Journal of Fungi

18 pages, 2575 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 (registering DOI) - 1 Sep 2025

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

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 (registering DOI) - 1 Sep 2025

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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10 pages, 584 KB

Open AccessArticle

Antifungal Susceptibilities of Rare Yeast Isolates

by Deniz Turan, Zafer Habip, Hakan Odabaşı, Esra Dömbekçi, Narin Gündoğuş, Merve Özmen and Sebahat Aksaray

J. Fungi 2025, 11(9), 645; https://doi.org/10.3390/jof11090645 (registering DOI) - 1 Sep 2025

Abstract

The recent increase in the number of rare yeasts isolated from clinical specimens is a cause for concern, requiring accurate identification of these yeasts and assessment of their antifungal susceptibility to guide treatment. In this regard, we identified 196 rare yeasts isolated from [...] Read more.

The recent increase in the number of rare yeasts isolated from clinical specimens is a cause for concern, requiring accurate identification of these yeasts and assessment of their antifungal susceptibility to guide treatment. In this regard, we identified 196 rare yeasts isolated from various clinical specimens, mostly urine and respiratory tract specimens of patients hospitalized in intensive care unit and wards, using MALDI-TOF MS, and assessed their susceptibility to amphotericin B, fluconazole, voriconazole, posaconazole, itraconazole, isavuconazole and anidulafungin using the EUCAST broth microdilution method. Among the rare yeast species we isolated, Candida lusitaniae (13.8%) was the most common, followed by Magnusiomyces capitatus (13.3%), Candida fabianii (12.2%), and Trichosporon asahii (11.7%). Antifungal susceptibility testing revealed high echinocandin MIC values against Magnusiomyces spp., Trichosporon spp., and Rhodotorula mucilaginosa isolates. Similarly, we found high MIC values for fluconazole against the isolates of Magnusiomyces spp., T. asahii, R. mucilaginosa, and several Candida spp., including Candida guilliermondii, Candida pararugosa, Candida rugosa, Candida pelliculosa, Candida norvegensis, and Candida fabianii. We found similar MIC values across phylogenetically closely related species. In conclusion, prompt identification of rare yeasts and assessment of their antifungal susceptibilities are essential for effective treatment of the infections they cause. Full article

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17 pages, 299 KB

Open AccessArticle

Rare Mould Fungaemia at a Tertiary Academic Hospital in Athens, Greece: A 15-Year Survey and Literature Review

by Maria Siopi, Angeliki Alevra, Dimitrios Mitsopoulos, Spyros Pournaras and Joseph Meletiadis

J. Fungi 2025, 11(9), 644; https://doi.org/10.3390/jof11090644 (registering DOI) - 1 Sep 2025

Abstract

Invasive infections caused by rare moulds (RM) are increasingly reported and often exhibit resistance to antifungal agents. Their epidemiology varies regionally, yet data from Greece are scarce. To address this gap, we conducted a 15-year retrospective study of RM fungaemia at a tertiary [...] Read more.

Invasive infections caused by rare moulds (RM) are increasingly reported and often exhibit resistance to antifungal agents. Their epidemiology varies regionally, yet data from Greece are scarce. To address this gap, we conducted a 15-year retrospective study of RM fungaemia at a tertiary academic hospital in Athens, Greece. All microbiologically confirmed cases in hospitalised patients between 2010 and 2024 were reviewed. Demographic and clinical data were retrieved from medical records. Incidence rates were calculated per 1000 admissions and 10,000 bed-days. Isolates were morphologically identified and, when available, molecularly characterised and tested for antifungal susceptibility according to EUCAST guidelines. Eight RM fungaemia episodes (0.8% of total fungaemias) were identified, with an incidence of 0.01/1000 admissions and 0.03/10,000 bed-days, without bacterial co-infections. Haematological malignancies (62%) were the most common underlying condition. Fusarium spp. were the predominant pathogens (6/8), followed by single cases due to Lomentospora prolificans and Acremonium spp. Amphotericin B showed the highest in vitro activity against Fusarium isolates (MIC 0.5–1 mg/L), followed by voriconazole (MICs 2–8 mg/L) whereas other azoles showed no in vitro activity (MICs ≥ 8 mg/L). Half of the infections were breakthrough, whereas in 3/8 cases, the diagnosis was established post-mortem (n = 2) or post-discharge. Among the five patients who received treatment, the crude mortality rate was 60%. This first epidemiological report on RM fungaemia in Greece highlights the predominance of Fusarium spp., the frequency of breakthrough infections, and the challenges in early diagnosis and management. Increased clinical awareness and regional surveillance are essential for optimising outcomes. Full article

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

18 pages, 1983 KB

Open AccessArticle

Rise and Fall of Phytophthora infestans Resistance to Non-Specific Fungicide in Experimental Populations

by Shao-Bin Fan, Meng Xie, Zu-Lei Xiang, Tong-Xin Xu, Wen-Jing Wang, Zong-Hua Wang, Hong-Li Hu, Li-Xia Chen, Li Tang, Jia-Sui Zhan and Li-Na Yang

J. Fungi 2025, 11(9), 643; https://doi.org/10.3390/jof11090643 (registering DOI) - 30 Aug 2025

Abstract

Background: Fungicide resistance is one of the major factors threatening social and ecological sustainability. Many issues associated with the evolutionary processes and mechanisms of fungicide resistance in pathogens remain poorly understood, and better knowledge of these issues through experimentally observing the rise [...] Read more.

Background: Fungicide resistance is one of the major factors threatening social and ecological sustainability. Many issues associated with the evolutionary processes and mechanisms of fungicide resistance in pathogens remain poorly understood, and better knowledge of these issues through experimentally observing the rise and fall of the resistance is critical for the development of effective management strategies to ensure food security and ecological health. Methods: An experimental evolution approach was used to continuously acclimate a series of Phytophthora infestans populations under different mancozeb conditions for 400 consecutive days. Results: We found that P. infestans developed mancozeb resistance after 200 days of acclimation. This resistance was associated with ABC transporters and endocytic proteins. Potentially due to fitness costs associated with aggressiveness, mancozeb resistance was reversible. And the pathogen exhibited comparable rates of resistance gain during acclimation and resistance loss during the reversal experiment. Conclusions: Our results suggest that this pathogen may also develop resistance to mancozeb. However, this type of resistance may not be persistent, implying the fungicides concerned could be reused in practice. These results provide new insights into the evolution of fungicide resistance and sustainable plant disease chemical management based on the fungicide dose chosen beyond that of potato blight, warranting further study on the resistance target gene. Full article

(This article belongs to the Special Issue Integrated Management of Plant Fungal Diseases)

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16 pages, 4570 KB

Open AccessArticle

Fusarium suttonianum Identified as the Causal Agent of Root Rot in Plukenetia volubilis in Peru

by Elvin Delgado-Mera, Angel David Hernández-Amasifuen, Ángel Tuesta-Casique, Julio Santiago Chumacero-Acosta, Gerry Antonio Cosme-Garate, Gladstone Alves da Silva, Fernando Marcelo Carvajal Vallejos, Ronan Xavier Corrêa and Mike Anderson Corazon-Guivin

J. Fungi 2025, 11(9), 642; https://doi.org/10.3390/jof11090642 (registering DOI) - 29 Aug 2025

Abstract

Sacha inchi (Plukenetia volubilis) is a high-value crop due to its high content of omega-3 fatty acids and its outstanding nutritional, pharmaceutical, and cosmetic properties. However, this species faces challenges from diseases, particularly root rot. In this study, we identified one [...] Read more.

Sacha inchi (Plukenetia volubilis) is a high-value crop due to its high content of omega-3 fatty acids and its outstanding nutritional, pharmaceutical, and cosmetic properties. However, this species faces challenges from diseases, particularly root rot. In this study, we identified one of the causal agents of root rot in sacha inchi using morphological observations, molecular methods, and pathogenicity tests. The pathogen was isolated from root tissues showing symptoms of Fusarium infection, observed in a plot in the Picota province. Morphological identification, DNA sequencing, and phylogenetic analysis using the ITS and TEF-1α markers revealed that the isolate causing root rot was Fusarium suttonianum (FSSC 20). Analysis of the PQ636870 (ITS) and PQ639345 (TEF-1α) sequences in the NCBI database, together with phylogenetic analysis, revealed 99.58% and 99.51% similarity with the ITS and TEF sequences, respectively, corresponding to F. suttonianum. Pathogenicity tests confirmed that this species induced the same symptoms observed in the field, fulfilling Koch’s postulates. This study represents the first report of F. suttonianum as a pathogen causing root rot in sacha inchi in Peru. This finding is critical for developing effective strategies for disease management and control, contributing to the sustainability and improvement of sacha inchi production in the region. Full article

(This article belongs to the Special Issue Fusarium, Alternaria, and Rhizoctonia: A Spotlight on Fungal Pathogens—3rd Edition)

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15 pages, 1121 KB

Open AccessArticle

Diversity and Distribution of Non-Reducing Polyketide Synthases (NR-PKSs) in Ascomycota (Fungi)

by Pritam Chattopadhyay and Goutam Banerjee

J. Fungi 2025, 11(9), 641; https://doi.org/10.3390/jof11090641 - 29 Aug 2025

Abstract

(1) Background: This study highlights the diversity and distribution of non-reducing polyketide synthases (NR-PKSs) in Ascomycota and their role in producing bioactive aromatic polyketides. (2) Methods: A reference dataset of non-NR-PKSs was compiled from published literature and cross-examined using NaPDoS2 and Kyoto Encyclopedia [...] Read more.

