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Journal of Biotechnology May 2022Species of the genus Aureobasidium are ubiquitous, polyextremotolerant, "yeast-like" ascomycetes used for the industrial production of pullulan and other products and as...
Species of the genus Aureobasidium are ubiquitous, polyextremotolerant, "yeast-like" ascomycetes used for the industrial production of pullulan and other products and as biocontrol agents in agriculture. Their application potential and wide-spread occurrence make Aureobasidium spp. interesting study objects. The availability of a fast and efficient genome editing method is an obvious advantage for future basic and applied research on Aureobasidium. In this study, we describe the development of a CRISPR/Cas9-based genome editing method using ribonucleoproteins (RNPs) in A. pullulans and A. melanogenum. We demonstrate that this method can be used for single and multiplex genome editing using only RNPs by targeting URA3 (encoding for orotidine-5'-phosphate decarboxylase), ADE2 (encoding for phosphoribosylaminoimidazole carboxylase) and ARG4 (encoding for argininosuccinate lyase). We demonstrate the applicability of Trichoderma reesei pyr4 and Aspergillus fumigatus pyrG to complement the URA3 deficiency. Further, we show that using RNPs improves the homologous recombination rate and 20 bp long homologous flanks are sufficient. Therefore, the repair cassettes can be constructed by a single PCR, abolishing the need for laborious and time-consuming cloning, which is necessary for previously described methods for CRISPR-mediated genome editing in these fungi. The here presented method allows fast and efficient genome editing for gene deletions, modifications, and insertions in Auresobasidium with a minimized risk of off-target effects.
Topics: Ascomycota; Aureobasidium; CRISPR-Cas Systems; Gene Editing; Ribonucleoproteins; Saccharomyces cerevisiae
PubMed: 35398275
DOI: 10.1016/j.jbiotec.2022.03.017 -
Frontiers in Nutrition 2021Curdlan is an exopolysaccharide, which is composed of glucose linked with β-(1,3)-glycosidic bond and is produced by bacteria, such as spp., spp., spp., spp.,... (Review)
Review
Curdlan is an exopolysaccharide, which is composed of glucose linked with β-(1,3)-glycosidic bond and is produced by bacteria, such as spp., spp., spp., spp., spp., and fungal sources like , etc. Curdlan has been utilized in the food and pharmaceutical industries for its prebiotic, viscosifying, and water-holding properties for decades. Recently, the usefulness of curdlan has been further explored by the pharmaceutical industry for its potential therapeutic applications. Curdlan has exhibited immunoregulatory and antitumor activity in preclinical settings. It was observed that curdlan can prevent the proliferation of malarial merozoites ; therefore, it may be considered as a promising therapy for the treatment of end-stage malaria. In addition, curdlan has demonstrated potent antiviral effects against human immunodeficiency virus (HIV) and virus. It has been suggested that the virucidal properties of curdlans should be extended further for other deadly viruses, such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the current severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2/COVID-19). The prebiotic property of curdlan would confer beneficial effects on the host by promoting the growth of healthy microbiota in the gut and consequently help to reduce gastrointestinal disorders. Therefore, curdlan can be employed in the manufacture of prebiotics for the management of various gastrointestinal dysbiosis problems. Studies on the mechanism of action of curdlan-induced suppression in microbial and tumor cells at the cellular and molecular levels would not only enhance our understanding regarding the therapeutic effectiveness of curdlan but also help in the discovery of new drugs and dietary supplements. The primary focus of this review is to highlight the therapeutic interventions of curdlan as an anticancer, anti-malaria, antiviral, and antibacterial agent in humans. In addition, our review provides the latest information about the chemistry and biosynthesis of curdlan and its applications for making novel dairy products, functional foods, and nutraceuticals and also details about the recent patents of curdlan and its derivatives.
PubMed: 34262922
DOI: 10.3389/fnut.2021.646988 -
Microbiology Spectrum Mar 2023Fungicide applications in agriculture and medicine can promote the evolution of resistant, pathogenic fungi, which is a growing problem for disease management in both...
