Journal of Fungi最新文献

Allergic bronchopulmonary aspergillosis (ABPA) is a well-known complication in children and young people with cystic fibrosis (CF) and without treatment causes structural lung damage. We performed a longitudinal observational study to identify clinical risk factors for ABPA in a cohort of children and young people with CF aged 8 to 17 years at baseline. Anonymised annual review UK CF Registry data from 2009 to 2019 for patients aged 8-17 years in 2009 were collected, with lung transplant recipients excluded. Baseline characteristics are presented for the whole group and cross-sectional comparisons made according to the presence of ABPA or not in 2009. Longitudinal analysis from 2009 to 2019 was completed on the group without ABPA in 2009 to identify predictors for the subsequent development of ABPA using a complementary log-log regression model. In 2009, there were 1612 patients, of which 1420 were ABPA-negative and 192 ABPA-positive. Aspergillus colonisation (p = 0.01) and IV antibiotic use (p < 0.0001) were associated with having ABPA in 2009. Longitudinal analysis of the group without ABPA in 2009 identified male gender, younger age, lower lung function, Pseudomonas aeruginosa infection, and Aspergillus colonisation to be significantly associated with the development of ABPA (p < 0.0001). Ivacaftor was significantly associated with reduced ABPA (OR 0.46, p = 0.01) but not lumacaftor/ivacaftor (OR 0.64, p = 0.28). Chronic oral macrolide use was significantly associated with increased risk of development of ABPA (OR 1.30, p < 0.0001). This study shows that lower lung function, Aspergillus colonisation, and Pseudomonas aeruginosa infection in children with CF were associated with the development of ABPA, highlighting the need for enhanced surveillance in these patients. This is the first study to show a protective association of ivacaftor and ABPA.

(1) Background: Endophytic fungi play an important role in plant growth and stress resistance. The presence of a special fungal taxon such as the dark septate endophytic (DSE) fungi in alpine environments is particularly important for plant resistance to environmental stresses. However, the composition of root endophytic fungi in different environments and between different host plants has not been well studied. (2) Results: A total of 408 culturable endophytic fungi were isolated from the roots of Saussurea involucrata and Rhodiola crenulata which were collected in 5 plots from the Tianshan and Karakoram Mountains of the Xinjiang region, belonging to 91 species, 54 genera, 31 families, and 3 phyla based on the morphological characteristics and molecular sequence. Among them, DSE fungi were the dominant group, accounting for 52.94%, and Leptodontidium orchidicola was the dominant species. In addition, we also compared the composition and diversity of root endophytic fungi from different plants and different sites, with emphasis on special fungal taxa such as DSE. (3) Conclusions: The composition and diversity of cultural endophytic fungi are significantly different in the two alpine medicinal plant species and across various locations. Some fungi showed the preferences of the host or environment. The endophytic fungal resources, especially DSE, were very rich in the two alpine medicinal plants, indicating that these fungi may play a crucial role in the ecological adaptation of host plants in harsh environments.

Pholiota nameko (T. Ito) S. Ito and S. Imai is an emerging wild mushroom species belonging to the genus Pholiota. Its unique brown-yellow appearance and significant biological activity have garnered increasing attention in recent years. However, there is a relative lack of research on the biological characteristics and genetics of P. nameko, which greatly limits the potential for an in-depth exploration of this mushroom in the research fields of molecular breeding and evolutionary biology. This study aimed to address that gap by employing Illumina and Nanopore sequencing technologies to perform whole-genome sequencing, de novo assembly, and annotation analysis of the P. nameko ZZ1 strain. Utilizing bioinformatics methods, we conducted a comprehensive analysis of the genomic characteristics of this strain and successfully identified candidate genes associated with its mating type, carbohydrate-active enzymes, virulence factors, pan-genome, and drug resistance functions. The genome of P. nameko ZZ1 is 24.58 Mb in size and comprises 33 contigs, with a contig N50 of 2.11 Mb. A hylogenetic analysis further elucidated the genetic relationship between P. nameko and other Pholiota, revealing a high degree of collinearity between P. nameko and ZZ1. In our enzyme analysis, we identified 246 enzymes in the ZZ1 genome, including 68 key carbohydrate-active enzymes (CAZymes), and predicted the presence of 11 laccases, highlighting the strain's strong potential for cellulose degradation. We conducted a pan-genomic analysis of five closely related strains of Pholiota, yielding extensive genomic information. Among these, there were 2608 core genes, accounting for 21.35% of the total genes, and 135 dispensable genes, highlighting significant genetic diversity among Pholiota and further confirming the value of pan-genomic analysis in uncovering species diversity. Notably, while we successfully identified the A-mating-type locus, composed of the homeodomain protein genes HD1 and HD2 in ZZ1, we were unable to obtain the B-mating-type locus due to technical limitations, preventing us from acquiring the pheromone receptor of the B-mating-type. We plan to supplement these data in future studies and explore the potential impact of the B-mating-type locus on the current findings. In summary, the genome data of ZZ1 presented in this study are not only valuable resources for understanding the genetic basis of this species, but also serve as a crucial foundation for subsequent genome-assisted breeding, research into cultivation technology, and the exploration of its nutritional and potential medicinal value.