(1) Background: This study highlights the diversity and distribution of non-reducing polyketide synthases (NR-PKSs) in Ascomycota and their role in producing bioactive aromatic polyketides. (2) Methods: A reference dataset of non-NR-PKSs was compiled from published literature and cross-examined using NaPDoS2 and Kyoto Encyclopedia of Genes and Genomes Ortholog (KEGG KO) databases. Signature domains were validated through Pfam and CDD, while phylogenetic classification was conducted by comparing the dataset with the NaPDoS2 reference tree. Cluster support was derived from KEGG KO and homology-based modeling. Additionally, NR-PKS clade distribution across KEGG genomes was analyzed, and co-expression patterns were examined using STRING. (3) Results: This study identified nine distinct clades of NR-PKSs, six of which are supported by unique KEGG Orthology (KO) numbers. These clades are as follows: clade 1: polyketide synthase A (PksA, K15316); clade 2: fusarubinsynthase 1 (Fsr1); clade 3: white A (WA, K15321); clade 4: polyketide synthase citrinin (PksCT); clade 5: zearalenone synthase 1 (Zea1, K15417); clade 6: orsellinic acid synthase A (OrsA, K15416); clade 7: aurofusarin polyketide synthase A (AptA, K15317); clade 8: monodictyphenone polyketide synthase G (MdpG, K15415); and clade 9: bikaverin polyketide synthase (Bik1). The present investigation also reports incongruency in the distribution of different NR-PKSs and fungi phylogeny within the phylum Ascomycota. (4) Conclusions: The distribution of NR-PKSs in Ascomycota defies phylogenetic boundaries, reflecting the impact of horizontal gene transfer, gene loss, and ecological adaptation. Full article

15 pages, 1874 KB

Open AccessArticle

Methods to Stimulate Sporulation and Freeze-Drying Strategies for the Conservation of Diplodia mutila, Diplodia seriata, Lasiodiplodia theobromae, and Neofusicoccum arbuti Isolated from Apple Trees with Canker and Dieback Symptoms

by Adrián Valdez-Tenezaca, Mauricio E. Gutiérrez, Matías Guerra, Jean Franco Castro, Sergio A. Covarrubias and Gonzalo A. Díaz

J. Fungi 2025, 11(9), 640; https://doi.org/10.3390/jof11090640 (registering DOI) - 29 Aug 2025

Abstract

Four Botryosphaeria spp. isolated from apple with dieback symptoms, Diplodia mutila, Diplodia seriata, Neofusicoccum arbuti, and Lasiodiplodia theobromae, were subjected to different conditions to induce sporulation, then freeze-dried and stored in glass vials and ampoules at a temperature of 4 [...] Read more.

Four Botryosphaeria spp. isolated from apple with dieback symptoms, Diplodia mutila, Diplodia seriata, Neofusicoccum arbuti, and Lasiodiplodia theobromae, were subjected to different conditions to induce sporulation, then freeze-dried and stored in glass vials and ampoules at a temperature of 4 ° C using two protective media (skimmed milk powder in water at 20% and a mixture of skimmed milk powder at 20% plus 5% inositol). Viability was assessed after storage periods of 1, 90, 180, and 365 days. Low-nutrient growth conditions on 2% water agar supplemented with pine needles, incubated under UV light (λ = 350 nm) and at 24 ° C, effectively stimulated sporulation of all four Botryosphaeriaceae species. The survival rate of the isolates was similar. Overall viability showed slight but significant differences depending on the type of protective medium and storage container used for the freeze-dried cultures (p < 0.001). Among the tested media, the highest viability was maintained in vacuum-sealed glass ampoules using either a medium containing 20% skimmed milk powder with 5% inositol or 20% skimmed milk powder alone. Full article

(This article belongs to the Special Issue Control of Postharvest Fungal Diseases, 2nd Edition)

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20 pages, 2520 KB

Open AccessArticle

Population, Physiological, and Genetic Insights into Carbendazim Resistance in Populations of the Phytopathogenic Fungus Microdochium nivale

by Guzalia Sh. Murzagulova, Olga A. Gogoleva, Egor A. Ryazanov, Karina A. Shatravina, Natalia V. Tendiuk, Ildar T. Sakhabutdinov, Sergey N. Ponomarev, Inna B. Chastukhina, Olga N. Makshakova, Mira L. Ponomareva and Vladimir Y. Gorshkov

J. Fungi 2025, 11(9), 639; https://doi.org/10.3390/jof11090639 - 29 Aug 2025

Abstract

Fungicide treatment is one of the most common methods for controlling fungal plant diseases. However, many phytopathogenic fungi develop resistance to fungicides. Addressing this agriculturally important issue requires comprehensive investigations into fungicide resistance. Our study aims to assess the degree and prevalence of [...] Read more.

