J. Fungi, Volume 9, Issue 10 (October 2023) – 88 articles

Among Boletales, the family Boletaceae has the highest diversity worldwide. Additionally, this fungal group has great ecological relevance because it not only includes mainly ectomycorrhizal but also saprotrophic species. Furthermore, some species are used as food and have sociocultural and economic importance worldwide. In Mexico, the Boletaceae family boasts a substantial number of species, yet our understanding of these species remains far from comprehensive. In this work, by using macro- and micromorphological and phylogenetic analyses of DNA sequences from multi-gene analyses based on ITS, nrLSU, rpb1, rpb2, and tef1, we report five new species belonging to the genera Aureoboletus and Chalciporus: A. ayuukii and A. elvirae from a Quercus scytophylla forest, A. readii from a mixed forest, C. perezsilvae from cloud forest, and C. piedracanteadensis from both a mixed coniferous forest and a Quercus-Pinus forest. In Mexico, four species of Aureoboletus are used as a food source, and in this work, we add another one, A. readii, which is traditionally consumed by members of the Tlahuica-Pjiekakjoo culture, who are located in the central part of the country. This work contributes to our knowledge of two genera of Boletaceae in a geographical area that is scarcely studied, and thus, our understanding of its biocultural relevance is enriched. Full article

Coevolution between the pathogen and host plant drives pathogenic effector diversity. However, the molecular mechanism behind host-specific pathogenesis remains to be explored. Here, we present a 43 Mb whole-genome sequence of Endomelanconiopsis endophytica strain LS29, a host-specific pathogen of the common subtropical tree Castanopsis fissa. We described its genome annotations and identified its effector candidates. By performing temporal transcriptome sequencing of E. endophytica on C. fissa during early infection, we found that E. endophytica repressed other microbes in order to attack the tissue of the host by producing antibiotics earlier than 24 h post-inoculation (hpi). Simultaneously, a variety of effectors were secreted to recognize the host plant, but most of them showed a significantly opposing expression regulation trend after 24 hpi, indicating that 24 hpi represents a key time point between host recognition and specific infection. Furthermore, a comparison of isoenzymes showed that only a few effectors were identified as specific effectors, which were involved in hydrolyzing the compounds of the plant cell wall and releasing fatty acids during the early infection of C. fissa. Our results determined host recognition timing and identified a specific catalog of effectors, which are crucial for revealing the molecular mechanism of host-specific pathogenesis. Full article

Emergomycosis is an endemic mycosis caused by the Emergomyces species. Infections due to this agent have been reported globally. Hence, the present systematic review on Emergomyces infections was conducted to study the disease epidemiology, underlying diseases and risk factors, causative agents, and treatment and outcome. The MEDLINE, Scopus, Embase, and Web of Science databases were searched systematically with appropriate keywords from January 1990 to October 2022. A total of 77 cases of emergomycosis were included in the analysis. Emergomycosis was most commonly seen in patients with human immunodeficiency virus (HIV) infection (n = 61, 79.2%) and HIV-uninfected patients with or without other comorbidities (n = 16, 20.8%). The underlying disease and risk factors significantly associated with emergomycosis in the HIV-infected patients were CD4+ T-cell counts less than 100 cells/mm³ (n = 55, 90.2%), anaemia (n = 30, 49.2%), and thrombocytopenia (n = 17, 27.9%), whereas in the HIV-uninfected patients, treatment with immunosuppressive drugs (n = 10, 62.5%), renal disease (n = 8, 50%), transplant recipients (n = 6, 37.5%), and diabetes mellitus (n = 4, 25%) were the significant risk factors associated with emergomycosis. Emergomyces africanus (n = 55, 71.4%) is the most common causative agent, followed by E. pasteurianus (n = 9, 11.7%) and E. canadensis (n = 5, 6.5%). E. africanus was most often isolated from HIV-infected patients (n = 54, 98.2%), whereas E. pasteurianus was most common in HIV-uninfected patients (n = 5, 55.6%). The all-cause mortality rate of the total cohort is 42.9%. No significant variation in the mortality rate is observed between the HIV-infected patients (n = 28, 36.4%) and the HIV-uninfected patients (n = 5, 6.5%). In conclusion, with an increase in the immunosuppressed population across the globe in addition to HIV infection, the case burden of emergomycosis may increase in the future. Hence, clinicians and mycologists should be vigilant and clinically suspicious of emergomycosis, which helps in early diagnosis and initiation of antifungal treatment to prevent disease mortality. Full article

