Journal of Fungi

21 pages, 1339 KiB

Open AccessArticle

Toxicity Assessment and Antifungal Potential of Copper(II) and Silver(I) Complexes with 1,10-Phenanthroline-5,6-dione Against Drug-Resistant Clinical Isolates of Cryptococcus gattii and Cryptococcus neoformans

by Lucas Giovanini, Ana Lucia Casemiro, Larissa S. Corrêa, Matheus Mendes, Thaís P. Mello, Lucieri O. P. Souza, Luis Gabriel Wagner, Christiane Fernandes, Matheus M. Pereira, Lais C. S. V. de Souza, Andrea R. S. Baptista, Josué de Moraes, Malachy McCann, Marta H. Branquinha and André L. S. Santos

J. Fungi 2025, 11(6), 436; https://doi.org/10.3390/jof11060436 - 6 Jun 2025

Abstract

The World Health Organization included Cryptococcus neoformans and Cryptococcus gattii in its priority fungal pathogen list due to their high mortality rates and frequent treatment failures. These facts have driven research toward the discovery of new compounds for the treatment of cryptococcosis. In [...] Read more.

The World Health Organization included Cryptococcus neoformans and Cryptococcus gattii in its priority fungal pathogen list due to their high mortality rates and frequent treatment failures. These facts have driven research toward the discovery of new compounds for the treatment of cryptococcosis. In this study, we investigated the therapeutic potential of two complexes, [Cu(phendione)₃](ClO₄)₂·4H₂O (Cu-phendione) and [Ag(phendione)₂]ClO₄ (Ag-phendione), against drug-resistant clinical isolates of C. gattii and C. neoformans. Both complexes demonstrated anti-Cryptococcus activity, with Cu-phendione exhibiting minimum inhibitory concentration (MIC) values of 6.25 μM for C. gattii and 3.125 μM for C. neoformans, while Ag-phendione showed an MIC of 1.56 μM for both Cryptococcus species. Notably, both Cu-phendione and Ag-phendione complexes exhibited enhanced antifungal activity against reference strains of C. neoformans and C. gattii. In silico analysis identified both complexes as highly promising, exhibiting good oral bioavailability, high gastrointestinal absorption, and moderate skin permeability. Moreover, neither complex demonstrated toxicity toward sheep erythrocytes at concentrations up to 62.5 μM, with a selectivity index (SI) exceeding 10 for Cu-phendione and 40 for Ag-phendione. In vivo testing using the Galleria mellonella model demonstrated that both complexes were non-toxic, with 100% larval survival at concentrations up to 1000 μM and SI exceeding 160 following a single administration. Interestingly, larvae exposed to Cu-phendione at concentrations of 15.6–31.25 μM exhibited a significant increase in the density of hemocytes, the immune cells responsible for defense in invertebrates. Furthermore, multiple treatments with 62.5 μM of complexes caused either no larval mortality, hemocyte alterations, or changes in silk production or coloration, indicating a lack of toxicity. These findings suggest that Cu-phendione and Ag-phendione may serve as promising antifungal alternatives against Cryptococcus, with minimal host toxicity. Full article

(This article belongs to the Special Issue Fungal Infections: Immune Defenses and New Therapeutic Strategies)

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9 pages, 598 KiB

Open AccessEditorial

Commemorating the Landmark Advances in Our Understanding of Mucormycosis by Dimitrios P. Kontoyiannis

by Thomas J. Walsh

J. Fungi 2025, 11(6), 435; https://doi.org/10.3390/jof11060435 - 6 Jun 2025

Abstract

Writing with the perspective of a mentor, friend, and colleague, I am elated to contribute to this commemorative issue of the Journal of Fungi, which is dedicated to the landmark contributions of Dr. Dimitrios P. Kontoyiannis, who has greatly advanced our understanding [...] Read more.

Writing with the perspective of a mentor, friend, and colleague, I am elated to contribute to this commemorative issue of the Journal of Fungi, which is dedicated to the landmark contributions of Dr. Dimitrios P. Kontoyiannis, who has greatly advanced our understanding of the epidemiology, pathogenesis, diagnosis, and treatment of mucormycosis. Through his efforts and leadership, the four pillars in the management of mucormycosis have been made much stronger: early diagnosis, the rapid initiation of antifungal therapy, augmentation of the host’s defenses, and surgical intervention. Full article

(This article belongs to the Special Issue Twenty-Five Years in Mucormycosis Research: A Themed Issue Honoring the Contributions of Professor Dimitrios P. Kontoyiannis)

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14 pages, 785 KiB

Open AccessReview

Advancements in Diagnosing Talaromycosis: Exploring Novel Strategies and Emerging Technologies

by Yihui Wang, Xiaoyue Wang, Liyan Xi and Sha Lu

J. Fungi 2025, 11(6), 434; https://doi.org/10.3390/jof11060434 - 6 Jun 2025

Abstract

Talaromycosis (TM) is an invasive fungal infection caused by Talaromyces marneffei (T. marneffei). It has high morbidity and mortality rates, particularly among immunocompromised people. Globally, approximately 17,300 cases and 4900 deaths are reported annually. TM often has vague clinical signs with [...] Read more.

Talaromycosis (TM) is an invasive fungal infection caused by Talaromyces marneffei (T. marneffei). It has high morbidity and mortality rates, particularly among immunocompromised people. Globally, approximately 17,300 cases and 4900 deaths are reported annually. TM often has vague clinical signs with limited current tests, leading to misdiagnosis, incorrect treatments, or the long-term use of expensive antifungal drugs, which raises healthcare costs and patient risks. Although accurate diagnosis is key for starting the right antifungal therapy and improving outcomes, there are not enough reliable and fast tests. Recent progress with monoclonal antibodies (mAbs) that have high specificity for antigens may boost diagnostic accuracy and cut misdiagnosis rates. This review explores current ways to diagnose TM, including culture, histopathology, and molecular methods such as polymerase chain reaction (PCR) and antigen detection. We also discuss the merits and weaknesses of each method and highlight how mAbs may help diagnose TM. We searched PubMed, Web of Science, and Google Scholar for English-language papers (1990—1 January 2025) using “Talaromycosis” OR “Talaromyces marneffei” plus diagnostic terms (‘diagnosis’, ‘molecular diagnostics’, ‘monoclonal antibody’, ‘lateral flow’, ‘antigen detection’, and ‘fungal diagnosis’). After deduplication and relevance screening, studies with original data or substantive discussion on T. marneffei diagnostics or mAb development were retained to inform this narrative review. Full article

(This article belongs to the Special Issue New Perspectives on Fungal Immunology)

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18 pages, 5964 KiB

Open AccessArticle

Species Identification and Fungicide Sensitivity of Fusarium spp. Causing Peanut Root Rot in Henan, China

by Min Li, Liting Chen, Qinqin Wang, Leiming He, Yun Duan, Xuewei Mao and Lin Zhou

J. Fungi 2025, 11(6), 433; https://doi.org/10.3390/jof11060433 - 6 Jun 2025

Abstract

Peanut Root Rot (PRR) is a devastating disease that significantly limits peanut production worldwide. Although PRR has been frequently reported in Henan Province of China, the predominant Fusarium species and their sensitivity to different fungicides remain unclear. Between 2021 and 2023, we surveyed [...] Read more.

Peanut Root Rot (PRR) is a devastating disease that significantly limits peanut production worldwide. Although PRR has been frequently reported in Henan Province of China, the predominant Fusarium species and their sensitivity to different fungicides remain unclear. Between 2021 and 2023, we surveyed 81 peanut fields across 17 cities in Henan Province, China, to assess PRR prevalence and Fusarium species distribution. A total of 1131 Fusarium isolates were identified based on the morphological characters and phylogenetic analyses and classified into 11 recognized Fusarium species: F. solani (56.06%), F. oxysporum (20.87%), F. neocosmosporiellum (13.62%), F. proliferatum (4.69%), F. acuminatum (1.33%), F. commune (1.15%), F. graminearum (1.06%), F. pseudograminearum (0.35%), F. ipomoeae (0.35%), F. lacertarum (0.26%), and F. armeniacum (0.26%). Pathogenicity assessments showed that all 11 Fusarium species were capable of causing PRR, with F. solani exhibiting the highest isolation frequency and widespread distribution in all areas. Furthermore, the four Fusarium species (F. solani, F. oxysporum, F. neocosmosporiellum, and F. proliferatum) were highly sensitive to the six fungicides, including prochloraz (EC₅₀ values of 0.02 ± 0.00~0.06 ± 0.01 mg/L), pydiflumetofen (EC₅₀ values of 0.31 ± 0.07~0.67 ± 0.06 mg/L), tetramycin (EC₅₀ values of 0.11 ± 0.02~0.58 ± 0.08 mg/L), tebuconazole (EC₅₀ values of 0.26 ± 0.07~0.65 ± 0.10 mg/L), prothioconazole (EC₅₀ values of 1.14 ± 0.16~3.15 ± 0.81 mg/L), and difenoconazole (EC₅₀ values of 0.62 ± 0.12~3.58 ± 0.76 mg/L). This comprehensive study is the first systematic documentation on the prevalence, virulence, and fungicide sensitivity of PRR pathogens in Henan Province. The findings of the current study will provide a theoretical basis for the effective management of peanut root rot in Henan, China. Full article

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27 pages, 2332 KiB

Open AccessArticle

Conversion of Soluble Compounds in Distillery Wastewater into Fungal Biomass and Metabolites Using Australian Ganoderma Isolates

by Aline D. O. Campos, Hashini J. Wahalathanthrige, Shane Russell, Mark D. Harrison and Peter James Strong

J. Fungi 2025, 11(6), 432; https://doi.org/10.3390/jof11060432 - 6 Jun 2025

Abstract

Stillage is an acidic residue from ethanol production that has a high carbon load. Here, Ganoderma isolates were assessed for the treatment of rum stillage while producing biomass and associated metabolites. Isolates grew in 25% raw stillage, removing up to 73% of soluble [...] Read more.