Fungicide treatment is one of the most common methods for controlling fungal plant diseases. However, many phytopathogenic fungi develop resistance to fungicides. Addressing this agriculturally important issue requires comprehensive investigations into fungicide resistance. Our study aims to assess the degree and prevalence of resistance to carbendazim—one of the most widely used fungicides—in populations of Microdochium nivale, the causal agent of the deleterious plant disease pink snow mold; to explore possible relationships between carbendazim resistance and physiological and genetic traits; and to gain insight into the molecular basis of carbendazim resistance in this species. We showed that carbendazim resistance is widespread in the analyzed M. nivale populations, and that the application of carbendazim increases the proportion of resistant strains. Nevertheless, carbendazim-resistant strains are present at high relative abundance in populations that have never been exposed to fungicides. Carbendazim resistance in M. nivale is strongly associated with sequence variations in the β-tubulin gene, resulting in amino acid sequence variability that leads to differential affinity for carbendazim. Additionally, we propose a metabarcoding-based approach employing a genetic marker linked to a specific phenotypic trait to assess the ratio of genotypes with contrasting properties within a particular fungal species in environmental communities. Full article

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

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13 pages, 1224 KB

Open AccessArticle

Predicting the Structural Effects of CUG Codon Translation on Uncharacterized Proteins in Candida albicans

by Michaela Čermáková and Olga Heidingsfeld

J. Fungi 2025, 11(9), 638; https://doi.org/10.3390/jof11090638 - 29 Aug 2025

Abstract

In the standard genetic code, the CUG triplet is translated as leucine. The pathogenic yeast Candida albicans and other CTG-clade yeasts contain tRNA_CAG, which is recognized by both leucine- and serine-tRNA synthetases. The CUG codon in these yeasts is translated most [...] Read more.

In the standard genetic code, the CUG triplet is translated as leucine. The pathogenic yeast Candida albicans and other CTG-clade yeasts contain tRNA_CAG, which is recognized by both leucine- and serine-tRNA synthetases. The CUG codon in these yeasts is translated most often as serine, and only in 3–5% of cases as leucine. Therefore, CTG Candida species have unstable proteomes. The effect of serine–leucine exchange on the structure and function of proteins has only been experimentally examined for a few cases. In C. albicans, CUG codons occur even in genes deemed to be essential. This means that serine–leucine ambiguity either does not affect the structure and function of the respective proteins, or that the presence of these amino acids at specific positions is associated with meaningful alteration of the proteins’ function. This study employed AlphaFold2 to evaluate the potential effects of serine-to-leucine exchange in 12 proteins encoded by essential genes lacking orthologs in other yeasts and human genomes. The low homology with known proteins allowed us to make only low-confidence predictions. The analyzed proteins could be grouped into subsets based on the structural outcomes. Structural changes were observed only in four proteins. The remaining eight proteins showed no significant differences between serine and leucine variants. Full article

(This article belongs to the Special Issue Protein Research in Pathogenic Fungi)

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26 pages, 2512 KB

Open AccessArticle

Potential Antioxidant and Neuroprotective Effect of Polysaccharide Isolated from Digüeñe Cyttaria espinosae

by Claudia Pérez, Fabián A. Figueroa, Ignacio Tello, Roberto T. Abdala-Díaz, Manuel Marí-Beffa, Viviana Salazar-Vidal, José Becerra, Javiera Gavilán and Jorge Fuentealba

J. Fungi 2025, 11(9), 637; https://doi.org/10.3390/jof11090637 - 29 Aug 2025

Abstract

Alzheimer’s disease (AD) is a significant global health challenge, further exacerbated by the anticipated increase in prevalence in the coming years. The accumulation of β-amyloid peptide plays a critical role in the onset of AD; however, emerging evidence suggests that soluble oligomers of [...] Read more.

Alzheimer’s disease (AD) is a significant global health challenge, further exacerbated by the anticipated increase in prevalence in the coming years. The accumulation of β-amyloid peptide plays a critical role in the onset of AD; however, emerging evidence suggests that soluble oligomers of β-amyloid may primarily drive the neuronal impairments associated with this condition. Additionally, neurodegenerative diseases like AD are linked to oxidative stress and reduced antioxidant capacity in the brain. Natural products, particularly polysaccharides extracted from mushrooms, have garnered interest due to their neuroprotective properties and the potential to enhance the value of natural sources in addressing human diseases. This study examines the antioxidant and neuroprotective properties of polysaccharides derived from Cyttaria espinosae Lloyd (CePs), a relatively underexplored fungus native to Chile. Using Fourier Transform Infrared Spectroscopy (FT-IR) and Gas Chromatography-Mass Spectrometry (GC-MS), we characterized CePs. We assessed their antioxidant capacity using DPPH and ABTS assays, yielding maximum inhibition rates of 32.14% and 19.10%, respectively, at a concentration of 10 mg mL⁻¹. CePs showed no toxicity in zebrafish embryos and maintained high cell viability in PC-12 cells exposed to amyloid β peptide (Aβ). Our findings suggest that CePs exhibit significant antioxidant and neuroprotective properties against Aβ peptide toxicity while remaining non-toxic to zebrafish embryos. This underscores the potential of the polysaccharides from this mushroom to serve as functional foods that mitigate oxidative stress and warrant further investigation into their mechanisms in the context of the physiopathology of Alzheimer’s disease. Full article