The genetic composition of Saccharomyces cerevisiae and its various phenotypes during fermentation significantly correlate to the quality of Chinese steamed bread (CSB). However, the systematic correlation between different S. cerevisiae and CSB has not been fully elucidated. Herein, we characterised CSBs prepared with 36 isolates of S. cerevisiae (designated S1-S36) to comparatively evaluate their correlations. CSBs 1, 2, 13, 21, 25 and 33 exhibited suitable total titratable acidity (TTA) values, pH values and large specific volumes. Texture analysis showed that CSBs 1, 25 and 33 exhibited higher springiness and cohesiveness values. CSBs 8, 25 and 33 exhibited low hardness, gumminess and chewiness values. At the micro level, CSBs 1, 25 and 33 showed a loose reticular structure with large holes and in which starch particles wrapped into gluten protein. Fifty-nine volatile flavour compounds belonging to six categories were determined in 10 selected CSBs, and CSBs 1, 25 and 33 contained more flavour and balanced substance categories. In addition, comparative genomic analysis revealed 33 non-synonymous mutations in the three strains with strong fermentation ability (S1, S25 and S33) and the three strains with weak fermentation ability (S18, S20 and S35) involving 19 genes, including: the respiration-related genes COS5, COS8 and COX10; the starch metabolism transcription factor MSS11; the general transcription factor SPT8; the cell aggregation-related gene FLO1 and the transporter gene SEO1. Other genes with different genotypes were also enriched in respiration-related gene ontology terms. These data offer preliminary experimental evidence regarding the application of S. cerevisiae S1, S25 and S33 in fermented foods derived from grains.

Nitrogen is an essential nutrient that frequently determines the growth rate of fungi. Nitrate transporter proteins (Nrts) play a crucial role in the cellular absorption of nitrate from the environment. Entomopathogenic fungi (EPF) have shown their potential in the biological control of pests. Thus, comprehending the mechanisms that govern the pathogenicity and stress tolerance of EPF is helpful in improving the effectiveness and practical application of these fungal biocontrol agents. In this study, we utilized homologous recombination to create MaNrtB deletion mutants and complementation strains. We systematically investigated the biological functions of the nitrate transporter protein gene MaNrtB in M. acridum. Our findings revealed that the disruption of MaNrtB resulted in delayed conidial germination without affecting conidial production. Stress tolerance assays demonstrated that the MaNrtB disruption strain was more vulnerable to UV-B irradiation, hyperosmotic stress, and cell wall disturbing agents, yet it exhibited increased heat resistance compared to the wild-type strain. Bioassays on the locust Locusta migratoria manilensis showed that the disruption of MaNrtB impaired the fungal virulence owing to the reduced appressorium formation on the insect cuticle and the attenuated growth in the locust hemolymph. These findings provide new perspectives for understanding the pathogenesis of EPF.

Infections by the major opportunistic pathogen of human Candida albicans are commonly treated with echinocandin (ECN) drugs. However, C. albicans can adapt to grow in the presence of certain amounts of ECNs. Prior studies by several laboratories have defined multiple genes, as well as mechanisms involving induced aneuploidy, that can govern this. Still, the mechanisms of ECN adaptation are not fully understood. Here, we use genome-wide profiling of chromatin accessibility by ATAC-seq to determine if ECN adaptation is reflected in changes in the chromatin landscape in the absence of aneuploidy. We find that drug adaptation is coupled with multiple changes in chromatin accessibility genome-wide, which occur predominantly in gene promoter regions. Areas of increased accessibilities in promoters are enriched with the binding motifs for at least two types of transcription factors: zinc finger and basic leucine zipper. We also find that chromatin changes are often associated with differentially expressed genes including genes with functions relevant to the ECN-adapted phenotype, such as cell wall biosynthesis. Consistent with this, we find that the cell wall is remodeled in ECN-adapted mutants, with chitin up and glucan down and increased cell surface exposure. A full understanding of ECN adaptation processes is of critical importance for the prevention of clinical resistance.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a widely adopted technique for bacterial and yeast identification in clinical laboratories but is less frequently applied to filamentous fungi due to inconsistent performance, limitations of commercial libraries, and variability of preparation methods. This study aimed to validate the efficiency of MALDI-TOF MS-based dermatophyte identification using the Bruker Biotyper system. Focusing on species from the Trichophyton, Nannizzia, Microsporum, and Epidermophyton genera, an in-house reference library was established and evaluated with clinical isolates. The expanded library, which combined the in-house and Bruker libraries, achieved significantly higher accuracy than the Bruker library alone, correctly identifying 90.7% (107/118) of isolates at the species level compared to 16.1% (19/118) by the Bruker library. This study presents an efficient, standardized MALDI-TOF MS protocol for routine dermatophyte identification and provides a review of the current status and influencing factors in MALDI-TOF MS-based dermatophyte identification strategies.

