Journal of Fungi

16 pages, 1720 KB

Open AccessArticle

Cloning and Characterization of the Mycovirus MpChrV2 from Macrophomina phaseolina

by Peimeng Sun, Luyang Song, Mengyuan Mu, Jiayi Ma, Xinyu Li, Kunni Tian, Mengyuan Zhang, Mingyue Zhang, Yuanyuan Zhang, Caiyi Wen, Jing Wang and Ying Zhao

J. Fungi 2025, 11(9), 675; https://doi.org/10.3390/jof11090675 - 12 Sep 2025

Abstract

Macrophomina phaseolina is a widely distributed soilborne phytopathogenic fungus that causes destructive diseases such as charcoal rot and stem canker, posing serious threats to crop yield and quality. In recent years, mycoviruses have gained attention as potential biological control agents. In this study, [...] Read more.

Macrophomina phaseolina is a widely distributed soilborne phytopathogenic fungus that causes destructive diseases such as charcoal rot and stem canker, posing serious threats to crop yield and quality. In recent years, mycoviruses have gained attention as potential biological control agents. In this study, a novel double-stranded RNA (dsRNA) virus was identified from M. phaseolina strain 22C-8, isolated from sesame (Sesamum indicum L.) charcoal rot samples in Fuyang, Anhui Province, China. The viral genome comprised four dsRNA segments, each encoding a single open reading frame (ORF) predicted to encode RNA-dependent RNA polymerase (RdRp), coat protein (CP), and two hypothetical proteins. Phylogenetic analysis classified the virus as a new member of the genus Betachrysovirus in the family Chrysoviridae, and it was designated Macrophomina phaseolina chrysovirus 2 (MpChrV2). Pathogenicity assays in sesame seedlings revealed that MpChrV2 infection significantly reduced the virulence of M. phaseolina strain 22C-8. In contrast, virus-free derivatives (22C-8-VF18), obtained via protoplast regeneration, caused more severe symptoms and exhibited enhanced growth rates, indicating that MpChrV2 alters fungal physiology and pathogenicity. These findings suggest that MpChrV2 possesses a typical hypovirulence phenotype and holds promise as a biocontrol agent for sesame charcoal rot. Full article

(This article belongs to the Special Issue Mycoviruses: Emerging Investigations on Virus-Fungal Host Interaction, 2nd Edition)

20 pages, 4975 KB

Open AccessArticle

The Transformation and Protein Expression of the Edible Mushroom Stropharia rugosoannulata Protoplasts by Agrobacterium-tumefaciens-Mediated Transformation

by Dongjie Yin and Hairong Xiong

J. Fungi 2025, 11(9), 674; https://doi.org/10.3390/jof11090674 - 12 Sep 2025

Abstract

Stropharia rugosoannulata is a cultivated edible mushroom characterized by its nutritional composition and efficient cellulolytic enzymatic systems. However, the lack of genetic tools has significantly impeded the investigation of its molecular mechanisms, severely constraining the study of functional genomic and precision breeding in [...] Read more.

Stropharia rugosoannulata is a cultivated edible mushroom characterized by its nutritional composition and efficient cellulolytic enzymatic systems. However, the lack of genetic tools has significantly impeded the investigation of its molecular mechanisms, severely constraining the study of functional genomic and precision breeding in S. rugosoannulata. It was demonstrated in this study that the Agrobacterium-tumefaciens-mediated genetic transformation (ATMT) system is applicable for the transformation of S. rugosoannulata protoplasts. Through this proposal, we successfully achieved the expression of exogenous genes (mCherry gene encoding red fluorescent protein, hph gene encoding hygromycin B phosphotransferase, and GUS gene encoding β-glucuronidase) and the endogenous mutant gene SDI encoding the iron-sulfur protein subunit of succinate dehydrogenase in S. rugosoannulata. Furthermore, this study employed endogenous promoters of GPD encoding glyceraldehyde-3-phosphate dehydrogenase and SDI to enhance transformation efficiency and drive target gene expression. This study establishes the feasibility of ATMT in S. rugosoannulata systems, while achieving stable expression of a panel of selectable marker genes and reporter genes critical for genetic research in S. rugosoannulata. Full article

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

12 pages, 2265 KB

Open AccessArticle

T-DNA Mutagenesis Reveals FpPer1 as a Dual-Function Regulator of Virulence and Fungicide Resistance in Fusarium pseudograminearum

by Haiyang Li, Panpan Zhang, Xueqian Song, Huiying Li, Cong Chen, Limin Wang, Zhifang Wang, Lingjun Hao, Yun Li, Xinlong Wang, Jiangang Kang, Honglian Li, Min Wang and Shengli Ding

J. Fungi 2025, 11(9), 673; https://doi.org/10.3390/jof11090673 - 12 Sep 2025

Abstract

Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, is a devastating wheat disease leading to significant yield losses worldwide. However, the pathogenic mechanism of F. pseudograminearum and its resistance to fungicides remain poorly understood. In this study, we identified a hypothetical gene [...] Read more.

Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, is a devastating wheat disease leading to significant yield losses worldwide. However, the pathogenic mechanism of F. pseudograminearum and its resistance to fungicides remain poorly understood. In this study, we identified a hypothetical gene encoding GPI-anchored protein, designated FpPer1, by screening a T-DNA insertion mutant library of F. pseudograminearum for tebuconazole resistance. The ΔFpper1 mutant exhibited increased sensitivity to the triazole antifungal drugs and fludioxonil. Additionally, the deletion of FpPER1 impaired fungal growth, conidiation, and pathogenicity in barley leaves and wheat coleoptiles. Furthermore, the ΔFpper1 mutant displayed enhanced susceptibility to various environmental stresses, including NaCl, CR, sorbitol, H₂O₂, and SDS. The mutant also showed reduced penetration peg formation and impaired reactive oxygen species (ROS) scavenging ability during infection. Subcellular localization analysis revealed that FpPer1-GFP co-localized with the endoplasmic reticulum (ER) marker RFP-HDEL in both conidia and hyphae, indicating its localization in the ER. In summary, our findings demonstrate that FpPER1 plays an important role in pathogenicity and fungicide resistance in F. pseudograminearum. This study not only provides a theoretical foundation for understanding fungal virulence mechanisms but also offers practical insights for developing novel fungicide strategies. Full article

(This article belongs to the Special Issue Plant Pathogens and Mycotoxins)

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20 pages, 1547 KB

Open AccessSystematic Review

What Do We Know About Cryptococcus spp. in Portugal? One Health Systematic Review in a Comprehensive 13-Year Retrospective Study (2013–2025)

by Ricardo Lopes, Andreia Garcês, Hugo Lima de Carvalho, Vanessa Silva, Filipe Sampaio, Cátia Fernandes, Gonçalo Barros, Alexandre Sardinha de Brito, Ana Rita Silva, Elsa Leclerc Duarte, Luís Cardoso and Ana Cláudia Coelho

J. Fungi 2025, 11(9), 672; https://doi.org/10.3390/jof11090672 - 12 Sep 2025

Abstract

Cryptococcosis, caused by the Cryptococcus neoformans and Cryptococcus gattii species complexes (pathogenic Cryptococcus spp.), is an environmentally acquired mycosis of One Health relevance. This study integrates a PRISMA-compliant systematic review (2000–2025) of Portuguese animal, human, and environmental reports with a 13-year retrospective dataset [...] Read more.