(This article belongs to the Special Issue Advances in Mushroom Bioactive Metabolites)

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19 pages, 3792 KB

Open AccessArticle

Biological and Genomic Insights into Fusarium acuminatum Causing Needle Blight in Pinus tabuliformis

by Linin Song, Yuying Xu, Tianjin Liu, He Wang, Xinyue Wang, Changxiao Fu, Xiaoling Xie, Yakubu Saddeeq Abubakar, Abah Felix, Ruixian Yang, Xinhong Jing, Guodong Lu, Jiandong Bao and Wenyu Ye

J. Fungi 2025, 11(9), 636; https://doi.org/10.3390/jof11090636 - 29 Aug 2025

Abstract

Chinese pine, Pinus tabuliformis, is one of the most important garden plants in northern China, and the planting of this species is of great significance for the improvement of the ecological environment. In this study, different fungi were isolated and purified from [...] Read more.

Chinese pine, Pinus tabuliformis, is one of the most important garden plants in northern China, and the planting of this species is of great significance for the improvement of the ecological environment. In this study, different fungi were isolated and purified from diseased Pinus tabuliformis samples collected in Xi’an city, Shaanxi Province. Of these fungal isolates, only one (isolate AP-3) was pathogenic to the healthy host plant. The pathogenic isolate was identified as Fusarium acuminatum by morphological characteristics and ITS and TEF-1α sequence analyses. The optimal growth conditions for this isolate were further analyzed as follows: Optimal temperature of 25 °C, pH of 11, soluble starch and sodium nitrate as the most preferred carbon and nitrogen sources, respectively. By combining Oxford Nanopore Technologies (ONT) long-read sequencing with Illumina short-read sequencing technologies, we obtained a 41.50 Mb genome assembly for AP-3, with 47.97% GC content and 3.04% repeats. This consisted of 14 contigs with an N50 of 4.64 Mb and a maximum length of 6.45 Mb. The BUSCO completeness of the genome assembly was 98.94% at the fungal level and 97.83% at the Ascomycota level. The genome assembly contained 13,408 protein-coding genes, including 421 carbohydrate-active enzymes (CAZys), 120 cytochrome P450 enzymes (CYPs), 3185 pathogen-host interaction (PHI) genes, and 694 candidate secreted proteins. To our knowledge, this is the first report of F. acuminatum causing needle blight of P. tabuliformis. This study not only uncovered the pathogen responsible for needle blight of P. tabuliformis, but also provided a systematic analysis of its biological characteristics. These findings provide an important theoretical basis for disease control in P. tabuliformis and pave the way for further research into the fungal pathogenicity mechanisms and management strategies. Full article

(This article belongs to the Special Issue Pathogenic Fungi: Morphogenesis, Pathogenicity and Biosynthesis of Secondary Metabolites—Second Edition)

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14 pages, 7994 KB

Open AccessArticle

Evaluation of the Potential Risk Posed by Emerging Yr5-Virulent and Predominant Races of Puccinia striiformis f. sp. tritici on Bread Wheat (Triticum aestivum L.) Varieties Grown in Türkiye

by Kadir Akan, Ahmet Cat, Medine Yurduseven, Yesim Sila Tekin, Mehmet Zahit Yeken and Mehmet Tekin

J. Fungi 2025, 11(9), 635; https://doi.org/10.3390/jof11090635 - 29 Aug 2025

Abstract

In this study, the reactions of 70 bread wheat varieties released in Türkiye to five prevalent Pst races, including the Yr5-virulent PSTr-27, were evaluated. Reaction tests of wheat varieties to all races revealed PSTr-27 as the most aggressive race, followed by PSTr-31, [...] Read more.

