Journal of Fungi

The emergence of pathogenic fungi is a major and rapidly growing problem (7% increase) that affects human and animal health, ecosystems, food security, and the economy worldwide. The Dermocystida group in particular has emerged relatively recently and includes species that affect both humans and animals. Within this group, one species in particular, Sphareothecum destruens, also known as the rosette agent, represents a major risk to global aquatic biodiversity and aquaculture, and has caused severe declines in wild fish populations in Europe and large losses in salmon farms in the USA. It is a species that has been associated with a healthy carrier for millions of years, but in recent decades, the host has managed to invade parts of Southeast Asia, Central Asia, Europe, and North Africa. In order to better understand the emergence of this new disease, for the first time, we have synthesized current knowledge on the distribution, detection, and prevalence of S. destruens, as well as the associated mortality curves, and the potential economic impact in countries where the healthy carrier has been introduced. Finally, we propose solutions and perspectives to manage and mitigate the emergence of this fungus in countries where it has been introduced. Full article

Mucormycosis has emerged as a group of severe infections mainly in immunocompromised patients. We analysed the epidemiology of mucormycosis in Greece in a multicentre, nationwide prospective survey of patients of all ages, during 2005–2022. A total of 108 cases were recorded. The annual incidence declined after 2009 and appeared stable thereafter, at 0.54 cases/million population. The most common forms were rhinocerebral (51.8%), cutaneous (32.4%), and pulmonary (11.1%). Main underlying conditions were haematologic malignancy/neutropenia (29.9%), haematopoietic stem cell transplantation (4.7%), diabetes mellitus (DM) (15.9%), other immunodeficiencies (23.4%), while 22.4% of cases involved immunocompetent individuals with cutaneous/soft-tissue infections after motor vehicle accident, surgical/iatrogenic trauma, burns, and injuries associated with natural disasters. Additionally, DM or steroid-induced DM was reported as a comorbidity in 21.5% of cases with various main conditions. Rhizopus (mostly R. arrhizus) predominated (67.1%), followed by Lichtheimia (8.5%) and Mucor (6.1%). Antifungal treatment consisted mainly of liposomal amphotericin B (86.3%), median dose 7 mg/kg/day, range 3–10 mg/kg/day, with or without posaconazole. Crude mortality was 62.8% during 2005–2008 but decreased significantly after 2009, at 34.9% (p = 0.02), with four times fewer haematological cases, fewer iatrogenic infections, and fewer cases with advanced rhinocerebral form. The increased DM prevalence should alert clinicians for timely diagnosis of mucormycosis in this patient population. Full article

In fungi, the most abundant transcription factor (TF) class contains a fungal-specific ‘GAL4-like’ Zn2C6 DNA binding domain (DBD), while the second class contains another fungal-specific domain, known as ‘fungal_trans’ or middle homology domain (MHD), whose function remains largely uncharacterized. Remarkably, almost a third of MHD-containing TFs in public sequence databases apparently lack DNA binding activity, since they are not predicted to contain a DBD. Here, we reassess the domain organization of these ‘MHD-only’ proteins using an in silico error-tracking approach. In a large-scale analysis of ~17000 MHD-only TF sequences present in all fungal phyla except Microsporidia and Cryptomycota, we show that the vast majority (>90%) result from genome annotation errors and we are able to predict a new DBD sequence for 14261 of them. Most of these sequences correspond to a Zn2C6 domain (82%), with a small proportion of C2H2 domains (4%) found only in Dikarya. Our results contradict previous findings that the MHD-only TF are widespread in fungi. In contrast, we show that they are exceptional cases, and that the fungal-specific Zn2C6–MHD domain pair represents the canonical domain signature defining the most predominant fungal TF family. We call this family CeGAL, after the highly characterized members: Cep3, whose 3D structure is determined, and GAL4, a eukaryotic TF archetype. We believe that this will not only improve the annotation and classification of the Zn2C6 TF but will also provide critical guidance for future fungal gene regulatory network analyses. Full article