Cryptococcosis, caused by the Cryptococcus neoformans and Cryptococcus gattii species complexes (pathogenic Cryptococcus spp.), is an environmentally acquired mycosis of One Health relevance. This study integrates a PRISMA-compliant systematic review (2000–2025) of Portuguese animal, human, and environmental reports with a 13-year retrospective dataset of laboratory-confirmed veterinary cryptococcosis cases (2013–2025). Clinical specimens were cultured and identified by MALDI-TOF mass spectrometry, and associations were assessed using χ² and Fisher’s exact tests. Of 1059 submissions, 48 (4.5%) were culture-positive: 6.8% of canine, 5.3% of feline samples, and 4.0% of avian samples, with no detections in other vertebrate groups (p = 0.705). Cryptococcus neoformans predominated in carnivores (73.7%), while Papiliotrema laurentii (formerly Cryptococcus laurentii) was most frequent in birds (86.2%). Infection was not associated with sex or age. Seasonality was evident, with a July peak and summer predominance (p = 0.010). Most cases were from the Centre region (62.5%), with significant regional variation of Cryptococcus spp. distribution (p < 0.001). The systematic review confirmed autochthonous C. gattii complex disease and widespread C. neoformans contamination in pigeon guano and arboreal niches. These findings demonstrate a compartmentalised eco-epidemiology, reinforcing the need for integrated molecular typing, antifungal susceptibility testing, and coordinated human–animal–environment surveillance to inform targeted prevention and control strategies in Portugal. Full article

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

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11 pages, 441 KB

Open AccessArticle

Characteristics and Outcomes of Hospitalized Patients with Histoplasmosis: Comparison of Immunocompromised and Non-Immunocompromised Adult Patients

by Liam M. Dalton, Carol A. Kauffman and Marisa H. Miceli

J. Fungi 2025, 11(9), 671; https://doi.org/10.3390/jof11090671 - 12 Sep 2025

Abstract

We sought to investigate the role of immunocompromise in patients with newly diagnosed histoplasmosis in an era when AIDS is less prevalent. We performed a retrospective comparison of immunocompromised and non-immunocompromised adults hospitalized at Michigan Medicine from 2015 to 2024. Of 51 patients, [...] Read more.

We sought to investigate the role of immunocompromise in patients with newly diagnosed histoplasmosis in an era when AIDS is less prevalent. We performed a retrospective comparison of immunocompromised and non-immunocompromised adults hospitalized at Michigan Medicine from 2015 to 2024. Of 51 patients, 37 (73%) were immunocompromised, 32 from solid organ transplantation or tumor necrosis factor antagonist/disease-modifying anti-rheumatic drugs. Of these 37, 34 had disseminated and 3 had pulmonary histoplasmosis; of the 14 non-immunocompromised patients, 8 had disseminated and 6 had pulmonary histoplasmosis, p = 0.004. Fever was the only symptom/sign that was more common in the immunocompromised cohort (86% vs. 36%, p = 0.003). Laboratory/radiological studies showed no major differences between immunocompromised and non-immunocompromised cohorts. Histoplasma urinary antigen was positive for all immunocompromised vs. 79% non-immunocompromised patients, p = 0.003. Median antigen levels were 17.5 (IQR 6.2–19.7) ng/mL for immunocompromised vs. 1.9 (0.6–19.7) ng/mL for non-immunocompromised patients, p = 0.004. Cultures for Histoplasma were more often positive in the immunocompromised cohort, p = 0.025. All-cause 90-day mortality was 14% in each cohort (five immunocompromised and two non-immunocompromised patients); all deaths occurred in those with disseminated histoplasmosis, and four were in the first week of hospitalization. Disseminated histoplasmosis in both immunocompromised and non-immunocompromised patients continues to be a serious, often fatal infection. Full article

(This article belongs to the Special Issue Invasive Fungal Infections: Recent Advances in Epidemiology, Diagnosis, and Treatment)

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15 pages, 647 KB

Open AccessArticle

Candidemia in a General Hospital in Kuwait: Epidemiology, Species Distribution, Risk Factors, and Antifungal Susceptibility Patterns over a 10-Year Period (2015–2024)

by Khalifa Al Benwan, Sarah Ahmed, Dalal Al Banwan and Maria John

J. Fungi 2025, 11(9), 670; https://doi.org/10.3390/jof11090670 - 12 Sep 2025

Abstract

This 10-year retrospective observational study (2015–2024) conducted at Al-Amiri Hospital in Kuwait aimed to analyze the epidemiology, species distribution, and key risk factors associated with Candida bloodstream infections. Data were collected on patient demographics and clinical risk factors, and the distribution of Candida [...] Read more.

This 10-year retrospective observational study (2015–2024) conducted at Al-Amiri Hospital in Kuwait aimed to analyze the epidemiology, species distribution, and key risk factors associated with Candida bloodstream infections. Data were collected on patient demographics and clinical risk factors, and the distribution of Candida species was determined based on isolates recovered from patients with confirmed candidemia. Multivariate logistic regression was performed to identify factors associated with candidemia outcomes. Cases significantly increased from 33 (2015–2016) to 93 (2023–2024), predominantly affecting elderly patients (≥65 years) and intensive care unit (ICU) admissions. A shift in species distribution was observed, with a decline in Candida albicans and a marked increase in Candidozyma auris (formerly Candida auris) and C. parapsilosis. Antifungal susceptibility patterns were species-specific: C. albicans, C. parapsilosis, and C. tropicalis remained highly susceptible to all tested antifungals, while Nakaseomyces glabratus (formerly Candida glabrata) showed fluconazole resistance in 25% of isolates. C. auris exhibited resistance to fluconazole (97%) and variable resistance to echinocandins and voriconazole. Echinocandins retained broad-spectrum activity across most species. Independent risk factors included ICU admission, advanced age, and comorbidities. N. glabratus and C. auris infections were linked to higher mortality. This study highlights the growing candidemia burden in Kuwait, driven by emerging non-albicans Candida (NAC) spp. and related species. Early species identification and susceptibility testing are crucial for effective treatment and improved outcomes, necessitating enhanced infection control and antifungal stewardship. Full article

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

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5 pages, 187 KB

Open AccessEditorial

Diagnosis and Treatment of Superficial Fungal Infections

by Suzana Otašević and Aleksandra Ignjatović

J. Fungi 2025, 11(9), 669; https://doi.org/10.3390/jof11090669 - 12 Sep 2025

Abstract

On a global scale, one of the major challenges associated with superficial fungal infections (SFIs) of the skin and mucosa is their extremely high prevalence, along with the considerable proportion of patients who develop chronic infections [...] Full article

(This article belongs to the Special Issue Diagnosis and Treatment of Superficial Fungal Infections)

16 pages, 6483 KB

Open AccessArticle

Surface Changes Induced by Brushing Increase Candida albicans Biofilms on 3D-Printed Denture Base Resin

by Rafaelly Camargo, Jonatas Silva de Oliveira, Amanda Costa Ferro, Beatriz Ribeiro Ribas, Alan Augusto Valério Alves and Janaina Habib Jorge

J. Fungi 2025, 11(9), 668; https://doi.org/10.3390/jof11090668 - 12 Sep 2025

Abstract

Studies assessing the long-term effects of brushing with cleaning and disinfecting agents on surface roughness and biofilm accumulation on the three-dimensionally (3D) printed resins remain scarce. This study aimed to evaluate the effects of different solutions and simulated brushing times on the surface [...] Read more.