Fungicide applications in agriculture and medicine can promote the evolution of resistant, pathogenic fungi, which is a growing problem for disease management in both settings. Nonpathogenic mycobiota are also exposed to fungicides, may become tolerant, and could turn into agricultural or medical problems, for example, due to climate change or in immunocompromised individuals. However, quantitative data about fungicide sensitivity of environmental fungi is mostly lacking. species are widely distributed and frequently isolated yeast-like fungi. One species, , is used as a biocontrol agent, but is also encountered in clinical samples, regularly. Here, we compared 16 clinical and 30 agricultural isolates based on whole-genome data and by sensitivity testing with the 3 fungicides captan, cyprodinil, and difenoconazole. Our phylogenetic analyses determined that 7 of the 16 clinical isolates did not belong to the species . These isolates clustered with other species, including , a recently separated species that expresses virulence traits that are mostly lacking in . Interestingly, the clinical isolates were significantly more fungicide sensitive than many isolates from agricultural samples, which implies selection for fungicide tolerance of non-target fungi in agricultural ecosystems. Environmental microbiota are regularly found in clinical samples and can cause disease, in particular, in immunocompromised individuals. Organisms of the genus belonging to this group are highly abundant, and some species are even described as pathogens. Many isolates from agricultural samples are tolerant to different fungicides, and it seems inevitable that such strains will eventually appear in the clinics. Selection for fungicide tolerance would be particularly worrisome for species , which is also found in the environment and exhibits virulence traits. Based on our observation and the strains tested here, clinical isolates are still fungicide sensitive. We, therefore, suggest monitoring fungicide sensitivity in species, such as and , and to consider the development of fungicide tolerance in the evaluation process of fungicides.
PubMed: 36943135
DOI: 10.1128/spectrum.05299-22 -
Bioresource Technology Oct 2023Pullulan is an exopolysaccharide produced by Aureobasidium pullulans, with interesting characteristics which lead to its application in industries such as... (Review)
Review
Pullulan is an exopolysaccharide produced by Aureobasidium pullulans, with interesting characteristics which lead to its application in industries such as pharmaceuticals, cosmetics, food, and others. To reduce production costs for industrial applications, cheaper raw materials such as lignocellulosic biomass can be utilized as a carbon and nutrient source for the microbial process. In this study, a comprehensive and critical review was conducted, encompassing the pullulan production process and the key influential variables. The main properties of the biopolymer were presented, and different applications were discussed. Subsequently, the utilization of lignocellulosics for pullulan production within the framework of a biorefinery concept was explored, considering the main published works that deal with materials such as sugarcane bagasse, rice husk, corn straw, and corn cob. Next, the main challenges and future prospects in this research area were highlighted, indicating the key strategies to favor the industrial production of pullulan from lignocellulosic biomasses.
Topics: Cellulose; Biomass; Fermentation; Saccharum
PubMed: 37423546
DOI: 10.1016/j.biortech.2023.129460 -
Genes Dec 2021Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to...
Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass () genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteobacteria were significantly enriched in unharvested leaf surface communities. These shifts were most prominent in the upland genotype DAC where the leaf surface showed the highest enrichment of Gammaproteobacteria, including taxa with 100% identity to those previously shown to have phytopathogenic function. Fertilization did not have any significant impact on bacterial or fungal communities. We also identified bacterial and fungal taxa present in both the leaf surface and leaf endosphere across all genotypes and treatments. These core taxa were dominated by , , and , in addition to , , and . Local core leaf bacterial and fungal taxa represent promising targets for plant microbe engineering and manipulation across various genotypes and harvest treatments. Our study showcases, for the first time, the significant impact that harvest treatment can have on bacterial and fungal taxa inhabiting switchgrass leaves and the need to include this factor in future plant microbial community studies.
Topics: Archaea; Bacteria; Biodiversity; Biofuels; Fungi; Microbiota; Panicum; Plant Leaves; RNA, Ribosomal, 16S; Rhizosphere; Soil Microbiology
PubMed: 35052362
DOI: 10.3390/genes13010022 -
GigaScience Oct 2022The great diversity of lifestyles and survival strategies observed in fungi is reflected in the many ways in which they reproduce and recombine. Although a complete...
BACKGROUND
The great diversity of lifestyles and survival strategies observed in fungi is reflected in the many ways in which they reproduce and recombine. Although a complete absence of recombination is rare, it has been reported for some species, among them 2 extremotolerant black yeasts from Dothideomycetes: Hortaea werneckii and Aureobasidium melanogenum. Therefore, the presence of diploid strains in these species cannot be explained as the product of conventional sexual reproduction.