Fungi from the Teratosphaeriaceae (Mycosphaerellales; Dothideomycetes; Ascomycota) have a wide range of lifestyles. Among these are a few species that are endolichenic fungi. However, the known diversity of endolichenic fungi from Teratosphaeriaceae is far less understood compared to other lineages of Ascomycota. We conducted five surveys from 2020 to 2021 in Yunnan Province of China, to explore the biodiversity of endolichenic fungi. During these surveys, we collected multiple samples of 38 lichen species. We recovered a total of 205 fungal isolates representing 127 species from the medullary tissues of these lichens. Most of these isolates were from Ascomycota (118 species), and the remaining were from Basidiomycota (8 species) and Mucoromycota (1 species). These endolichenic fungi represented a wide variety of guilds, including saprophytes, plant pathogens, human pathogens, as well as entomopathogenic, endolichenic, and symbiotic fungi. Morphological and molecular data indicated that 16 of the 206 fungal isolates belonged to the family Teratosphaeriaceae. Among these were six isolates that had a low sequence similarity with any of the previously described species of Teratosphaeriaceae. For these six isolates, we amplified additional gene regions and conducted phylogenetic analyses. In both single gene and multi-gene phylogenetic analyses using ITS, LSU, SSU, RPB2, TEF1, ACT, and CAL data, these six isolates emerged as a monophyletic lineage within the family Teratosphaeriaceae and sister to a clade that included fungi from the genera Acidiella and Xenopenidiella. The analyses also indicated that these six isolates represented four species. Therefore, we established a new genus, Intumescentia gen. nov., to describe these species as Intumescentia ceratinae, I. tinctorum, I. pseudolivetorum, and I. vitii. These four species are the first endolichenic fungi representing Teratosphaeriaceae from China. Full article

Methanol, which produced in large quantities from low-quality coal and the hydrogenation of CO₂, is a potentially renewable one-carbon (C1) feedstock for biomanufacturing. The methylotrophic yeast Pichia pastoris is an ideal host for methanol biotransformation given its natural capacity as a methanol assimilation system. However, the utilization efficiency of methanol for biochemical production is limited by the toxicity of formaldehyde. Therefore, reducing the toxicity of formaldehyde to cells remains a challenge to the engineering design of a methanol metabolism. Based on genome-scale metabolic models (GSMM) calculations, we speculated that reducing alcohol oxidase (AOX) activity would re-construct the carbon metabolic flow and promote balance between the assimilation and dissimilation of formaldehyde metabolism processes, thereby increasing the biomass formation of P. pastoris. According to experimental verification, we proved that the accumulation of intracellular formaldehyde can be decreased by reducing AOX activity. The reduced formaldehyde formation upregulated methanol dissimilation and assimilation and the central carbon metabolism, which provided more energy for the cells to grow, ultimately leading to an increased conversion of methanol to biomass, as evidenced by phenotypic and transcriptome analysis. Significantly, the methanol conversion rate of AOX-attenuated strain PC110-AOX1-464 reached 0.364 g DCW/g, representing a 14% increase compared to the control strain PC110. In addition, we also proved that adding a co-substrate of sodium citrate could further improve the conversion of methanol to biomass in the AOX-attenuated strain. It was found that the methanol conversion rate of the PC110-AOX1-464 strain with the addition of 6 g/L sodium citrate reached 0.442 g DCW/g, representing 20% and 39% increases compared to AOX-attenuated strain PC110-AOX1-464 and control strain PC110 without sodium citrate addition, respectively. The study described here provides insight into the molecular mechanism of efficient methanol utilization by regulating AOX. Reducing AOX activity and adding sodium citrate as a co-substrate are potential engineering strategies to regulate the production of chemicals from methanol in P. pastoris. Full article

