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Volume 11
Issue 3
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J. Fungi, Volume 11, Issue 3 (March 2025) – 74 articles

Cover Story (view full-size image): Cercospora beticola, the most important fungal pathogen in sugar beets, has a long incubation period (IP) and is classified as a hemibiotroph. A single infection period under controlled conditions resulted in minor IP differences among host genotypes and individual plants, greater differences among leaves within plants, and substantial variation within individual leaves. A GIS approach enabled the tracking of lesion appearance and growth for up to 27 days. The first lesions appeared 10 days after inoculation; however, the number of lesions increased for another 7 to 17 days, while lesion growth was limited. The asymptomatic fungal colonization of tissue was associated with thick hyphae, which became thinner after the appearance of lesions. Despite the lengthy incubation period, evidence of a C. beticola biotroph phase is lacking. View this paper
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10 pages, 3191 KiB  
Article
Calcium-Induced Regulation of Sanghuangporus baumii Growth and the Biosynthesis of Its Triterpenoids
by Zengcai Liu, Ying Yu, Shiyuan Wang and Li Zou
J. Fungi 2025, 11(3), 238; https://doi.org/10.3390/jof11030238 - 20 Mar 2025
Viewed by 262
Abstract
Sanghuangporus baumii, a fungus used in traditional Chinese medicine, produces important pharmacological compounds such as triterpenoids, but at levels significantly lower than those required for medical use. This study investigated the effects of various concentrations of Ca2+ on S. baumii mycelial [...] Read more.
Sanghuangporus baumii, a fungus used in traditional Chinese medicine, produces important pharmacological compounds such as triterpenoids, but at levels significantly lower than those required for medical use. This study investigated the effects of various concentrations of Ca2+ on S. baumii mycelial growth and the heterologous biosynthesis of S. baumii triterpenoids. Under induction by 10 mM Ca2+, the growth rate (0.39 cm/d) and biomass (4.48 g/L) of S. baumii mycelia were 1.03% and 10.05% higher than those in the 0 mM Ca2+-treatment group, respectively. In contrast, 200 mM Ca2+ significantly inhibited the growth rate and biomass of the mycelia. Notably, the total triterpenoid content reached its peak (17.71 mg/g) in the 200 mM Ca2+-treatment group, with a significant increase in the Ca2+ content (3869.97 µg/g) in the mycelia. Subsequently, the differential metabolic pathways and related genes between the S. baumii groups were examined using transcriptomic analysis. The results indicated that the increase in the growth rate and biomass of S. baumii mycelia was primarily due to elevated soluble sugar content, whereas the growth inhibition was associated with the toxic effects of H2O2. The observed differences in triterpenoid content were mainly attributed to the activation of the terpenoid backbone biosynthesis pathway and the AACT gene. Finally, the AACT gene was cloned and transformed into yeast cells, thus creating strain Sc-AA1. Upon treatment at the optimal Ca2+ concentration, the squalene content of strain Sc-AA1 reached 0.78 mg/g, 2.89-fold higher than that in the control group. These findings are significant for the heterologous biosynthesis of triterpenoids from S. baumii. Our study demonstrates the feasibility of producing triterpenoids in Saccharomyces cerevisiae and provides a foundation for future optimization toward achieving industrially relevant yields. Full article
(This article belongs to the Special Issue New Trends in Yeast Metabolic Engineering)
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31 pages, 10034 KiB  
Article
What Are “Lingzhi Wang” or “Zhu Lingzhi”? Notes on Ganoderma (Ganodermataceae, Polyporales) Species Characterized by Diminutive Pilei and Gracile Stipes from Hainan Island, Tropical China
by Run Tian, Hua-Zhi Qin, Qing Zhong, Zhi-Qun Liang, Xue-Yan Zhang, Xiao-Dong Mu, Lin Xu, Ting-Chi Wen, Xiang-Dong Chen and Nian-Kai Zeng
J. Fungi 2025, 11(3), 237; https://doi.org/10.3390/jof11030237 - 20 Mar 2025
Viewed by 317
Abstract
Species of Ganoderma (Ganodermataceae, Polyporales) have been extensively utilized in traditional Chinese medicine for over two millennia, owing to their remarkable medicinal properties and diverse chemical constituents. Hainan Island, located in tropical China, harbors a rich diversity of Ganoderma species. Among these, certain [...] Read more.
Species of Ganoderma (Ganodermataceae, Polyporales) have been extensively utilized in traditional Chinese medicine for over two millennia, owing to their remarkable medicinal properties and diverse chemical constituents. Hainan Island, located in tropical China, harbors a rich diversity of Ganoderma species. Among these, certain varieties referred to as “Lingzhi Wang” or “Zhu Lingzhi” by indigenous communities are distinguished by their diminutive pilei and slender stipes. Despite their traditional recognition, these species have been subject to morphological confusion. In this study, specimens labeled as “Lingzhi Wang” or “Zhu Lingzhi” were subjected to comprehensive morphological examinations and molecular phylogenetic analyses. The findings reveal that the Ganoderma species characterized by small pilei and gracile stipes encompass at least five distinct species. Among these, two are new to science: G. baisuzhenii and G. shennongii. The remaining three species, G. bambusicola, G. flexipes, and G. subflexipes, have been previously described. Taxonomically, G. bambusicola was reported for the first time on the Chinese mainland. This study provides a clearer taxonomic framework for these medicinally significant fungi. Full article
(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 3rd Edition)
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35 pages, 1520 KiB  
Review
The Hidden Fortress: A Comprehensive Review of Fungal Biofilms with Emphasis on Cryptococcus neoformans
by Hope M. Pruitt, Jinyi C. Zhu, Sean P. Riley and Meiqing Shi
J. Fungi 2025, 11(3), 236; https://doi.org/10.3390/jof11030236 - 19 Mar 2025
Viewed by 371
Abstract
Biofilms are structurally organized communities of microorganisms that adhere to a variety of surfaces. These communities produce protective matrices consisting of polymeric polysaccharides, proteins, nucleic acids, and/or lipids that promote shared resistance to various environmental threats, including chemical, antibiotic, and immune insults. While [...] Read more.
Biofilms are structurally organized communities of microorganisms that adhere to a variety of surfaces. These communities produce protective matrices consisting of polymeric polysaccharides, proteins, nucleic acids, and/or lipids that promote shared resistance to various environmental threats, including chemical, antibiotic, and immune insults. While algal and bacterial biofilms are more apparent in the scientific zeitgeist, many fungal pathogens also form biofilms. These surprisingly common biofilms are morphologically distinct from the multicellular molds and mushrooms normally associated with fungi and are instead an assemblage of single-celled organisms. As a collection of yeast and filamentous cells cloaked in an extracellular matrix, fungal biofilms are an extreme threat to public health, especially in conjunction with surgical implants. The encapsulated yeast, Cryptococcus neoformans, is an opportunistic pathogen that causes both pulmonary and disseminated infections, particularly in immunocompromised individuals. However, there is an emerging trend of cryptococcosis among otherwise healthy individuals. C. neoformans forms biofilms in diverse environments, including within human hosts. Notably, biofilm association correlates with increased expression of multiple virulence factors and increased resistance to both host defenses and antifungal treatments. Thus, it is crucial to develop novel strategies to combat fungal biofilms. In this review, we discuss the development and treatment of fungal biofilms, with a particular focus on C. neoformans. Full article
(This article belongs to the Special Issue Human Fungal Pathogens: Emerging Threats, Diagnostic and Therapeutic Innovations and Global Impacts)
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16 pages, 2485 KiB  
Article
The Effect of Different Types of Fertilizers on the Growth of Cassava and the Fungal Community in Rhizosphere Soil
by Qinyun Liu, Xiaojing Lu, Chunyu Xiang, Shan Yu, Jie Zhang, Kaimian Li, Wenjun Ou, Songbi Chen and Jie Cai
J. Fungi 2025, 11(3), 235; https://doi.org/10.3390/jof11030235 - 19 Mar 2025
Viewed by 251
Abstract
With the growing importance of cassava worldwide, developing efficient and eco-friendly fertilizer strategies is crucial for sustainable cassava production. Diverse fertilizer treatments can significantly influence soil properties and plant growth. In this study, we investigated the effects of three fertilizer treatments—organic fertilizer (OF), [...] Read more.