The diversity of Lycoperdaceae in Israel was studied. Molecular phylogenetic relationships within the family, and genus Lycoperdon in particular, were inferred using original ITS rDNA sequences of 58 samples belonging to 25 species from Israel and six other countries, together with 66 sequences stored in the GenBank database. The current molecular phylogenetic study recovered the family Lycoperdaceae as a monophyletic group, which was supported in both maximum likelihood and Bayesian analyses. The clades corresponding to the genera Apioperdon, Bovista, Calvatia, Disciseda, and Lycoperdon were revealed. The taxonomic structure of the named genera was partially resolved. Within the genus Lycoperdon, some species received significant statistical support; however, their relationships, as well as the problem of the genus monophyly, mostly remained questionable. As a result of a thorough literature survey, extensive sample collection, and studies of the material stored in the Herbarium of the Institute of Evolution, University of Haifa (HAI, Israel), fifteen species representing five genera were found in the territory of Israel. Six species, namely Apioperdon pyriforme, Bovista aestivalis, Calvatia candida, Lycoperdon decipiens, L. niveum, and L. perlatum, are new additions to the diversity of Lycoperdaceae in Israel. Detailed macro- and micromorphological descriptions, ecology, geography, and critical notes, together with light microscopy photos and SEM micrographs, are provided. In-depth discussion on some taxonomically challenging species is presented. Full article

Verticillium dahliae, a virulent soil-borne fungus, elicits Verticillium wilt in numerous dicotyledonous plants through intricate pathogenic mechanisms. Ubiquitination, an evolutionarily conserved post-translational modification, marks and labels proteins for degradation, thereby maintaining cellular homeostasis. Within the ubiquitination cascade, ubiquitin ligase E3 demonstrates a unique capability for target protein recognition, a function often implicated in phytopathogenic virulence. Our research indicates that two ubiquitin ligase E3s, VdBre1 and VdHrd1, are intrinsically associated with virulence. Our findings demonstrate that the deletion of these two genes significantly impairs the ability of V. dahliae to colonize the vascular bundles of plants and to form typical penetration pegs. Furthermore, transcriptomic analysis suggests that VdBre1 governs the lipid metabolism pathway, while VdHrd1 participates in endoplasmic-reticulum-related processes. Western blot analyses reveal a significant decrease in histone ubiquitination and histone H3K4 trimethylation levels in the ΔVdBre1 mutant. This research illuminates the function of ubiquitin ligase E3 in V. dahliae and offers fresh theoretical perspectives. Our research identifies two novel virulence-related genes and partially explicates their roles in virulence-associated structures and gene regulatory pathways. These findings augment our understanding of the molecular mechanisms inherent to V. dahliae. Full article

In England, Cryphonectria parasitica was detected for the first time in 2011 in a nursery and in 2016 in the wider environment. Surveys between 2017 and 2020 identified the disease at different sites in Berkshire, Buckinghamshire, Cornwall, Derbyshire, Devon, Dorset, London, West Sussex, and the island of Jersey, while the present study comprises the results of the 2020–2023 survey with findings in Derbyshire, Devon, Kent, Nottinghamshire, Herefordshire, Leicestershire, London, West Sussex, and the islands of Jersey and Guernsey. A total of 226 suspected samples were collected from 72 surveyed sites, as far north as Edinburgh and as far west as Plymouth (both of which were negative), and 112 samples tested positive by real-time PCR and isolation from 35 sites. The 112 isolates were tested for the vegetative compatibility group (VCG), mating type, and Cryphonectria hypovirus 1 (CHV1). Twelve VCGs were identified, with two of them (EU-5 and EU-22) being the first records in the UK. Both mating types were present (37% MAT-1 and 63% MAT-2), but only one mating type was present per site and VCG, and perithecia were never observed. Cryphonectria hypovirus 1 (CHV1), consistently subtype-I haplotype E-5, was detected in three isolates at a low concentration (5.9, 21.1, and 33.0 ng/µL) from locations in London, Nottinghamshire, and Devon. Full article

