Journal of Fungi

23 pages, 14052 KiB

Open AccessArticle

Composition and Biodiversity of Culturable Endophytic Fungi in the Roots of Alpine Medicinal Plants in Xinjiang, China

by Mengyan Hou, Jun Zhu, Chunyan Leng, Xinjie Huang, Mingshu Yang, Yifei Yin, Yongmei Xing and Juan Chen

J. Fungi 2025, 11(2), 113; https://doi.org/10.3390/jof11020113 - 3 Feb 2025

Abstract

(1) Background: Endophytic fungi play an important role in plant growth and stress resistance. The presence of a special fungal taxon such as the dark septate endophytic (DSE) fungi in alpine environments is particularly important for plant resistance to environmental stresses. However, the [...] Read more.

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

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19 pages, 6703 KiB

Open AccessArticle

Whole-Genome Sequencing and Fine Map Analysis of Pholiota nameko

by Yan He, Bo Liu, Xiaoqi Ouyang, Mianyu He, Hongyan Hui, Bimei Tang, Liaoliao Feng, Min Ren, Guoliang Chen, Guangping Liu and Xiaolong He

J. Fungi 2025, 11(2), 112; https://doi.org/10.3390/jof11020112 - 3 Feb 2025

Abstract

Pholiota nameko (T. Ito) S. Ito and S. Imai is an emerging wild mushroom species belonging to the genus Pholiota. Its unique brown–yellow appearance and significant biological activity have garnered increasing attention in recent years. However, there is a relative lack of [...] Read more.

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

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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17 pages, 3339 KiB

Open AccessArticle

MaNrtB, a Putative Nitrate Transporter, Contributes to Stress Tolerance and Virulence in the Entomopathogenic Fungus Metarhizium acridum

by Jia Wang, Yuneng Zou, Yuxian Xia and Kai Jin

J. Fungi 2025, 11(2), 111; https://doi.org/10.3390/jof11020111 - 1 Feb 2025

Abstract

Nitrogen is an essential nutrient that frequently determines the growth rate of fungi. Nitrate transporter proteins (Nrts) play a crucial role in the cellular absorption of nitrate from the environment. Entomopathogenic fungi (EPF) have shown their potential in the biological control of pests. [...] Read more.

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

(This article belongs to the Special Issue Fungi and Insect Interactions: Pathogenicity, Immune Defenses and Biocontrol)

23 pages, 4688 KiB

Open AccessArticle

Echinocandin Adaptation in Candida albicans Is Accompanied by Altered Chromatin Accessibility at Gene Promoters and by Cell Wall Remodeling

by Sudisht K. Sah, Anshuman Yadav, Tyler Stahl, Jeffrey J. Hayes, Michael Bulger and Elena Rustchenko

J. Fungi 2025, 11(2), 110; https://doi.org/10.3390/jof11020110 - 1 Feb 2025

Abstract

Infections by the major opportunistic pathogen of human Candida albicans are commonly treated with echinocandin (ECN) drugs. However, C. albicans can adapt to grow in the presence of certain amounts of ECNs. Prior studies by several laboratories have defined multiple genes, as well [...] Read more.

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

(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)

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19 pages, 3447 KiB

Open AccessArticle

Hemileia vastatrix in Coffea spp.: Distribution of Urediniospores Grouped by Size and Insights into Morphological Structures

by Gabriela Pelayo-Sánchez, María de Jesús Yáñez-Morales, Roney Solano-Vidal, Hilda Victoria Silva-Rojas, Dionicio Alvarado-Rosales, Simón Morales-Rodriguez, Luis Felipe Jiménez-García, Reyna Lara-Martínez, Iván Ramírez-Ramírez and Jorge M. Valdez-Carrasco

J. Fungi 2025, 11(2), 109; https://doi.org/10.3390/jof11020109 - 31 Jan 2025

Abstract

Hemileia vastatrix coffee leaf rust reduces Mexican coffee production by 51%. We aimed to analyze the size and distribution of H. vastatrix urediniospores among coffee plantations, as well as the morphological structures of the uredinium. In 2015, 65 leaf samples with rust [...] Read more.