With the growing importance of cassava worldwide, developing efficient and eco-friendly fertilizer strategies is crucial for sustainable cassava production. Diverse fertilizer treatments can significantly influence soil properties and plant growth. In this study, we investigated the effects of three fertilizer treatments—organic fertilizer (OF), chemical fertilizer combined with organic fertilizer (CFOF), and reduced chemical fertilizer combined with organic fertilizer (RFOF)—on the fungal community structure, chemical properties (SOM, AP, AN, and AK), and enzyme activities (NP, SC, CAT, and UE) in cassava rhizosphere. Our results demonstrated that these fertilizer treatments significantly enhanced cassava growth and yield compared to the control (CK) without fertilization. Soil chemical properties (SOM, AN, AP, and AK) and enzyme activities (NP, SC, CAT, and UE) were notably improved following fertilization. High-throughput sequencing revealed the significant alterations in the relative abundance of specific fungal taxa. Environmental parameters, particularly UE, SC, CAT, and AP, showed strong correlations with fungal community structure. These findings highlight the critical role of combined organic and chemical fertilizers in promoting cassava productivity and soil health. Understanding these interactions provides a foundation for optimizing fertilization practices to enhance crop yields and support sustainable agriculture. Full article
(This article belongs to the Section Fungi in Agriculture and Biotechnology)
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9 pages, 451 KiB  
Communication
Advancing Dermatomycosis Diagnosis: Evaluating a Microarray-Based Platform for Rapid and Accurate Fungal Detection—A Pilot Study
by Vittorio Ivagnes, Elena De Carolis, Carlotta Magrì, Riccardo Torelli, Brunella Posteraro and Maurizio Sanguinetti
J. Fungi 2025, 11(3), 234; https://doi.org/10.3390/jof11030234 - 19 Mar 2025
Viewed by 207
Abstract
Dermatomycosis, including the most prevalent onychomycosis, significantly impacts patients’ quality of life due to its chronic nature and high recurrence rate. Conventional diagnostic methods are often limited by low sensitivity and specificity and prolonged turnaround times. This study evaluates the EUROArray Dermatomycosis Platform, [...] Read more.
Dermatomycosis, including the most prevalent onychomycosis, significantly impacts patients’ quality of life due to its chronic nature and high recurrence rate. Conventional diagnostic methods are often limited by low sensitivity and specificity and prolonged turnaround times. This study evaluates the EUROArray Dermatomycosis Platform, a microarray-based molecular assay, for its performance in identifying fungi causing dermatomycosis. Forty reference fungal strains, covering on-panel and off-panel species, and 120 clinical samples from patients with suspected dermatomycosis were analyzed. The platform’s accuracy was compared to microscopy and/or culture as the diagnostic standard. The assay demonstrated 100% analytical sensitivity and 97.1% analytical specificity, correctly identifying 33 of 34 fungal species while misclassifying one. In clinical samples, the assay showed good sensitivity (78.6%) and high specificity (91.7%), detecting additional positive cases missed by culture, which highlights the assay’s ability to identify non-viable fungi and low fungal loads. The assay achieved a positive predictive value of 75.9% and a negative predictive value of 92.8%, reinforcing its diagnostic reliability. Despite some discordances, the assay provides rapid results and broad-spectrum fungal detection, positioning it as a valuable complement to conventional diagnostics. Future improvements, including expanding the identification panel and optimizing sample handling, could further enhance its clinical utility. Full article
(This article belongs to the Special Issue Diagnosis and Treatment of Superficial Fungal Infections)
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17 pages, 2013 KiB  
Article
Fungal Sinusitis Spreading to the Sellar Region Mimicking a Pituitary Tumor: Case Report and Literature Review
by Sandra Pekic Djurdjevic and Valentina Arsic Arsenijevic
J. Fungi 2025, 11(3), 233; https://doi.org/10.3390/jof11030233 - 19 Mar 2025
Viewed by 328
Abstract
Chronic fungal sinusitis (FS) can cause bone erosion and extend to the sellar region, often misdiagnosed as pituitary tumors or malignancies. We report a 56-year-old immunocompetent female with sphenoid FS presenting as a giant sellar mass compressing the optic chiasm, with normal pituitary [...] Read more.
Chronic fungal sinusitis (FS) can cause bone erosion and extend to the sellar region, often misdiagnosed as pituitary tumors or malignancies. We report a 56-year-old immunocompetent female with sphenoid FS presenting as a giant sellar mass compressing the optic chiasm, with normal pituitary function. The surgery successfully resolved her symptoms, and a histological examination confirmed the presence of a fungal hyphal mass. We conducted a literature review of 52 publications on FS cases with bone erosion and inflammatory extension to the sellar region, which included analyses of 67 patients (35 females, mean age 49.6 years, half immunocompetent). The most common symptom was headache (73.1%), followed by visual complaints (71.7%), visual deterioration (40.3%), ophthalmoplegia (38.8%), and visual field defects (13.4%). Symptom duration averaged 4.5 months in 65.7% of cases. Aspergillus was the most frequent (71.6%). Hormonal abnormalities included hypopituitarism (25.4%) and hyperprolactinemia (13.4%). Surgery was performed in 92.5% of patients. Common diagnoses included pituitary abscess (41.8%), fungal granuloma (16.4%), aspergillosis (16.4%) and allergic FS (14.9%). Antifungal therapy was administered in 53.7% of cases. Cure was achieved in 67.2%, while the mortality rate was 10.4%. Early recognition of fungal involvement, supported by a multidisciplinary approach, is essential for the accurate diagnosis and effective treatment. This highlights the need for vigilance to improve the outcomes in similar cases. Full article
(This article belongs to the Special Issue Diagnosis and Management of Human Mold Infections)
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9 pages, 3533 KiB  
Brief Report
Trends in Antifungal Resistance Among Candida Species: An Eight-Year Retrospective Study in the Galveston–Houston Gulf Coast Region
by Michael D. Nguyen and Ping Ren
J. Fungi 2025, 11(3), 232; https://doi.org/10.3390/jof11030232 - 19 Mar 2025
Viewed by 327
Abstract
Fungal systemic infections are a growing global health concern, particularly among immunocompromised individuals. Candida species are the leading cause of invasive fungal infections, with C. albicans historically being the most prevalent. The emergence of C. auris, known for its multidrug resistance, presents [...] Read more.
Fungal systemic infections are a growing global health concern, particularly among immunocompromised individuals. Candida species are the leading cause of invasive fungal infections, with C. albicans historically being the most prevalent. The emergence of C. auris, known for its multidrug resistance, presents additional challenges for treatment and infection control. This study retrospectively analyzed minimal inhibitory concentration (MIC) data for common Candida species isolated from patients in the Galveston–Houston Gulf Coast region from the EPIC Laboratory Information System (LIS) between October 2016 and September 2024. Antifungal susceptibility was assessed using the SensititreTM YeastOneTM YO9 AST Plate and interpreted per Clinical and Laboratory Standard Institute (CLSI) guidelines. A total of 1206 clinical yeast isolates from over 29 species were identified, with Candida species accounting for 94.5% (1140). C. albicans (30.7%), C. glabrata (23.5%), C. parapsilosis (12.2%), and C. tropicalis (10.4%) were the most prevalent. C. auris (6.2%) emerged in late 2021 in our region, showing high MICs against fluconazole (92%) and amphotericin B (32.2%). While C. albicans, C. parapsilosis, and C. tropicalis remained susceptible to echinocandins, fluconazole resistance showed an increasing trend. C. glabrata exhibited variable susceptibility to both echinocandins and azoles. These findings highlight the urgent need for enhanced antifungal stewardship, improved diagnostics, and novel therapeutic strategies. Continued regional surveillance and targeted interventions are essential to mitigating the impact of antifungal resistance. Full article
(This article belongs to the Special Issue Public Health Action on Fungal Infections and Antimicrobial Resistance)
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17 pages, 2912 KiB  
Article
Protein Phosphatases MoPtc5, MoPtc1, and MoPtc2 Contribute to the Vegetative Growth, Stress Adaptation, and Virulence of Magnaporthe oryzae
by Jules Biregeya, Frankline Jagero Otieno, Meilian Chen, Anjago Wilfred Mabeche, Abah Felix, Nsanzinshuti Aimable, Yakubu Saddeeq Abubakar, Osakina Aron, Guodong Lu, Zonghua Wang, Yonghe Hong and Wei Tang
J. Fungi 2025, 11(3), 231; https://doi.org/10.3390/jof11030231 - 18 Mar 2025
Viewed by 251
Abstract
Protein phosphatases are crucial enzymes that regulate key cellular processes such as the cell cycle, gene transcription, and translation in eukaryotes. Seven PP2C protein phosphatases have been identified in Magnaporthe oryzae. However, their synergistic roles in the pathology and physiology of M. [...] Read more.
Protein phosphatases are crucial enzymes that regulate key cellular processes such as the cell cycle, gene transcription, and translation in eukaryotes. Seven PP2C protein phosphatases have been identified in Magnaporthe oryzae. However, their synergistic roles in the pathology and physiology of M. oryzae remain poorly investigated. By qRT-PCR analysis, we found that PTC1 and PTC2 are significantly upregulated in the PTC5 deletion mutant. The double deletion of the MoPTC5/MoPTC1 and MoPTC5/MoPTC2 genes significantly reduced hyphal growth, conidiophore formation, sporulation, and virulence in M. oryzae. In addition, the double-knockout mutants were increasingly sensitive to different osmotic, oxidative, and cell wall stresses. Western blot analysis revealed that MoPtc5 plays a synergistic function with MoPtc1 and MoPtc2 in the regulation of MoMps1 and MoOsm1 phosphorylation levels. Lastly, appressorium formation and turgor generation were remarkably affected in the ΔMoptc5ΔMoptc1 and ΔMoptc5ΔMoptc2 double-deletion mutants. These findings demonstrate the overlapping roles of PP2c protein phosphatase in the fungal development and pathogenesis of M. oryzae. Full article
(This article belongs to the Special Issue Growth and Virulence of Plant Pathogenic Fungi, 2nd Edition)
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25 pages, 9613 KiB  
Article
A New Root and Trunk Rot Disease of Grapevine Plantlets Caused by Fusarium in Four Species Complexes
by José Manoel Ferreira de Lima Cruz, Otília Ricardo de Farias, Brunno Cassiano Lemos Araújo, Alejandra Valencia Rivera, Cláudia Rita de Souza and Jorge Teodoro de Souza
J. Fungi 2025, 11(3), 230; https://doi.org/10.3390/jof11030230 - 17 Mar 2025
Viewed by 354
Abstract
Grapevines are propagated by grafting, but the rootstocks used in commercial plantations are susceptible to several diseases. In this study, we focused on a novel root and trunk rot disease of grapevine plantlets that show symptoms during cold storage, before field establishment. Our [...] Read more.
Grapevines are propagated by grafting, but the rootstocks used in commercial plantations are susceptible to several diseases. In this study, we focused on a novel root and trunk rot disease of grapevine plantlets that show symptoms during cold storage, before field establishment. Our objectives were to study the aetiology, symptomatology, plant resistance responses, and mode of action of the pathogen that was initially identified as Fusarium. The characterisation of this pathosystem was performed by isolation, pathogenicity assays, genetic diversity studies with BOX-PCR, and identification by sequencing a fragment of the tef1 gene. Scanning electron microscopy and X-ray spectroscopy were used to study the mode of action and plant resistance responses. The results showed that 12 species of Fusarium, initially isolated from both healthy and diseased plantlets, and classified into 4 species complexes, were pathogenic to grapevines. Comparative analyses between diseased and healthy roots showed typical resistance responses in diseased plantlets, including tyloses formation, translocation of Ca, and accumulation of Si. Field experiments confirmed that 100% of the diseased plantlets died within 90 days of transplantation. This study contributes to a better understanding of root and trunk rot disease under cold storage and provides insights for the development of management strategies. Full article
(This article belongs to the Section Fungal Pathogenesis and Disease Control)
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19 pages, 7233 KiB  
Article
Whole-Genome Sequencing of Flammulina filiformis and Multi-Omics Analysis in Response to Low Temperature
by Xinmin Liang, Jing Han, Yuqin Cui, Xueqin Shu, Mengting Lei, Bo Wang, Dinghong Jia, Weihong Peng, Xiaolan He and Xun Liu
J. Fungi 2025, 11(3), 229; https://doi.org/10.3390/jof11030229 - 17 Mar 2025
Viewed by 360
Abstract
The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon [...] Read more.
The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon and multi-omics data (transcriptome and metabolome) analyses of the mycelia, primordia, and fruiting bodies were conducted in the present study. Genome sequencing based on PacBio HiFi and Hi-C resulted in a 36.3 Mb genome sequence that mapped to 12 chromosomes, comprising 11,886 protein-coding genes. A total of 25 cold-responsive (COR) genes and 520 cold-adapted enzymes were identified in the genome. Multi-omics analyses showed that the pathways related to carbohydrate metabolism in the mycelia under low temperature (10 °C) were significantly enriched. Further examination of the expression profiles of carbohydrate-active enzymes (CAZymes) involved in carbohydrate metabolism revealed that out of 515 CAZyme genes in F. filiformis, 58 were specifically upregulated in mycelia under low-temperature conditions. By contrast, the expression levels of these genes in primordia and fruiting bodies reverted to those prior to low-temperature exposure. These indicate that CAZyme genes are important for the low-temperature adaptation of F. filiformis. This research contributes to the targeted breeding of F. filiformis. Full article
(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)
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18 pages, 2249 KiB  
Article
Culturable Yeast Diversity Associated with Industrial Cultures of the Microalga Microchloropsis gaditana and Their Ability to Produce Lipids and Biosurfactants
by Madalena Matos, Mónica A. Fernandes, Inês Costa, Natacha Coelho, Tamára F. Santos, Veronica Rossetto, João Varela and Isabel Sá-Correia
J. Fungi 2025, 11(3), 228; https://doi.org/10.3390/jof11030228 - 17 Mar 2025
Viewed by 487
Abstract
The marine oleaginous microalga Microchloropsis gaditana (formerly Nannochloropsis gaditana) exhibits a high capacity to thrive in a broad range of environmental conditions, being predominantly utilized as feed in aquaculture. This article reports the characterization of the culturable yeast population present during the [...] Read more.