With only four classes of antifungal drugs available for the treatment of invasive systemic fungal infections, the number of resistant fungi is increasing, highlighting the urgent need for novel antifungal drugs. Ergosterol, an essential component of cell membranes, and its synthetic pathway have been targeted for antifungal drug development. Sterol-C4-methyl monooxygenase (Erg25p), which is a greater essential target than that of existing drugs, represents a promising drug target. However, the development of antifungal drugs must consider potential side effects, emphasizing the importance of evaluating their selective toxicity against fungi. In this study, we knocked in ERG25 of Candida glabrata and its human ortholog, SC4MOL, in ERG25-deleted Saccharomyces cerevisiae. Utilizing these strains, we evaluated 1181-0519, an Erg25p inhibitor, that exhibited selective toxicity against the C. glabrata ERG25 knock-in strain. Furthermore, 1181-0519 demonstrated broad-spectrum antifungal activity against pathogenic Candida species, including Candida auris. The approach of utilizing a gene that is functionally conserved between yeast and humans and subsequently screening for molecular target drugs enables the identification of selective inhibitors for both species. Full article

Postharvest diseases seriously restrict developments in the passion fruit industry. In this study, we aimed to identify the postharvest pathogen affecting passion fruit, investigate its pathogenicity, and explore relevant control methods. The pathogen was isolated from rotting passion fruit and identified using morphological characteristics, ITS sequences, and phylogenetic tree analyses. Additionally, preliminary studies were conducted to assess the biological characteristics of the pathogen and evaluate the efficacy of various treatments for disease control. The fungus on the passion fruit called B4 was identified as Diaporthe passiflorae. Optimal conditions for mycelial growth were observed at 25–30 °C and pH 5–6, with starch as the carbon source and peptone as the nitrogen source. Infection by D. passiflorae accelerated fruit decay, reduced the h° value of the peel, and increased the peel cell membrane permeability when compared to the control. Notably, treatments with appropriate concentrations of ɛ-poly-l-lysine, salicylic acid, and melatonin showed inhibitory effects on the pathogen’s growth in vitro and may thus be potential postharvest treatments for controlling brown rot caused by D. passiflorae in passion fruit. The results provide a scientific basis for the development of strategies to control postharvest decay and extend the storage period of passion fruit. Full article

Assaying changes in the amount of DNA in single cells is a well-established method for studying the effects of various perturbations on the cell cycle. A drawback of this method is the need for a fixation procedure that does not allow for in vivo study nor simultaneous monitoring of additional parameters such as fluorescence of tagged proteins or genetically encoded indicators. In this work, we report on a method of Histone Abundance Quantification (HAQ) of live yeast harboring a GFP-tagged histone, Htb2. We show that it provides data highly congruent with DNA levels, both in Saccharomyces cerevisiae and Ogataea polymorpha yeasts. The protocol for the DNA content assay was also optimized to be suitable for both Ogataea and Saccharomyces yeasts. Using the HAQ approach, we demonstrate the expected effects on the cell cycle progression for several compounds and conditions and show usability in conjunction with additional fluorophores. Thus, our data provide a simple approach that can be utilized in a wide range of studies where the effects of various stimuli on the cell cycle need to be monitored directly in living cells. Full article

Although fungi occupy only a small proportion of the microbial community in the intestinal tract of mammals, they play important roles in host fat accumulation, nutrition metabolism, metabolic health, and immune development. Here, we investigated the dynamics and assembly of gut fungal communities in plateau pikas inhabiting six altitudinal gradients across warm and cold seasons. We found that the relative abundances of Podospora and Sporormiella significantly decreased with altitudinal gradients in the warm season, whereas the relative abundance of Sarocladium significantly increased. Alpha diversity significantly decreased with increasing altitudinal gradient in the warm and cold seasons. Distance-decay analysis showed that fungal community similarities were significantly and negatively correlated with elevation. The co-occurrence network complexity significantly decreased along the altitudinal gradients as the total number of nodes, number of edges, and degree of nodes significantly decreased. Both the null and neutral model analyses showed that stochastic or neutral processes dominated the gut fungal community assembly in both seasons and that ecological drift was the main ecological process explaining the variation in the gut fungal community across different plateau pikas. Homogeneous selection played a weak role in structuring gut fungal community assembly during the warm season. Collectively, these results expand our understanding of the distribution patterns of gut fungal communities and elucidate the mechanisms that maintain fungal diversity in the gut ecosystems of small mammals. Full article