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

(This article belongs to the Special Issue Rust Fungi)

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17 pages, 11584 KiB

Open AccessArticle

The Endoplasmic Reticulum Membrane Protein Complex Is Important for Deoxynivalenol Production and the Virulence of Fusarium graminearum

by Lei Chen, Yaxian Liu, Yu Wang, Yaxin Zhang, Saisai Wang, Liyuan Zhang, Kai Lu, Xiaochen Chen, Hansong Dong and Shenshen Zou

J. Fungi 2025, 11(2), 108; https://doi.org/10.3390/jof11020108 - 31 Jan 2025

Abstract

Fusarium graminearum is recognized as the pathogen responsible for wheat head blight. It produces deoxynivalenol (DON) during infection, which endangers human health. DON biosynthesis occurs within toxisomes in the endoplasmic reticulum (ER). In eukaryotes, the ER membrane protein complex (EMC) is critical for [...] Read more.

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

(This article belongs to the Special Issue Fusarium, Alternaria and Rhizoctonia: A Spotlight on Fungal Pathogens, 2nd Edition)

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13 pages, 1184 KiB

Open AccessArticle

Identification of Challenging Dermatophyte Species Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

by Tsung-Fu Tsai, Yun-Chen Fan, Jang-Jih Lu, Chun-Chih Chien, Hsin-Yao Wang and Pei-Lun Sun

J. Fungi 2025, 11(2), 107; https://doi.org/10.3390/jof11020107 - 31 Jan 2025

Abstract

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a widely adopted technique for bacterial and yeast identification in clinical laboratories but is less frequently applied to filamentous fungi due to inconsistent performance, limitations of commercial libraries, and variability of preparation methods. This [...] Read more.

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

(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)

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23 pages, 2002 KiB

Open AccessArticle

Harnessing Filamentous Fungi for Enzyme Cocktail Production Through Rice Bran Bioprocessing

by Ana M. Yélamos, Jose F. Marcos, Paloma Manzanares and Sandra Garrigues

J. Fungi 2025, 11(2), 106; https://doi.org/10.3390/jof11020106 - 31 Jan 2025

Abstract

Valorization of agri-food residues has garnered significant interest for obtaining value-added compounds such as enzymes or bioactive molecules. Rice milling by-products, such as rice bran, have limited commercial value and may pose environmental challenges. Filamentous fungi are recognized for their ability to grow [...] Read more.

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

(This article belongs to the Special Issue Filamentous Fungi as Excellent Industrial Strains: Development and Applications, 2nd Edition)

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17 pages, 1707 KiB

Open AccessArticle

Trichoderma brevicompactum 6311: Prevention and Control of Phytophthora capsici and Its Growth-Promoting Effect

by Jien Zhou, Junfeng Liang, Xueyan Zhang, Feng Wang, Zheng Qu, Tongguo Gao, Yanpo Yao and Yanli Luo

J. Fungi 2025, 11(2), 105; https://doi.org/10.3390/jof11020105 - 30 Jan 2025

Abstract

Pepper Phytophthora blight caused by Phytophthora capsici results in substantial losses in global pepper cultivation. The use of biocontrol agents with the dual functions of disease suppression and crop growth promotion is a green and sustainable way of managing this pathogen. In this [...] Read more.

Pepper Phytophthora blight caused by Phytophthora capsici results in substantial losses in global pepper cultivation. The use of biocontrol agents with the dual functions of disease suppression and crop growth promotion is a green and sustainable way of managing this pathogen. In this study, six biocontrol strains of Trichoderma with high antagonistic activity against P. capsici were isolated and screened from the rhizosphere soil of healthy peppers undergoing long-term continuous cultivation. Morphological identification and molecular biological identification revealed that strains 2213 and 2221 were T. harzianum, strains 5111, 6311, and 6321 were T. brevicompactum, and strain 7111 was T. virens. The results showed that T. brevicompactum 6311 had the greatest inhibitory effect against P. capsici. The inhibition rate of 6311 on the mycelial growth of P. capsici was 82.22% in a double-culture test, whereas it reached 100% in a fermentation liquid culture test. Meanwhile, the pepper fruit tests showed that 6311 was 29% effective against P. capsici on pepper, and a potting test demonstrated that the preventive and controlling effect of 6311 on pepper epidemics triggered by P. capsici was 55.56%. The growth-promoting effect, germination potential, germination rate, radicle-embryonic axis length, germination index, and fresh weight of peppers cultured in the 6311 fermentation broth were significantly increased compared with the results for the control group. Scanning electron microscopy revealed that 6311 achieved the parasitism of P. capsici, producing siderophores and the growth hormone indoleacetic acid (IAA) to achieve disease-suppressive and growth-promoting functions. Transcriptomic results indicated that genes encoding proteins involved in plant disease resistance, namely flavanone 3-hydroxylase (F3H) and growth transcription factor (AUX22), were generally upregulated after the application of 6311. This study demonstrated that 6311 exhibits significant bioprotective and growth-promoting functions. Full article