Fusarium graminearum is recognized as the pathogen responsible for wheat head blight. It produces deoxynivalenol (DON) during infection, which endangers human health. DON biosynthesis occurs within toxisomes in the endoplasmic reticulum (ER). In eukaryotes, the ER membrane protein complex (EMC) is critical for the ER's normal operation. However, the specific role of the EMC in F. graminearum remains poorly understood. In this study, six EMC subunits (FgEmc1-6) were identified in F. graminearum, and all of them were localized to the toxisomes. Our results demonstrate that the EMC is indispensable for vegetative growth and asexual and sexual reproduction, which are the fundamental life processes of F. graminearum. Importantly, EMC deletion led to reduced virulence in wheat spikes and petioles. Further investigation revealed that in ΔFgemc1-6, the expression of trichothecene (TRI) genes is decreased, the biosynthesis of lipid droplets (LDs) is diminished, toxisome formation is impaired, and DON production is reduced. Additionally, defects in the formation of the infection cushion were observed in ΔFgemc1-6. In conclusion, the EMC is involved in regulating growth and virulence in F. graminearum. This study enhances our understanding of the EMC functions in F. graminearum and offers valuable insights into potential targets for managing wheat head blight.

Valorization of agri-food residues has garnered significant interest for obtaining value-added compounds such as enzymes or bioactive molecules. Rice milling by-products, such as rice bran, have limited commercial value and may pose environmental challenges. Filamentous fungi are recognized for their ability to grow on residues and for their capacity to produce large amounts of metabolites and enzymes of industrial interest. Here, we used filamentous fungi to produce enzyme cocktails from rice bran, which, due to its polysaccharide composition, serves as an ideal substrate for the growth of fungi producing cellulases and xylanases. To this end, sixteen fungal strains were isolated from rice bran and identified at the species level. The species belonged to the genera Aspergillus, Penicillium, and Mucor. The Aspergillus species displayed the highest efficiency in cellulase and xylanase activities, especially A. niger var. phoenicis and A. amstelodami. A. terreus, A. tritici, and A. montevidensis stood out as xylanolytic isolates, while P. parvofructum exhibited good cellulase activity. A. niger var. phoenicis followed by A. terreus showed the highest specific enzymatic activities of α- and β-D-galactosidase, α-L-arabinofuranosidase, α- and β-D-glucosidase, and β-D-xylosidase. Additionally, proteomic analysis of A. terreus, A. niger var. phoenicis, and P. parvofructum exoproteomes revealed differences in enzyme production for rice bran degradation. A. niger var. phoenicis had the highest levels of xylanases and cellulases, while P. parvofructum excelled in proteases, starch-degrading enzymes, and antifungal proteins. Finally, two Penicillium isolates were notable as producers of up to three different antifungal proteins. Our results demonstrate that filamentous fungi can effectively valorize rice bran by producing enzyme cocktails of industrial interest, along with bioactive peptides, in a cost-efficient manner, aligning with the circular bio-economy framework.

Hemileia vastatrix coffee leaf rust reduces Mexican coffee production by 51%. We aimed to analyze the size and distribution of H. vastatrix urediniospores among coffee plantations, as well as the morphological structures of the uredinium. In 2015, 65 leaf samples with rust symptoms were collected from 17 coffee cultivars grown at various altitudes (229-1649 m) under different environmental conditions in 14 regions of four Mexican states. A total of 30 spores per sample were measured and grouped using the Ward centroid method, and the group distribution was analyzed. Uredinia morphology was examined via electron microscopy, and the identity of the rust was confirmed. We identified eight significant spore groups. Groups 8h and 3a had the smallest and largest spores, respectively, which were distributed in two and one state, respectively, at different altitudes. The spores in groups 1b-7f were variable within the intermediate size range, and their distribution was at least one group per state under temperate, warm, and humid conditions. The uredinium had double-cell walls in the pedicels and urediniospores, a split septum, spores with hilum and protuberances, and an oval spore shape; anastomosis was detected on vegetative hyphae and haustoria. These findings may reflect gaps in knowledge in the biological cycle of this rust.