RESULTS
Genome sequencing revealed that the ratio of diploid to haploid strains in both H. werneckii and A. melanogenum is about 2:1. Linkage disequilibrium between pairs of polymorphic loci and a high degree of concordance between the phylogenies of different genomic regions confirmed that both species are clonal. Heterozygosity of diploid strains is high, with several hybridizing genome pairs reaching the intergenomic distances typically seen between different fungal species. The origin of diploid strains collected worldwide can be traced to a handful of hybridization events that produced diploids, which were stable over long periods of time and distributed over large geographic areas.
CONCLUSIONS
Our results, based on the genomes of over 100 strains of 2 black yeasts, show that although they are clonal, they occasionally form stable and highly heterozygous diploid intraspecific hybrids. The mechanism of these apparently rare hybridization events, which are not followed by meiosis or haploidization, remains unknown. Both extremotolerant yeasts, H. werneckii and even more so A. melanogenum, a close relative of the intensely recombining and biotechnologically relevant Aureobasidium pullulans, provide an attractive model for studying the role of clonality and ploidy in extremotolerant fungi.
Topics: Ascomycota; Genomics; Hybridization, Genetic; Inbreeding; Phylogeny; Yeasts
PubMed: 36200832
DOI: 10.1093/gigascience/giac095 -
Persoonia Jun 2023Novel species of fungi described in this study include those from various countries as follows: , on whitefly, on bark of , from soil under , on leaf spot of , and...
Novel species of fungi described in this study include those from various countries as follows: , on whitefly, on bark of , from soil under , on leaf spot of , and on leaf spot of . , on fully submersed siliceous schist in high-mountain streams, and on the lower part and apothecial discs of on a twig. , on decaying wood, from moist soil with leaf litter, on a trunk of a living unknown hardwood tree species, and on dead twigs of unidentified plant. , on sandy soil in a plantation of . , on dead bark of , and on dead bark of . , on fruit lesion of . , on corticioid , on sp. , on calcareous soils in dry forests and park habitats. , on sandy soil under , and on leaves of . , on decaying bark of logs, on unidentified woody substrate, from soil, on the trunk of , and on elephant dung. , on infected leaves of . , (incl. gen. nov.) from . , on acidic soil. , on dead leaf of , and on dead leaves of . , on dead culms of , (incl. gen. nov.) on culms of , (incl. gen. nov.) on branch of , on dead standing culms of , on culms of , and on dead bamboo sticks. , half-buried and moss-covered pieces of rotting wood in grass-grown path. , on soil. , (incl. gen. nov.) from resin of ssp. , from sooty mould community on , and from a gallery of on . , on mossy areas of laurel forest areas planted with , and from a biofilm covering a biodeteriorated limestone wall. , from hypersaline sea water, and from water sample collected from hypersaline lagoon. , on culm of , on , (incl. gen. nov.) on culms of , on nest of cases of bag worm moths () on , on leaves of , on stems of , from the roots of × , and (incl. gen. nov.) on leaf of . , on decaying leaves of sp. from pond. , on the bark of fallen trees of , from surface-sterilised, asymptomatic roots of , on soil in mixed forest, on calcareous soil in mixed forest, on acidic soils, from roots of × , on leaves of sp., and from soil. , on calcareous soil. , on pupa, buried in soil, on larva, buried in soil, and on pupa, buried in soil. , on dead leaf of . , on clay loamy soils. , (incl. gen. nov.) on leaves of . , on recently dead stem of , (incl. gen. nov.) from water, and from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes. : Crous PW, Osieck ER, Shivas RG, et al. 2023. Fungal Planet description sheets: 1478-1549. Persoonia 50: 158- 310. https://doi.org/10.3767/persoonia.2023.50.05.
PubMed: 38567263
DOI: 10.3767/persoonia.2023.50.05 -
International Journal of Molecular... Dec 2021Global reports on multidrug resistance (MDR) and life-threatening pathogens such as SARS-CoV-2 and have stimulated researchers to explore new antimicrobials that are... (Review)
Review
Global reports on multidrug resistance (MDR) and life-threatening pathogens such as SARS-CoV-2 and have stimulated researchers to explore new antimicrobials that are eco-friendly and economically viable. In this context, biodegradable polymers such as nisin, chitin, and pullulan play an important role in solving the problem. Pullulan is an important edible, biocompatible, water-soluble polymer secreted by that occurs ubiquitously. It consists of maltotriose units linked with α-1,6 glycosidic bonds and is classed as Generally Regarded as Safe (GRAS) by the Food and Drug Administration (FDA) in the USA. Pullulan is known for its antibacterial, antifungal, antiviral, and antitumor activities when incorporated with other additives such as antibiotics, drugs, nanoparticles, and so on. Considering the importance of its antimicrobial activities, this polymer can be used as a potential antimicrobial agent against various pathogenic microorganisms including the multidrug-resistant (MDR) pathogens. Moreover, pullulan has ability to synthesize biogenic silver nanoparticles (AgNPs), which are remarkably efficacious against pathogenic microbes. The pullulan-based nanocomposites can be applied for wound healing, food packaging, and also enhancing the shelf-life of fruits and vegetables. In this review, we have discussed biosynthesis of pullulan and its role as antibacterial, antiviral, and antifungal agent. Pullulan-based films impregnated with different antimicrobials such as AgNPs, chitosan, essential oils, and so on, forming nanocomposites have also been discussed as natural alternatives to combat the problems posed by pathogens.
Topics: Anti-Bacterial Agents; Anti-Infective Agents; Antifungal Agents; COVID-19; Chitin; Chitosan; Drug Resistance, Multiple; Food Packaging; Glucans; Humans; Metal Nanoparticles; Nanocomposites; Nisin; Polymers; SARS-CoV-2
PubMed: 34948392
DOI: 10.3390/ijms222413596 -
New Biotechnology Jul 2019Fructo-oligosaccharide (FOS) mixtures produced by fermentation contain large amounts of non-prebiotic sugars. Here we propose a mixed culture of Aureobasidium pullulans...
Fructo-oligosaccharide (FOS) mixtures produced by fermentation contain large amounts of non-prebiotic sugars. Here we propose a mixed culture of Aureobasidium pullulans and Saccharomyces cerevisiae cells to produce FOS and consume the small saccharides simultaneously, thereby increasing FOS purity in the mixture. The use of immobilised A. pullulans in co-culture with encapsulated S. cerevisiae, inoculated after 10 h fermentation, enhanced FOS production in a 5 L bioreactor. Using this strategy, a maximal FOS concentration of 119 g L, and yield of 0.59 g g, were obtained after 20 h fermentation, increasing FOS productivity from about 4.9 to 5.9 g L h compared to a control fermentation of immobilized A. pullulans in monoculture. In addition, the encapsulated S. cerevisiae cells were able to decrease the glucose in the medium to about 7.6% (w/w) after 63 h fermentation. This provided a final fermentation mixture with 2.0% (w/w) sucrose and a FOS purity of over 67.0% (w/w). Moreover, a concentration of up to 58.0 g L of ethanol was obtained through the enzymatic transformation of glucose. The resulting pre-purified FOS mixture could improve the separation and purification of FOS in downstream treatments, such as simulated moving bed chromatography.
Topics: Ascomycota; Bioreactors; Coculture Techniques; Fermentation; Fructose; Oligosaccharides
PubMed: 30708187
DOI: 10.1016/j.nbt.2019.01.009 -
Biotechnology Advances 2022Aureobasidium spp. can use a wide range of substrates and are widely distributed in different environments, suggesting that they can sense and response to various... (Review)
Review
Aureobasidium spp. can use a wide range of substrates and are widely distributed in different environments, suggesting that they can sense and response to various extracellular signals and be adapted to different environments. It is true that their pullulan, lipid and liamocin biosynthesis and cell growth are regulated by the cAMP-PKA signaling pathway; Polymalate (PMA) and pullulan biosynthesis is controlled by the Ca and TORC1 signaling pathways; the HOG1 signaling pathway determines high osmotic tolerance and high pullulan and liamocin biosynthesis; the Snf1/Mig1 pathway controls glucose repression on pullulan and liamocin biosynthesis; DHN-melanin biosynthesis and stress resistance are regulated by the CWI signaling pathway and TORC1 signaling pathway. In addition, the HSF1 pathway may control cell growth of some novel strains of A. melanogenum at 37 °C. However, the detailed molecular mechanisms of high temperature growth and thermotolerance of some novel strains of A. melanogenum and glucose derepression in A. melanogenum TN3-1 are still unclear.
Topics: Aureobasidium; Glucose; Mechanistic Target of Rapamycin Complex 1; Saccharomyces cerevisiae; Signal Transduction
PubMed: 34974157
DOI: 10.1016/j.biotechadv.2021.107898