2-24EW had the best effect on flavor and quality of wine followed by SLY-4EW and HX-13EW. These research results can provide references for the use of β-glucosidases from non- yeasts to improve the flavor complexity, typicality, and quality of wines.
PubMed: 36294622
DOI: 10.3390/jof8101057 -
Philosophical Transactions of the Royal... May 2018Anthropogenic resource supplementation can shape wildlife disease directly by altering the traits and densities of hosts and parasites or indirectly by stimulating prey,... (Review)
Review
Anthropogenic resource supplementation can shape wildlife disease directly by altering the traits and densities of hosts and parasites or indirectly by stimulating prey, competitor or predator species. We first assess the direct epidemiological consequences of supplementation, highlighting the similarities and differences between food provisioning and two widespread forms of nutrient input: agricultural fertilization and aquatic nutrient enrichment. We then review an aquatic disease system and a general model to assess whether predator and competitor species can enhance or overturn the direct effects of enrichment. All forms of supplementation can directly affect epidemics by increasing host population size or altering parasite production within hosts, but food provisioning is most likely to aggregate hosts and increase parasite transmission. However, if predators or competitors increase in response to supplementation, they could alter resource-fuelled outbreaks in focal hosts. We recommend identifying the traits of hosts, parasites or interacting species that best predict epidemiological responses to supplementation and evaluating the relative importance of these direct and indirect mechanisms. Theory and experiments should examine the timing of behavioural, physiological and demographic changes for realistic, variable scenarios of supplementation. A more integrative view of resource supplementation and wildlife disease could yield broadly applicable disease management strategies.This article is part of the theme issue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'.
Topics: Animals; Chlorophyta; Competitive Behavior; Daphnia; Fish Diseases; Fishes; Food Chain; Host-Pathogen Interactions; Humans; Metschnikowia; Models, Statistical; Mycoses; Predatory Behavior; Spores, Fungal
PubMed: 29531153
DOI: 10.1098/rstb.2017.0101 -
Emerging biotechnologies and non-thermal technologies for winemaking in a context of global warming.Frontiers in Microbiology 2023In the current situation, wine areas are affected by several problems in a context of global warming: asymmetric maturities, pH increasing, high alcohol degree and flat... (Review)
Review
In the current situation, wine areas are affected by several problems in a context of global warming: asymmetric maturities, pH increasing, high alcohol degree and flat wines with low freshness and poor aroma profile. The use of emerging biotechnologies allows to control or manage such problems. Emerging non- as are very useful for controlling pH by the formation of stable lactic acid from sugars with a slight concomitant alcohol reduction. Lower pH improves freshness increasing simultaneously microbiological stability. The use of spp. (specially and ) or promotes a better aroma complexity and improves wine sensory profile by the expression of a more complex metabolic pattern and the release of extracellular enzymes. Some of them are also compatible or synergic with the acidification by , and is an interesting biotool for reductive winemaking and bioprotection. The use of bioprotection is a powerful tool in this context, allowing oxidation control by oxygen depletion, the inhibition of some wild microorganisms, improving the implantation of some starters and limiting SO. This can be complemented with the use of reductive yeast derivatives with high contents of reducing peptides and relevant compounds such as glutathione that also are interesting to reduce SO. Finally, the use of emerging non-thermal technologies as Ultra High-Pressure Homogenization (UHPH) and Pulsed Light (PL) increases wine stability by microbial control and inactivation of oxidative enzymes, improving the implantation of emerging non- and lowering SO additions. GRAPHICAL ABSTRACT.
PubMed: 37869658
DOI: 10.3389/fmicb.2023.1273940 -
Frontiers in Bioscience (Elite Edition) Jan 2023The vineyard is a great reservoir of autochthonous yeast strains whose composition is defined by different regional (edaphology, orography or climatology) and...
BACKGROUND
The vineyard is a great reservoir of autochthonous yeast strains whose composition is defined by different regional (edaphology, orography or climatology) and anthropological factors (cultivation systems or cultural practices). Most of this yeast diversity corresponds to non- strains, some of which have potential use in winemaking.
METHODS
The oenological potential of 29 different native non- strains belonging to 4 species (, , and spp.) was evaluated, using the autochthonous XG3 strain as a control. Microfermentations with pure culture of each strain were performed in duplicate and the basic parameters and major volatiles of wines were analysed following official methodology. The best strain within each species was selected using a quantification matrix including the relevant oenological characteristics.
RESULTS
The fermentative ability of non- was lower than in all cases, but with differences among species. and showed higher fermentation rates than , whereas spp. presented a low fermentative power. At chemical level all non- strains reduced the alcoholic content, the higher alcohols and the volatile acidity of wines and increased the content of glycerol, with differences among strains within a given species. and increased the total acidity of wines. The latter and spp. strains produced lactic acid, which decreased the wine pH in the case of . According to their oenological traits the best rated strains of each species were Lt93, Td315, Mf278 and Sb474. In addition, the data obtained in pure fermentations were correlated to those chemical and aromatic compounds obtained with these non- strains in sequential fermentations.
CONCLUSIONS
Autochthonous strains of non- yeast species contribute distinctive chemical characteristics to the wines. The correlations observed between wines fermented with the different non- indigenous strains in pure and sequential fermentations suggest that their contribution to wine properties remains stable regardless of must composition or winemaking techniques.
Topics: Saccharomyces cerevisiae; Vitis; Wine; Glycerol
PubMed: 36959102
DOI: 10.31083/j.fbe1501001 -
Frontiers in Microbiology 2021Biosurfactants are potential biomolecules that have extensive utilization in cosmetics, medicines, bioremediation and processed foods. Yeast produced biosurfactants...
Biosurfactants are potential biomolecules that have extensive utilization in cosmetics, medicines, bioremediation and processed foods. Yeast produced biosurfactants offer thermal resistance, antioxidant activity, and no risk of pathogenicity, illustrating their promising use in food formulations. The present study is aimed to assess potential of biosurfactant screened from a novel yeast and their inhibition against food spoilage fungi. A novel asexual ascomycetes yeast strain CIG-6A producing biosurfactant, was isolated from the gut of stingless bee from Churdhar, HP, India. The phylogenetic analysis revealed that the strain CIG-6A was closely related to , showing 94.38% sequence similarity in the D1D2 region for which the name f.a., sp. nov., is proposed. The strain CIG-6A was able to produce sophorolipid biosurfactant under optimum conditions. Sophorolipid biosurfactant from strain CIG-6A effectively reduced the surface tension from 72.8 to 35 mN/m. Sophorolipid biosurfactant was characterized using TLC, FTIR, GC-MS and LC-MS techniques and was a mixture of both acidic and lactonic forms. Sophorolipid assessed promising activity against pathogenic fungi viz. (MTCC 9913), (MTCC 350), and (MTCC 2190). The inhibitory effect of biosurfactant CIG-6A against was studied and MIC was 49 μgm/ml, further confirmed through confocal laser scanning microscopy. We illustrated the antifungal activity of sophorolipid biosurfactant from genus for the first time and suggested a novel antifungal compound against food spoilage and human fungal pathogen.
PubMed: 34149670
DOI: 10.3389/fmicb.2021.678668 -
Microorganisms Oct 2021Wine reflects the specificity of a , including the native microbiota. In contrast to the use of commercial starters, a way to maintain wines' microbial identities,...
Wine reflects the specificity of a , including the native microbiota. In contrast to the use of commercial starters, a way to maintain wines' microbial identities, guaranteeing at the same time the predictability and reproducibility of the wines, is the selection of autochthonous and non- strains towards optimal enological characteristics for the chosen area of isolation. This field has been explored but there is a lack of a compendium covering the main methods to use. Autochthonous wine yeasts from different areas of Slovakia were identified and tested, in the form of colonies grown either on nutrient agar plates or in grape must micro-fermentations, for technological and qualitative enological characteristics. Based on the combined results, PDA W 10, 5-1-1 and 125/14 were selected as potential wine starters. This paper, as a mixture of experimental and review contributions, provides a compendium of methods used to select autochthonous wine yeasts. Thanks to the presence of images, this compendium could guide other researchers in screening their own yeast strains for wine production.
PubMed: 34835348
DOI: 10.3390/microorganisms9112223 -
Current Biology : CB Jul 2020While sequencing and characterizing the mitochondrial genomes of 71 strains from the yeast genus Metschnikowia [1] (close cousin to the model species Candida albicans),...
While sequencing and characterizing the mitochondrial genomes of 71 strains from the yeast genus Metschnikowia [1] (close cousin to the model species Candida albicans), we uncovered one of the most extreme examples of mitochondrial genome architectural diversity observed to date. These Metschnikowia mitochondrial DNAs (mtDNAs) capture nearly the entire known gene-size and intron-content range for cox1 and cob across all eukaryotic life and show remarkable differences in structure and noncoding content. This genomic variation can be seen both among species and between strains of the same species, raising the question: why are Metschnikowia mitogenomes so malleable?
Topics: DNA, Mitochondrial; Electron Transport Complex IV; Genetic Variation; Genome, Fungal; Introns; Metschnikowia; Mitochondria; Saccharomyces cerevisiae Proteins
PubMed: 32693070
DOI: 10.1016/j.cub.2020.05.075