Journal of Fungi

20 pages, 3541 KiB

Open AccessReview

Immunoregulation in Fungal Infections: A Review and Update on the Critical Role of Myeloid-Derived Suppressor Cells

by Valéria de Lima Kaminski, Ana Luiza Oliveira Menezes, Kauan Gonçalves de Lima, Stephani Leonelo de Almeida, Diego Vinícius Alves da Silva, Filipe Nogueira Franco, Nycolas Willian Preite and Flávio Vieira Loures

J. Fungi 2025, 11(7), 496; https://doi.org/10.3390/jof11070496 - 30 Jun 2025

Abstract

Myeloid-derived suppressor cells (MDSCs) are a heterogeneous group of immune cells that play a central role in regulating host immune responses during fungal infections. Their recruitment is mediated by pathogen recognition receptors, particularly Dectin-1 and CARD9 signaling, which promote the production of reactive [...] Read more.

Myeloid-derived suppressor cells (MDSCs) are a heterogeneous group of immune cells that play a central role in regulating host immune responses during fungal infections. Their recruitment is mediated by pathogen recognition receptors, particularly Dectin-1 and CARD9 signaling, which promote the production of reactive oxygen species (ROS) and IL-1β. Once activated, MDSCs suppress T-cell and natural killer cell functions through immunosuppressive cytokines like IL-10 and TGF-β, as well as enzymes such as arginase-1 and indoleamine 2,3-dioxygenase 1 (IDO-1). This review explores the role of MDSCs in fungal infections caused by Candida spp., Paracoccidioides brasiliensis, Aspergillus spp., and Cryptococcus neoformans, emphasizing their impact on immune modulation and disease progression. The emerging evidence suggests that fungal bioactive compounds, such as polysaccharides, can influence MDSC activity and restore immune balance. Notably, therapies targeting MDSCs have demonstrated promise in both fungal infections. In particular, infections with P. brasiliensis and C. neoformans show improved T-cell responses following MDSC-targeted interventions. Additionally, polysaccharides from Grifola frondosa and exposure to Aspergillus sydowii affect MDSC behavior, supporting the potential of modulating these cells therapeutically. Together, these findings highlight the relevance of MDSCs in fungal pathogenesis and underscore their potential as targets for immunotherapeutic strategies in infectious diseases. Full article

(This article belongs to the Special Issue Fungal Cell Biology)

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24 pages, 10260 KiB

Open AccessArticle

Functional Characterization of Deubiquitinase UBP Family and Proteomic Analysis of Aaubp14-Mediated Pathogenicity Mechanism in Alternaria alternata

by Jiejing Tang, Hang Zhou, Chen Jiao and Hongye Li

J. Fungi 2025, 11(7), 495; https://doi.org/10.3390/jof11070495 - 29 Jun 2025

Abstract

The Alternaria alternata tangerine pathotype causes Alternaria brown spot, a devastating disease of susceptible tangerine varieties and their hybrids. Alternaria citri toxin (ACT) is the primary virulence factor, but the regulatory mechanisms governing ACT synthesis remain unclear. Deubiquitinating enzymes maintain ubiquitination homeostasis and [...] Read more.

The Alternaria alternata tangerine pathotype causes Alternaria brown spot, a devastating disease of susceptible tangerine varieties and their hybrids. Alternaria citri toxin (ACT) is the primary virulence factor, but the regulatory mechanisms governing ACT synthesis remain unclear. Deubiquitinating enzymes maintain ubiquitination homeostasis and regulate fungal pathogenicity, yet their role in A. alternata remains unexplored. We characterized 13 ubiquitin-specific protease (UBP) family members in A. alternata tangerine pathotype. Six UBP genes (Aaubp2, