Journal of Fungi

Background: We sought to characterize the outcomes of patients with primary pulmonary coccidioidomycosis whose post-treatment complement fixation (CF) titer increased by more than 2 dilutions (serologic rebound) after discontinuation of antifungal treatment. Methods. We conducted a retrospective chart review of patients with primary pulmonary coccidioidomycosis and identified immunocompetent, non-pregnant adults who received antifungal treatment and then experienced a serologic rebound after treatment discontinuation. We compared these to matched controls similarly treated who did not have serologic rebound. Results. Fifty-eight patients experienced serologic rebound. Thirty (52%) of these were associated with symptoms. Nine were associated with radiographic progression. The median time to serologic rebound was 3.5 months. Antifungal treatment was reinitiated in 37 (63.7%) patients. Four of the 58 (6.9%) with rebounded serology subsequently developed extra-thoracic dissemination. Compared with matched controls, patients with rebounded serology were more likely to have post-treatment symptoms, reinitiation of antifungal therapy, and a longer duration of clinical follow-up. However, they were not more likely to experience extra-thoracic dissemination. Conclusion: Serological rebound, manifested in at least 2-dilution rise of CF titer following antifungal treatment of primary pulmonary coccidioidomycosis, was uncommon, but resulted in longer clinical follow-up. Continued monitoring of such patients is important to identify the patients who develop subsequent symptoms, as well as extra-thoracic dissemination. Full article

Interactions between different kingdoms of microorganisms in humans are common but not well described. A recent analysis of the mycobiome has described the presence of different fungi and their positive and/or negative interactions with bacteria and other fungi. In chronic respiratory diseases, these different microorganisms form mixed biofilms to live inside. The interactions between Gram-negative bacteria and filamentous fungi in these biofilms have attracted more attention recently. In this review, we analyse the microbiota of the respiratory tract of healthy individuals and patients with chronic respiratory disease. Additionally, we describe the regulatory mechanisms that rule the mixed biofilms of Aspergillus fumigatus and Gram-negative bacteria and the effects of this biofilm on clinical presentations. Full article

Kiwifruit brown spot caused by Corynespora cassiicola is the most significant fungal disease in Sichuan, resulting in premature defoliation, which had a significant impact on yield and fruit quality. The objective of the study was to determine the occurrence regularity and suitability of kiwifruit brown spot in Sichuan. The occurrence of the disease in the main producing region was continuously monitored, the maximum entropy (MaxEnt) model was used to predict its potential distribution, and the key environmental variables were identified using the jackknife method. The results indicated that kiwifruit brown spot was widely distributed across the entire producing region in Sichuan, predominantly affecting the variety “Hongyang”. The incidence (p < 0.01) and disease index (p < 0.05) showed a significant positive correlation with the cultivar, and decreased with the altitude increasing. The average area under the ROC curve (AUC) of 10 replicates was 0.933 ± 0.012, with an accuracy of 84.44% in a field test, confirming the reliability of the predicted results. The highly suitable distribution areas of kiwifruit brown spot were mainly located in the Chengdu and Ya’an regions. The entire Panzhihua region was an unsuitable distribution area, and the entire Pujiang County and Mingshan District were highly suitable distribution areas. The key environmental variables affecting the potential distribution of kiwifruit brown spot included isothermality (24.3–33.7%), minimum temperature in August (16.3–23.6 °C), maximum temperature in July (25.5–31.2 °C), minimum temperature in June (15.6–20.9 °C), precipitation in August (158–430 mm), and average temperature in October (15.6–18.8 °C). This study provides a theoretical basis for the reasonable layout of the cultivar and the precise prevention and control of the disease. Full article

We studied the taxonomy of Pluteus podospileus and similar species using morphological and molecular (nrITS, TEF1-α) data, including a detailed study of the type collections of P. inflatus var. alneus, Pluteus minutissimus f. major, and P. granulatus var. tenellus. Within the P. podospileus complex, we phylogenetically confirmed six species in Europe, five in Asia, and eight in North America. Based on our results, we recognize P. seticeps as a separate species occurring in North America, while P. podospileus is limited to Eurasia. We describe six new species and a new variety: P. absconditus, P. fuscodiscus, P. gausapatus, P. inexpectatus, P. millsii, and P. notabilis and its variety, P. notabilis var. insignis. We elevate Pluteus seticeps var. cystidiosus to species rank as Pluteus cystidiosus. Based on the holotype of P. inflatus var. alneus, collections of P. inflatus identified by Velenovský, and several modern collections, we resurrect the name P. inflatus. Based on molecular analyses of syntypes of Pluteus minutissimus f. major and a holotype of Pluteus granulatus var. tenellus, we synonymize them under P. inflatus. We also increase our knowledge about the morphology and distribution of P. cutefractus Full article