The marine oleaginous microalga Microchloropsis gaditana (formerly Nannochloropsis gaditana) exhibits a high capacity to thrive in a broad range of environmental conditions, being predominantly utilized as feed in aquaculture. This article reports the characterization of the culturable yeast population present during the scale-up process of M. gaditana cultivation at Necton S.A. facilities, from 5 L flasks until tubular photobioreactors. The 146 yeast isolates obtained, molecularly identified based on D1/D2 and ITS nucleotide sequences, belong to the species Rhodotorula diobovata, R. mucilaginosa, R. taiwanensis, R. sphaerocarpa, Vishniacozyma carnescens, Moesziomyces aphidis, and Meyerozyma guilliermondii. The yeast abundance was found to increase throughout upscaling stages. The yeast populations isolated from microalgal cultures and water samples share phylogenetically close isolates, indicating a possible common source. The impressive high percentage of red yeasts isolated (90%) is consistent with the recognized role of carotenoid pigments in yeast photoprotection. Sixty yeast isolates were tested for lipid (Nile Red staining) and biosurfactant (oil drop dispersion and emulsification index) production. Results revealed that these capacities are common features. Microbial lipids and biosurfactants have promising biotechnological applications. Moreover, biosurfactants can fulfill various physiological roles and provide advantages in natural environments contributing to the promising use of yeasts as probiotics in microalgae production. Full article
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21 pages, 4962 KiB  
Article
Genome Sequencing and Comparative Transcriptomic Analysis of Rice Brown Spot Pathogen Bipolaris oryzae Adaptation to Osmotic Stress
by Chun Wang, Kexin Yang, Sauban Musa Jibril, Ruoping Wang, Chengyun Li and Yi Wang
J. Fungi 2025, 11(3), 227; https://doi.org/10.3390/jof11030227 - 17 Mar 2025
Viewed by 340
Abstract
Rice brown spot disease, caused by Bipolaris oryzae, is a significant fungal disease that poses a major threat to global rice production. Despite its widespread impact, genomic studies of B. oryzae remain limited, particularly those involving high-quality genomic data. In this study, [...] Read more.
Rice brown spot disease, caused by Bipolaris oryzae, is a significant fungal disease that poses a major threat to global rice production. Despite its widespread impact, genomic studies of B. oryzae remain limited, particularly those involving high-quality genomic data. In this study, we performed whole-genome sequencing of the B. oryzae strain RBD1, which was isolated from the demonstration field for upland rice cultivation in Haozhiba Village, Lancang County, Pu’er City, Yunnan Province, China, using a combination of second-generation Illumina sequencing and third-generation Single-Molecule Real-Time (SMRT) sequencing. The assembled genome was 37.5 Mb in size with a G + C content of 49.39%, containing 42 contigs with a contig N50 of 2.0 Mb. Genomic analysis identified genes related to carbon, nitrogen, and lipid metabolism, highlighting the strain’s metabolic flexibility under diverse environmental conditions and host interactions. Additionally, we identified pathogenicity-related genes involved in MAPK signaling, G protein signaling, and oxidative stress responses. Under 1.2 M sorbitol-induced osmotic stress, we observed significant differences in growth responses between RBD1 and the rice blast fungus Magnaporthe oryzae H7. Transcriptomic analysis using Illumina sequencing revealed that RBD1 responds to osmotic stress by enhancing carbohydrate metabolism, fatty acid degradation, and amino acid synthesis, while H7 primarily relies on protein synthesis to enhance growth tolerance. This study provides a valuable foundation for understanding the pathogenic mechanisms of rice brown spot and future disease control strategies. Full article
(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)
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1 pages, 129 KiB  
Correction
Correction: Ellsworth, M.; Ostrosky-Zeichner, L. Isavuconazole: Mechanism of Action, Clinical Efficacy, and Resistance. J. Fungi 2020, 6, 324
by Misti Ellsworth and Luis Ostrosky-Zeichner
J. Fungi 2025, 11(3), 226; https://doi.org/10.3390/jof11030226 - 17 Mar 2025
Viewed by 158
Abstract
In the original article [...] Full article
37 pages, 12685 KiB  
Article
Diversity of Alternaria Section Nimbya in Iran, with the Description of Eight New Species
by Abdollah Ahmadpour, Youbert Ghosta, Zahra Alavi, Fatemeh Alavi, Alireza Poursafar and Pabulo Henrique Rampelotto
J. Fungi 2025, 11(3), 225; https://doi.org/10.3390/jof11030225 - 15 Mar 2025
Viewed by 426
Abstract
Alternaria includes endophytes, saprophytes, and pathogens affecting both plants and animals, with a global distribution across various hosts and substrates. It is categorized into 29 sections, each defined by a type species and six monophyletic lineages. The Alternaria section Nimbya comprises 10 species [...] Read more.
Alternaria includes endophytes, saprophytes, and pathogens affecting both plants and animals, with a global distribution across various hosts and substrates. It is categorized into 29 sections, each defined by a type species and six monophyletic lineages. The Alternaria section Nimbya comprises 10 species primarily associated with the families Juncaceae and Cyperaceae, functioning as either saprophytes or plant pathogens. In this study, 189 fungal strains were collected from multiple locations across six provinces in Iran. The isolates were initially classified based on morphological characteristics and ISSR-PCR molecular marker banding patterns. Multi-gene phylogenetic analyses of 38 selected strains, using ITS–rDNA, GAPDH, TEF1, RPB2, and Alt a 1 gene sequences, combined with morphological data, led to the identification of 13 species, including eight new species, namely Alternaria caricifolia, A. cyperi, A. juncigena, A. junci-inflexi, A. persica, A. schoenoplecti, A. salkadehensis, and A. urmiana. In addition, this work identified new host associations (matrix nova) for three previously known species: A. caricicola on Cyperus sp., A. cypericola on Eleocharis sp., and A. junci-acuti on Carex sp. The study provides detailed morphological descriptions and illustrations of all identified species, discusses their habitats, distribution, and phylogenetic relationships within section Nimbya, and presents a key for species identification within this section in Iran. Furthermore, these findings highlight the significance of studying fungal biodiversity in Iran and contribute to a better understanding of species distribution and host range within the Alternaria section Nimbya. Full article
(This article belongs to the Collection Fungal Biodiversity and Ecology)
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9 pages, 514 KiB  
Communication
Evaluation of Serum Biomarkers for Improved Diagnosis of Candidemia
by Amélie Kinet-Poleur, Corentin Deckers, Imane Saad Albichr, Pierre Bogaerts, Patrick M. Honoré, Pierre Bulpa, Nathalie Ausselet, Frederic Foret, François Kidd, Te-Din Huang and Isabel Montesinos
J. Fungi 2025, 11(3), 224; https://doi.org/10.3390/jof11030224 - 15 Mar 2025
Viewed by 337
Abstract
Background: Candidemia, associated with high morbidity and mortality, remains challenging to diagnose due to the limitations of blood cultures. Serological biomarkers offer faster detection, enabling earlier treatment and improving outcomes. Methods: This study, conducted at CHU UCL Namur (August 2023–January 2025), evaluated three [...] Read more.
Background: Candidemia, associated with high morbidity and mortality, remains challenging to diagnose due to the limitations of blood cultures. Serological biomarkers offer faster detection, enabling earlier treatment and improving outcomes. Methods: This study, conducted at CHU UCL Namur (August 2023–January 2025), evaluated three diagnostic biomarkers for candidemia: CAGTA IgG VirClia Monotest, Wako β-D-glucan test, and CandId OLM RT-PCR. A total of 35 candidemia cases and 20 controls were included. Results: CAGTA IgG VirClia Monotest demonstrated low sensitivity (46%) and moderate specificity (75%). Both Wako β-D-glucan test and CandId OLM RT-PCR exhibited higher sensitivity (74% and 71%, respectively) and excellent specificity (100%). The combined use of Wako β-D-glucan test and CandId OLM RT-PCR further enhanced diagnostic performance, achieving 91% sensitivity and 100% specificity. Misidentification between Candida albicans and Candida dubliniensis was observed with CandId PCR, underlining a potential limitation in species-level discrimination. Conclusions: Both Wako β-D-glucan test and CandID OLM RT-PCR outperformed CAGTA IgG VirClia Monotest in diagnosing candidemia, and their combination significantly improved diagnostic accuracy, albeit at a higher cost. These findings highlight the potential of integrating multiple biomarkers into diagnostic workflows to optimize early detection, though further studies are needed to refine strategies and address challenges. Full article
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18 pages, 1064 KiB  
Review
Transcription Factors in Biocontrol Fungi
by Han-Jian Song, Xiao-Feng Li, Xin-Ran Pei, Zhan-Bin Sun and Han-Xu Pan
J. Fungi 2025, 11(3), 223; https://doi.org/10.3390/jof11030223 - 15 Mar 2025
Viewed by 442
Abstract
Transcription factors are extensively found in fungi and are involved in the regulation of multiple biological processes, including growth, development, conidiation, morphology, stresses tolerance, and virulence, as well as the production of secondary metabolites. Biocontrol is a complex biological process through which several [...] Read more.
Transcription factors are extensively found in fungi and are involved in the regulation of multiple biological processes, including growth, development, conidiation, morphology, stresses tolerance, and virulence, as well as the production of secondary metabolites. Biocontrol is a complex biological process through which several biocontrol behaviors, such as the secretion of cell wall-degrading enzymes and the production of secondary metabolites, are regulated by transcription factors. To date, biocontrol-related transcription factors have been reported in several biocontrol fungi, such as Beauveria bassiana, Clonostachys rosea, Coniothyrium minitans, and different species in the genera Metarhizium, Trichoderma, and Arthrobotrys. However, comprehensive reviews summarizing and analyzing transcription factors with biocontrol potential in these fungi are scarce. This review begins by giving a basic overview of transcription factors and their functions. Then, the role of biocontrol-related transcription factors in biocontrol fungi is discussed. Lastly, possible approaches for further work on transcription factors in biocontrol fungi are suggested. This review provides a basis for further elaborating the molecular mechanisms of transcription factors in the context of biocontrol. Full article
(This article belongs to the Section Fungi in Agriculture and Biotechnology)
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18 pages, 15921 KiB  
Article
Variation of Arbuscular Mycorrhizal Fungi Communities Between Root and Rhizosphere Soil of Endangered Plant Heptacodium miconioides Along Elevation Gradient
by Yueling Li, Guangyu Luo, Shijie Wu, Dang Yang, Pengpeng Lv, Zexin Jin and Junmin Li
J. Fungi 2025, 11(3), 222; https://doi.org/10.3390/jof11030222 - 14 Mar 2025
Viewed by 403
Abstract
Arbuscular mycorrhizal fungi (AMF) are considered crucial for the survival of many endangered plant species. However, the dynamics of AMF communities in the roots and rhizosphere soil of Heptacodium miconioides, particularly along elevation gradients, remain underexplored. This study investigates AMF colonization, spore [...] Read more.
Arbuscular mycorrhizal fungi (AMF) are considered crucial for the survival of many endangered plant species. However, the dynamics of AMF communities in the roots and rhizosphere soil of Heptacodium miconioides, particularly along elevation gradients, remain underexplored. This study investigates AMF colonization, spore density, and community structure in the root and rhizosphere soil of H. miconioides across an elevation range from 306 to 1028 m a.s.l., employing high-throughput sequencing. Our results show that AMF colonization and spore density in H. miconioides increased with elevation. Glomus was the dominant genus in both root and rhizosphere samples. Elevation significantly influenced the AMF community structure and diversity in the root, with alpha diversity decreasing linearly with elevation. In contrast, no significant elevation-related changes were observed in the rhizosphere soil alpha diversity. The difference in AMF beta diversity between the root and rhizosphere soil was lowest at the highest elevation. Compared to the rhizosphere soil, the degree and degree centralization of AMF community co-occurrence networks in the root showed a significant increase at higher elevations. Variations in soil properties, particularly soil pH, available phosphorus, and total nitrogen levels strongly influenced AMF communities in rhizosphere soil, while nitrate nitrogen, available potassium, and acid phosphatase were correlated with AMF communities in the root. These findings highlight the impact of elevation on AMF communities in both root and rhizosphere soil, providing valuable insights for the habitat restoration and conservation efforts for this species. Full article
(This article belongs to the Special Issue Fungal Communities in Various Environments)
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24 pages, 6703 KiB  
Article
Different Proteostasis Mechanisms Facilitate the Assembly of Individual Components on the Chitin Synthase 3 Complex at the Endoplasmic Reticulum
by Noelia Sánchez, Rosario Valle and César Roncero
J. Fungi 2025, 11(3), 221; https://doi.org/10.3390/jof11030221 - 14 Mar 2025
Viewed by 360
Abstract
Chitin synthase 3 complex assembly begins at the endoplasmic reticulum where the formation of a Chs3/Chs7 complex facilitates its exit from the ER and its transport along the secretory route. In the present study, our work shows that orphan molecules of Chs7 can [...] Read more.
Chitin synthase 3 complex assembly begins at the endoplasmic reticulum where the formation of a Chs3/Chs7 complex facilitates its exit from the ER and its transport along the secretory route. In the present study, our work shows that orphan molecules of Chs7 can exit the ER and are later recycled from the early Golgi by coat protein I (COPI) machinery via the adaptor complex Erv41/Erv46. Moreover, an eventual excess of the protein in the Golgi is recognized by the GGA complex and targeted to the vacuole for degradation through the ESCRT machinery. Non-oligomerizable versions of Chs3 can also exit the ER individually and follow a similar route to that of Chs7. We therefore demonstrate the traffic of unassembled CS3 subunits and describe the cellular mechanisms that guarantee the correct assembly of this protein complex at the ER while providing a default traffic route to the vacuole in case of its failure. This traffic route is shared with canonical ER adaptors, such as Erv29 and Erv14, and other components of protein complexes. The comparative analysis of their traffic allows us to discern a cellular program that combines COPI recycling, proteasomal degradation, and vacuolar disposal for maintaining protein homeostasis at the ER. Full article
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15 pages, 5978 KiB  
Article
Fungal-Infected Weeds: A Potential Source of Leaf Spot Disease in Rubber Trees from Southern Thailand
by Narit Thaochan, Chaninun Pornsuriya, Thanunchanok Chairin, Kodeeyah Thoawan, Putarak Chomnunti and Anurag Sunpapao
J. Fungi 2025, 11(3), 220; https://doi.org/10.3390/jof11030220 - 14 Mar 2025
Viewed by 494
Abstract
The rubber tree (Hevea brasiliensis) is an economically important crop in Thailand. Severe defoliation caused by emerging diseases has been reported to substantially reduce rubber yields during the leaf fall phase. The classical disease dispersal patterns of fungi in rubber tree [...] Read more.