(This article belongs to the Special Issue Fungal Biotechnology and Application 3.0)

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10 pages, 3108 KiB

Open AccessCommunication

High Host Preferences in Epiphytic Lichens Across Diverse Phorophyte Species in the Mediterranean Region

by Gregorio Aragón, Isabel Martínez, Marcelino de la Cruz and Pilar Hurtado

J. Fungi 2025, 11(2), 104; https://doi.org/10.3390/jof11020104 - 30 Jan 2025

Abstract

Contrary to the assumption that epiphytic lichens, which obtain water and nutrients from the atmosphere, do not exhibit host species preference, this notion is challenged by the limited number of studies that cover a wide geographical range and diverse phorophyte species (hereafter referred [...] Read more.

Contrary to the assumption that epiphytic lichens, which obtain water and nutrients from the atmosphere, do not exhibit host species preference, this notion is challenged by the limited number of studies that cover a wide geographical range and diverse phorophyte species (hereafter referred to as “host species”). To investigate this assumption, we evaluated the host preference of 709 epiphytic lichen species across the Mediterranean basin, examining 72 host species. The research is based on field studies conducted by the authors, supplemented with bibliographic records to expand the study area and the number of host species. We define “host preference” as the association of an epiphytic lichen species with a single host species. Our findings reveal a high prevalence of lichens exhibiting host preference both locally (exceeding 30% of lichen species in each of six geographic areas) and regionally (25% across the entire dataset). This host preference remained consistent even with increased sampling extent, which can be attributed to factors such as hosts with diverse bark types, the wide climatic range of some species, and host species associated with extreme environmental conditions within the Mediterranean region. Overall, we conclude that host bias for epiphytic lichen species remains consistent in Mediterranean landscapes, contributing to a diverse array of epiphytic species and high levels of host species preference. This research provides valuable insights into the complex interactions between lichens and their host species, offering a deeper understanding of biodiversity within Mediterranean landscapes. Full article

(This article belongs to the Section Fungal Evolution, Biodiversity and Systematics)

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12 pages, 1273 KiB

Open AccessCase Report

Erythema Nodosum Associated with Kerion: A Case Series and Narrative Review of the Literature

by Teerapong Rattananukrom, Isaías Uh-Sánchez, Carlos Atoche-Dieguez, Nixma Eljure, Carlos Garcia-Rementeria and Roberto Arenas

J. Fungi 2025, 11(2), 103; https://doi.org/10.3390/jof11020103 - 29 Jan 2025

Abstract

Kerion is a form of inflammatory tinea capitis, a fungal infection caused by various zoophilic, geophilic, and anthropophilic pathogens. Erythema nodosum (EN), a form of septal panniculitis, can be considered a dermatophyte id reaction that occurs outside the primary site of dermatophyte infection. [...] Read more.

Kerion is a form of inflammatory tinea capitis, a fungal infection caused by various zoophilic, geophilic, and anthropophilic pathogens. Erythema nodosum (EN), a form of septal panniculitis, can be considered a dermatophyte id reaction that occurs outside the primary site of dermatophyte infection. The association between EN and kerion is rarely reported, with most cases following Trichophyton mentagrophytes scalp infections. Here, we describe three cases of EN associated with kerion caused by T. mentagrophytes, successfully treated with itraconazole or griseofulvin plus prednisone. Additionally, we conducted a narrative review of the literature, identifying 23 reported cases of EN associated with kerion on PubMed. The most commonly reported fungus was T. mentagrophytes (78.25%). In 52.17% of cases, patients developed EN after initiating antifungal treatment, with a mean onset time of 11.58 days (SD 7.3). Griseofulvin remains a mainstay treatment. The mean time for EN resolution was 8.31 days (SD 4.15), and the median duration of treatment for kerion leading to a complete response was 6 weeks (IQR 6–8). Scarring alopecia is a common sequela following kerion, and the use of corticosteroids has been recommended as adjunct therapy to minimize the risk of scarring. Full article