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a highly infectious positive RNA virus, has spread from its epicenter to other countries with increased mortality and morbidity. Its expansion has hampered humankind’s social, economic, and health realms to a large extent. Globally, investigations are underway to understand the complex pathophysiology of coronavirus disease (COVID-19) induced by SARS-CoV-2. Though numerous therapeutic strategies have been introduced to combat COVID-19, none are fully proven or comprehensive, as several key issues and challenges remain unresolved. At present, natural products have gained significant momentum in treating metabolic disorders. Mushrooms have often proved to be the precursor of various therapeutic molecules or drug prototypes. The plentiful bioactive macromolecules in edible mushrooms, like polysaccharides, proteins, and other secondary metabolites (such as flavonoids, polyphenols, etc.), have been used to treat multiple diseases, including viral infections, by traditional healers and the medical fraternity. Some edible mushrooms with a high proportion of therapeutic molecules are known as medicinal mushrooms. In this review, an attempt has been made to highlight the exploration of bioactive molecules in mushrooms to combat the various pathophysiological complications of COVID-19. This review presents an in-depth and critical analysis of the current therapies against COVID-19 versus the potential of natural anti-infective, antiviral, anti-inflammatory, and antithrombotic products derived from a wide range of easily sourced mushrooms and their bioactive molecules. Full article

We analyzed the global expression patterns of telomerase-negative mutants from haploid cells of Ustilago maydis to identify the gene network required for cell survival in the absence of telomerase. Mutations in either of the telomerase core subunits (trt1 and ter1) of the dimorphic fungus U. maydis cause deficiencies in teliospore formation. We report the global transcriptome analysis of two ter1Δ survivor strains of U. maydis, revealing the deregulation of telomerase-deleted responses (TDR) genes, such as DNA-damage response, stress response, cell cycle, subtelomeric, and proximal telomere genes. Other differentially expressed genes (DEGs) found in the ter1Δ survivor strains were related to pathogenic lifestyle factors, plant–pathogen crosstalk, iron uptake, meiosis, and melanin synthesis. The two ter1Δ survivors were phenotypically comparable, yet DEGs were identified when comparing these strains. Our findings suggest that teliospore formation in U. maydis is controlled by key pathogenic lifestyle and meiosis genes. Full article

Fungi represents a rich repository of taxonomically restricted, yet chemically diverse, secondary metabolites that are synthesised via specific metabolic pathways. An enzyme’s specificity and biosynthetic gene clustering are the bottleneck of secondary metabolite evolution. Trichoderma harzianum M10 v1.0 produces many pharmaceutically important molecules; however, their specific biosynthetic pathways remain uncharacterised. Our genomic-based analysis of this species reveals the biosynthetic diversity of its specialised secondary metabolites, where over 50 BGCs were predicted, most of which were listed as polyketide-like compounds associated clusters. Gene annotation of the biosynthetic candidate genes predicted the production of many medically/industrially important compounds including enterobactin, gramicidin, lovastatin, HC-toxin, tyrocidine, equisetin, erythronolide, strobilurin, asperfuranone, cirtinine, protoilludene, germacrene, and epi-isozizaene. Revealing the biogenetic background of these natural molecules is a step forward towards the expansion of their chemical diversification via engineering their biosynthetic genes heterologously, and the identification of their role in the interaction between this fungus and its biotic/abiotic conditions as well as its role as bio-fungicide. Full article

Background: The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels—showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella. Objectives: The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella. Methodology: Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale. Results and Conclusions: The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species. Full article

Soil salinity is a limiting factor in crop productivity. Inoculating crops with microorganisms adapted to salt stress is an alternative to increasing plant salinity tolerance. Few studies have simultaneously propagated arbuscular mycorrhizal fungi (AMF) and dark septate fungi (DSF) using different sources of native inoculum from halophyte plants and evaluated their effectiveness. In alfalfa plants as trap culture, this study assessed the infectivity of 38 microbial consortia native from rhizosphere soil (19) or roots (19) from six halophyte plants, as well as their effectiveness in mitigating salinity stress. Inoculation with soil resulted in 26–56% colonization by AMF and 12–32% by DSF. Root inoculation produced 10–56% and 8–24% colonization by AMF and DSF, respectively. There was no difference in the number of spores of AMF produced with both inoculum types. The effective consortia were selected based on low Na but high P and K shoot concentrations that are variable and are relevant for plant nutrition and salt stress mitigation. This microbial consortia selection may be a novel and applicable model, which would allow the production of native microbial inoculants adapted to salinity to diminish the harmful effects of salinity stress in glycophyte plants in the context of sustainable agriculture. Full article

Sclerotinia sclerotiorum, a fungal pathogen, causes world-wide crop losses and additional disease management strategies are needed. Modeling the climate niche of this fungus may offer a tool for the selection of biological control organisms and cultural methods of control. Maxent, a modeling technique, was used to characterize the climate niche for the fungus. The technique requires disease occurrence data, bioclimatic data layers, and geospatial analysis. A cross-correlation was performed with ArcGIS 10.8.1, to reduce nineteen bioclimatic variables (WorldClim) to nine variables. The model results were evaluated by AUC (area under the curve). A final model was created with the random seed procedure of Maxent and gave an average AUC of 0.935 with an AUC difference of −0.008. The most critical variables included annual precipitation (importance: 14.1%) with a range of 450 mm to 2500 mm and the mean temperature of the coldest quarter0 (importance: 55.6%) with a range of −16 °C to 24 °C, which contributed the most to the final model. A habitat suitability map was generated in ArcGIS 10.8.1 from the final Maxent model. The final model was validated by comparing results with another occurrence dataset. A Z-Score statistical test confirmed no significant differences between the two datasets for all suitability areas. Full article

Synthetic dyes are generally not safe for human health or the environment, leading to the continuous search and growing demand for natural pigments that are considered safer, biodegrade more easily, and are environmentally beneficial. Among micro-organisms, fungi represent an emerging source of pigments due to their many benefits; therefore, they are readily viable on an industrial scale. Among all the bioactive pigments produced by fungi, melanin is an enigmatic, multifunctional pigment that has been studied for more than 150 years. This dark pigment, which is produced via the oxidative polymerization of phenolic compounds, has been investigated for its potential to protect life from all kingdoms, including fungi, from biotic and abiotic stresses. Over time, the research on fungal melanin has attracted a significant amount of scientific interest due to melanin’s distinct biological activities and multifarious functionality, which is well-documented in the literature and could possibly be utilized. This review surveys the literature and summarizes the current discourse, presenting an up-to-date account of the research performed on fungal melanin that encompasses its types, the factors influencing its bioactivity, the optimization of fermentation conditions to enhance its sustainable production, its biosynthetic pathways, and its extraction, as well as biochemical characterization techniques and the potential uses of melanin in a wide range of applications in various industries. A massive scope of work remains to circumvent the obstacles to obtaining melanin from fungi and exploring its future prospects in a diverse range of applications. Full article

Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota. Full article

Data about the relationship between their molecular types, virulence factors, clinical presentation, antifungal susceptibility profile, and outcome are still limited for Cryptococcus deuterogattii. This study aimed to evaluate the molecular and phenotypic characteristics of 24 C. deuterogattii isolates from the southeast region of Brazil. The molecular characterization was performed by multilocus sequence typing (MLST). The antifungal susceptibility profile was obtained according to CLSI-M27-A3 and EUCAST-EDef 7.1 methods. The virulence factors were evaluated using classic techniques. The isolates were divided into four populations. The molecular analysis suggests recombinant events in most of the groups evaluated. Resistance and susceptibility dose-dependent to fluconazole were evidenced in four isolates (16%) by EUCAST and in four isolates (16%) by CLSI methods. The agreement at ±two dilutions for both methods was 100% for itraconazole, ketoconazole, and voriconazole, 96% for amphotericin B, and 92% for fluconazole. Significant differences in virulence factor expression and antifungal susceptibility to itraconazole and amphotericin B were found. The mixed infection could be suggested by the presence of variable sequence types, differences in virulence factor production, and decreased antifungal susceptibility in two isolates from the same patient. The data presented herein corroborate previous reports about the molecular diversity of C. deuterogattii around the world. Full article