The Chilean matorral is a heavily threatened Mediterranean-type ecosystem due to human-related activities such as anthropogenic fires. Mycorrhizal fungi may be the key microorganisms to help plants cope with environmental stress and improve the restoration of degraded ecosystems. However, the application of mycorrhizal fungi in the restoration of the Chilean matorral is limited because of insufficient local information. Consequently, we assessed the effect of mycorrhizal inoculation on the survival and photosynthesis at set intervals for two years after a fire event in four native woody plant species, namely: Peumus boldus, Quillaja saponaria, Cryptocarya alba, and Kageneckia oblonga, all dominant species of the matorral. Additionally, we assessed the enzymatic activity of three enzymes and macronutrient in the soil in mycorrhizal and non-mycorrhizal plants. The results showed that mycorrhizal inoculation increased survival in all studied species after a fire and increased photosynthesis in all, but not in P. boldus. Additionally, the soil associated with mycorrhizal plants had higher enzymatic activity and macronutrient levels in all species except in Q. saponaria, in which there was no significant mycorrhization effect. The results suggest that mycorrhizal fungi could increase the fitness of plants used in restoration initiatives after severe disturbances such as fires and, consequently, should be considered for restoration programs of native species in threatened Mediterranean ecosystems. Full article

Soil-borne beneficial microbes establish symbioses with plant hosts and play key roles during growth and development therein. In this study, two fungal strains, FLP7 and B9, were isolated from the rhizosphere microbiome associated with Choy Sum (Brassica rapa var. parachinensis) and barley (Hordeum vulgare), respectively. Sequence analyses of the internal transcribed spacer and 18S ribosomal RNA genes combined with colony and conidial morphology identified FLP7 and B9 to be Penicillium citrinum strains/isolates. Plant–fungus interaction assays revealed that isolate B9 showed significant growth promotion effects in Choy Sum plants cultivated in normal soil, as well as under phosphate-limiting conditions. In comparison to the mock control, B9-inoculated plants showed a 34% increase in growth in aerial parts and an 85% upsurge in the fresh weight of roots when cultivated in sterilized soil. The dry biomass of such fungus-inoculated Choy Sum increased by 39% and 74% for the shoots and roots, respectively. Root colonization assays showed that P. citrinum associates directly with the root surface but does not enter or invade the root cortex of the inoculated Choy Sum plants. Preliminary results also indicated that P. citrinum can promote growth in Choy Sum via volatile metabolites too. Interestingly, we detected relatively higher amounts of gibberellins and cytokinins in axenic P. citrinum culture filtrates through liquid chromatography–mass spectrometry analyses. This could plausibly explain the overall growth induction in P. citrinum-inoculated Choy Sum plants. Furthermore, the phenotypic growth defects associated with the Arabidopsis ga1 mutant could be chemically complemented by the exogenous application of P. citrinum culture filtrate, which also showed accumulation of fungus-derived active gibberellins. Our study underscores the importance of transkingdom beneficial effects of such mycobiome-assisted nutrient assimilation and beneficial fungus-derived phytohormone-like metabolites in the induction of robust growth in urban farmed crops. Full article

Bacterial and fungal adhesins mediate microbial aggregation, biofilm formation, and adhesion to host. We divide these proteins into two major classes: professional adhesins and moonlighting adhesins that have a non-adhesive activity that is evolutionarily conserved. A fundamental difference between the two classes is the dissociation rate. Whereas moonlighters, including cytoplasmic enzymes and chaperones, can bind with high affinity, they usually dissociate quickly. Professional adhesins often have unusually long dissociation rates: minutes or hours. Each adhesin has at least three activities: cell surface association, binding to a ligand or adhesive partner protein, and as a microbial surface pattern for host recognition. We briefly discuss Bacillus subtilis TasA, pilin adhesins, gram positive MSCRAMMs, and yeast mating adhesins, lectins and flocculins, and Candida Awp and Als families. For these professional adhesins, multiple activities include binding to diverse ligands and binding partners, assembly into molecular complexes, maintenance of cell wall integrity, signaling for cellular differentiation in biofilms and in mating, surface amyloid formation, and anchorage of moonlighting adhesins. We summarize the structural features that lead to these diverse activities. We conclude that adhesins resemble other proteins with multiple activities, but they have unique structural features to facilitate multifunctionality. Full article