High levels of carbon dioxide are known to inhibit the growth of microorganisms. A total of twenty strains of filamentous fungi and yeasts were isolated from habitats with enriched carbon dioxide concentration. Most strains were derived from modified atmosphere packed (MAP) food products or mofettes and were cultivated under an atmosphere of 20% CO₂ and 80% O₂. The influence of CO₂ on fungal cell membrane fatty acid profiles was examined in this study. Major changes were the increase in linolenic acid (C_18:3 cis 9, 12, 15) and, additionally in most strains, linoleic acid (C_18:2 cis 9, 12) with a maximum of 24.8%, at the expense of oleic (C_18:1 cis 9), palmitic (C_16:0), palmitoleic (C_16:1 cis 9) and stearic acid (C_18:0). The degree of fatty acid unsaturation increased for all of the strains in the study, which consequently led to lower melting temperatures of the cell membranes after incubation with elevated levels of CO₂, indicating fluidization of the membrane and a potential membrane malfunction. Growth was reduced in 18 out of 20 strains in laboratory experiments and a change in pigmentation was observed in several strains. Two of the isolated strains, strain WT5 and strain WR1, were found to represent a hitherto undescribed yeast for which the new genus and species Stenotrophomyces fumitolerans (MB# 849906) is proposed. Full article

tRNA methylations, including base modification and 2’-O-methylation of ribose moiety, play critical roles in the structural stabilization of tRNAs and the fidelity and efficiency of protein translation. These modifications are catalyzed by tRNA methyltransferases (TRMs). Some of the TRMs from yeast can fully function only by a single subunit. In this study, after performing the primary bioinformatic analyses, the progress of the studies of yeast single-subunit TRMs, as well as the studies of their homologues from yeast and other types of eukaryotes and the corresponding TRMs from other types of organisms was systematically reviewed, which will facilitate the understanding of the evolutionary origin of functional diversity of eukaryotic single-subunit TRM. Full article

Brown-rot fungi lack many enzymes associated with complete wood degradation, such as lignin-attacking peroxidases, and have developed alternative mechanisms for rapid wood breakdown. To identify the effects of culture conditions and wood substrates on gene expression, we grew Fibroporia radiculosa in submerged cultures containing Wiley milled wood (5 days) and solid wood wafers (30 days), using aspen, pine, and spruce as a substrate. The comparative analysis revealed that wood species had a limited effect on the transcriptome: <3% of genes were differentially expressed between different wood species substrates. The comparison between gene expression during growth on milled wood and wood wafer conditions, however, indicated that the genes encoding plant cell wall-degrading enzymes, such as glycoside hydrolases and peptidases, were activated during growth on wood wafers, confirming previous reports. On the other hand, it was shown for the first time that the genes encoding Fenton chemistry enzymes, such as hydroquinone biosynthesis enzymes and oxidoreductases, were activated during submerged growth on ground wood. This illustrates the diversity of wood-decay reactions encoded in fungi and activated at different stages of this process. Full article

Mushroom dietary fiber is a type of bioactive macromolecule derived from the mycelia, fruiting bodies, or sclerotia of edible or medicinal fungi. The use of mushroom dietary fiber as a prebiotic has recently gained significant attention for providing health benefits to the host by promoting the growth of beneficial microorganisms; therefore, mushroom dietary fiber has promising prospects for application in the functional food industry and in drug development. This review summarizes methods for the preparation and modification of mushroom dietary fiber, its degradation and metabolism in the intestine, its impact on the gut microbiota community, and the generation of short-chain fatty acids (SCFAs); this review also systematically summarizes the beneficial effects of mushroom dietary fiber on host health. Overall, this review aims to provide theoretical guidance and a fresh perspective for the prebiotic application of mushroom dietary fiber in the development of new functional foods and drugs. Full article