(This article belongs to the Section Fungal Pathogenesis and Disease Control)

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16 pages, 1512 KiB

Open AccessArticle

Proteomic Approach to Study the Effect of Pneumocystis jirovecii Colonization in Idiopathic Pulmonary Fibrosis

by Jonás Carmona-Pírez, Rocío Salsoso, Eléna Charpentier, Cinta Olmedo, Francisco J. Medrano, Lucas Román, Carmen de la Horra, Yaxsier de Armas, Enrique J. Calderón and Vicente Friaza

J. Fungi 2025, 11(2), 102; https://doi.org/10.3390/jof11020102 - 29 Jan 2025

Abstract

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and interstitial disease with an unclear cause, believed to involve genetic, environmental, and molecular factors. Recent research suggested that Pneumocystis jirovecii (PJ) could contribute to disease exacerbations and severity. This article explores how PJ colonization [...] Read more.

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and interstitial disease with an unclear cause, believed to involve genetic, environmental, and molecular factors. Recent research suggested that Pneumocystis jirovecii (PJ) could contribute to disease exacerbations and severity. This article explores how PJ colonization might influence the pathogenesis of IPF. We performed a proteomic analysis to study the profile of control and IPF patients, with/without PJ. We recruited nine participants from the Virgen del Rocio University Hospital (Seville, Spain). iTRAQ and bioinformatics analyses were performed to identify differentially expressed proteins (DEPs), including a functional analysis of DEPs and of the protein–protein interaction networks built using the STRING database. We identified a total of 92 DEPs highlighting the protein vimentin when comparing groups. Functional differences were observed, with the glycolysis pathway highlighted in PJ-colonized IPF patients; as well as the pentose phosphate pathway and miR-133A in non-colonized IPF patients. We found 11 protein complexes, notably the JAK-STAT signaling complex in non-colonized IPF patients. To our knowledge, this is the first study that analyzed PJ colonization’s effect on IPF patients. However, further research is needed, especially on the complex interactions with the AKT/GSK-3β/snail pathway that could explain some of our results. Full article

(This article belongs to the Special Issue Proteomic Studies of Pathogenic Fungi and Hosts)

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19 pages, 11996 KiB

Open AccessArticle

Visualizing Oral Infection Dynamics of Beauveria bassiana in the Gut of Tribolium castaneum

by Lautaro Preisegger, Juan Cruz Flecha, Fiorella Ghilini, Daysi Espin-Sánchez, Eduardo Prieto, Héctor Oberti, Eduardo Abreo, Carla Huarte-Bonnet, Nicolás Pedrini and Maria Constanza Mannino

J. Fungi 2025, 11(2), 101; https://doi.org/10.3390/jof11020101 - 28 Jan 2025

Abstract

The ability of entomopathogenic fungi, such as Beauveria bassiana, to infect insects by penetrating their cuticle is well documented. However, some insects have evolved mechanisms to combat fungal infections. The red flour beetle (Tribolium castaneum), a major pest causing significant [...] Read more.

The ability of entomopathogenic fungi, such as Beauveria bassiana, to infect insects by penetrating their cuticle is well documented. However, some insects have evolved mechanisms to combat fungal infections. The red flour beetle (Tribolium castaneum), a major pest causing significant economic losses in stored product environments globally, embeds antifungal compounds within its cuticle as a protective barrier. Previous reports have addressed the contributions of non-cuticular infection routes, noting an increase in mortality in beetles fed with conidia. In this study, we further explore the progression and dynamics of oral exposure in the gut of T. castaneum after feeding with an encapsulated B. bassiana conidia formulation. First, we characterized the formulation surface using atomic force microscopy, observing no significant topological differences between capsules containing and not containing conidia. Confocal microscopy confirmed uniform conidia distribution within the hydrogel matrix. Then, larvae and adult insects fed with the conidia-encapsulated formulation exhibited B. bassiana distributed throughout the alimentary canal, with a higher presence of conidia before the pyloric chamber. More conidia were found in the larval midgut and hindgut compared to adults, but no germinated conidia were observed in the epithelium. These results suggest that the presence of conidia obstructs the gut, impairing the insect’s ability to ingest, process, and absorb nutrients. This disruption may weaken the host, increasing its susceptibility to infections and, ultimately, leading to death. By providing the first direct observation of fungal conidia within the alimentary canal of T. castaneum, this study highlights a novel aspect of fungal–host interaction and opens new avenues for advancing fungal-based pest control strategies by exploiting stage-specific vulnerabilities. Full article