Stillage is an acidic residue from ethanol production that has a high carbon load. Here, Ganoderma isolates were assessed for the treatment of rum stillage while producing biomass and associated metabolites. Isolates grew in 25% raw stillage, removing up to 73% of soluble organic carbon, 77% soluble nitrogen, and 74% phenolic compounds. Isolate G2 demonstrated faster removal of organic carbon and nitrogen. Biomass and metabolite production were benchmarked against a nutrient medium. In stillage, maximum values of the following were obtained: 8.2 g·L⁻¹ biomass; 52.8% crude protein; 22.1 mg·g⁻¹ extractable protein; antioxidants of 17.2 mg TE·g⁻¹ (2,2′-azino-di-(3-ethylbenzothiazoline-6-sulfonic acid), ABTS) and 16.6 µmol Fe²⁺·g⁻¹ (ferric reducing antioxidant power, FRAP); 2.9 mg GAE·g⁻¹ phenolic compounds (gallic acid equivalents); 1.2% lipids; and 11% β-glucans. In the nutrient medium, the following were obtained: 6.9 g·L⁻¹ biomass; 56.4% crude protein; 38.7 mg·g⁻¹ extractable protein; antioxidants of 24.9 mg TE·g⁻¹ (ABTS) and 25.9 µmol Fe²⁺·g⁻¹ (FRAP); 6.0 mg GAE·g⁻¹ phenolic compounds; 0.7% lipids; and 13% β-glucans. To our knowledge, this is the first report detailing the biomass metabolite content of Ganoderma mycelium using rum stillage. The production of edible biomass containing bioactive products demonstrates the potential of using Ganoderma strains to valorize this residue. Full article

(This article belongs to the Section Fungi in Agriculture and Biotechnology)

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26 pages, 38794 KiB

Open AccessArticle

New Contributions to the Species Diversity of the Genus Hydnum (Hydnaceae, Cantharellales) in China: Four New Taxa and Newly Recorded Species

by Yong-Lan Tuo, Libo Wang, Xue-Fei Li, Hang Chu, Minghao Liu, Jiajun Hu, Zheng-Xiang Qi, Xiao Li, Yu Li and Bo Zhang

J. Fungi 2025, 11(6), 431; https://doi.org/10.3390/jof11060431 - 4 Jun 2025

Abstract

Hydnum, a well-defined genus in the family Hydnaceae (order Cantharellales), is characterized by its distinctive spine-bearing hymenophores. In this study, we performed a multi-locus phylogenetic analysis (ITS-nrLSU-tef1) of Hydnum species. Integrating morphological examinations and phylogenetic evidence, we identified and [...] Read more.

Hydnum, a well-defined genus in the family Hydnaceae (order Cantharellales), is characterized by its distinctive spine-bearing hymenophores. In this study, we performed a multi-locus phylogenetic analysis (ITS-nrLSU-tef1) of Hydnum species. Integrating morphological examinations and phylogenetic evidence, we identified and delineated five Hydnum species in China, which include four novel species (Hydnum crassipedum, H. albomarginatum, H. fulvostriatum, and H. bifurcatum) and the first record (H. orientalbidum) in Anhui Province. This study provides a comprehensive morphological description (including macroscopic morphology and microscopic structure), hand-drawn illustrations (encompassing basidiocarps, basidiospores, basidia, and pileipellis hyphae), morphological comparative analysis with similar species, and comparative phylogenetic analysis with related taxa. Furthermore, we developed a dichotomous key for identifying Hydnum species distributed in China. Full article

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

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9 pages, 685 KiB

Open AccessArticle

An Optimized In-House Protocol for Cryptococcus neoformans DNA Extraction from Whole Blood: “Comparison of Lysis Buffer and Ox-Bile Methods”

by Fredrickson B Wasswa, Kennedy Kassaza, Kirsten Nielsen and Joel Bazira

J. Fungi 2025, 11(6), 430; https://doi.org/10.3390/jof11060430 - 4 Jun 2025

Abstract

Cryptococcus neoformans (C. neoformans) is a capsulated yeast that enters the body through inhalation and migrates via the bloodstream to the central nervous system, causing cryptococcal meningitis. Diagnosis methods are culture, serology, and India ink staining, which require cerebrospinal fluid (CSF) or whole blood. [...] Read more.

Cryptococcus neoformans (C. neoformans) is a capsulated yeast that enters the body through inhalation and migrates via the bloodstream to the central nervous system, causing cryptococcal meningitis. Diagnosis methods are culture, serology, and India ink staining, which require cerebrospinal fluid (CSF) or whole blood. Molecular methods are used for epidemiological studies and require expensive commercial DNA extraction kits. This study aimed to develop an economical in-house method for extracting C. neoformans DNA from whole blood. C. neoformans cells of varying McFarland standards were spiked into expired blood, then lysed using laboratory-prepared lysis buffer and ox-bile solution, followed by organic DNA extraction. Ordinary PCR targeting the CNAG 04922 gene was performed. To determine the limit of detection, serial dilutions of C. neoformans were made, and DNA extraction was performed on other parts cultured on yeast extract peptone dextrose agar to determine colony-forming units (CFU). The lysis buffer method successfully extracted DNA from as low as the average of 62 CFU in 0.9 mL of expired blood with superior quality and high yield compared to ox-bile. The lysis buffer method yielded higher DNA quality and quantity than ox-bile and detected low concentrations of C. neoformans in expired blood. This method presents a cost-effective alternative for molecular diagnosis in resource-limited settings. Full article

(This article belongs to the Special Issue Prevention and Treatment of Cryptococcal Meningitis)

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21 pages, 11439 KiB

Open AccessArticle

CBC Complex Regulates Hyphal Growth, Sclerotial Quantity, and Pathogenicity in the Necrotrophic Fungus Botrytis cinerea

by Yinshan Zhang, Xueting Chen, Guihua Li, Qingming Qin, Mingzhe Zhang and Jianchun Qin

J. Fungi 2025, 11(6), 429; https://doi.org/10.3390/jof11060429 - 2 Jun 2025

Abstract

The cap-binding protein complex (CBC), comprising Cbp20 and Cbp80, is crucial for gene expression, yet its role in the notorious crop pathogen Botrytis cinerea remains unclear. Immunoprecipitation coupled with LC-MS/MS demonstrated that BcCbp20 interacts with BcCbp80. Yeast two-hybrid, GST pull-down, and Split-luciferase complementation [...] Read more.

The cap-binding protein complex (CBC), comprising Cbp20 and Cbp80, is crucial for gene expression, yet its role in the notorious crop pathogen Botrytis cinerea remains unclear. Immunoprecipitation coupled with LC-MS/MS demonstrated that BcCbp20 interacts with BcCbp80. Yeast two-hybrid, GST pull-down, and Split-luciferase complementation assays confirmed that the conserved RNA recognition motif (RRM, 54–127 aa) of BcCbp20 and the N-terminal MIF4G domain (1–370 aa, 1–577 aa) of BcCbp80 constitute the core interaction regions. Genetic transformation experiments revealed that BcCBP80 exerts a more dominant role than BcCBP20 in regulating hyphal morphology, growth rate, conidiophore development, and conidial yield. Furthermore, BcCBP20 and BcCBP80 differentially regulate sclerotium formation to maintain sclerotial quantity. Based on pathogenicity assays, BcCBP80 associated with infection cushion development, with this phenotypic alteration possibly being among the factors correlated with altered pathogenicity. However, the increased sensitivity of ΔBccbp20 to various stress factors may be the primary reason for the diminished pathogenicity. Taken together, these results indicate that BcCBP20 and BcCBP80 play important roles in multiple aspects of B. cinerea growth, development, stress response, and pathogenicity. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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21 pages, 2936 KiB

Open AccessArticle

Adaptation Under Pressure: Resistance and Stress Response Interplay in Clinical Aspergillus fumigatus Isolates

by Ivana Segéňová, Ján Víglaš, Tomáš Pagáč and Petra Olejníková

J. Fungi 2025, 11(6), 428; https://doi.org/10.3390/jof11060428 - 2 Jun 2025

Abstract

Understanding the interplay between antifungal resistance, stress adaptation, and virulence in Aspergillus fumigatus is critical for more effective treatment outcomes. In this study, we investigate six clinical isolates of A. fumigatus from the hospitals of the Czech Republic, focusing on their resistance profiles, [...] Read more.

Understanding the interplay between antifungal resistance, stress adaptation, and virulence in Aspergillus fumigatus is critical for more effective treatment outcomes. In this study, we investigate six clinical isolates of A. fumigatus from the hospitals of the Czech Republic, focusing on their resistance profiles, stress responses, and survival mechanisms under antifungal pressure. Notably, we have shown that azole-susceptible strains were able to form persister cells under supra-MIC concentrations, highlighting an emerging non-genetic survival mechanism. Stress response profiling demonstrated differential susceptibility to agents targeting signal transduction pathways, as principal component analysis proved that even azole-resistant strains might rely on these pathways. Combinatorial treatment with posaconazole and dithiothreitol enhanced antifungal efficacy regardless of the susceptibility of the strains. Fitness assays revealed that azole resistance imposed a competitive disadvantage in azole-free conditions. In vivo virulence assessment in Galleria mellonella larvae revealed strain-specific pathogenicity that did not directly correlate with resistance. Together, our findings illustrate the multifactorial nature of fungal survival and emphasize that stress adaptation, tolerance, and persistence significantly affect treatment efficacy and outcomes, even in the absence of classical resistance mechanisms. Targeting stress response pathways emerges as a promising strategy to enhance the efficacy of existing antifungal agents and manage resistance in A. fumigatus. Full article