Pichia pastoris is the most widely used microorganism for the production of secreted industrial proteins and therapeutic proteins. Recently, this yeast has been repurposed as a cell factory for the production of chemicals and natural products. In this review, the general physiological properties of P. pastoris are summarized and the readily available genetic tools and elements are described, including strains, expression vectors, promoters, gene editing technology mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, and adaptive laboratory evolution. Moreover, the recent achievements in P. pastoris-based biosynthesis of proteins, natural products, and other compounds are highlighted. The existing issues and possible solutions are also discussed for the construction of efficient P. pastoris cell factories. Full article

Candida auris has emerged as a significant fungal threat due to its rapid worldwide spread since its first appearance, along with its potential for antimicrobial resistance and virulence properties. This study was designed to examine virulence characteristics, the efficacy of ceragenins, and biofilm-derived drug resistance in seven C. auris strains isolated from Turkish intensive care patients. It was observed that none of the tested strains exhibited proteinase or hemolysis activity; however, they demonstrated weak phospholipase and esterase activity. In addition, all strains were identified as having moderate to strong biofilm formation characteristics. Upon determining the minimum inhibitory concentrations (MIC) of ceragenins, it was discovered that CSA-138 exhibited the highest effectiveness with a MIC range of 1–0.5 µg/mL, followed by CSA-131 with a MIC of 1 µg/mL. Also, antimicrobial agents destroyed mature biofilms at high concentrations (40–1280 µg/mL). The investigation revealed that the strains isolated from Türkiye displayed weak exoenzyme activities. Notably, the ceragenins exhibited effectiveness against these strains, suggesting their potential as a viable treatment option. Full article

M. bicuspidata var. bicuspidata 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, Daphnia dentifera 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. Full article

Based on published anatomical-morphological and ecological characteristics and phylogenetic evidence, six species of the Ganoderma genus are known to occur in Europe, namely, G. applanatum (Pers.) Pat., G. adspersum (Schulzer) Donk, G. pfeifferi Bres., G. resinaceum Boud., G. carnosum Pat., and G. lucidum (Curtis) P. Karst. Molecular markers (DNA sequences of selected genes or intergenic spacers) revolutionized our view of fungal variability. Every one of the four most frequently used molecular markers (ITS (internal transcribed spacer) and partial sequences of LSU (rRNA large subunit), tef1-α (translation elongation factor 1-alpha), and Rpb2 (RNA polymerase II second largest subunit)) provides a different view on the variability of European species of the Ganoderma genus. Both the lowest intraspecies variability and the best species differentiation (interspecies divergence) were observed for the LSU marker, and based on our data, this marker could be recommended for identification and species delineation in European Ganoderma spp. The sequences of the most frequently used ITS marker were unable to discriminate between G. lucidum and G. carnosum, and in general, this species pair showed the lowest interspecies divergence using all markers tested. Surprisingly, up to now, hidden variability has been detected in several Ganoderma spp., indicating the existence of possible cryptic taxa within the European Ganoderma morphospecies. Full article

Paraphoma chrysanthemicola is a newly identified endophytic fungus. The focus of most studies on P. chrysanthemicola has been on its isolation, identification and effects on plants. However, the limited genomic information is a barrier to further research. Therefore, in addition to studying the morphological and physiological characteristics of P. chrysanthemicola, we sequenced its genome and compared it with that of Paraphoma sp. The results showed that sucrose, peptone and calcium phosphate were suitable sources of carbon, nitrogen and phosphorus for this strain. The activities of amylase, cellulase, chitosanase, lipase and alkaline protease were also detected. Sequencing analysis revealed that the genome of P. chrysanthemicola was 44.1 Mb, with a scaffold N50 of 36.1 Mb and 37,077 protein-coding genes. Gene Ontology (GO) annotation showed that mannose-modified glycosylation was predominant in monosaccharide utilisation. The percentage of glycoside hydrolase (GH) modules was the highest in the carbohydrate-active enzymes database (CAZy) analysis. Secondary metabolite-associated gene cluster analysis identified melanin, dimethylcoprogen and phyllostictine A biosynthetic gene clusters (>60% similarity). The results indicated that P. chrysanthemicola had a mannose preference in monosaccharide utilisation and that melanin, dimethylcoprogen and phyllostictine A were important secondary metabolites for P. chrysanthemicola as an endophytic fungus. Full article