The rubber tree (Hevea brasiliensis) is an economically important crop in Thailand. Severe defoliation caused by emerging diseases has been reported to substantially reduce rubber yields during the leaf fall phase. The classical disease dispersal patterns of fungi in rubber tree plantations might be derived from weeds in adjacent fields. However, this hypothesis remains untested. Therefore, in this study, we collected and isolated fungi from symptomatic weed samples in rubber tree plantations in Krabi Province in southern Thailand. We found that Parameria sp. were dominant, showing the development of conidiomata on leaves. A total of 25 symptomatic Parameria sp. leaves were collected and tested for their pathogenicity on rubber tree leaves. The tests produced six fungal isolates, WC001, WC002, WL001, WL002, WN001, and WN002, that caused spots on the rubber tree leaves similar to those observed on the weeds. Morphological characterization revealed that fungal isolates WC001 and WC002 were Colletotrichum sp., WL001 and WL002 were Lasiodiplodia sp., and WN001 and WN002 were Neopestalotiopsis sp. Multigene phylogenetic analyses of combined act, gapdh, ITS, and tub2 regions identified WC001 and WC002 as Colletotrichum siamense, while analyses of ITS, tub2, and tef1-α regions identified WL001 and WL002 as Lasiodiplodia brasiliensis and WN001 and WN002 as Neopestalotiopsis cubana. The occurrence of fungal diseases in rubber trees is significantly associated with leafy weeds in and around rubber tree plantations that could constitute reservoirs of fungal pathogens. The strategies used to control weeds have to be further considered in the future. Full article
(This article belongs to the Special Issue Current Trends in Mycological Research in Southeast Asia)
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14 pages, 3272 KiB  
Article
Optimization of Protoplast Preparation and Establishment of PEG-Mediated Genetic Transformation Method in Cordyceps cicadae
by Haikun Qi, Haihua Ruan, Tao Wu, Hongyang Zhang, Rui Dong and Yanjun Jiang
J. Fungi 2025, 11(3), 219; https://doi.org/10.3390/jof11030219 - 13 Mar 2025
Viewed by 537
Abstract
Cordyceps cicadae (C. cicadae) is an important edible medicinal fungus; however, owing to its wild growth and lack of genome annotation, construction of a stable genetic transformation system in C. cicadae is greatly limited, impeding the extensive exploitation of C. cicadae [...] Read more.
Cordyceps cicadae (C. cicadae) is an important edible medicinal fungus; however, owing to its wild growth and lack of genome annotation, construction of a stable genetic transformation system in C. cicadae is greatly limited, impeding the extensive exploitation of C. cicadae in industry. Here, we successfully established an efficient plasmid transformation method within protoplasts of C. cicadae by PEG mediation using pCas9-EGFP as a marker plasmid. In order to overcome low transformation efficiency and acquire sufficient protoplasts for transformation, the influence of enzyme species, enzymatic hydrolysis time, enzymatic hydrolysis temperature, and fungal age on protoplast preparation were analyzed sequentially, and the optimal conditions for protoplast preparation were determined as follows: 2-day-old C. cicadae mycelia with 1.5% lywallzyme hydrolysis at 34 °C for 5 h. Our results indicate that no less than 5.1 × 107 CFU/mL protoplasts could be acquired. Additionally, five osmotic pressure stabilizers including potassium chloride (KCl), sodium chloride (NaCl), glucose, mannitol, and sucrose were employed to enhance the regeneration of protoplasts, among which sucrose exhibited the highest regeneration rate of 10.43%. The transformation efficiency of plasmid was 37.3 CFU/µg DNA. On this basis, a genetic transformation method was successfully constructed, laying the foundation for further gene editing and metabolic engineering of C. cicadae. Full article
(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)
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9 pages, 239 KiB  
Article
Epidemiological Profile of Otomycosis at the Peace Hospital of Ziguinchor (Senegal)
by Abdoulaye Diop, Hussein Younes, Papa Samba Diop, Kalilou Diallo, Youssouph Sambou, Khadim Diongue, Mouhamadou Ndiaye, Mame Ngoné Coly, Habibou Sarr, Evelyne Siga Diom and Daouda Ndiaye
J. Fungi 2025, 11(3), 218; https://doi.org/10.3390/jof11030218 - 12 Mar 2025
Viewed by 384
Abstract
The investigation of the fungal etiologies of otomycoses is a rare occurrence in Senegal. The present study aspires to ascertain the profile of these mycoses within the confines of Ziguinchor. Conducted from 3 February 2021 to 31 August 2022, this retrospective descriptive study [...] Read more.
The investigation of the fungal etiologies of otomycoses is a rare occurrence in Senegal. The present study aspires to ascertain the profile of these mycoses within the confines of Ziguinchor. Conducted from 3 February 2021 to 31 August 2022, this retrospective descriptive study encompassed a total of 82 patients presenting with clinically suspected otomycosis within the otolaryngology (ENT) department of the Ziguinchor Peace Hospital (ZPH). In this study, two samples were collected from the external auditory canal (EAC) of each patient using sterile swabs. These samples were first observed by direct microscopy and then cultured at 30 °C on Sabouraud chloramphenicol with or without cycloheximide. The identification of the isolates was based on their macroscopic, microscopic, and physiological characteristics. The mycological examination was positive in 70 patients, with a prevalence of 85.37%. The most prevalent fungal isolates were Aspergillus section Nigri (30%), Aspergillus section Flavi (20%), and Candida albicans/Candida dubliniensis (10%). Of the clinical signs examined, auricular pruritus (p = 1.7033 × 10−6) was the only one to demonstrate a positive correlation with the onset of otomycosis. These results indicate that fungal agents play a significant role in the pathogenesis of otitis externa, underscoring the importance of mycological diagnosis in ensuring optimal patient management. Full article
13 pages, 654 KiB  
Article
Epidemiology and Clinical Features of Candida Bloodstream Infections: A 10-Year Retrospective Study in a Korean Teaching Hospital
by Shi Nae Yu, Sun In Hong, Jung Wan Park, Min Hyok Jeon and Oh Hyun Cho
J. Fungi 2025, 11(3), 217; https://doi.org/10.3390/jof11030217 - 12 Mar 2025
Viewed by 436
Abstract
Candida species are major pathogens of bloodstream infections (BSIs) in hospitalized patients, with high mortality. This study examined Candida species distribution, clinical characteristics, and the mortality of patients with Candida BSIs. Adult patients (≥16 years) with Candida BSIs at a teaching hospital (2014–2023) [...] Read more.
Candida species are major pathogens of bloodstream infections (BSIs) in hospitalized patients, with high mortality. This study examined Candida species distribution, clinical characteristics, and the mortality of patients with Candida BSIs. Adult patients (≥16 years) with Candida BSIs at a teaching hospital (2014–2023) were retrospectively reviewed. Over 10 years, 487 Candida isolates were obtained from 462 patients. C. albicans was the most frequent (38.2%), followed by C. glabrata (21.1%), C. parapsilosis (20.5%), and C. tropicalis (13.3%). The annual incidence of Candida BSIs remained stable (p = 0.525). However, non-albicans species BSIs increased 1.61-fold compared to C. albicans (95% CI: 1.19–2.19, p = 0.002). Fluconazole-non-susceptible Candida isolates increased after 2021 (p = 0.040). The overall 30-day mortality was 40.6%. In the multivariate analysis, a high Charlson comorbidity index (aHR: 1.20, 95% CI: 1.07–1.35, p = 0.001) and high SOFA score (aHR: 1.12, 95% CI: 1.02–1.23, p = 0.022) were the strongest predictors of 30-day mortality. Meanwhile, C. parapsilosis BSIs (aHR: 0.46, 95% CI: 0.22–0.99, p = 0.047) and central venous catheter removal at any time (aHR: 0.22, 95% CI: 0.13–0.37, p < 0.001) were associated with reduced 30-day mortality. The mortality of patients with Candida BSIs was mainly determined by disease severity, while catheter removal was associated with improved survival. Full article
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14 pages, 3688 KiB  
Article
Construction of Overexpression Vector with TYR7523 Gene and Its Effect on Browning in Macrocybe gigantea
by Jinyun Gao, Shuqing Song, Xinqian Liu, Zhuanlin Mo and Meihua Mo
J. Fungi 2025, 11(3), 216; https://doi.org/10.3390/jof11030216 - 12 Mar 2025
Viewed by 353
Abstract
Macrocybe gigantea is a rare high-temperature edible fungus known for its resistance to browning. Previous studies suggested that the anti-browning property of the SCAU4 strain might be associated with low expression levels of the TYR7523 gene. In this study, an overexpression vector for [...] Read more.