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

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13 pages, 983 KiB

Open AccessArticle

Exploring the Antifungal Potential of Lawsone-Loaded Mesoporous Silica Nanoparticles Against Candida albicans and Candida glabrata: Growth Inhibition and Biofilm Disruption

by Fatemeh Nikoomanesh, Mahsa Sedighi, Mahdi Mahmmoodi Bourang, Mitra Rafiee, André Luis Souza dos Santos and Maryam Roudbary

J. Fungi 2025, 11(6), 427; https://doi.org/10.3390/jof11060427 - 1 Jun 2025

Abstract

The incidence of fungal infections is significantly rising, posing a challenge due to the limited class of antifungal drugs. There is a necessity to combat emerging resistant fungal infections by developing novel antifungal agents. This study aimed to evaluate the antifungal effects of [...] Read more.

The incidence of fungal infections is significantly rising, posing a challenge due to the limited class of antifungal drugs. There is a necessity to combat emerging resistant fungal infections by developing novel antifungal agents. This study aimed to evaluate the antifungal effects of lawsone (LAW), a natural component extracted from herbal medicine, and LAW-loaded mesoporous silica nanoparticles (LAW-MSNs) on growth, biofilm formation, and expression of ALS1 and EPA1 genes contributing to cell adhesion of Candida spp. Twenty C. albicans and twenty C. glabrata isolates, including ten fluconazole-resistant and ten fluconazole-susceptible isolates, were examined. The findings of the study indicated that LAW and LAW-MSNs inhibited Candida isolates growth at MIC range of 0.31–>5 µg/mL and significantly reduced biofilm formation in C. albicans and C. glabrata. Moreover, both LAW and LAW-MSNs downregulated the expression of the adhesion genes ALS1 and EPA1 in C. albicans and C. glabrata. Based on the obtained findings, LAW emerged as a promising antifungal candidate. However, the nano-formulation (LAW-MSNs) improved its antifungal properties. Full article

(This article belongs to the Special Issue Antifungal Resistance Mechanisms from a One Health Perspective)

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17 pages, 4454 KiB

Open AccessArticle

UvPomt, an O-Methyltransferase Interacting with UvMAT1-1-3, for Regulating Growth, Stress Tolerance, and Virulence in Ustilaginoidea virens

by Zhi Li, Junjie Yu, Mina Yu, Huijuan Cao, Tianqiao Song, Shuchen Wang, Zhongqiang Qi, Yan Du, Xiayan Pan and Yongfeng Liu

J. Fungi 2025, 11(6), 426; https://doi.org/10.3390/jof11060426 - 31 May 2025

Abstract

Rice false smut (RFS), caused by Ustilaginoidea virens (teleomorph: Villosiclava virens), is a devastating fungal disease that severely impacts global rice production by reducing both yield and grain quality. While the mating-type gene UvMAT1-1-3 is known to regulate both sexual and asexual [...] Read more.

Rice false smut (RFS), caused by Ustilaginoidea virens (teleomorph: Villosiclava virens), is a devastating fungal disease that severely impacts global rice production by reducing both yield and grain quality. While the mating-type gene UvMAT1-1-3 is known to regulate both sexual and asexual reproduction in U. virens, its regulatory mechanism remains unclear. In this study, an interacting protein of UvMAT1-1-3, a putative O-methyltransferase (UvPomt), was identified using yeast two-hybrid screening, and its interaction was further confirmed by co-localization microscopy. A quantitative reverse transcription PCR (qRT-PCR) analysis showed a significant up-regulation of UvPomt expression during the early infection stage of U. virens. Functional characterization revealed that ΔUvPomt mutants exhibited reduced fungal pathogenicity, vegetative growth, conidial production, and stress adaptation. Furthermore, a Western blot analysis revealed that the UvMAT1-1-3 protein level was reduced in ΔUvPomt mutants, whereas the UvPomt protein level was elevated in ΔUvMAT1-1-3 mutants. Taken together, these findings suggest a potential reciprocal regulation between UvPomt and UvMAT1-1-3. Understanding UvPomt’s function could provide a potential molecular target for controlling RFS disease. Full article

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

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8 pages, 2203 KiB

Open AccessCommunication

CRYPTOMICSDB: Revealing the Molecular Landscape of Cryptococcosis

by Yohana Porto Calegari-Alves, Camila Innocente-Alves, Renata Pereira Costa, Aline Martins Faustino, Karyn Scheffler Schirma Farias, Mateus Boiani, Bruno Samuel Ardenghi Gonçalves, Marcio Dorn, Walter Orlando Beys-da-Silva and Lucélia Santi

J. Fungi 2025, 11(6), 425; https://doi.org/10.3390/jof11060425 - 31 May 2025

Abstract

Cryptococcosis is a serious fungal infection mainly caused by two Cryptococcus species, Cryptococcus gattii and Cryptococcus neoformans species complexes. Even though it is considered a dangerous disease, this infection is also neglected worldwide and its research is not adequately funded. The molecular understanding [...] Read more.

Cryptococcosis is a serious fungal infection mainly caused by two Cryptococcus species, Cryptococcus gattii and Cryptococcus neoformans species complexes. Even though it is considered a dangerous disease, this infection is also neglected worldwide and its research is not adequately funded. The molecular understanding of the infection, which could help in the development of specific treatments and appropriate management, is hampered, as molecular data are not of easy access. With that purpose, our group developed a Cryptococcus molecular database, grouping published molecular data on gene and protein differential expression that occurred due to the infection. CRYPTOMICSDB presents a user-friendly interface, and users can search for both pathogen or host information and visualize data on experimental approaches, animal models or cell culture, Cryptococcus species and strain, genes and proteins. The database features 19,462 and 986,507 total genes related to the pathogen and host views, respectively. CRYPTOMICSDB is a powerful tool that can help health workers and microbiology researchers to better understand the molecular impact caused by cryptococcosis infection process. Full article

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

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25 pages, 2090 KiB

Open AccessArticle

The Growth, Pathogenesis, and Secondary Metabolism of Fusarium verticillioides Are Epigenetically Modulated by Putative Heterochromatin Protein 1 (FvHP1)

by Andrés G. Jacquat, Natalia S. Podio, María Carmen Cañizares, Pilar A. Velez, Martín G. Theumer, Vanessa A. Areco, María Dolores Garcia-Pedrajas and José S. Dambolena

J. Fungi 2025, 11(6), 424; https://doi.org/10.3390/jof11060424 - 31 May 2025

Abstract

Fusarium verticillioides is a globally prevalent phytopathogenic fungus responsible for multiple diseases in maize and a major producer of the mycotoxin fumonisin B1 (FB1), a highly toxic fungal secondary metabolite (FSM). The histone code, which includes reversible modifications such as acetylation and methylation, [...] Read more.

Fusarium verticillioides is a globally prevalent phytopathogenic fungus responsible for multiple diseases in maize and a major producer of the mycotoxin fumonisin B1 (FB1), a highly toxic fungal secondary metabolite (FSM). The histone code, which includes reversible modifications such as acetylation and methylation, plays a critical role in regulating chromatin structure and gene expression. In fungi, di- and tri-methylation of histone H3 at lysine 9 (H3K9me2/3) serves as a key epigenetic mark associated with heterochromatin formation and transcriptional repression. In this study, we identified and characterized a putative heterochromatin protein 1 (HP1) family member in F. verticillioides, designated FvHP1, based on conserved domain architecture and phylogenetic analyses. FvHP1 retains essential residues required for H3K9me2/3 recognition, supporting its functional conservation within the HP1 protein family. Phenotypic analysis of the ΔFvHP1 mutant revealed impaired vegetative growth, reduced conidiation and virulence, and altered FB1 mycotoxin production. Additionally, the accumulation of red pigment in the mutant was linked to the deregulation of secondary metabolism, specifically the overproduction of fusarubin-type naphthoquinones, such as 8-O-methylnectriafurone. These results support the role of FvHP1 in facultative heterochromatin-mediated repression of sub-telomeric biosynthetic gene clusters, including the pigment-associated PGL1 cluster. Our findings provide new insights into the epigenetic regulation of fungal pathogenicity and metabolite production, as well as the first evidence of a functional HP1 homolog in F. verticillioides. Full article

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

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16 pages, 5155 KiB

Open AccessArticle

Histopathological Study of Host–Pathogen Interactions Between Cordyceps javanica PSUC002 and Hypothenemus hampei

by Sinlapachai Senarat, Peerasak Bunsap, Pisit Poolprasert, Anjaree Inchan, Natthawut Charoenphon, Peerapon Sornying and Narit Thaochan

J. Fungi 2025, 11(6), 423; https://doi.org/10.3390/jof11060423 - 30 May 2025

Abstract

The use of entomopathogenic fungi (EPF), such as Cordyceps javanica, to reduce insect pest populations is gaining traction since it is an environmentally safe approach that can control many pests at different life stages. Here, we focus on the histopathology of the [...] Read more.