Studies assessing the long-term effects of brushing with cleaning and disinfecting agents on surface roughness and biofilm accumulation on the three-dimensionally (3D) printed resins remain scarce. This study aimed to evaluate the effects of different solutions and simulated brushing times on the surface roughness and biofilm formation on heat-cured and 3D-printed denture base resins. Discs samples (10 mm × 1.2 mm) were prepared and randomly assigned to brushing treatments using the following solutions: distilled water, disinfectant liquid soap and dentifrice. The specimens (n = 9) were subjected to 10,000, 20,000 and 50,000 cycles to simulate 1, 2 and 5 years of brushing, respectively. The control group consisted of unbrushed samples. Surface roughness (Ra) was measured. Candida albicans biofilm formation was evaluated by counting colony forming units, cellular metabolic activity, and qualitative and quantitative analysis through confocal fluorescence microscopy. A significant increase in roughness was observed in both resins after two years of simulated brushing, mainly with dentifrice. After two years of brushing, an increase in the number of cells and metabolism of C. albicans was observed, in agreement with the fluorescence and biofilm thickness results. Brushing with dentifrice increased the roughness of heat-cured and 3D-printed resins and potentially increased C. albicans biofilm formation. Full article

(This article belongs to the Section Fungal Cell Biology, Metabolism and Physiology)

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20 pages, 9792 KB

Open AccessArticle

Discovery and Identification of Four Novel Species of Distoseptispora (Distoseptisporaceae, Distoseptisporales) on Decaying Wood from Hainan and Fujian Provinces, China

by Wenwen Liu, Changzhun Yin, Yang Jiang, Xigang Yan, Xingsheng Wang, Xiuguo Zhang and Shi Wang

J. Fungi 2025, 11(9), 667; https://doi.org/10.3390/jof11090667 - 11 Sep 2025

Abstract

Decaying wood, as a unique substrate, which contains cellulose, hemicellulose, lignin, and nitrogen-containing compounds, harbors significant fungal biodiversity, particularly among dematiaceous hyphomycete species. This study uses a combination of morphological and molecular systematics methods. Phylogenetic analyses of ITS, LSU, RPB2 and TEF1 sequences [...] Read more.

Decaying wood, as a unique substrate, which contains cellulose, hemicellulose, lignin, and nitrogen-containing compounds, harbors significant fungal biodiversity, particularly among dematiaceous hyphomycete species. This study uses a combination of morphological and molecular systematics methods. Phylogenetic analyses of ITS, LSU, RPB2 and TEF1 sequences were conducted using the maximum likelihood (ML) and the Bayesian inference (BI) method. Combined with the morphological characteristics, four new species of Distoseptispora, D. bawanglingensis sp. nov., D. changjiangensis sp. nov., D. daanyuanensis sp. nov. and D. jianfenglingensis sp. nov., were identified from decaying wood collected in Hainan and Fujian provinces, China. This study provides detailed descriptions, illustrations, and phylogenetic trees with the aim of clarifying the taxonomic status of these four new species, thereby enhancing our understanding of the species diversity of Distoseptispora in Hainan and Fujian provinces, China. Full article

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

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10 pages, 646 KB

Open AccessPerspective

Can We Have Guidelines or Just Guidance for Rare Fungal Infections?

by Nancy N. Vuong and Dimitrios P. Kontoyiannis

J. Fungi 2025, 11(9), 666; https://doi.org/10.3390/jof11090666 - 11 Sep 2025

Abstract

In this perspective, we discuss the limitations of medical guidelines as it relates to the management of uncommon invasive fungal infections (IFIs) or infrequent manifestations of more common IFIs. We emphasize the difficulties to define “gold standards” for diagnostics and treatment based on [...] Read more.

In this perspective, we discuss the limitations of medical guidelines as it relates to the management of uncommon invasive fungal infections (IFIs) or infrequent manifestations of more common IFIs. We emphasize the difficulties to define “gold standards” for diagnostics and treatment based on limited and low-quality evidence. We posit that such “guidelines” based on scarce data may be suboptimal and could be in some cases even harmful. Specifically, guidelines are often seen as rigid rules to follow which can prevent a critical examination of the nuanced management of individual patients with rare IFIs. We also emphasize that guidelines are often not updated frequently enough and therefore may not reflect the current treatment landscape. For all those reasons, we suggest that the term “guidance” may be more appropriate than “guidelines” for rare IFIs. Finally, we pose several questions regarding constructing future “Guidelines”/“Guidance for such entities”. Full article

(This article belongs to the Special Issue Current and Future Development of Mycology: The 10th Anniversary of Journal of Fungi)

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12 pages, 607 KB

Open AccessArticle

Virulence of Candida Isolates in Patients with Tuberculosis and Oral/Oesophageal Candidiasis: Co-Infection Evaluation

by Rayana Larissa Pinheiro Soares Ferreira, Alessandra Teixeira Macedo, Conceição de Maria Pedrozo e Silva de Azevedo, Sirlei Garcia Marques, Marliete Carvalho Costa, João Carlos Maia Dornelas de Oliveira, Paulo Henrique Fonseca do Carmo, Yankee Costa Magalhães Diniz, Heylane Ferreira Cutrim, Cristina Andrade Monteiro, Maria Rosa Quaresma Bomfim, Daniel Assis Santos, Rodrigo Assuncao Holanda and Julliana Ribeiro Alves Santos

J. Fungi 2025, 11(9), 665; https://doi.org/10.3390/jof11090665 - 11 Sep 2025

Abstract

Tuberculosis (TB) is an infection caused by Mycobacterium tuberculosis complex (MTBC), which can be exacerbated by fungal infections. This study evaluated the clinical characteristics and virulence of Candida spp. in patients with tuberculosis. Antifungal sensitivity, phospholipase and proteinase production, biofilm formation, phagocytic index, [...] Read more.

Tuberculosis (TB) is an infection caused by Mycobacterium tuberculosis complex (MTBC), which can be exacerbated by fungal infections. This study evaluated the clinical characteristics and virulence of Candida spp. in patients with tuberculosis. Antifungal sensitivity, phospholipase and proteinase production, biofilm formation, phagocytic index, and reactive oxygen (ROS) and nitrogen (RNS) species were assessed. Candida spp. were isolated from 14 patients, 28.5% women and 71.4% men, mainly from sputum and tracheal secretions. Five (35.7%) patients were co-infected with Mycobacterium, Candida, and HIV. Candida albicans (78.6%) and Candida tropicalis (21.4%) were identified in all 14 patients. All isolates showed sensitivity to amphotericin B and dose-dependent responses to fluconazole (16 μg/mL). Phospholipase activity was detected in 35.7% of the isolates, whereas all isolates showed proteinase activity (100%). A significant difference in phospholipase activity, phagocytosis, and production of reactive oxygen species (ROS) and nitrogen species (RNS) was observed when Candida isolates from patients with TB, living with or without HIV, were compared to Candida isolates from healthy individuals. All isolates were biofilm producers. This study highlights the relevance of mycoses diagnosis in patients with TB, since Candida spp. may be more virulent and contribute to the deterioration of the clinical condition. Full article

(This article belongs to the Special Issue Recent Advances in Systemic and Emerging Mycoses)

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9 pages, 442 KB

Open AccessOpinion

The Use of Genetics and Immunology in the Diagnosis and Care of Advanced Coccidioidomycosis: Where Are We Going?

by Kavitha Thiagarajan, Shikha Mishra, Rob Purdie, Bianca Torres, Royce H. Johnson and Manish J. Butte

J. Fungi 2025, 11(9), 664; https://doi.org/10.3390/jof11090664 - 11 Sep 2025

Abstract

Coccidioidomycosis (CM) is an endemic disease in the western United States, northern Mexico, and Central and South America. The severity of coccidioidal infection is highly variable, with potential factors including comorbidities and the patient’s innate and adaptive immune response. Based on data from [...] Read more.

Coccidioidomycosis (CM) is an endemic disease in the western United States, northern Mexico, and Central and South America. The severity of coccidioidal infection is highly variable, with potential factors including comorbidities and the patient’s innate and adaptive immune response. Based on data from a predominantly healthy and mainly Caucasian male survey conducted nearly a century ago, approximately 60% of infections are asymptomatic, with an estimated 40% of people experiencing some respiratory symptoms; with 10% of those diagnosed with CM. Disseminated disease occurs in approximately 1% of cases and can involve the meninges and, potentially, any place in the body. It is not yet fully understood why some people experience severe disease while many people do not; it is understood that the immune response has a major role. Immunomodulators, including dupilumab and interferon-gamma (IFN-γ), have shown promise in treating patients with disseminated infection. This article summarizes the latest genetic and immunologic evidence demonstrating immune dysfunction. Immunomodulators and potential therapeutic strategies based on the above are reviewed. Full article

(This article belongs to the Special Issue Personalized Mycology)

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20 pages, 10422 KB

Open AccessArticle

Metagenomic Insights into Disease-Induced Microbial Dysbiosis and Elemental Cycling Alterations in Morchella Cultivation Soils: Evidence from Two Distinct Regions

by Zong-Lin Deng, Feng-Ming Yu, Xiang Ma, Qi Zhao and Jian-Kui Liu

J. Fungi 2025, 11(9), 663; https://doi.org/10.3390/jof11090663 - 10 Sep 2025

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Abstract

Soil-borne diseases represent a major constraint on the sustainable cultivation of morel mushrooms (Morchella spp.), yet the microbial ecological mechanisms driving disease occurrence and progression remain poorly understood. In this study, we conducted comparative metagenomic analyses of rhizosphere and root-adhering soils associated [...] Read more.

Soil-borne diseases represent a major constraint on the sustainable cultivation of morel mushrooms (Morchella spp.), yet the microbial ecological mechanisms driving disease occurrence and progression remain poorly understood. In this study, we conducted comparative metagenomic analyses of rhizosphere and root-adhering soils associated with healthy and diseased Morchella crops from two major production regions in China, aiming to elucidate shifts in microbial community composition, assembly processes, and functional potential. Disease conditions were linked to pronounced microbial dysbiosis, with community assembly shifting from stochastic to deterministic processes, particularly within fungal communities under host selection and pathogen pressure. Co-occurrence network analysis revealed substantial reductions in connectivity, modularity, and clustering coefficients in diseased soils, indicating the loss of ecological stability and keystone taxa. Functional annotations using CAZy, COG, and KEGG databases showed that healthy soils were enriched in genes related to carbohydrate metabolism, aerobic respiration, and ecosystem resilience, whereas diseased soils exhibited higher abundance of genes associated with stress responses, proliferation, and host defense. Furthermore, elemental cycling analysis demonstrated that healthy soils supported pathways involved in aerobic carbon degradation, nitrogen fixation, phosphate transport, and sulfur oxidation, while diseased soils favored fermentation, denitrification, phosphorus limitation responses, and reductive sulfur metabolism. Collectively, these results highlight the importance of microbial functional integrity in maintaining soil health and provide critical insights into microbiome-mediated disease dynamics, offering a foundation for developing microbiome-informed strategies for sustainable fungal crop management. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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13 pages, 1331 KB

Open AccessReview

Malassezia Folliculitis: An Underdiagnosed Mimicker of Acneiform Eruptions

by Natalia V. Chalupczak and Shari R. Lipner

J. Fungi 2025, 11(9), 662; https://doi.org/10.3390/jof11090662 - 10 Sep 2025

Viewed by 247

Abstract

Malassezia folliculitis, previously known as Pityrosporum folliculitis, is a common yet frequently misdiagnosed dermatologic condition caused by Malassezia yeast overgrowth in hair follicles. Its monomorphic, pruritic papules and pustules closely mimic acne vulgaris, often leading to inappropriate antibiotic use. This review summarizes current [...] Read more.

Malassezia folliculitis, previously known as Pityrosporum folliculitis, is a common yet frequently misdiagnosed dermatologic condition caused by Malassezia yeast overgrowth in hair follicles. Its monomorphic, pruritic papules and pustules closely mimic acne vulgaris, often leading to inappropriate antibiotic use. This review summarizes current evidence on the epidemiology, clinical presentation, diagnostic challenges, and management of Malassezia folliculitis. A high index of clinical suspicion is critical in patients with recalcitrant acneiform eruptions. Diagnosis is supported by dermoscopy, potassium hydroxide preparation, Wood’s lamp, and response to antifungal therapy. Topical and oral antifungal agents are highly effective although relapses are common and access to off-label treatments may be limited. Greater awareness of the distinct clinical features of Malassezia folliculitis and treatment response can improve diagnostic accuracy and enhance patient outcomes. Full article

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

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16 pages, 2522 KB

Open AccessArticle

The Predicted Structure of S. cerevisiae Ssp1 Reveals Parallel Evolution in the Pil1 BAR Domain Family Proteins of Ascomycetes

by Yasuyuki Suda and Aaron M. Neiman

J. Fungi 2025, 11(9), 661; https://doi.org/10.3390/jof11090661 - 9 Sep 2025

Viewed by 384

Abstract

BAR domains are a superfamily of widely conserved membrane binding motifs. In fungi, Pil1 family proteins are BAR domain containing proteins involved in organizing the plasma membrane. S. pombe encodes a sporulation-specific Pil1 family protein, Meu14, which has a specialized role in shaping [...] Read more.

BAR domains are a superfamily of widely conserved membrane binding motifs. In fungi, Pil1 family proteins are BAR domain containing proteins involved in organizing the plasma membrane. S. pombe encodes a sporulation-specific Pil1 family protein, Meu14, which has a specialized role in shaping the forespore membrane during sporulation. The functional analog of Meu14 in S. cerevisiae is Ssp1. While Ssp1 has no primary sequence homology to Pil1 or Meu14, AlphaFold predicts that it contains a Pil1-related BAR domain. Consistent with this structural prediction, mutation of residues in the putative lipid binding face of Ssp1 or in a residue implicated in multimerization disrupt sporulation. Characterization of the mutant proteins indicates that the BAR domain is necessary for recruitment of Ssp1 to the highly curved leading edge of the prospore membrane and multimerization of Ssp1 at that location is required for assembly of the leading edge complex. The distribution of Pil1 family proteins across an evolutionary tree of Ascomycetes reveals that Meu14 and Ssp1 arose independently in the lineages leading to S. pombe and S. cerevisiae, respectively. Full article

(This article belongs to the Special Issue Current and Future Development of Mycology: The 10th Anniversary of Journal of Fungi)

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14 pages, 1290 KB

Open AccessArticle

Secreted Protein VdCUE Modulates Virulence of Verticillium dahliae Without Interfering with BAX-Induced Cell Death

by Haonan Yu, Haiyuan Li, Xiaochen Zhang, Mengmeng Wei, Xiaoping Hu and Jun Qin

J. Fungi 2025, 11(9), 660; https://doi.org/10.3390/jof11090660 - 8 Sep 2025

Viewed by 127

Abstract

Verticillium wilt, caused by Verticillium dahliae, severely threatens various crops and trees worldwide. This study aimed to characterize the function of a CUE (coupling of ubiquitin conjugation to endoplasmic reticulum (ER) degradation)-domain-containing protein, VdCUE, in V. dahliae, which exhibits sequence divergence [...] Read more.

Verticillium wilt, caused by Verticillium dahliae, severely threatens various crops and trees worldwide. This study aimed to characterize the function of a CUE (coupling of ubiquitin conjugation to endoplasmic reticulum (ER) degradation)-domain-containing protein, VdCUE, in V. dahliae, which exhibits sequence divergence between the defoliating strain XJ592 and the non-defoliating strain XJ511. We generated ∆VdCUE-knockout mutants and evaluated their phenotypes in growth and virulence. Functional analyses included verifying the signal peptide activity of VdCUE, testing its ability to induce cell death or inhibit BAX-induced cell death in Nicotiana benthamiana leaves, and identifying host targets via yeast two-hybrid screening. The ∆VdCUE mutants showed reduced formation of melanized microsclerotia but no other obvious growth defects. Cotton plants infected with the ∆VdCUE mutants exhibited a significantly lower disease index and defoliation rate. VdCUE was confirmed to be secreted via a functional signal peptide, but it neither triggered cell death nor inhibited BAX-induced cell death. Three putative host targets were identified and supported by AI-based three-dimensional structural modeling, including tRNA-specific 2-thiouridylase, peptidyl-prolyl cis-trans isomerase, and 40S ribosomal protein, which may mediate VdCUE-dependent virulence regulation. These findings reveal VdCUE as a key virulence factor in V. dahliae, contributing to our understanding of its pathogenic mechanism. Full article

(This article belongs to the Special Issue Growth and Virulence of Plant Pathogenic Fungi, 2nd Edition)

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13 pages, 1876 KB

Open AccessArticle

Azole Resistance in Aspergillus Species Isolated from Clinical Samples: A Nine-Year Single-Center Study in Turkey (2015–2023)

by Zeynep Yazgan, Reyhan Çalışkan and Gökhan Aygün

J. Fungi 2025, 11(9), 659; https://doi.org/10.3390/jof11090659 - 7 Sep 2025

Viewed by 449

Abstract

Azole-resistant mycotic infections pose an escalating global health threat, with an estimated 6.5 million invasive fungal infections (IFIs) annually leading to 3.8 million deaths, 68% directly caused by IFIs. While azole antifungals are the cornerstone of treatment, emerging resistance, mainly due to gene [...] Read more.

Azole-resistant mycotic infections pose an escalating global health threat, with an estimated 6.5 million invasive fungal infections (IFIs) annually leading to 3.8 million deaths, 68% directly caused by IFIs. While azole antifungals are the cornerstone of treatment, emerging resistance, mainly due to gene mutations and efflux pump overexpression, is a major concern. This study, spanning 2015–2023, investigated azole resistance in clinical Aspergillus isolates in Turkey, a region lacking comprehensive surveillance. Of 200 causative isolates, A. fumigatus accounted for 45% and respiratory samples 57%. Overall azole resistance was 7%, rising to 11% for A. fumigatus. Findings highlight the persistent challenge of azole resistance, emphasizing the critical need for continued local and global surveillance to inform treatment guidelines and public health interventions. Despite limitations, including a single-center focus, this research provides crucial epidemiological insights into the evolving landscape of antifungal resistance in Turkey. Full article

(This article belongs to the Special Issue Azole Resistance in Aspergillus spp., 2nd Edition)

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16 pages, 1969 KB

Open AccessArticle

Rme1: Unveiling a Novel Repressor in the Cellulolytic Pathway of Trichoderma reesei

by Amanda Cristina Campos Antoniêto, David Batista Maués, Marcelo Candido, Iasmin Cartaxo Taveira and Roberto N. Silva

J. Fungi 2025, 11(9), 658; https://doi.org/10.3390/jof11090658 - 6 Sep 2025

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Abstract

Thefilamentous fungus Trichoderma reesei is renowned for its exceptional ability to secrete cellulolytic enzymes, which play a crucial role in the hydrolysis of lignocellulose biomass. The expression of fungal cellulases is meticulously regulated at the transcriptional level, depending on the carbon source available [...] Read more.

Thefilamentous fungus Trichoderma reesei is renowned for its exceptional ability to secrete cellulolytic enzymes, which play a crucial role in the hydrolysis of lignocellulose biomass. The expression of fungal cellulases is meticulously regulated at the transcriptional level, depending on the carbon source available in the medium. To obtain new insights into the transcriptional network controlling cellulase expression in T. reesei, we analyzed RNA-Seq data and identified and characterized a new transcription factor, Rme1, that regulates the expression of cellulolytic genes. Combining functional genomics and protein-DNA interaction assay, we showed that Rme1 acts as a repressor of cellulase production in T. reesei by directly regulating two critical genes involved in cellulose degradation: the cellobiohydrolase cel7a and the carbon catabolite repressor cre1. This is the first report of a transcription factor regulating Cre1. This study contributes to a better understanding of the complex regulation of the cellulolytic system of T. reesei and may be useful for the genetic modification of strains for the biorefinery industry. Full article

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

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10 pages, 632 KB

Open AccessBrief Report

Healthcare Resource Utilization, Treatment Costs, and Mortality in Patients with Malignancies or Transplantation Who Develop Invasive Aspergillosis

by Thomas J. Walsh, Craig I. Coleman, Melissa Johnson, Belinda Lovelace and Barbara D. Alexander

J. Fungi 2025, 11(9), 657; https://doi.org/10.3390/jof11090657 - 6 Sep 2025

Viewed by 287

Abstract

Objectives: Invasive aspergillosis (IA) poses significant risks to patients with malignancies or transplantation; however, estimates of burden-of-illness in patients with IA are sparse. We sought to assess in-hospital and outpatient healthcare resource utilization, all-cause treatment costs, and mortality in patients admitted with [...] Read more.

Objectives: Invasive aspergillosis (IA) poses significant risks to patients with malignancies or transplantation; however, estimates of burden-of-illness in patients with IA are sparse. We sought to assess in-hospital and outpatient healthcare resource utilization, all-cause treatment costs, and mortality in patients admitted with IA with hematologic or non-hematologic malignancies, bone marrow transplant/hematopoietic cell transplantation (BMT/HCT), or solid organ transplantation (SOT). Methods: This claims study utilized United States IQVIA data. Adults admitted for IA were identified by diagnosis codes during the patient selection period (October 2015–November 2022). IA patients were stratified into cohorts including recent hematologic or non-hematologic malignancies, or a history of BMT/HCT or SOT. We assessed hospital and intensive care unit (ICU) length-of-stay (LOS), all-cause index hospital treatment costs, and inpatient mortality or need for hospice in each cohort, as well as the need for re-admission and total treatment costs for up to six-months after admission, and all-cause mortality at end of study follow-up. Results: Among 1190 patients admitted for IA, 317 had hematologic malignancies, 155 non-hematologic malignancies, 133 BMT/HCT and 173 SOT. Across these cohorts, IA was associated with protracted (median LOS = 12–18 days; ICU LOS = 10–13 days) and costly (median = USD 79,058–USD 172,342) index hospitalizations ending in death or hospice in 28.1% (89/317) to 36.1% (48/133) of patients. Among those surviving to discharge, between 53.1% (34/64) and 63.4% (97/153) were re-admitted within six months. Total median treatment costs at six months ranged from USD 213,378 to USD 397,857. All-cause mortality was 33.6% (52/155) to 40.6% (54/133) at end of study follow-up. Conclusions: Hospitalizations for IA in patients with malignancies or transplantation are long, costly, and end with readmission, hospice, or death in more than one-third of patients. Full article

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

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12 pages, 704 KB

Open AccessArticle

The Prognostic Value of (1→3)-β-D-Glucan in COVID-19 Patients with and Without Secondary Fungal Disease

by Udari Welagedara, Jessica Price, Raquel Posso, Matt Backx and P. Lewis White

J. Fungi 2025, 11(9), 656; https://doi.org/10.3390/jof11090656 - 5 Sep 2025

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Abstract

Background: The presence of (1→3)-β-D-Glucan (BDG) in serum may be indicative of invasive fungal disease (IFD), but even without IFD, elevated BDG can be associated with adverse patient outcomes. Methods: COVID-19-infected patients (n = 125) who were screened for IFD with [...] Read more.