Aphelids are a holomycotan group, represented exclusively by parasitoids infecting algae. They form a sister lineage to Fungi in the phylogenetic tree and represent a key group for reconstruction of the evolution of Holomycota and for analysis of the origin of Fungi. The newly assembled genome of Aphelidium insullamus (Holomycota, Aphelida) with a total length of 18.9 Mb, 7820 protein-coding genes and a GC percentage of 52.05% was obtained by a hybrid assembly based on Oxford Nanopore long reads and Illumina paired reads. In order to trace the origin and the evolution of fungal osmotrophy and its presence or absence in Aphelida, we analyzed the set of main fungal transmembrane transporters, which are proteins of the Major Facilitator superfamily (MFS), in the predicted aphelid proteomes. This search has shown an absence of a specific fungal protein family Drug:H⁺ antiporters-2 (DAH-2) and specific fungal orthologs of the sugar porters (SP) family, and the presence of common opisthokont’s orthologs of the SP family in four aphelid genomes. The repertoire of SP orthologs in aphelids turned out to be less diverse than in free-living opisthokonts, and one of the most limited among opisthokonts. We argue that aphelids do not show signs of similarity with fungi in terms of their osmotrophic abilities, despite the sister relationships of these groups. Moreover, the osmotrophic abilities of aphelids appear to be reduced in comparison with free-living unicellular opisthokonts. Therefore, we assume that the evolution of fungi-specific traits began after the separation of fungal and aphelid lineages, and there are no essential reasons to consider aphelids as a prototype of the fungal ancestor. Full article

Ganoderma lucidum exhibits the ability to synthesize a diverse range of biologically active molecules with significant pharmaceutical potential, including xylomannan and fucogalactan, which have demonstrated antitumor activity. However, there exists considerable intra-species variability in the capacity to produce these metabolites at high concentrations, likely reflecting the high genomic diversity observed from a limited number of strains sequenced to date. We employed high-throughput shotgun sequencing to obtain the complete genome sequence of G. lucidum strain 5.1, which is distinguished by its remarkable xylomannan synthesis capabilities. Through the utilization of semi-automatic reordering based on conformation capture (Hi-C) data, we substantially enhanced the assembly process, resulting in the generation of 12 chromosome-level scaffolds with a cumulative length of 39 Mbp. By employing both de novo and homology-based approaches, we performed comprehensive annotation of the genome, thereby identifying a diverse repertoire of genes likely involved in polysaccharide biosynthesis. The genome sequence generated in this study serves as a valuable resource for elucidating the molecular mechanisms underlying the medicinal potential of Ganoderma species, discovering novel pharmaceutically valuable compounds, and elucidating the ecological mechanisms of the species. Furthermore, the chromosome contact map obtained for the first time for this species extends our understanding of 3D fungal genomics and provides insights into the functional and structural organization within the fungal kingdom. Full article

Histoplasmosis is a globally distributed systemic infection caused by the dimorphic fungus Histoplasma capsulatum (H. capsulatum). This fungus can cause a wide spectrum of clinical manifestations, and the diagnosis of progressive disseminated histoplasmosis is often a challenge for clinicians. Although microscopy and culture remain the gold standard diagnostic tests for Histoplasma identification, matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has emerged as a method of microbial identification suitable for the confirmation of dimorphic fungi. However, to our knowledge, there are no entries for H. capsulatum spectra in most commercial databases. In this review, we describe the case of disseminated histoplasmosis in a patient living with HIV admitted to our university hospital that we failed to identify by the MALDI-TOF method due to the limited reference spectrum of the instrument database. Furthermore, we highlight the utility of molecular approaches, such as conventional polymerase chain reaction (PCR) and DNA sequencing, as alternative confirmatory tests to MALDI-TOF technology for identifying H. capsulatum from positive cultures. An overview of current evidence and limitations of MALDI-TOF-based characterization of H. capsulatum is also presented. Full article