(This article belongs to the Special Issue Fungi and Insect Interactions: Pathogenicity, Immune Defenses and Biocontrol)

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15 pages, 3090 KiB

Open AccessArticle

MaPac2, a Transcriptional Regulator, Is Involved in Conidiation, Stress Tolerances and Pathogenicity in Metarhizium acridum

by Xiaobin Hu, Baicheng Li, Yan Li, Yuxian Xia and Kai Jin

J. Fungi 2025, 11(2), 100; https://doi.org/10.3390/jof11020100 - 28 Jan 2025

Abstract

The Gti1/Pac2 protein family, which is highly conserved across fungi, is pivotal in processes such as fungal development, spore formation, protein export, toxin production, and virulence. Despite its importance, the precise functions of Pac2 within entomopathogenic fungi have yet to be fully understood. [...] Read more.

The Gti1/Pac2 protein family, which is highly conserved across fungi, is pivotal in processes such as fungal development, spore formation, protein export, toxin production, and virulence. Despite its importance, the precise functions of Pac2 within entomopathogenic fungi have yet to be fully understood. In our study, the MaPac2 gene from M. acridum was identified, and its functions were explored. Studying the domain of the protein showed that MaPac2 comprises 422 amino acids with a characteristic Gti1/Pac2 family domain (Pfam09729). Additionally, MaPac2 is predicted to have an N-terminal protein kinase A phosphorylation site and a potential cyclin-dependent kinase phosphorylation site, highlighting its potential regulatory roles in the fungus. Our findings indicate that the inactivation of MaPac2 resulted in faster germination of conidia and a marked reduction in conidial production. Furthermore, stress tolerance tests revealed that the absence of MaPac2 significantly bolstered the fungal resilience to UV-B radiation, heat shock, SDS exposure, and stresses induced by hyperosmotic conditions and oxidative challenges. Virulence assessments through bioassays indicated no substantial differences among the WT, MaPac2-disrupted strain, and CP strains in the topical inoculation trials. Interestingly, deletion of MaPac2 increased the fungal virulence by intrahemocoel injection. Furthermore, we found that disruption of MaPac2 impaired fungal cuticle penetration due to the diminished appressorium formation but increased the fungal growth in locust hemolymph. These findings provide further insights into the roles played by Gti1/Pac2 in insect pathogenic fungi. Full article

(This article belongs to the Collection Entomopathogenic and Nematophagous Fungi)

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24 pages, 2933 KiB

Open AccessReview

Exploring Psilocybe cubensis Strains: Cultivation Techniques, Psychoactive Compounds, Genetics and Research Gaps

by Eyal Kurzbaum, Tomáš Páleníček, Amiel Shrchaton, Sara Azerrad and Yaron Dekel

J. Fungi 2025, 11(2), 99; https://doi.org/10.3390/jof11020099 - 28 Jan 2025

Abstract

Psilocybe cubensis, a widely recognized psychoactive mushroom species, has played a significant role in both historical and modern therapeutic practices. This review explores the complex interplay between genetic diversity, strain variability and environmental factors that shape the biosynthesis of key psychoactive compounds, [...] Read more.

Psilocybe cubensis, a widely recognized psychoactive mushroom species, has played a significant role in both historical and modern therapeutic practices. This review explores the complex interplay between genetic diversity, strain variability and environmental factors that shape the biosynthesis of key psychoactive compounds, including psilocybin and psilocin. With many strains exhibiting substantial variability in their phenotypic characteristics and biochemical content, understanding and documenting this diversity is crucial for optimizing therapeutic applications. The review also highlights advances in cultivation techniques, such as submerged fermentation of the mycelium, and innovative analytical methodologies that have improved the precision of compound quantification and extraction. Although there is limited scientific information on P. cubensis due to nearly four decades of regulatory restrictions on psychedelic research, recent developments in genetic and biochemical studies are beginning to provide valuable insights into its therapeutic potential. Furthermore, this review emphasizes key knowledge gaps and offers insights into future research directions to advance the cultivation, scientific documentation of strain diversity, regulatory considerations and therapeutic use of P. cubensis. Full article