In this study, the reactions of 70 bread wheat varieties released in Türkiye to five prevalent Pst races, including the Yr5-virulent PSTr-27, were evaluated. Reaction tests of wheat varieties to all races revealed PSTr-27 as the most aggressive race, followed by PSTr-31, PSTr-28, PSTr-29, and PSTr-30. Notably, only seven varieties (Kıraç 66, İkizce 96, Dinç, Altındane, Ziyabey 98, Bayraktar 2000, and Shiro) exhibited moderately resistant reactions to PSTr-27, while the remaining varieties were susceptible. The presence of nine important resistance (Yr) genes in these varieties was also screened at the molecular level. Yr5, Yr15, and Yr26 genes were not detected in any of the varieties and Yr10 and YrSP genes were each detected in only one variety, while the other genes were detected in different ratios. Molecular screening showed that 19 varieties with no resistance genes used in this study displayed susceptible reactions; however, ten varieties that did not carry any resistance genes showed resistant reactions to one or more races, suggesting the presence of unknown or novel resistance sources. Furthermore, gene combinations, particularly Yr10 + Yr18, significantly provided resistance to all Pst races studied. These findings highlight that continual monitoring of PSTr-27, and other Pst races is needed, since it can be a serious threat to wheat production in Türkiye and neighboring countries. Full article

(This article belongs to the Special Issue Crop Fungal Diseases Management)

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13 pages, 1330 KB

Open AccessCase Report

Pulmonary Verruconis Infection in an Immunocompetent Patient: A Case Report and Literature Review

by Lulu Xu and Lili Tao

J. Fungi 2025, 11(9), 634; https://doi.org/10.3390/jof11090634 - 29 Aug 2025

Abstract

Verruconis species are thermophilic, darkly pigmented fungi commonly found in hot environments. Despite their environmental ubiquity, fewer than fifty human infections have been reported, with V. gallopava responsible for most cases. While infections primarily occur in immunocompromised individuals, only six cases in immunocompetent [...] Read more.

Verruconis species are thermophilic, darkly pigmented fungi commonly found in hot environments. Despite their environmental ubiquity, fewer than fifty human infections have been reported, with V. gallopava responsible for most cases. While infections primarily occur in immunocompromised individuals, only six cases in immunocompetent patients have been documented. We describe a case of pulmonary Verruconis infection in a 75-year-old immunocompetent woman. Despite broad-spectrum antifungal treatments, including liposomal amphotericin B and voriconazole, the patient’s condition deteriorated. Bronchoalveolar lavage (BAL) revealed hyphal forms, and fungal culture identified a Verruconis species. Antifungal susceptibility tests showed low minimal inhibitory concentrations (MICs) for amphotericin B (1 μg/mL) and voriconazole (0.5 μg/mL). Clinical manifestations of Verruconis infection in immunocompetent pneumonia patients are non-specific. Structural lung disease was identified as the primary risk factor in such hosts. BAL fungal cultures and metagenomics are valuable tools in diagnosing rare fungal infections. Treatment regimens vary, with amphotericin B and triazoles being the most commonly used antifungal agents. Currently, there are no standardized guidelines for diagnosis or treatment. Further studies are needed to establish clinical protocols. Full article

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15 pages, 3555 KB

Open AccessArticle

First Report of Colletotrichum kahawae Causing Anthracnose on Buckwheat (Fagopyrum tataricum) in China and Biological Characterization of the Pathogen

by Xin Liu, Guang Wang, Daowang Sun, Jing Tan, Jiaxing Xie, Binxin Zhai, Chunyan Huang, Wenjie Lu and Lihua Wang

J. Fungi 2025, 11(9), 633; https://doi.org/10.3390/jof11090633 - 29 Aug 2025

Abstract

Buckwheat (Fagopyrum tataricum) is native to Yunnan, China, and as a miscellaneous grain crop with high nutritional value, it has received increased attention from farmers and enterprises in recent years. In June 2024, we observed severe anthracnose in the buckwheat cultivation [...] Read more.

Buckwheat (Fagopyrum tataricum) is native to Yunnan, China, and as a miscellaneous grain crop with high nutritional value, it has received increased attention from farmers and enterprises in recent years. In June 2024, we observed severe anthracnose in the buckwheat cultivation area in Malu Township and Jiache Township, Huize County, Qujing City, Yunnan Province, China. In this study, six isolates (SM01–SM06) of anthracnose with similar morphology were obtained using the tissue isolation method, which was due to the fact that this disease is highly pathogenic to buckwheat. The strain SM02 was selected as a representative isolate for biological characterization and molecular phylogenetic analysis, and a phylogenetic tree was constructed based on the ACT, CHS, and ITS genes to determine its taxonomic status. The selected SM02 isolate was further identified as Colletotrichum kahawae. Biological characterization showed that the representative strain SM02 exhibited optimal growth for in vitro cultivation under a photoperiod, temperature, pH, carbon source, and nitrogen source of 12L:12D, 25 °C, pH 7.0, glucose, and beef extract, respectively. Host range testing demonstrated that C. kahawae might infect important field crops, including maize, wheat, oats, and potatoes. In conclusion, C. kahawae causes buckwheat anthracnose in China, which might hinder the production of buckwheat. This study provides insight into anthracnose disease in buckwheat and provides a basis for further investigations to assess and implement effective disease management strategies. Full article

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

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20 pages, 1480 KB

Open AccessReview

A Comprehensive Overview of Candida albicans as the Leading Pathogen in Vulvovaginal Candidiasis

by Nika Srb, Jasminka Talapko, Tomislav Meštrović, Rajko Fureš, Mirjana Stupnišek, Andrea Milostić Srb and Ivana Škrlec

J. Fungi 2025, 11(9), 632; https://doi.org/10.3390/jof11090632 - 28 Aug 2025

Abstract

Candida albicans is the primary etiological agent of vulvovaginal candidiasis (VVC), a widespread fungal infection affecting millions of women worldwide. Although often self-limiting, VVC can become recurrent or severe, significantly impacting quality of life. The pathogenesis of C. albicans is driven by key [...] Read more.