Candida tropicalis is one of the most pathogenic species within the genus. Increased antifungal resistance has been reported, which is in part due to the organism’s ability to form biofilms. In natural products derived from plants, such as essential oils (EOs) or their major components, there is significant potential to develop new antifungals or to both enhance the efficacy and reduce the toxicity of conventional antifungals. This study aimed to evaluate the effect of combining an EO of Lippia origanoides or thymol with fluconazole on an azole-resistant C. tropicalis strain. Synergism was observed in the combination of fluconazole with the EO and with thymol, and minimal inhibitory concentrations for fluconazole decreased at least 32-fold. As a consequence of the synergistic interactions, mitochondrial membrane potential was reduced, and mitochondrial superoxide production increased. Alteration in nuclear morphology, cell surface, and ultrastructure was also observed. In conclusion, the synergistic interaction between L. origanoides EO or thymol with fluconazole reverted the azole-resistant C. tropicalis phenotype. These findings suggest that L. origanoides EO or thymol alone, or in combination with fluconazole, have the potential for development as antifungal therapies for this yeast, including resistant strains. Full article

In a survey to evaluate the potential of lichens associated with gypsum areas as sources of new antifungal metabolites, six species of lichens were collected in the gypsum outcrops of the Sorbas Desert (Diploschistes ocellatus and Seirophora lacunosa) and the Tabernas Desert (Cladonia foliacea, Acarospora placodiformis, Squamarina lentigera and Xanthoparmelia pokornyi) in southern Spain. Raw lichen acetone extracts were tested against a panel of seven phytopathogenic fungi, including Botrytis cinerea, Colletotrichum acutatum, Fusarium oxysporum f.sp cubense TR4, Fusarium ploriferaum, Magnaporthe grisea, Verticillium dahliae and Zymoseptoria tritici. Active extracts of Cladonia foliacea, Xanthoparmelia pokornyi and Squamarina lentigera were analyzed by HPLC-MS/MS and Molecular Networking to identify possible metabolites responsible for the antifungal activity. A total of ten depside-like metabolites were identified by MS/MS dereplication and NMR experiments, of which one was a new derivative of fumaroprotocetraric acid. The compounds without previously described biological activity were purified and tested against the panel of fungal phytopathogens. Herein, the antifungal activity against fungal phytopathogens of 4′-O-methylpaludosic acid, divaricatic acid and stenosporic acid is reported for the first time. Stenosporic and divaricatic acids displayed a broad antifungal spectrum against seven relevant fungal phytopathogens in a micromolar range, including the extremely resistant fungus F. oxysporum f. sp. cubense Tropical Race 4 (TR4). 4′-O-methylpaludosic acid exhibited specific antifungal activity against the wheat pathogen Z. tritici, with an IC50 of 38.87 µg/mL (87.1 µM) in the absorbance-based assay and 24.88 µg/mL (55.52 µM) in the fluorescence-based assay. Full article

Purpose: This study aimed to identify the antagonistic bacteria from the rhizosphere of healthy bananas that can effectively suppress the Fusarium wilt of banana, and to further investigate the inhibitory mechanism. Method: The primary and secondary screening techniques were implemented using the double-plate and fermentation antagonism methods. The strain was identified based on physiological and biochemical tests, 16S rRNA gene sequencing, and specific gene amplification. The effects of crude extract on the protein content, lipid peroxidation, and pectinase activity of mycelia were determined from the identified isolates. Results: Two antagonistic bacteria, JF-4 and JF-5, were screened and initially identified as Bacillus subtilis (GenBank: OR125631) and B. amylum (GenBank: OR125632). The greenhouse experiment showed that the biological control efficiency of the two antagonists against the Fusarium wilt of banana was 48.3% and 40.3%, respectively. The catalase content produced by lipid peroxidation increased significantly after treatment with the crude extracts of JF-4 and JF-5 at concentrations of 0.69 μmol/L and 0.59 μmol/L, respectively. The protein and ergosterol content and pectinase activity decreased significantly. The two antagonistic bacteria might inhibit the growth of pathogens by enhancing lipid peroxidation and decreasing the synthesis of cell metabolites. Twenty compounds were identified by gas chromatography–mass spectrometry (GC-MS). B. subtilis JF-4 was further sequenced and assembled to obtain a complete circular chromosome genome of 681,804,824 bp. The genome consisted of a 4,310,825-bp-long scaffold. Conclusion: The findings of this study may help elucidate the mechanism behind this biocontrol isolate. Full article