Macrocybe gigantea is a rare high-temperature edible fungus known for its resistance to browning. Previous studies suggested that the anti-browning property of the SCAU4 strain might be associated with low expression levels of the TYR7523 gene. In this study, an overexpression vector for the TYR7523 gene was constructed and introduced into SCAU4 mycelium using an Agrobacterium-mediated transformation method. After three rounds of hygromycin resistance screening, successful transformants were identified through PCR amplification and validated by qRT-PCR analysis, confirming a 3.47-fold upregulation of TYR7523 expression. The overexpression strain OE7523 was compared with the wild-type SCAU4 strain in terms of growth rate, browning degree, and tyrosinase activity. Although there was no significant difference in growth rate on the mother culture medium, OE7523 showed faster growth on the stock culture and mycelium culture medium. In the late storage period, OE7523 exhibited a higher browning degree and tyrosinase activity than SCAU4, suggesting a potential role of TYR7523 in fruiting body browning. Physiological analyses indicated that low TYR7523 expression may contribute to storage tolerance, while high expression influenced postharvest browning and preservation duration. The results provide data support for further study on the function of TYR7523 gene of Macrocybe gigantea. Full article
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23 pages, 3511 KiB  
Article
Adaptative Divergence of Cryptococcus neoformans: Phenetic and Metabolomic Profiles Reveal Distinct Pathways of Virulence and Resistance in Clinical vs. Environmental Isolates
by Camila Botelho Miguel, Geovana Pina Vilela, Lara Mamede Almeida, Mariane Andrade Moreira, Glicélia Pereira Silva, Jamil Miguel-Neto, Melissa Carvalho Martins-de-Abreu, Ferdinando Agostinho, Javier Emilio Lazo-Chica, Mariana Santos Cardoso, Siomar de Castro Soares, Aristóteles Góes-Neto and Wellington Francisco Rodrigues
J. Fungi 2025, 11(3), 215; https://doi.org/10.3390/jof11030215 - 12 Mar 2025
Viewed by 559
Abstract
Cryptococcus neoformans is a life-threatening fungal pathogen that primarily affects immunocompromised individuals. While antiretroviral therapy has reduced incidence in developed nations, fluconazole-resistant strains and virulent environmental isolates continue to pose challenges, especially because they have many mechanisms of adaptability, supporting their survival. This [...] Read more.
Cryptococcus neoformans is a life-threatening fungal pathogen that primarily affects immunocompromised individuals. While antiretroviral therapy has reduced incidence in developed nations, fluconazole-resistant strains and virulent environmental isolates continue to pose challenges, especially because they have many mechanisms of adaptability, supporting their survival. This study explores the phenetic and metabolomic adaptations of C. neoformans in clinical and environmental contexts to understand the factors influencing pathogenicity and resistance. Methods: An in silico observational study was conducted with 16 C. neoformans isolates (6 clinical, 9 environmental, and 1 reference) from the NCBI database. Molecular phenetic analysis used MEGA version 11.0.13 and focused on efflux pump protein sequences. Molecular phenetic relationships were assessed via the UPGMA clustering method with 1000 bootstrap replicates. The enzymatic profiling of glycolytic pathways was conducted with dbCAN, and metabolomic pathway enrichment analysis was performed in MetaboAnalyst 6.0 using the KEGG pathway database. Results: Molecular phenetic analysis revealed distinct clustering patterns among isolates, reflecting adaptations associated with clinical and environmental niches. Clinical isolates demonstrated enriched sulfur metabolism and glutathione pathways, likely adaptations to oxidative stress in host environments, while environmental isolates favored methane and glyoxylate pathways, suggesting adaptations for survival in carbon-rich environments. Conclusion: Significant phenetic and metabolomic distinctions between isolates reveal adaptive strategies for enhancing virulence and antifungal resistance, highlighting potential therapeutic targets. Full article
(This article belongs to the Special Issue Multidrug-Resistant Fungi, 2nd Edition)
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19 pages, 6313 KiB  
Article
Distribution Pattern and Assembly Process of Fungal Communities Along Altitude Gradient in Sediments of the Yellow River Basin
by Kang Fang, Guoce Xu, Xin Chen, Jing Li, Yuting Cheng and Yifan Cheng
J. Fungi 2025, 11(3), 214; https://doi.org/10.3390/jof11030214 - 11 Mar 2025
Viewed by 410
Abstract
Microorganisms have a profound impact on the stability and ecological health of aquatic environments. Fungi, as important components of river ecosystems, play critical roles as decomposers and symbionts. A comprehensive understanding of the mechanisms underlying fungal community assembly is essential for the effective [...] Read more.
Microorganisms have a profound impact on the stability and ecological health of aquatic environments. Fungi, as important components of river ecosystems, play critical roles as decomposers and symbionts. A comprehensive understanding of the mechanisms underlying fungal community assembly is essential for the effective conservation and management of river ecosystems. However, the distribution patterns and assembly process of fungal communities along elevation gradients in river sediments remain poorly understood. In this study, ITS amplicon sequencing, a neutral community model, and a null model were employed to analyze the distribution patterns and assembly processes of fungal communities in sediments along the altitudinal gradient of the Yellow River. The results indicated that Ascomycota (47.79%) and Basidiomycota (15.68%) were identified as the dominant phyla in the sediments, collectively accounting for 63.47% of the total relative abundance of the community. In the three different altitudinal gradients, the fungal community diversity (Shannon) showed a gradually decreasing trend with increasing altitude. The co-line networks of fungal communities exhibited positive interactions and had more complex and compact networks in the sediments of the Tibetan Plateau area (YRA). Environmental factors in the sediments played an important role in shaping the structure of fungal communities, with lead (Pb), total nitrogen (TN), silt, and total organic carbon (TOC) being the main factors driving changes in community structure, contributing 15.5%, 12.3%, 10.7%, and 10.2%, respectively. In the community assembly process, deterministic processes were found to dominate, with homogenizing selection contributing the most (69.66%). These research results help us understand the distribution patterns of fungal communities along altitudinal gradients and the mechanisms of community assembly, and also provide a scientific basis for biodiversity conservation and the rational use of biological resources. Full article
(This article belongs to the Special Issue Fungal Communities in Various Environments)
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27 pages, 1925 KiB  
Review
Fungal Stress Responses and the Importance of GPCRs
by Daniela Lara-Martínez, Fabiola Estefania Tristán-Flores, Juan Antonio Cervantes-Montelongo and Guillermo Antonio Silva-Martínez
J. Fungi 2025, 11(3), 213; https://doi.org/10.3390/jof11030213 - 11 Mar 2025
Viewed by 975
Abstract
G-protein-coupled receptors (GPCRs) play a crucial role in the gene regulation of processes related to the response to different types of stress in fungi. These receptors act as sensors of extracellular signals and transmit the information to the interior of the cell through [...] Read more.
G-protein-coupled receptors (GPCRs) play a crucial role in the gene regulation of processes related to the response to different types of stress in fungi. These receptors act as sensors of extracellular signals and transmit the information to the interior of the cell through G-proteins. In the presence of different and specific types of stresses, GPCRs activate signaling cascades that culminate in the activation of transcription factors, which regulate the expression of genes associated with the stress response, including those induced by changes in environmental pH. GPCR-mediated gene regulation allows fungi to adapt to adverse conditions such as osmotic, thermal, oxidative, or nutritional stress, as well as fluctuations in environmental pH. This review focuses on the understanding of how GPCRs modulate the stress response in fungi and their crucial role in advancing our knowledge of the physiology and adaptability of these microorganisms in their changing environment. Full article
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19 pages, 4352 KiB  
Article
Occurrence and Diversity of Fungi and Their Mycotoxin Production in Common Edible and Medicinal Substances from China
by Ling Chen, Junhui Wu, Shuhong Zhang, Xinqi Liu, Meiping Zhao, Weipeng Guo, Jumei Zhang, Wei Chen, Zhenjie Liu, Meiqing Deng and Qingping Wu
J. Fungi 2025, 11(3), 212; https://doi.org/10.3390/jof11030212 - 10 Mar 2025
Viewed by 583
Abstract
Edible and medicinal substances can be contaminated by fungi during harvesting, processing, and storage, leading to mycotoxin production and quality deterioration. The distribution of mycotoxigenic fungi in edible and medicinal substances was investigated in this study. Fungi and mycotoxins were detected in 163 [...] Read more.