Candida albicans is the primary etiological agent of vulvovaginal candidiasis (VVC), a widespread fungal infection affecting millions of women worldwide. Although often self-limiting, VVC can become recurrent or severe, significantly impacting quality of life. The pathogenesis of C. albicans is driven by key virulence factors, including hyphal transformation, biofilm formation, and immune evasion, which all facilitate persistence and resistance to host defenses. Epidemiological data indicate that up to 75% of women experience at least one episode of VVC, with 5–10% developing recurrent vulvovaginal candidiasis. The condition typically presents with vaginal itching, burning, erythema, edema, and an abnormal discharge. Diagnosis relies on both clinical presentation and microbiological confirmation; however, misdiagnosis remains common due to symptom overlap with other vaginal infections and conditions in general. Azole antifungals remain the cornerstone of treatment; however, increasing resistance (particularly in non-albicans Candida species) poses substantial therapeutic challenges. Consequently, the emergence of antifungal-resistant strains underscores the need for novel treatment strategies, including probiotics and natural antifungal agents. Preventive measures—including maintaining vaginal microbiota balance, avoiding unnecessary antibiotic usage, and improving hygiene practices—play a pivotal role in reducing disease burden due to C. albicans. Given the rising incidence of VVC and the burden of recurrent cases, further research is essential to develop targeted therapeutic interventions. This comprehensive review highlights the evolving epidemiology, pathogenesis, and clinical challenges of C. albicans-associated VVC, emphasizing the need for improved diagnostic strategies, alternative therapeutic approaches, and targeted preventive measures to reduce disease burden and enhance patient outcomes. Full article

(This article belongs to the Special Issue Fungi in Vulvovaginal Infections)

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20 pages, 1813 KB

Open AccessArticle

Impact of Antibiotic Therapy on the Upper Respiratory Tract and Gut Mycobiome in Patients with Cystic Fibrosis

by Cristina Zubiria-Barrera, Malena Bos, Robert Neubert, Jenny Fiebig, Michael Lorenz, Michael Hartmann, Jochen G. Mainz, Hortense Slevogt and Tilman E. Klassert

J. Fungi 2025, 11(9), 631; https://doi.org/10.3390/jof11090631 (registering DOI) - 28 Aug 2025

Abstract

Patients with cystic fibrosis (CF) are frequently exposed to antibiotic treatments, which can alter the fungal communities (mycobiome) across their mucosal sites. This pilot study investigated the impact of antibiotic exposure on the mycobiome by analyzing fungal community dynamics in the upper respiratory- [...] Read more.

Patients with cystic fibrosis (CF) are frequently exposed to antibiotic treatments, which can alter the fungal communities (mycobiome) across their mucosal sites. This pilot study investigated the impact of antibiotic exposure on the mycobiome by analyzing fungal community dynamics in the upper respiratory- (nasal lavage) and gastrointestinal- (stool samples) tracts of 12 patients with CF following (a) long-term antibiotic treatment over a three-year period and (b) short-term antibiotic therapy during acute pulmonary exacerbations. Mycobiome profiles of the samples obtained from 38 healthy individuals were also analyzed and used for comparison purposes. The ITS1 region of the fungal rRNA gene cluster was sequenced to characterize and quantify the fungal community composition in both cohorts. Compared to healthy controls, samples from the patients with CF who had undergone long-term antibiotic treatment revealed a significantly increased fungal biomass in both sino-nasal and stool samples. Moreover, diversity metrics revealed significant differences in nasal lavage samples, whereas the stool samples showed no significant variation. Candida spp. was significantly enriched in both nasal and stool samples from CF patients. Further analyses demonstrated a strong positive correlation between the relative abundance of Candida spp. and the cumulative antibiotic intake over the three-year period in sino-nasal samples, but not in stool samples. Acute antibiotic treatment during a pulmonary exacerbation episode also led to a marked increase in the abundance of Candida spp. in sino-nasal samples. These findings highlight the increased sensitivity of the sino-nasal mycobiome to both chronic and acute antibiotic exposure in CF patients, as characterized by a site-specific fungal overgrowth, particularly of Candida spp. Full article