The uncertainty response of soil fungi community to climate warming in alpine agroecosystems will limit our ability to fully exploit and utilize soil fungi resources, especially in alpine regions. In this study, a warming experiment was conducted in one perennial leguminous agroecosystem [i.e., alfalfa (Medicago sativa)], perennial gramineous agroecosystem (i.e., Elymus nutans) and annual gramineous agroecosystem [i.e., highland barley (Hordeum vulgare L)] in Tibet since 2016 to investigate the response of soil fungi community to climate warming. Soils at two layers (i.e., 0–10 cm and 10–20 cm) were collected in August 2017 to estimate soil fungi community based on the ITS method. The α-diversity, community composition and functional group abundance of soil fungi in the leguminous agroecosystem were more sensitive to climate warming. The α-diversity of soil fungi in the perennial gramineous agroecosystem were more sensitive to climate warming, but topology parameters of soil fungi species cooccurrence network in the annual gramineous agroecosystem were more sensitive to climate warming. Compared with 0–10 cm, soil fungal α-diversity, community composition and functional group abundance at 10–20 cm were more sensitive to climate warming. The topological parameters of soil fungi species cooccurrence network at 0–10 cm in the gramineous agroecosystem were more sensitive to climate warming, but those at 10–20 cm in the leguminous agroecosystem were more sensitive to climate warming. Warming increased the differences of soil fungi α-diversity and functional composition. For the Medicago sativa agroecosystem, warming increased the abundance of soil pathogenic fungi but decreased the abundance of soil symbiotic and saprophytic fungi at 10–20 cm. Therefore, responses of the soil fungi community to climate warming varied with agroecosystem types and soil depth. Climate warming can alter the differences of the soil fungi community among agroecosystems. Changes in soil fungi community caused by climate warming may be detrimental to the growth of alpine crops, at least for perennial Medicago sativa in Tibet. Full article

Histoplasmosis is one of the most under-diagnosed and under-reported endemic mycoses in the United States. Histoplasma capsulatum is the causative agent of this disease. To date, molecular epidemiologic studies detailing the phylogeographic structure of H. capsulatum in the United States have been limited. We conducted genomic sequencing using isolates from histoplasmosis cases reported in the United States. We identified North American Clade 2 (NAm2) as the most prevalent clade in the country. Despite high intra-clade diversity, isolates from Minnesota and Michigan cases were predominately clustered by state. Future work incorporating environmental sampling and veterinary surveillance may further elucidate the molecular epidemiology of H. capsulatum in the United States and how genomic sequencing can be applied to the surveillance and outbreak investigation of histoplasmosis. Full article

Fungal phytopathogens are the major agents responsible for causing severe damage to and losses in agricultural crops worldwide. Botrytis cinerea, Colletotrichum acutatum, Fusarium proliferatum, and Magnaporthe grisea are included in the top ten fungal phytopathogens that impose important plant diseases on a broad range of crops. Microbial natural products can be an attractive alternative for the biological control of phytopathogens. The objective of this work was to develop and validate a High-throughput Screening (HTS) platform to evaluate the antifungal potential of chemicals and natural products against these four important plant pathogens. Several experiments were performed to establish the optimal assay conditions that provide the best reproducibility and robustness. For this purpose, we have evaluated two media formulations (SDB and RPMI-1640), several inoculum concentrations (1 × 10⁶, 5 × 10⁵ and 5 × 10⁶ conidia/mL), the germination curves for each strain, each strain’s tolerance to dimethyl sulfoxide (DMSO), and the Dose Response Curves (DRC) of the antifungal control (Amphotericin B). The assays were performed in 96-well plate format, where absorbance at 620 nm was measured before and after incubation to evaluate growth inhibition, and fluorescence intensity at 570 nm excitation and 615 nm emission was monitored after resazurin addition for cell viability evaluation. Quality control parameters (RZ’ Factors and Signal to Background (S/B) ratios) were determined for each assay batch. The assay conditions were finally validated by titrating 40 known relevant antifungal agents and testing 2400 microbial natural product extracts from the MEDINA Library through both HTS agar-based and HTS microdilution-based set-ups on the four phytopathogens. Full article