Background: The presence of (1→3)-β-D-Glucan (BDG) in serum may be indicative of invasive fungal disease (IFD), but even without IFD, elevated BDG can be associated with adverse patient outcomes. Methods: COVID-19-infected patients (n = 125) who were screened for IFD with fungal biomarkers were evaluated to assess the prognostic value of BDG. BDG was correlated with patients’ mortality, considering the influences of IFD and anti-fungal therapy (AFT). Results: A BDG concentration > 31 pg/mL was associated with significant mortality in the absence of documented IFD and without subsequent antifungal therapy (≤31 pg/mL: 28% vs. >31 pg/mL: 91%; p = 0.0001). In patients without IFD but with BDG > 31 pg/mL, mortality dropped to 50% when AFT was administered. In patients with BDG > 31 pg/mL and neither IFD nor AFT, the average probability of death was 3.38-fold greater. Conclusions: Elevated serum BDG is associated with significant mortality in COVID-19-infected patients without IFD, irrespective of AFT. A BDG-associated proinflammatory response might be driving the high mortality. BDG serves as a prognostic marker in COVID-19-infected patients with or without IFD. When BDG is very low (≤31 pg/mL) the likelihood of death remains consistent with the background mortality rates for COVID-19 within the ICU. Full article

(This article belongs to the Special Issue Recent Advances in Clinical Mycology)

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15 pages, 3471 KB

Open AccessArticle

Identification and Biocontrol of Fusarium oxysporum Affecting Lucky Bamboo (Dracaena sanderiana Hort. ex. Mast.)

by Merve Şenol Kotan

J. Fungi 2025, 11(9), 655; https://doi.org/10.3390/jof11090655 - 4 Sep 2025

Viewed by 429

Abstract

Lucky bamboo is an economically crucial ornamental plant worldwide due to its durability, rapid growth capacity, and versatile uses. However, diseases caused by various fungal pathogens negatively affect bamboo production, resulting in yield losses. In the present study, fungal agents causing disease in [...] Read more.

Lucky bamboo is an economically crucial ornamental plant worldwide due to its durability, rapid growth capacity, and versatile uses. However, diseases caused by various fungal pathogens negatively affect bamboo production, resulting in yield losses. In the present study, fungal agents causing disease in Dracaena sanderiana were isolated and evaluated for their pathogenicity. The MF-1 and MF-2 isolates that showed pathogenicity were characterized morphologically and molecularly. Chitinase enzymes were partially purified from four different bacteria and biochemically characterized, and the antifungal activities of these bacteria and chitinases were evaluated. As a result of the diagnosis, both isolates were identified as Fusarium oxysporum with ~99% similarity. It was determined that the partially purified chitinases from Pseudomonas chlororaphis C-37A and Agrobacterium radiobacter A-16 had the highest activity with values of 9.44 and 1.02 EU/mL, respectively. Additionally, the pH and temperature values at which C-37A’s chitinase exhibited optimal activity were determined to be 8 and 30 °C, while those for A-16’s chitinase were found to be pH 4 and 40 °C. After 120 min, C-37A’s chitinase retained 50% of its activity at 90 °C, while A-16’s chitinase retained 80% of its activity at 40 °C. C-37A inhibited the growth of MF-1 and MF-2 by 83% and 75%, respectively. Additionally, the inhibition rates of A-16, Bacillus megaterium M-3, and KBA-10 ranged from 68% to 29%. In chitinase applications, the highest inhibition rates of 28% (MF-1) and 23% (MF-2) were obtained from C-37A chitinase. In conclusion, it was observed that bioagent bacteria provide sustainable biological effects against F. oxysporium in D. Sanderiana, and that the chitinase enzyme purified from these isolates can be used as a biocontrol agent in agriculture, as well as potentially evaluated in various industrial applications. Full article

(This article belongs to the Special Issue Biological Control of Fungal Plant Pathogens)

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11 pages, 1782 KB

Open AccessArticle

Investigating the Potential Involvement of Glutathione S-Transferases in Defence Against Powdery Scab in Potato

by Sadegh Balotf, Richard Wilson and Calum Wilson

J. Fungi 2025, 11(9), 654; https://doi.org/10.3390/jof11090654 - 4 Sep 2025

Viewed by 383

Abstract

Glutathione S-transferases (GSTs) are key enzymes in plant defences involved in detoxification, redox regulation, and the modulation of secondary metabolism, playing essential roles in the response to pathogen infections. Despite prior genome-wide predictions of GSTs in potato, little is known about their specific [...] Read more.

Glutathione S-transferases (GSTs) are key enzymes in plant defences involved in detoxification, redox regulation, and the modulation of secondary metabolism, playing essential roles in the response to pathogen infections. Despite prior genome-wide predictions of GSTs in potato, little is known about their specific roles in defending against Spongospora subterranea. This study re-analyses our previously generated transcriptomics and proteomics datasets to explore the role of GSTs in two contrasting potato cultivars, ‘Iwa’ (susceptible) and ‘Gladiator’ (resistant), after inoculation with S. subterranea. A total of 69 and 41 GSTs were identified in the transcriptomics and proteomics data, respectively. The majority of these GSTs were upregulated in the resistant cultivar but not in the susceptible cultivar. The upregulation of GSTs in ‘Gladiator’ suggests a more efficient antioxidant and detoxification response following S. subterranea infection. Chromosomal mapping revealed a high number of GSTs on chromosome 9, suggesting a hotspot for GSTs in the potato genome. This research provides direct evidence of the potential involvement of GSTs in resistance to S. subterranea, offering insights into potential targets for breeding resistant potato cultivars. Full article

(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition)

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15 pages, 693 KB

Open AccessArticle

The Evolving Threat of Fusarium Wilt TR4 to Small-Scale Mixed Cultivar Banana Production in the Red River Basin of Northern Vietnam

by Chung Huy Nguyen, Thi Tho Nguyen, Diane Mostert, Altus Viljoen, Elizabeth Kearsley and Guy Blomme

J. Fungi 2025, 11(9), 653; https://doi.org/10.3390/jof11090653 - 4 Sep 2025

Viewed by 483

Abstract

Fusarium wilt (Foc) TR4 was first reported in Northern Vietnam in 2018. Since then, it has rapidly spread across most northern provinces along the Red River basin banana production landscapes, impacting Cavendish (Musa AAA genome) production. The other main banana cultivars which [...] Read more.

Fusarium wilt (Foc) TR4 was first reported in Northern Vietnam in 2018. Since then, it has rapidly spread across most northern provinces along the Red River basin banana production landscapes, impacting Cavendish (Musa AAA genome) production. The other main banana cultivars which are widely grown in this production zone are Pisang Awak (Musa ABB genome) and Pisang Mas (Musa AA genome). Field surveys were conducted in 2022/2023 across this banana production region to assess pathogen spread from Cavendish monocropping systems into adjacent smaller-scale mixed cultivar systems. Across 130 sites, a total of 210 banana pseudostem tissue samples were collected from symptomatic Cavendish, Pisang Awak and Pisang Mas plants. Foc TR4 incursions into mixed small-to-mid-sized Cavendish–Pisang Awak plantations were confirmed, and the pathogen was also recorded in Pisang Awak plantations and backyard gardens that did not contain any Cavendish mats. A screenhouse-based Foc TR4 screening trial including seven commonly cultivated Musa varieties in Northern Vietnam indicated that Pisang Awak and Pisang Mas are susceptible to the pathogen. While Pisang Awak, an important local variety, is known to be susceptible to both Foc Race 1 and TR4, recent field observations suggest a limited susceptibility of Pisang Awak to Foc TR4 in mixed cultivar plantation settings. Local farmers similarly reported observing reduced susceptibility, with several having already replanted TR4-affected Cavendish fields with Pisang Awak as part of their disease management strategy. No infections were observed on field-grown Pisang Mas plants in TR4-affected mixed banana cultivar production landscapes. These results and insights provide solutions for the revival of TR4-affected Cavendish production fields or landscapes, through the cultivation of less susceptible local cultivars. In addition, the introduction, validation and scaling of Formosana (i.e., GCTCV-218, a Cavendish somaclone with moderate resistance to Foc TR4) should be envisaged. Full article

(This article belongs to the Section Environmental and Ecological Interactions of Fungi)

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20 pages, 1040 KB

Open AccessReview

The Structural and Functional Diversities of Bacteria Inhabiting Plant Woody Tissues and Their Interactions with Fungi

by Rana Haidar, Amira Yacoub, Ouiza Mesguida, Rémy Guyoneaud, Eléonore Attard and Patrice Rey

J. Fungi 2025, 11(9), 652; https://doi.org/10.3390/jof11090652 - 3 Sep 2025

Viewed by 599

Abstract

In recent studies, the bacterial and fungal communities associated with plant wood have received considerable attention. Due to microorganisms’ vertical migration from roots to leaves, these communities provide critical links between the rhizosphere and phyllosphere microbiome. Recent investigations have shown that anatomical and [...] Read more.