Hericium rajendrae is an emerging species in the genus Hericium with few members. Despite being highly regarded due to its rarity, knowledge about H. rajendrae remains limited. In this study, we sequenced, de novo assembled, and annotated the complete genome of H. rajendrae NPCB A08, isolated from the Qinling Mountains in Shaanxi, China, using the Illumina NovaSeq and Nanopore PromethION technologies. Comparative genomic analysis revealed similarities and differences among the genomes of H. rajendrae, H. erinaceus, and H. coralloides. Phylogenomic analysis revealed the divergence time of the Hericium genus, while transposon analysis revealed evolutionary characteristics of the genus. Gene family variation reflected the expansion and contraction of orthologous genes among Hericium species. Based on genomic bioinformation, we identified the candidate genes associated with the mating system, carbohydrate-active enzymes, and secondary metabolite biosynthesis. Furthermore, metabolite profiling and comparative gene clusters analysis provided strong evidence for the biosynthetic pathway of erinacines in H. rajendrae. This work provides the genome of H. rajendrae for the first time, and enriches the genomic content of the genus Hericium. These findings also facilitate the application of H. rajendrae in complementary drug research and functional food manufacturing, advancing the field of pharmaceutical and functional food production involving H. rajendrae. Full article

Sesquiterpenes are a type of abundant natural product with widespread applications in several industries. They are biosynthesized by sesquiterpene synthases (STSs). As valuable and abundant biological resources, mushroom-forming fungi are rich in new sesquiterpenes and STSs, which remain largely unexploited. In the present study, we collected information on 172 STSs from mushroom-forming fungi with experimentally characterized products from the literature and sorted them to develop a dataset. Furthermore, we analyzed and discussed the phylogenetic tree, catalytic products, and conserved motifs of STSs. Phylogenetic analysis revealed that the STSs were clustered into four clades. Furthermore, their cyclization reaction mechanism was divided into four corresponding categories. This database was used to predict 12 putative STS genes from the edible fungi Flammulina velutipes. Finally, three FvSTSs were selected to experimentally characterize their functions. FvSTS03 predominantly produced Δ-cadinol and FvSTS08 synthesized β-barbatene as the main product; these findings were consistent with those of the functional prediction analysis. A product titer of 78.8 mg/L β-barbatene was achieved in Saccharomyces cerevisiae via metabolic engineering. Our study findings will help screen or design STSs from fungi with specific product profiles as functional elements for applications in synthetic biology. Full article

Fungal endophytes are harboured in the leaves of every individual plant host and contribute to plant health, leaf senescence, and early decomposition. In grasslands, fungal endophytes and their hosts often coexist with large herbivores. However, the influence of grazing by large herbivores on foliar fungal endophyte communities remains largely unexplored. We conducted a long-term (18 yr) grazing experiment to explore the effects of grazing on the community composition and diversity of the foliar fungal endophytes of two perennial grassland species (i.e., Artemisia capillaris and Stipa bungeana) across one growing season. Grazing significantly increased the mean fungal alpha diversity of A. capillaris in the early season. In contrast, grazing significantly reduced the mean fungal alpha diversity of endophytic fungi of S. bungeana in the late season. Grazing, growing season, and their interactions concurrently structured the community composition of the foliar fungal endophytes of both plant species. However, growing season consistently outperformed grazing and environmental factors in shaping the community composition and diversity of both plant species. Overall, our findings demonstrate that the foliar endophytic fungal community diversity and composition differed in response to grazing between A. capillaris and S. bungeana during one growing season. The focus on this difference will enhance our understanding of grazing’s impact on ecological systems and improve land management practices in grazing regions. This variation in the effects of leaf nutrients and plant community characteristics on foliar endophytic fungal community diversity and composition may have a pronounced impact on plant health and plant–fungal interactions. Full article

Intertidal zones comprise diverse habitats and directly suffer from the influences of human activities. Nevertheless, the seasonal fluctuations in fungal diversity and community structure in these areas are not well comprehended. To address this gap, samples of seawater and sediment were collected seasonally from the estuary and swimming beaches of Qingdao’s intertidal areas in China and were analyzed using a metabarcoding approach targeting ITS2 rDNA regions. Compared to the seawater community dominated by Ciliophora and Agaricomycetes, the sediment community was rather dominated by Dothideomycetes and Eurotiomycetes. Furthermore, the seawater community shifted with the seasons but not with the locations, while the sediment community shifted seasonally and spatially, with a specific trend showing that Cladosporium, Alternaria, and Aureobasidium occurred predominantly in the estuarine habitats during winter and in the beach habitats during spring. These spatiotemporal shifts in fungal communities’ composition were supported by the PERMANOVA test and could be explained partially by the environmental variables checked, including temperature, salinity, and total organic carbon. Unexpectedly, the lowest fungal richness was observed in the summer sediments from two swimming beaches which were attracting a high influx of tourists during summer, leading to a significant anthropogenic influence. Predicted trophic modes of fungal taxa exhibited a seasonal pattern with an abundance of saprotrophic fungi in the summer sediments, positively correlating to the temperature, while the taxa affiliated with symbiotroph and pathotroph-saprotroph occurred abundantly in the winter and spring sediments, respectively. Our results demonstrate the space–time shifts in terms of the fungal community, as well as the trophic modes in the intertidal region, providing in-depth insights into the potential influence of environmental factors and human activity on intertidal mycobiomes. Full article