Fungi work as decomposers to break down organic carbon, deposit recalcitrant carbon, and transform other elements such as nitrogen. The decomposition of biomass is a key function of wood-decaying basidiomycetes and ascomycetes, which have the potential for the bioremediation of hazardous chemicals present in the environment. Due to their adaptation to different environments, fungal strains have a diverse set of phenotypic traits. This study evaluated 320 basidiomycetes isolates across 74 species for their rate and efficiency of degrading organic dye. We found that dye-decolorization capacity varies among and within species. Among the top rapid dye-decolorizing fungi isolates, we further performed genome-wide gene family analysis and investigated the genomic mechanism for their most capable dye-degradation capacity. Class II peroxidase and DyP-type peroxidase were enriched in the fast-decomposer genomes. Gene families including lignin decomposition genes, reduction-oxidation genes, hydrophobin, and secreted peptidases were expanded in the fast-decomposer species. This work provides new insights into persistent organic pollutant removal by fungal isolates at both phenotypic and genotypic levels. Full article

Despite recent studies suggesting that marine fungi are ubiquitous in oceanic systems and involved in organic matter degradation, their role in the carbon cycle of the oceans is still not characterized and fungal respiration and production are understudied. This study focused on determining fungal growth efficiencies and its susceptibility to temperature differences and nutrient concentration. Hence, respiration and biomass production of three fungal isolates (Rhodotorula mucilaginosa, Rhodotorula sphaerocarpa, Sakaguchia dacryoidea) were measured in laboratory experiments at two temperatures and two nutrient concentrations. We found that fungal respiration and production rates differed among species, temperature, and nutrient concentration. Fungal respiration and production were higher at higher temperatures, but higher fungal growth efficiencies were observed at lower temperatures. Nutrient concentration affected fungal respiration, production, and growth efficiency, but its influence differed among species. Altogether, this study provides the first growth efficiency estimates of pelagic fungi, providing novel insights into the role of fungi as source/sink of carbon during organic matter remineralization. Further research is now needed to unravel the role of pelagic fungi in the marine carbon cycle, a topic that gains even more importance in times of increasing CO₂ concentrations and global warming. Full article

We sequenced over 200 recent specimens of Lecanora s.lat. from Brazil, delimiting 28 species in our material. Many seem to represent undescribed species, some of which being morphologically and chemically similar to each other or to already described species. Here, we present a phylogenetic analysis based on ITS, including our specimens and GenBank data. We describe nine new species. The purpose of the paper is to illustrate the diversity of the genus in Brazil, not to focus on segregate genera. However, we found that all Vainionora species cluster together and these will be treated separately. Other Lecanora species with dark hypothecium clustered in several different clades. Species with the morphology of Lecanora caesiorubella, in which currently several subspecies with different chemistry and distribution are recognized, fall apart in different, distantly related clades, so they cannot be regarded as subspecies but should be recognized at species level. A key is given for the Lecanora species from Brazil. Full article

Pneumocystis jirovecii pneumonia (PJP) in immunocompromised patients entails high mortality and requires adequate laboratory diagnosis. We compared the performance of a real time-PCR assay against the immunofluorescence assay (IFA) in the routine of a large microbiology laboratory. Different respiratory samples from HIV and non-HIV-infected patients were included. The retrospective analysis used data from September 2015 to April 2018, which included all samples for which a P. jirovecii test was requested. A total of 299 respiratory samples were tested (bronchoalveolar lavage fluid (n = 181), tracheal aspirate (n = 53) and sputum (n = 65)). Forty-eight (16.1%) patients fulfilled the criteria for PJP. Five positive samples (10%) had only colonization. The PCR test was found to have a sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of 96%, 98%, 90% and 99%, compared to 27%, 100%, 100% and 87%, for the IFA, respectively. PJ-PCR sensitivity and specificity were >80% and >90% for all tested respiratory samples. Median cycle threshold values in definite PJP cases were 30 versus 37 in colonized cases (p < 0.05). Thus, the PCR assay is a robust and reliable test for the diagnosis PJP in all respiratory sample types. Ct values of ≥36 could help to exclude PJP diagnosis. Full article