In recent studies, the bacterial and fungal communities associated with plant wood have received considerable attention. Due to microorganisms’ vertical migration from roots to leaves, these communities provide critical links between the rhizosphere and phyllosphere microbiome. Recent investigations have shown that anatomical and chemical wood characteristics shape the microbiota inhabiting living or dead wood tissues, leading to variation in the observed decomposition of these materials. Despite the fact that bacteria have limited ability to degrade polymeric lignocelluloses compared to fungi, those inhabiting wood tissues have demonstrated a significant role in these habitats. Bacteria and fungi coexist in wood and form differing relationships with each other, with consequences for community structures that, in turn, impact plant health. The aim of this review is to present an overview of current insights regarding bacterial profiles and functions in lignocellulosic plants and their interaction with fungal communities colonising the same habitat. A better understanding of plant–bacteria–fungi interactions will allow for better exploitation of these tripartite interactions and possibly improve plant health. Full article

(This article belongs to the Section Environmental and Ecological Interactions of Fungi)

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20 pages, 2925 KB

Open AccessArticle

Mycoremediation of Petroleum-Contaminated Soil Using Native Ganoderma and Trametes Strains from the Ecuadorian Amazon

by Isabel Cipriani-Avila, Cony Decock, Aracely Zambrano-Romero, Katherine Zaldumbide, Mónica Garcés-Ruiz, Jazel Caiza-Olmedo, Ana Gordillo, Verónica Luna and Patrick A. Gerin

J. Fungi 2025, 11(9), 651; https://doi.org/10.3390/jof11090651 - 2 Sep 2025

Viewed by 672

Abstract

Petroleum-contaminated soils are a major environmental concern worldwide. In Ecuador, extensive oil spills in the Amazon have led to widespread hydrocarbon pollution, threatening ecosystems and posing health risks to nearby communities. Conventional remediation techniques are resource-intensive and may render soil unsuitable for future [...] Read more.

Petroleum-contaminated soils are a major environmental concern worldwide. In Ecuador, extensive oil spills in the Amazon have led to widespread hydrocarbon pollution, threatening ecosystems and posing health risks to nearby communities. Conventional remediation techniques are resource-intensive and may render soil unsuitable for future use. In contrast, mycoremediation—using fungi to degrade toxic contaminants—offers a sustainable alternative. White-rot fungi, known for their ligninolytic enzyme systems such as laccases and peroxidases, are capable of degrading a wide range of organic pollutants, including petroleum hydrocarbons. This study assessed the enzymatic activity of 16 fungal strains from the phyla Ascomycota and Basidiomycota isolated in the Ecuadorian Amazon. Plate-based screening and quantitative laccase activity assays confirmed positive enzymatic activity in all strains. The five strains with the highest enzymatic activity were Ganoderma cf. parvulum QCAM7791, Trametes menziesii QCAM7783, Trametes menziesii QCAM7788, Trametes menziesii QCAM7790, and Trametes meyenii QCAM7785, which were selected for a 60-day soil microcosm experiment under controlled laboratory conditions. These strains removed over 96% of total petroleum hydrocarbons from contaminated soil, demonstrating high biodegradation efficiency. These results highlight the promise of native fungal strains as bioremediation agents for petroleum-contaminated soils. Further studies should focus on evaluating their performance under field conditions and their potential integration into large-scale remediation strategies. Full article

(This article belongs to the Special Issue Fungi Activity on Remediation of Polluted Environments, 2nd Edition)

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18 pages, 3054 KB

Open AccessArticle

Harnessing Epigenetic Modifiers Reveals MAPK-Mediated Regulation Mechanisms in Hadal Fungi of Alternaria alternata Under High Hydrostatic Pressure

by Qingqing Peng, Qifei Wei and Xi Yu

J. Fungi 2025, 11(9), 650; https://doi.org/10.3390/jof11090650 - 2 Sep 2025

Viewed by 451

Abstract

High hydrostatic pressure (HHP) significantly modulates microbial metabolism, while chemical epigenetic modifiers are known to reactivate silent biosynthetic gene clusters and induce novel natural products. However, the mechanisms by which these epigenetic modifiers regulate fungal responses under differential pressure conditions, and how such [...] Read more.

High hydrostatic pressure (HHP) significantly modulates microbial metabolism, while chemical epigenetic modifiers are known to reactivate silent biosynthetic gene clusters and induce novel natural products. However, the mechanisms by which these epigenetic modifiers regulate fungal responses under differential pressure conditions, and how such regulation affects natural product biosynthesis, remain completely unexplored. Here, we investigated the hadal fungus Alternaria alternata CIEL23 isolated from 7332 m sediments in the Mariana Trench under epigenetic modifier treatment with contrasting pressures (0.1 MPa vs. 40 MPa). Our results revealed that epigenetic perturbations and high pressure significantly altered fungal phenotypes, gene expression, and secondary metabolite composition. Transcriptome-level analysis of epigenetic regulatory mechanisms under epigenetic modifiers in both pressure conditions (0.1 MPa and 40 MPa) demonstrated that the addition of epigenetic modifiers regulated MAPK pathway-related gene expression in response to the environment stimuli. Under dual stress conditions, the IG, CWI, and HOG branches of the MAPK pathway showed significantly altered activity patterns. These changes were associated with differential the regulation of genes related to hyphal growth, cell wall remodeling, cell cycle progression, and osmolyte synthesis, suggesting the coordinated modulation of multiple cellular processes. These findings provide the mechanistic link between epigenetic modification induced HHP-response changes and regulation in hadal fungi. Our study not only advances understanding of hadal fungal response to dual stressors but also unlocks new possibilities for harnessing their stress-driven metabolic versatility for biotechnological applications. Full article

(This article belongs to the Section Environmental and Ecological Interactions of Fungi)

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16 pages, 2071 KB

Open AccessArticle

Potential Protective Role of Amphibian Skin Bacteria Against Water Mold Saprolegnia spp.

by Sara Costa, Diogo Neves Proença, Artur Alves, Paula V. Morais and Isabel Lopes

J. Fungi 2025, 11(9), 649; https://doi.org/10.3390/jof11090649 - 2 Sep 2025

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Abstract

Amphibian populations have experienced a severe decline over the past 40 years, driven primarily by environmental pollution, habitat destruction, climate change, and disease. This work reports, for the first time, saprolegniosis in Pelophylax perezi egg masses and saprolegniosis in amphibians in Portugal. After [...] Read more.

Amphibian populations have experienced a severe decline over the past 40 years, driven primarily by environmental pollution, habitat destruction, climate change, and disease. This work reports, for the first time, saprolegniosis in Pelophylax perezi egg masses and saprolegniosis in amphibians in Portugal. After isolation and phylogenetic analysis, the pathogen was identified as Saprolegnia australis. Following this, the present work intended to screen a collection of P. perezi skin bacteria for the existence of bacterial strains with inhibitory action against the newly identified S. australis SC1 and two other species, Saprolegnia diclina SAP 1010 UE and Saprolegnia australis SAP 1581 UE. The results showed that various bacterial species could inhibit the growth of these three species of oomycetes. Bacteria with the most significant antagonistic action against Saprolegnia spp. predominantly belonged to the genus Bacillus, followed by Serratia, Pseudomonas, and Aeromonas. Despite variations in bacterial diversity among frog populations, the present study also demonstrated the presence of bacteria on frogs’ skin that were capable of inhibiting Saprolegnia spp., as evidenced by in vitro challenge assays. These findings highlight the protective function of bacteria present in amphibian skin. The observed bacterial diversity may contribute to the metabolic redundancy of the frog skin microbiome, helping to maintain its functional capacity despite shifts in the community composition. Additionally, the study found that, when providing a more advantageous environment for pathogen growth—in this case a peptone–glucose (PG) medium instead of R2A—the percentage of bacteria with moderate-to-strong antagonistic activity dropped by 13% to 4%. In conclusion, the presence of bacteria capable of inhibiting Saprolegnia spp. in adult individuals and across different environmental conditions may contribute to lowering the susceptibility of frog adults towards Saprolegnia spp., compared with that in the early stages of development, like the tadpole or egg stages. Full article