(This article belongs to the Special Issue Current and Future Research Trends on Medicinal Mushrooms, 2nd Edition)

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17 pages, 2248 KiB

Open AccessArticle

Species Identification and Orthologous Allergen Prediction and Expression in the Genus Aspergillus

by Maria C. Zuleta, Oscar M. Gómez, Elizabeth Misas, Susana Torres, Álvaro L. Rúa-Giraldo, Juan G. McEwen, Ana M. Garcia, Clayton L. Borges, Orville Hernández and Angela M. López

J. Fungi 2025, 11(2), 98; https://doi.org/10.3390/jof11020098 - 27 Jan 2025

Abstract

The genus Aspergillus comprises a diverse group of fungi that can cause a range of health issues, including systemic infections and allergic reactions. In this regard, A. fumigatus has been recognized as the most prevalent allergen-producing species. This genus taxonomic classification has been [...] Read more.

The genus Aspergillus comprises a diverse group of fungi that can cause a range of health issues, including systemic infections and allergic reactions. In this regard, A. fumigatus has been recognized as the most prevalent allergen-producing species. This genus taxonomic classification has been subject to frequent updates, which has generated considerable difficulties for its classification when traditional identification methodologies are employed. To demonstrate the feasibility of this approach, we sequenced the whole genomes of 81 Aspergillus isolates and evaluated a WGS-based pipeline for precise species identification. This pipeline employed two methodologies: (i) BLASTn web using four barcode genes and (ii) species tree inference by OrthoFinder. Furthermore, we conducted a prediction of allergenic capacity based on a homology analysis across all the isolated species and confirmed by RT-qPCR the expression of three orthologous allergens (Asp f 1, Asp f 3 and Asp f 22) in fifteen different Aspergillus species. The species-level identification rate with the barcoding and the species tree were calculated at 64.2% and 100%, respectively. The results demonstrated that A. fumigatus, A. flavus and A. niger were the most prevalent species. The species A. hortae, A. uvarum, A. spinulosporus, A. sydowii, A. westerdijkiae, A. amoenus and A. rhizopodus identified in this study represent the inaugural report of their presence in our region. The results of the homology analysis indicated the presence of orthologous allergens in a wide range of non-fumigatus species. This study presents a novel approach based on WGS that enables the classification of new species within the genus Aspergillus and reports the genomic sequences of a great diversity of species isolated in our geographic area that had never been reported before. Additionally, this approach enables the prediction of allergens in species other than A. fumigatus and demonstrates their genetic expression, thereby contributing to the understanding of the allergenic potential of different species within this fungal genus. Full article

(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)

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11 pages, 1186 KiB

Open AccessArticle

Revision of Entrophosporales, with Three Genera and an Identification Key for All Species Currently Attributed to This Order

by Gladstone Alves da Silva, Ewald Sieverding, Daniele Magna Azevedo de Assis, Bruno Tomio Goto, Mike Anderson Corazon-Guivin and Fritz Oehl

J. Fungi 2025, 11(2), 97; https://doi.org/10.3390/jof11020097 - 26 Jan 2025

Abstract

The objective of the present study was to revise the recently described order Entrophosporales of the Glomeromycetes. The single family Entrophosporaceae had been divided into three genera, Entrophospora, Claroideoglomus and Albahypha, due to molecular phylogenetic or morphological analyses, but recently these [...] Read more.

The objective of the present study was to revise the recently described order Entrophosporales of the Glomeromycetes. The single family Entrophosporaceae had been divided into three genera, Entrophospora, Claroideoglomus and Albahypha, due to molecular phylogenetic or morphological analyses, but recently these three genera were combined within the type genus of the family, Entrophospora. Our new studies now suggest once more three genera, but Entrophospora and Claroideoglomus were not separated again. In the present study, we resurrected Albahypha with A. drummondii and A. furrazolae comb. nov. and established Alborhynchus gen. nov. with A. walkeri comb. nov. Morphologically, all glomoid morphs of the three genera have hyaline to white subtending hyphae with one spore wall continuous with the subtending hyphal wall. However, the genera can easily be differentiated from each other and from other glomoid species of the Glomeromycetes by the combination of the characteristics of the subtending hyphae, the staining reaction of the spore wall layers in Melzer’s reagent and phylogeny. In conclusion, the three AMF genera, currently recognized in the Entrophosporales, can unequivocally be identified by molecular phylogeny or by morphological characteristics of their spores and their subtending hyphae. An identification key distinguishes all AMF species currently attributed to Entrophosporales. Full article