Mycelial ageing is associated with ROS and autophagy in Lentinula edodes. However, the underlying cellular and molecular mechanisms between ROS and autophagy remain obscure. This study induced autophagy in L. edodes mycelia through exogenous H₂O₂ treatment. Results showed that 100 μM H₂O₂ treatment for 24 h significantly inhibited mycelial growth. H₂O₂ caused the depolarisation of MMP and accumulation of TUNEL-positive nuclei, which was similar to the ageing phenotype of L. edodes mycelia. Transcriptome analysis showed that differentially expressed genes were enriched in the mitophagic, autophagic, and MAPK pathways. LeAtg8 and LeHog1 were selected as hub genes. RNA and protein levels of LeATG8 increased in the H₂O₂-treated mycelia. Using fluorescent labelling, we observed for the first time the classic ring structure of autophagosomes in a mushroom, while 3D imaging suggested that these autophagosomes surrounded the nuclei to degrade them at specific growth stages. Phospho-LeHOG1 protein can translocate from the cytoplasm to the nucleus to regulate mycelial cells, resisting ROS-induced oxidative stress. Furthermore, LeATG8 expression was suppressed when LeHOG1 phosphorylation was inhibited. These results suggest that the LeATG8-dependent autophagy in L. edodes mycelial is closely associated with the activity or even phosphorylation of LeHOG1. Full article

Color is a crucial feature to consider when breeding and improving strains of Auricularia cornea. To uncover the mechanism of white strain formation in A. cornea, this study selected parental strains that were homozygous for the color trait and analyzed the genetic laws of A. cornea color through genetic population construction, such as test-cross, back-cross, and self-cross populations, and the statistical analysis of color trait segregation. Moreover, the study developed SSR molecular markers to construct a genetic linkage map, perform the fine mapping the color-controlling genetic locus, and verify candidate genes using yeast two-hybrid, transcriptome analysis, and different light treatments. The results of the study indicated that the color trait of A. cornea is controlled by two pairs of alleles. When both pairs of loci are dominant, the fruiting body is purple, while when both pairs of loci are recessive or one pair of loci is recessive, the fruiting body is white. Based on the linkage map, the study finely mapped the color locus within Contig9_29,619bp-53,463bp in the A. cornea genome and successfully predicted the color-controlling locus gene A18078 (AcveA), which belongs to the Velvet factor family protein and has a conserved structure domain of the VeA protein. It can form a dimer with the VelB protein to inhibit pigment synthesis in filamentous fungi. Lastly, the study validated the interaction between AcVeA and VelB (AcVelB) in A. cornea at the gene, protein, and phenotype levels, revealing the mechanism of inhibition of pigment synthesis in A. cornea. Under dark conditions, dimerization occurs, allowing it to enter the nucleus and inhibit pigment synthesis, leading to a lighter fruiting body color. However, under light conditions, the dimer content is low and cannot enter the nucleus to inhibit pigment synthesis. In summary, this study clarified the mechanism of white strain formation in A. cornea, which could aid in improving white strains of A. cornea and studying the genetic basis of color in other fungi. Full article

Cobweb disease is a fungal disease that can cause serious damage to edible mushrooms worldwide. To investigate cobweb disease in Morchella sextelata in Guizhou Province, China, we isolated and purified the pathogen responsible for the disease. Through morphological and molecular identification and pathogenicity testing on infected M. sextelata, we identified Cladobotryum mycophilum as the cause of cobweb disease in this region. This is the first known occurrence of this pathogen causing cobweb disease in M. sextelata anywhere in the world. We then obtained the genome of C. mycophilum BJWN07 using the HiFi sequencing platform, resulting in a high-quality genome assembly with a size of 38.56 Mb, 10 contigs, and a GC content of 47.84%. We annotated 8428 protein-coding genes in the genome, including many secreted proteins, host interaction-related genes, and carbohydrate-active enzymes (CAZymes) related to the pathogenesis of the disease. Our findings shed new light on the pathogenesis of C. mycophilum and provide a theoretical basis for developing potential prevention and control strategies for cobweb disease. Full article