Edible and medicinal substances can be contaminated by fungi during harvesting, processing, and storage, leading to mycotoxin production and quality deterioration. The distribution of mycotoxigenic fungi in edible and medicinal substances was investigated in this study. Fungi and mycotoxins were detected in 163 commercially available edible and medicinal substances using standard microbiological techniques and high-performance liquid chromatography. A total of 92.0% of samples contained fungi (0.5–5.3 lg colony-forming units (CFU)·g−1); 208 fungal strains belonging to 16 genera were identified, predominantly Aspergillus and Penicillium. Aspergillus section Nigri (30.3%) produced fumonisin B2, which was distributed mainly in radix and rhizome samples. Thirteen samples had mycotoxins, of which ochratoxin A was the most common, followed by aflatoxins and zearalenone (ZEN). One Nelumbinis semen sample contained 10.75 μg·kg−1 AFB1, and one Raisin tree semen sample contained 484.30 μg·kg−1 ZEN, which exceeded regulatory limits in Europe and China. These findings highlight the potential risks associated with fungal contamination and mycotoxins in edible and medicinal substances. Enhanced quality control measures are essential to reduce contamination during harvesting, processing, and storage. Expanded mycotoxin screening, improved preservation techniques, and stricter regulatory standards need to be implemented to ensure consumer safety. Full article
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29 pages, 23714 KiB  
Article
Intra-Leaf Variability of Incubation Period Sheds New Light on the Lifestyle of Cercospora beticola in Sugar Beets
by Erich-Christian Oerke and Ulrike Steiner
J. Fungi 2025, 11(3), 211; https://doi.org/10.3390/jof11030211 - 9 Mar 2025
Viewed by 554
Abstract
The length of incubation period, i.e., the time between first contact of host and pathogen and the appearance of symptoms, varies among diseases and depends on environmental conditions. Cercospora beticola is the most important fungal pathogen in sugar beet production worldwide, as Cercospora [...] Read more.
The length of incubation period, i.e., the time between first contact of host and pathogen and the appearance of symptoms, varies among diseases and depends on environmental conditions. Cercospora beticola is the most important fungal pathogen in sugar beet production worldwide, as Cercospora leaf spot (CLS) reduces the leaf area contributing to yield formation. Using sugar beet cultivars differing in CLS resistance, a single infection period of C. beticola resulted in minor differences in the incubation period among host genotypes and among individual plants of cultivars, greater differences among leaves within plants, and substantial variation within individual leaves. Under greenhouse conditions not suitable for secondary infections, the first CLS lesions appeared 10 days after inoculation; however, the number of leaf spots and CLS severity further increased significantly for another 7 to 17 days. A geographic information system approach enabled the tracking of colony appearance and growth of all CLSs on inoculated leaves for up to 27 days. Asymptomatic colonization of leaves was associated with thick hyphae which switched to thin hyphae or melanization after lesion appearance. The lifestyle of C. beticola—intercellular tissue colonization, triggering of necrotic host reaction—is discussed considering the experimental results as well as literature resources. Full article
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28 pages, 458 KiB  
Review
Aspergillus in Children and Young People with Cystic Fibrosis: A Narrative Review
by Emily Chesshyre, Eva Wooding, Emily Sey and Adilia Warris
J. Fungi 2025, 11(3), 210; https://doi.org/10.3390/jof11030210 - 9 Mar 2025
Viewed by 723
Abstract
Cystic fibrosis is a severe, inherited, life-limiting disorder, and over half of those living with CF are children. Persistent airway infection and inflammation, resulting in progressive lung function decline, is the hallmark of this disorder. Aspergillus colonization and infection is a well-known complication [...] Read more.
Cystic fibrosis is a severe, inherited, life-limiting disorder, and over half of those living with CF are children. Persistent airway infection and inflammation, resulting in progressive lung function decline, is the hallmark of this disorder. Aspergillus colonization and infection is a well-known complication in people with CF and can evolve in a range of Aspergillus disease phenotypes, including Aspergillus bronchitis, fungal sensitization, and allergic bronchopulmonary aspergillosis (ABPA). Management strategies for children with CF are primarily aimed at preventing lung damage and lung function decline caused by bacterial infections. The role of Aspergillus infections is less understood, especially during childhood, and therefore evidence-based diagnostic and treatment guidelines are lacking. This narrative review summarizes our current understanding of the impact of Aspergillus on the airways of children and young people with CF. Full article
(This article belongs to the Special Issue Fungal Infections in Non-neutropenic Patients)
16 pages, 3272 KiB  
Article
Antifungal Polyacetylenic Deoxyglycosides Isolated from Endophytic Fungus Xylaria sp. VDL4 Associated with Vaccinium dunalianum
by Jiao Yao, Sai Huang, Lingfeng He, Shengyun Wei, Wei Yang, Qiangxin Zhang, Weihua Wang, Xiaoqin Yang, Sida Xie, Yunxian Li, Ping Zhao and Guolei Zhu
J. Fungi 2025, 11(3), 209; https://doi.org/10.3390/jof11030209 - 8 Mar 2025
Viewed by 552
Abstract
One novel C10 polyacetylene rhamnoside, 4,6,8-decatriyne-1-O-α-L-rhamnopyranoside, named xylariside A (1), together with two novel C10 polyacetylene quinovopyranosides, 4,6,8-decatriyne-1-O-α-D-quinovopyranoside, xylariside B (2), and 8E-decaene-4,6-diyne-1-O-α-D-quinovopyranoside, xylariside C (3), were [...] Read more.
One novel C10 polyacetylene rhamnoside, 4,6,8-decatriyne-1-O-α-L-rhamnopyranoside, named xylariside A (1), together with two novel C10 polyacetylene quinovopyranosides, 4,6,8-decatriyne-1-O-α-D-quinovopyranoside, xylariside B (2), and 8E-decaene-4,6-diyne-1-O-α-D-quinovopyranoside, xylariside C (3), were obtained from the solid fermentation of Xylaria sp. VDL4, an endophytic fungus isolated from Vaccinium dunalianum wight (Ericaceae). Their chemical structures were elucidated through a combination of spectroscopic techniques. The antifungal activities of these compounds were evaluated in vitro against four phytopathogenic fungi (Fusarium oxysporum, Botrytis cinerea, Phytophthora capsici, and Fusarium solani). Compound 2 demonstrated significant antifungal activities, with minimum inhibitory concentration (MIC) values ranging from 3.91 to 7.81 μg/mL. Compound 2’s effectiveness levels were similar to those of the reference drugs thiabendazole and carbendazim (each MIC = 0.98−15.62 μg/mL). Xylariside B (2) was further evaluated against B. cinerea in vivo. It exhibited remarkable efficacy in both the prevention and treatment of tomato and strawberry gray mold. Molecular docking studies confirmed the antifungal mechanism of compound 2 by revealing its binding interactions with key enzyme targets in B. cinerea, thereby supporting the observed in vitro and in vivo results. Additionally, compound 2 showed effective inhibition of α-glucosidase, with IC50 values of 5.27 ± 0.0125 μg/mL. Full article
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