Neutrophils are critical phagocytic cells in innate immunity, playing a significant role in defending against invasive fungal pathogens. This study aimed to explore the transcriptional activation of human neutrophils in response to different fungal pathogens, including Candida albicans and Aspergillus fumigatus, compared to the bacterial pathogen Escherichia coli. We identified distinct transcriptional profiles and stress-related pathways in neutrophils during fungal infections, highlighting their functional diversity and adaptability. The transcriptional response was largely redundant across all pathogens in immune-relevant categories and cytokine pathway activation. However, differences in the magnitude of differentially expressed genes (DEGs) were observed, with A. fumigatus inducing a lower transcriptional effect compared to C. albicans and E. coli. Notably, specific gene signatures associated with cell death were differentially regulated by fungal pathogens, potentially increasing neutrophil susceptibility to autophagy, pyroptosis, and neutrophil extracellular trap (NET) formation. These findings provide valuable insights into the complex immunological responses of neutrophils during fungal infections, offering new avenues for diagnostic and therapeutic strategies, particularly in the management of invasive fungal diseases. Full article

As a unique ecosystem, Karst caves harbor an impressive diversity of specific fungi. However, the factors and mechanisms that shape fungal biodiversity in caves remain elusive. In this study, we explored the assembly patterns of fungal communities based on our previous research in eight representative Karst caves in Southwest China. Our results indicated that dispersal limitation plays a crucial role in shaping the overall fungal community as well as specific communities in rock, sediment, and water samples. However, “Undominated” processes contributed more than dispersal limitation in air samples. Interestingly, the dominant assembly processes varied between caves. Consistently, environmental selection had a minor impact on the assembly of fungal communities. Among the examined spatial and environmental variables, latitude, longitude, altitude, and temperature were found to significantly influence fungal communities irrespective of substrate type. These findings provide valuable insights into the ecological factors governing fungal community assembly in Karst caves. Full article

Candidemia is the fourth most common healthcare-related bloodstream infection. In recent years, incidence rates of Candida parapsilosis have been on the rise, with differences in prevalence and antifungal susceptibility between countries. The aim of the present study was to evaluate temporal changes in prevalence and antifungal susceptibility of C. parapsilosis among other species causing candidemia. All candidemia episodes from January 2015 to August 2022 were evaluated in order to depict time trends in prevalence of C. parapsilosis sensu stricto among all Candida species recovered from blood cultures as well as fluconazole- and voriconazole-non-susceptibility rates. Secondary analyses evaluated time trends in prevalence and antifungal non-susceptibility according to clinical settings. The overall prevalence of C. parapsilosis was observed to increase compared to the prevalence of other Candida species over time (p-trend = 0.0124). From 2019, the number of C. parapsilosis sensu stricto isolates surpassed C. albicans, without an increase in incidence rates. Overall rates of fluconazole- and voriconazole-non-susceptible C. parapsilosis sensu stricto were both 3/44 (6.8%) in 2015 and were 32/51 (62.7%) and 27/51 (52.9%), respectively, in 2022 (85% cross-non-susceptibility). The risk of detecting fluconazole- or voriconazole-non-susceptibility was found to be higher in C. parapsilosis compared to other Candida species (odds ratio (OR) = 1.60, 95% CI [1.170, 2.188], p-value < 0.0001 and OR = 12.867, 95% CI [6.934, 23.878], p-value < 0.0001, respectively). This is the first study to report C. parapsilosis sensu stricto as the most prevalent among Candida spp. isolated from blood cultures, with worrisome fluconazole- and voriconazole-non-susceptibility rates, unparalleled among European and North American geographical regions. Full article