(This article belongs to the Section Fungal Evolution, Biodiversity and Systematics)

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43 pages, 2093 KiB

Open AccessReview

Comprehensive Review of Environmental Surveillance for Azole-Resistant Aspergillus fumigatus: A Practical Roadmap for Hospital Clinicians and Infection Control Teams

by Masato Tashiro, Yuichiro Nakano, Tomoyuki Shirahige, Satoshi Kakiuchi, Ayumi Fujita, Takeshi Tanaka, Takahiro Takazono and Koichi Izumikawa

J. Fungi 2025, 11(2), 96; https://doi.org/10.3390/jof11020096 - 25 Jan 2025

Abstract

Abstract: As azole-resistant Aspergillus fumigatus emerges globally, healthcare facilities face mounting challenges in managing invasive aspergillosis. This review synthesizes worldwide azole resistance data to reveal profound regional variability, demonstrating that findings from other regions cannot be directly extrapolated to local settings. Consequently, [...] Read more.

Abstract: As azole-resistant Aspergillus fumigatus emerges globally, healthcare facilities face mounting challenges in managing invasive aspergillosis. This review synthesizes worldwide azole resistance data to reveal profound regional variability, demonstrating that findings from other regions cannot be directly extrapolated to local settings. Consequently, hospital-level environmental surveillance is crucial for tailoring interventions to local epidemiology and detecting resistant strains in real-time. We outline practical approaches—encompassing sampling site prioritization, diagnostic workflows (culture-based and molecular), and PDCA-driven continuous improvement—so that even resource-limited facilities can manage resistant isolates more effectively. By linking real-time surveillance findings with clinical decisions, hospitals can tailor antifungal stewardship programs and swiftly adjust prophylaxis or treatment regimens. Our approach aims to enable accurate, ongoing evaluations of emerging resistance patterns, ensuring that institutions maintain efficient and adaptive programs. Ultimately, we advocate for sustained, collaborative efforts worldwide, where facilities adapt protocols to local conditions, share data through international networks, and contribute to a global knowledge base on resistance mechanisms. Through consistent application of these recommendations, healthcare systems can better preserve azole efficacy, safeguard immunocompromised populations, and refine infection control practices in the face of evolving challenges. Full article

11 pages, 1182 KiB

Open AccessCase Report

Moesziomyces aphidis Bloodstream Infection in Oncologic Patient: First Report in Poland

by Beata Sulik-Tyszka, Jolanta Małyszko, Agnieszka Pęczuła and Sylwia Jarzynka

J. Fungi 2025, 11(2), 95; https://doi.org/10.3390/jof11020095 - 24 Jan 2025

Abstract

Moesziomyces spp. (Pseudozyma) is a genus recognized as a new opportunistic human pathogen, causing systemic infections including premature neonates and adult patients. These fungi’s natural resistance to caspofungin enables them to spread through vascular catheter colonization, making them a new etiological [...] Read more.

Moesziomyces spp. (Pseudozyma) is a genus recognized as a new opportunistic human pathogen, causing systemic infections including premature neonates and adult patients. These fungi’s natural resistance to caspofungin enables them to spread through vascular catheter colonization, making them a new etiological agent associated with fungal bloodstream infections (FBIs) and a significant contributor to high mortality rates. In this report, we present a case of fungemia caused by Moesziomyces aphidis species in a patient with medical history that revealed pancreatic cancer infiltrating the duodenum and bile ducts. During hospitalization, the M. aphidis was cultured twice from peripheral blood samples on Sabouraud agar. The strain was sensitive to amphotericin B and voriconazole. In vitro susceptibility testing revealed resistance to fluconazole, caspofungin, anidulafungin, and micafungin. Antifungal therapy with voriconazole resulted in the resolution of clinical symptoms associated with fungal infection. Related to M. aphidis fungemia, we reviewed a total of three cases in Europe published in the PubMed database between 2003 and 2024. To the best of our knowledge, this is the first case of M. aphidis FBI in Poland and the fourth case in an adult patient in Europe. Full article

(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)

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