The use of entomopathogenic fungi (EPF), such as Cordyceps javanica, to reduce insect pest populations is gaining traction since it is an environmentally safe approach that can control many pests at different life stages. Here, we focus on the histopathology of the coffee berry borer, Hypothenemus hampei, infected by C. javanica. Morphological observation revealed that C. javanica conidia germinated within 12 h following inoculation according to light microscopic and ultrastructural levels. The fungus thoroughly penetrated the fat body and muscular tissue between 84 and 120 h post-inoculation. Transmission electron microscopy (TEM) confirmed the hyphal invasion of the cuticle at 12 h post-inoculation, with progressive tissue disruption and organelle degeneration, especially mitochondria and rough endoplasmic reticulum in adipocytes. All organelles were completely degenerated at 96 h post-inoculation. There was evidence of a connection between C. javanica activity and the coffee berry borer that might cause histopathological changes in the host defense against the pathogen, pointing to increased mortality and potential control of coffee berry borer in natural populations. Additionally, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) confirmed that apoptotic cells were slightly increased in the adipose tissue and integument of the coffee berry borer. The ability of C. javanica to fatally infect the coffee berry borer suggests that it could be deployed as a biological control agent in the field. Full article

(This article belongs to the Special Issue Current Trends in Mycological Research in Southeast Asia)

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50 pages, 1608 KiB

Open AccessReview

A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions

by Muyun Xie, Jing Wang, Feixiang Wang, Jinfeng Wang, Yunjin Yan, Kun Feng and Baixiong Chen

J. Fungi 2025, 11(6), 422; https://doi.org/10.3390/jof11060422 - 30 May 2025

Abstract

Edible fungi, a group of globally significant macrofungi, are highly valued for their unique flavors and substantial nutritional and medicinal properties. Understanding the molecular mechanisms governing their growth, development, gene function, biosynthesis of valuable compounds, and environmental adaptation is crucial for enhancing yield [...] Read more.

Edible fungi, a group of globally significant macrofungi, are highly valued for their unique flavors and substantial nutritional and medicinal properties. Understanding the molecular mechanisms governing their growth, development, gene function, biosynthesis of valuable compounds, and environmental adaptation is crucial for enhancing yield and quality, providing essential scientific support for industrial progress. Genomics, transcriptomics, and proteomics, as cornerstone life science technologies, offer powerful, integrated approaches to decipher genetic codes, reveal gene expression patterns, and elucidate complex metabolic networks in edible fungi. These advancements are transitioning research from traditional cultivation methods towards deeper molecular biology exploration. This review synthesizes key progress in applying genomics, transcriptomics, and proteomics to edible fungi, with a particular focus on metabolism-related research and the fundamentals of metabolic network construction. It discusses how these technologies, independently and in preliminary integration, uncover critical steps and regulatory mechanisms within endogenous metabolic pathways. While acknowledging the importance of metabolomics and epigenomics as cutting-edge areas, this review focuses on the “classical triad” of genomics, transcriptomics, and proteomics due to their technological maturity, data accessibility, and established application base in elucidating core metabolic mechanisms in edible fungi. The goal is to deepen the understanding of edible fungi metabolic mechanisms, providing a vital theoretical basis and practical insights for optimizing cultivation, enabling genetic improvement, harnessing bioactive substances, and promoting industrial upgrading, thereby boosting the overall efficiency and competitiveness of the edible fungi industry. Full article

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

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14 pages, 4510 KiB

Open AccessCommunication

Long-Read Draft Genome Sequences of Two Fusarium oxysporum f. sp. cubense Isolates from Banana (Musa spp.)

by Jiaman Sun, Jinzhong Zhang, Donald M. Gardiner, Peter van Dam, Gang Fu, Brett J. Ferguson, Elizabeth A. B. Aitken and Andrew Chen

J. Fungi 2025, 11(6), 421; https://doi.org/10.3390/jof11060421 - 30 May 2025

Abstract

Fusarium oxysporum f. sp. cubense (Foc) causes Fusarium wilt, a devastating epidemic disease that has caused widespread damage to banana crops worldwide. We report the draft genomes of Foc race 1 (16117) and Foc tropical race 4 (Fusarium odoratissimum) (CNSD1) isolates [...] Read more.

Fusarium oxysporum f. sp. cubense (Foc) causes Fusarium wilt, a devastating epidemic disease that has caused widespread damage to banana crops worldwide. We report the draft genomes of Foc race 1 (16117) and Foc tropical race 4 (Fusarium odoratissimum) (CNSD1) isolates from China, assembled using PacBio HiFi sequencing reads, with functional annotation performed. The strains group in distinct lineages within the Fusarium oxysporum species complex. This genetic resource will contribute towards understanding the pathogenicity and evolutionary dynamics of Foc populations in banana-growing regions around the world. Full article

(This article belongs to the Section Fungi in Agriculture and Biotechnology)

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16 pages, 5768 KiB

Open AccessArticle

Integrated Transcriptomics and Metabolomics Provide Insight into Degeneration-Related Molecular Mechanisms of Morchella importuna During Repeated Subculturing

by Wenyan Huo, Xuelian He, Yu Liu, Liguang Zhang, Lu Dai, Peng Qi, Ting Qiao, Suying Hu, Pengpeng Lu and Junzhi Li

J. Fungi 2025, 11(6), 420; https://doi.org/10.3390/jof11060420 - 30 May 2025

Abstract

This study investigated Morchella importuna strain degeneration during repeated subculturing and employed metabolomics, transcriptomics, and other techniques to explore its molecular mechanisms. Significant metabolic and transcriptional differences were observed between normal mycelia (NM) and degenerated mycelia (DG). Metabolomic analysis revealed 699 differentially expressed [...] Read more.

This study investigated Morchella importuna strain degeneration during repeated subculturing and employed metabolomics, transcriptomics, and other techniques to explore its molecular mechanisms. Significant metabolic and transcriptional differences were observed between normal mycelia (NM) and degenerated mycelia (DG). Metabolomic analysis revealed 699 differentially expressed metabolites (DEMs) that were predominantly enriched in secondary metabolite biosynthesis pathways, particularly flavonoids and indole alkaloids. Total flavonoid content was markedly higher in NM than in DG, with most flavonoid compounds showing reduced levels in degenerated strains. Transcriptomic profiling revealed 2691 differentially expressed genes (DEGs), primarily associated with metabolic pathways and genetic information processing. Integrated analysis showed that metabolic dynamics were regulated by DEGs, with pyruvate metabolism being significantly enriched. The FunBGCeX tool identified biosynthetic gene clusters (BGCs) in the M. importuna genome, highlighting the critical role of the non-reducing polyketide synthase (NR-PKS) gene in flavonoid biosynthesis. This gene exhibited significantly downregulated expression in DG strains. These findings indicate that M. importuna degeneration resulted from systemic dysregulation of gene expression networks and metabolic pathway reorganization. The results presented herein also provide theoretical insights into degeneration mechanisms and potential prevention strategies for this edible fungus. Full article

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

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6 pages, 207 KiB

Open AccessEditorial

Ascomycota: Diversity, Taxonomy and Phylogeny, 2nd Edition: Editorial

by Asha J. Dissanayake and Jian-Kui Liu

J. Fungi 2025, 11(6), 419; https://doi.org/10.3390/jof11060419 - 30 May 2025

Abstract

It’s crucial to emphasize a universal conservation of all life on the earth, including not only plants and animals but also fungi [...] Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 2nd Edition)

19 pages, 11326 KiB

Open AccessArticle

A Novel Plate Compartment–Confrontation Method Discovered That Volatile Organic Compounds Produced by Saccharomyces cerevisiae Inhibit Botrytis cinerea and Fusarium graminearum

by Ying Meng, Jing Wang, Hui Xu, Yaqi Yu and Yongheng Liang

J. Fungi 2025, 11(6), 418; https://doi.org/10.3390/jof11060418 - 29 May 2025

Abstract

Biological control of plant diseases is important for crop production. Botrytis cinerea and Fusarium graminearum are two common pathogenic fungi which result in great harm to crop production, processing, and storage of foodstuffs. Yeasts have unique advantages to be the focus of biological [...] Read more.

Biological control of plant diseases is important for crop production. Botrytis cinerea and Fusarium graminearum are two common pathogenic fungi which result in great harm to crop production, processing, and storage of foodstuffs. Yeasts have unique advantages to be the focus of biological control of plant diseases through multiple mechanisms, including producing volatile organic compounds (VOCs) with inhibitory effect. However, the discontinuous display of inhibitory effect by yeast VOCs on pathogenic fungi is restricted by the conventional confrontation method, and the inhibitory mechanisms are unclear. We developed a new method to detect the inhibitory effect of Saccharomyces cerevisiae (yeast) VOCs on B. cinerea and F. graminearum. Our results showed that the yeast VOCs inhibited the growth and development of B. cinerea and F. graminearum and the strength of the inhibitory effect is positively related to the yeast inoculation amount. We confirmed the inhibition effect of ethyl acetic, one of the main yeast VOCs, on both pathogenic fungi. We further found that the deletion or overexpression of the ethyl acetic synthesis-related genes (ATF1 and/or ATF2) did not change the inhibitory effect much. The overexpression of ATF1 changed the main composition of VOCs. One of the changed VOCs, phenethyl acetic, even had stronger inhibitory effect than ethyl acetic on F. graminearum when they were added alone. These results suggest that the inhibitory effect of yeast VOCs on pathogenic fungi is a complex module. The lonely added individual component of VOCs may inhibit the growth and development of pathogenic fungi, while the partial alternation of VOC composition through gene modification may not be enough to change the total inhibitory effect. Full article

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

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