Peroxidase (Prx)-related genes are reported to be involved in the metabolism of hydrogen peroxide (H₂O₂) in plants. Here, we found that the expression of the PdePrx12 gene was upregulated in wild-type (WT) poplar line NL895 infected with the pathogens Botryosphaeria dothidea strain 3C and Alternaria alternata strain 3E. The PdePrx12 gene was cloned in the poplar line NL895 and its overexpression (OE) and reduced-expression (RE) vectors were constructed. OE and RE transgenic lines were then generated. The H₂O₂ content in the leaves was measured by DAB staining and spectrophotometric analysis, and the data revealed that the OE line had a reduced H₂O₂ content, whereas the RE line had an increased H₂O₂ content. These transgenic and WT plants were also inoculated with the 3C/3E pathogens. The leaf area infected by pathogen 3C/3E was determined and the OE line was found to have a larger area of infection, whereas the RE line was found to have a smaller area of infection. This result suggested PdePRX12 is involved in disease resistance in poplar. Given these results, this study demonstrated that when poplar is infected by pathogens, the expression of PdePrx12 is inhibited, leading to an increase in H₂O₂ content, thereby enhancing disease resistance. Full article

d-lactic acid, a chiral organic acid, can enhance the thermal stability of polylactic acid plastics. Microorganisms such as the yeast Pichia pastoris, which lack the natural ability to produce or accumulate high amounts of d-lactic acid, have been metabolically engineered to produce it in high titers. However, tolerance to d-lactic acid remains a challenge. In this study, we demonstrate that cell flocculation improves tolerance to d-lactic acid and increases d-lactic acid production in Pichia pastoris. By incorporating a flocculation gene from Saccharomyces cerevisiae (ScFLO1) into P. pastoris KM71, we created a strain (KM71-ScFlo1) that demonstrated up to a 1.6-fold improvement in specific growth rate at high d-lactic acid concentrations. Furthermore, integrating a d-lactate dehydrogenase gene from Leuconostoc pseudomesenteroides (LpDLDH) into KM71-ScFlo1 resulted in an engineered strain (KM71-ScFlo1-LpDLDH) that could produce d-lactic acid at a titer of 5.12 ± 0.35 g/L in 48 h, a 2.6-fold improvement over the control strain lacking ScFLO1 expression. Transcriptomics analysis of this strain provided insights into the mechanism of increased tolerance to d-lactic acid, including the upregulations of genes involved in lactate transport and iron metabolism. Overall, our work represents an advancement in the efficient microbial production of d-lactic acid by manipulating yeast flocculation. Full article

(1) Background: Acetaminophen (APAP), an active component of many analgesic and antipyretic drugs, is one of the most concerning trace contaminants in the environment and is considered as an emergent pollutant of marine and aquatic ecosystems. Despite its biodegradability, APAP has become a recalcitrant compound due to the growth of the global population, the ease of availability, and the inefficient wastewater treatment applied. (2) Methods: In this study, we used a transcriptomic approach to obtain functional and metabolic insights about the metabolization of APAP by a phenol-degrading fungal strain, Penicillium chrysogenum var. halophenolicum. (3) Results: We determined that the transcriptomic profile exhibited by the fungal strain during APAP degradation was very dynamic, being characterized by an abundance of dysregulated transcripts which were proportional to the drug metabolization. Using a systems biology approach, we also inferred the protein functional interaction networks that could be related to APAP degradation. We proposed the involvement of intracellular and extracellular enzymes, such as amidases, cytochrome P450, laccases, and extradiol-dioxygenases, among others. (4) Conclusions: Our data suggested that the fungus could metabolize APAP via a complex metabolic pathway, generating nontoxic metabolites, which demonstrated its potential in the bioremediation of this drug. Full article