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

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15 pages, 419 KB

Open AccessArticle

Isavuconazole Therapy for Patients with Hematologic Diseases and Hematopoietic Cell Transplantation with and Without Breakthrough Invasive Fungal Infections

by Fabián Herrera, Diego Torres, Gustavo Mendez, Noelia Mañez, Rosana Jordán, Adriana Manzur, Myrna Cabral, Manuel Alderete, Natalia García Allende, José Benso, Claudia Salgueira, María Laura Pereyra, Hugo Peretti, Carla Niveyro, Maximiliano Castro, Federico Pollastrelli, Silvina García Rojas, Juan Dapás, Agustina Risso Patrón, Verónica Fernández, Rocío Gago and Javier Afeltra Show full author list Hide full author list

J. Fungi 2025, 11(9), 648; https://doi.org/10.3390/jof11090648 - 1 Sep 2025

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Abstract

There are no data available on the effectiveness and safety of isavuconazole (ISA) for treating breakthrough invasive fungal infections (bIFIs). A retrospective and prospective cohort study was conducted between January 2020 and March 2025 in 13 centers in Argentina. Hematologic diseases (HD) and [...] Read more.

There are no data available on the effectiveness and safety of isavuconazole (ISA) for treating breakthrough invasive fungal infections (bIFIs). A retrospective and prospective cohort study was conducted between January 2020 and March 2025 in 13 centers in Argentina. Hematologic diseases (HD) and hematopoietic cell transplantation (HCT) patients who received ISA for IFI were included and followed for 12 weeks. Patients with proven and probable bIFIs and non-bIFIs were compared. One hundred and sixty-three patients were included. IFIs were classified as proven (13.5%), probable (26.9%) and possible (59.5%). Among 66 proven and probable IFIs, 53% were bIFIs, with aspergillosis and mucormycosis being the most common. Twenty-three (34.8%) patients had acute myelogenous leukemia, and 40.9% had received HCT. Forty-eight (72.7%) patients experienced neutropenia, with a median duration of 26 days (interquartile range [IQR] 16–44). Fluconazole and posaconazole were the most frequently received antifungal prophylaxis. ISA was prescribed as first-line therapy in 31 (46.9%) patients. The other 35 received ISA as a continuation therapy, mainly as a step-down therapy after liposomal amphotericin B. Four (6.1%) patients developed adverse effects, and one discontinued ISA. The 90-day overall clinical response between patients with bIFI vs. non-bIFI was 91.4% vs. 70.9% (p = 0.052). The 90-day overall and IFI-related mortality rates were, respectively, 11.4% vs. 32.3% (p = 0.068) and 5.7% vs. 9.7% (p = 0.659). The study data evidence ISA effectiveness and safety for the treatment of HD and HCT patients with and without bIFIs. Full article

(This article belongs to the Special Issue Personalized Mycology)

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18 pages, 5056 KB

Open AccessArticle

The First Whole Genome Sequence and Methylation Profile of Gerronema lapidescens QL01

by Yanming Qiao, Zhiyuan Jia, Yuying Liu, Na Zhang, Chun Luo, Lina Meng, Yajie Cheng, Minglei Li, Xiuchao Xie and Jianzhao Qi

J. Fungi 2025, 11(9), 647; https://doi.org/10.3390/jof11090647 - 1 Sep 2025

Viewed by 454

Abstract

Gerronema lapidescens (Lei Wan), a valued medicinal basidiomycete traditionally employed for antiparasitic and digestive ailments, faces severe conservation threats due to unsustainable wild harvesting and the absence of reliable cultivation protocols. To address this crisis and unlock its pharmacotherapeutic potential, we present the [...] Read more.

Gerronema lapidescens (Lei Wan), a valued medicinal basidiomycete traditionally employed for antiparasitic and digestive ailments, faces severe conservation threats due to unsustainable wild harvesting and the absence of reliable cultivation protocols. To address this crisis and unlock its pharmacotherapeutic potential, we present the first chromosome-scale genome assembly and comprehensive methylome profile for the wild strain G. lapidescens QL01, domesticated from the Qinling Mountains. A multi-platform sequencing strategy (Illumina and PacBio HiFi) yielded a high-quality 82.23 Mb assembly anchored to 11 chromosomes, exhibiting high completeness (98.4% BUSCO) and 46.03% GC content. Annotation predicted 15,847 protein-coding genes, with 81.12% functionally assigned. Genome-wide analysis identified 8.46 million high-confidence single-nucleotide polymorphisms (SNPs). Notably, methylation profiling revealed 3.25 million methylation events, with elevated densities on chromosomes 4, 9, and 10, suggesting roles in gene silencing and environmental adaptation. Phylogenomic analyses clarified the evolutionary status of G. lapidescens, whilst gene family evolution indicated moderate dynamics reflecting niche adaptation. Carbohydrate-Active enzymes (CAZymes) analysis identified 521 enzymes, including 211 Glycoside Hydrolases (GHs), consistent with organic matter degradation. Additionally, 3279 SSRs were catalogued as molecular markers. This foundational resource elucidates G. lapidescens’s genetic architecture, epigenetic regulation, evolutionary history, and enzymatic toolkit, underpinning future research into medicinal compound biosynthesis, environmental adaptation, germplasm conservation, and sustainable cultivation. Full article

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16 pages, 6039 KB

Open AccessArticle

Blue Light Receptor WC-2 Regulates Ganoderic Acid Biosynthesis in Ganoderma lingzhi

by Yan Xu, Xiong-Min Huang, Zi-Xu Wang, Ying-Jie Zhao, Dong-Mei Lv and Jun-Wei Xu

J. Fungi 2025, 11(9), 646; https://doi.org/10.3390/jof11090646 - 1 Sep 2025

Viewed by 538

Abstract

Ganoderic acid (GA) is a key bioactive component with pharmacological properties that is found in Ganoderma lingzhi, a renowned medicinal mushroom. Currently, the regulatory mechanisms underlying GA biosynthesis in G. lingzhi remain to be further elucidated. In this study, blue light induction [...] Read more.

Ganoderic acid (GA) is a key bioactive component with pharmacological properties that is found in Ganoderma lingzhi, a renowned medicinal mushroom. Currently, the regulatory mechanisms underlying GA biosynthesis in G. lingzhi remain to be further elucidated. In this study, blue light induction was found to significantly enhance the GA content in G. lingzhi. To explore the regulatory mechanism of GA biosynthesis in response to blue light, the blue light receptor WC-2 was identified, and its regulatory role was characterized. The deletion of wc-2 resulted in a significant reduction in both GA content and the accumulation of intermediates compared to the wild-type control strain, largely due to the strong downregulation of key GA biosynthetic genes. Additionally, decreased asexual spore production and reduced expression of sporulation-specific genes were observed with the deletion of wc-2. The overexpression of wc-2 led to greatly enhanced GA accumulation. Under blue light induction, the maximum contents of GA-Mk, GA-T, GA-S, and GA-Me were 2.27-, 2.51-, 2.49-, and 2.08-fold higher, respectively, compared to the control kept in darkness. These results demonstrate that the blue light receptor WC-2 functions as a positive regulator of GA biosynthesis in G. lingzhi, influencing the expression of genes involved in GA biosynthesis and asexual spore production, thereby advancing our understanding of the intricate regulatory network of GA biosynthesis. Full article

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