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17 pages, 1969 KB

Open AccessArticle

Shifting Paradigms in Antifungal Prophylaxis and Their Effects on Candidemia Outcomes in Hematological Malignancies: A 14-Year Experience from a Single Tertiary Center

by Fazıl Çağrı Hunutlu, Fahir Özkalemkaş, Beyza Ener, Dilay Demirayak, Büşra Çalışır, Hikmet Öztop, İbrahim Ethem Pınar, Vildan Gürsoy, Tuba Ersal, Tuba Güllü Koca, Emin Halis Akalın and Vildan Özkocaman

J. Fungi 2025, 11(9), 630; https://doi.org/10.3390/jof11090630 - 28 Aug 2025

Abstract

Evolving antifungal prophylaxis approaches have reshaped candidemia patterns and outcomes in hematological malignancy (HM) patients. This study aimed to evaluate temporal changes in candidemia incidence, species distribution, and factors associated with mortality in relation to prophylaxis practices. Adult HM patients with candidemia between [...] Read more.

Evolving antifungal prophylaxis approaches have reshaped candidemia patterns and outcomes in hematological malignancy (HM) patients. This study aimed to evaluate temporal changes in candidemia incidence, species distribution, and factors associated with mortality in relation to prophylaxis practices. Adult HM patients with candidemia between 2009 and 2023 were included. Clinical and microbiological data were analyzed, and candidemia rates were compared across different prophylaxis periods. Sixty-six patients were identified, with acute myeloid leukemia (AML) being the most common underlying malignancy (40.9%). Non-albicans Candida species predominated, especially C. krusei and C. tropicalis. In AML patients, candidemia incidence significantly decreased over time (β = −0.694, p = 0.004), with the lowest rates observed during the extended-release posaconazole tablet era (2016–2023). However, 30-day mortality remained high (53%) and unchanged across periods. Multivariate analysis identified C. tropicalis and total parenteral nutrition as independent risk factors for 30-day mortality (OR: 4.3 and 4.6, p < 0.05), while antifungal prophylaxis was protective (OR: 0.07, p = 0.017). In patients with AML, posaconazole prophylaxis, particularly in the extended-release tablet formulation, significantly reduced the incidence of candidemia. However, overall 30-day mortality rates remained high, with C. tropicalis being a major contributor. Thus, individualized prophylaxis and treatment strategies are crucial for improving outcomes. Full article

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15 pages, 2359 KB

Open AccessArticle

Trichoderma harzianum Cellobiohydrolase Thph2 Induces Reactive Oxygen Species-Mediated Resistance Against Southern Corn Leaf Blight in Maize

by Bo Lang, Hongyi Liu, Gaoyue Si, Xifen Zhang, Cheng Zhang, Jing Wang and Jie Chen

J. Fungi 2025, 11(9), 629; https://doi.org/10.3390/jof11090629 - 27 Aug 2025

Abstract

The pathogenic plant fungus Bipolaris maydis is responsible for southern corn leaf blight (SCLB), a widespread agricultural disease that significantly reduces maize yield in various agroecological zones. The present research focuses on characterizing the role of Trichoderma harzianum cellobiohydrolase (CBH) Thph2 in induced [...] Read more.

The pathogenic plant fungus Bipolaris maydis is responsible for southern corn leaf blight (SCLB), a widespread agricultural disease that significantly reduces maize yield in various agroecological zones. The present research focuses on characterizing the role of Trichoderma harzianum cellobiohydrolase (CBH) Thph2 in induced maize resistance to SCLB by triggering the production of reactive oxygen species (ROS) in leaves. First of all, we demonstrated the potential activities of Thph2 in triggering ROS burst and PDC in a model plant, Nicotiana benthamiana. Cell death, ROS burst, and programmed cell death (PCD) were observed in N. benthamiana leaves following transient expression of Thph2, indicating its defensive role against Sclerotinia sclerotiorum infection. The removal of the signal peptide from Thph2 resulted in the complete loss of the cell death phenotype and the accumulation of reactive oxygen species (ROS), confirming that Thph2 functions as a microbial elicitor that primes host plant immunity through ROS-mediated signaling, thereby inducing systemic resistance (ISR). Furthermore, the Thph2 protein conferred resistance against B. maydis in maize, significantly increasing reactive oxygen species (ROS) accumulation (1.5-fold compared to the control) at 48 h post-inoculation (hpi),and leading to the reduction in the lesion area of SCLB by 15.9% at 2 days post-inoculation (dpi). Our results demonstrated that the Thph2 protein markedly enhanced the expression of lox5, aos, and hpl in maize leaves, thereby confirming its function in triggering plant defense mechanisms primarily via the jasmonic acid signaling pathway. This research reveals new molecular mechanisms by which T. harzianum enhances plant defense and showcases the biocontrol efficacy of Thph2 against southern corn leaf blight (SCLB). 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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