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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 -
Frontiers in Microbiology 2023Finding alternatives to the use of chemical inputs to preserve the sanitary and organoleptic quality of food and beverages is essential to meet public health... (Review)
Review
Finding alternatives to the use of chemical inputs to preserve the sanitary and organoleptic quality of food and beverages is essential to meet public health requirements and consumer preferences. In oenology, numerous manufacturers already offer a diverse range of bio-protection yeasts to protect must against microbiological alterations and therefore limit or eliminate sulphites during winemaking. Bio-protection involves selecting non- yeasts belonging to different genera and species to induce negative interactions with indigenous microorganisms, thereby limiting their development and their impact on the matrix. Although the effectiveness of bio-protection in the winemaking industry has been reported in numerous journals, the underlying mechanisms are not yet well understood. The aim of this review is to examine the current state of the art of field trials and laboratory studies that demonstrate the effects of using yeasts for bio-protection, as well as the interaction mechanisms that may be responsible for these effects. It focuses on the yeast , particularly recommended for the bio-protection of grape musts.
PubMed: 37664122
DOI: 10.3389/fmicb.2023.1252973 -
FEMS Microbiology Ecology Jul 2023Bee-fungus associations are common, and while most studies focus on entomopathogens, emerging evidence suggests that bees associate with a variety of symbiotic fungi... (Review)
Review
Bee-fungus associations are common, and while most studies focus on entomopathogens, emerging evidence suggests that bees associate with a variety of symbiotic fungi that can influence bee behavior and health. Here, we review nonpathogenic fungal taxa associated with different bee species and bee-related habitats. We synthesize results of studies examining fungal effects on bee behavior, development, survival, and fitness. We find that fungal communities differ across habitats, with some groups restricted mostly to flowers (Metschnikowia), while others are present almost exclusively in stored provisions (Zygosaccharomyces). Starmerella yeasts are found in multiple habitats in association with many bee species. Bee species differ widely in the abundance and identity of fungi hosted. Functional studies suggest that yeasts affect bee foraging, development, and pathogen interactions, though few bee and fungal taxa have been examined in this context. Rarely, fungi are obligately beneficial symbionts of bees, whereas most are facultative bee associates with unknown or ecologically contextual effects. Fungicides can reduce fungal abundance and alter fungal communities associated with bees, potentially disrupting bee-fungi associations. We recommend that future study focus on fungi associated with non-honeybee species and examine multiple bee life stages to document fungal composition, abundance, and mechanistic effects on bees.
Topics: Bees; Animals; Fungicides, Industrial; Ecosystem; Mycobiome; Porifera; Metschnikowia; Fungi
PubMed: 37422442
DOI: 10.1093/femsec/fiad077 -
Archives of Microbiology Aug 2023Recently, there has been growing interest in the characterization of native yeasts for their use in production of wines with regional characteristics. This study aimed...
Recently, there has been growing interest in the characterization of native yeasts for their use in production of wines with regional characteristics. This study aimed to investigate Saccharomyces and non-Saccharomyces yeasts present in the spontaneous fermentation of Tannat and Marselan grape musts collected from Concordia (Entre Ríos, Argentina) over 2019, 2020, and 2021 vintages. The evolution of these fermentative processes was carried out by measuring total soluble solids, total acidity, volatile acidity, pH, ethanol concentration, and total carbon content. Isolated Saccharomyces and non-Saccharomyces yeasts were identified based on colony morphology in WL medium, 5.8S-ITS-RFLP analysis, and 26S rDNA D1/D2 gene sequencing. Two hundred and ten yeast colonies were isolated and identified as Pichia kudriavzevii, Saccharomyces cerevisiae, Hanseniaspora uvarum, Metschnikowia pulcherrima, Candida albicans, Candida parapsilosis, Pichia occidentalis, Pichia bruneiensis, Hanseniaspora opuntiae, Issatchenkia terricola, and Hanseniaspora vineae. P. kudriavzevii isolated from all vintages was associated with the spontaneous fermentation of grape musts from the Concordia region.
Topics: Vitis; Fermentation; Yeasts; Wine; Saccharomyces cerevisiae; DNA, Ribosomal
PubMed: 37550458
DOI: 10.1007/s00203-023-03646-1 -
Life (Basel, Switzerland) Dec 2023Consumers today seek safe functional foods with proven health-promoting properties. Current evidence shows that a healthy diet can effectively alleviate oxidative stress...
Consumers today seek safe functional foods with proven health-promoting properties. Current evidence shows that a healthy diet can effectively alleviate oxidative stress levels and reduce inflammatory markers, thereby preventing the occurrence of many types of cancer, hypertension, and cardiovascular and neurological pathologies. Nevertheless, as fruits and vegetables are mainly consumed fresh, they can serve as vectors for the transmission of pathogenic microorganisms associated with various disease outbreaks. As a result, there has been a surge in interest in the microbiome of fruits and vegetables. Therefore, given the growing interest in sweet cherries, and since their microbial communities have been largely ignored, the primary purpose of this study is to investigate their culturome at various maturity stages for the first time. A total of 55 microorganisms were isolated from sweet cherry fruit, comprising 23 bacteria and 32 fungi species. Subsequently, the selected isolates were molecularly identified by amplifying the 16S rRNA gene and ITS region. Furthermore, it was observed that the communities became more diverse as the fruit matured. The most abundant taxa included and among the bacteria, and , , and among the fungi.
PubMed: 38137924
DOI: 10.3390/life13122323 -
Mycopathologia Dec 2023The majority of Candida species are known as non-pathogenic yeasts and rarely involved in human diseases. However, recently case reports of human infections caused by...
The majority of Candida species are known as non-pathogenic yeasts and rarely involved in human diseases. However, recently case reports of human infections caused by non-albicans Candida species have increased, mostly in immunocompromised hosts. Our study aimed to describe and characterize as thoroughly as possible, a new species of the Metschnikowia clade, named here Candida massiliensis (PMML0037), isolated from a clinical sample of human sputum. We targeted four discriminant genetic regions: "Internal Transcribed Spacers" of rRNA, D1/D2 domains (28S large subunit rRNA) and part of the genes encoding Translation Elongation Factor 1-α and β-tubulin2. The genetic data were compared to morphological characters, from scanning electron microscopy (TM 4000 Plus, SU5000), physiological, including the results of oxidation and assimilation tests of different carbon sources by the Biolog system, and chemical mapping by Energy-Dispersive X-ray Spectroscopy. Lastly, the in vitro antifungal susceptibility profile was performed using the E-test™ exponential gradient method. The multilocus analysis supported the genetic position of Candida massiliensis (PMML0037) as a new species of the Metschnikowia clade, and the phenotypic analysis highlighted its unique morphological and chemical profile when compared to the other Candida/Metschnikowia species included in the study.
Topics: Humans; DNA, Ribosomal Spacer; Phylogeny; DNA, Fungal; Candida; Yeasts; RNA, Ribosomal; Metschnikowia; RNA, Ribosomal, 28S; Sequence Analysis, DNA; Mycological Typing Techniques
PubMed: 37728680
DOI: 10.1007/s11046-023-00792-4 -
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 -
Journal of Fungi (Basel, Switzerland) Oct 2023var. is a pathogenic yeast which can affect aquacultured and marine-cultured animals such as brine shrimp, ridgetail white prawn, chinook salmon, giant freshwater... (Review)
Review
var. is a pathogenic yeast which can affect aquacultured and marine-cultured animals such as brine shrimp, ridgetail white prawn, chinook salmon, giant freshwater prawn, the Chinese mitten crab, marine crab, the mud crab, the mangrove land crab, the Chinese grass shrimp, sea urchins, sea urchins, and even snails, causing a milky disease, and it has caused big economic losses in aquacultural and marine-cultural industries in the past. However, the detailed mechanisms and the reasons for the milky disease in the diseased aquatic animals are still completely unknown. So far, only some antimycotics, killer toxins and Massoia lactone haven been found to be able to actively control and kill its growth. The ecofriendly, green and renewable killer toxins and Massoia lactone have high potential for application in controlling the milky disease.
PubMed: 37888280
DOI: 10.3390/jof9101024 -
Anais Da Academia Brasileira de Ciencias 2023Harsh and extreme environments, such as Antarctica, offer unique opportunities to explore new microbial taxa and biomolecules. Given the limited knowledge on microbial...
Harsh and extreme environments, such as Antarctica, offer unique opportunities to explore new microbial taxa and biomolecules. Given the limited knowledge on microbial diversity, this study aimed to compile, analyze and compare a subset of the biobank of Antarctic fungi maintained at the UNESP's Central of Microbial Resources (CRM-UNESP). A total of 711 isolates (240 yeasts and 471 filamentous fungi) from marine and terrestrial samples collected at King George Island (South Shetland Islands, Antarctica) were used with the primary objective of investigating their presence in both marine and terrestrial environments. Among the yeasts, 13 genera were found, predominantly belonging to the phylum Basidiomycota. Among the filamentous fungi, 34 genera were represented, predominantly from the phylum Ascomycota. The most abundant genera in the marine samples were Metschnikowia, Mrakia, and Pseudogymnoascus, while in the terrestrial samples, they were Pseudogymnoascus, Leucosporidium, and Mortierella. Most of the genera and species of the CRM-UNESP biobank of Antarctic fungi are being reported as an important target for biotechnological applications. This study showed the relevance of the CRM-UNESP biobank, highlighting the importance of applying standard methods for the preservation of the biological material and associated data (BMaD), as recommended in national and international standards.
Topics: Antarctic Regions; Biological Specimen Banks; Fungi; Yeasts; Ascomycota; Basidiomycota
PubMed: 38126380
DOI: 10.1590/0001-3765202320230603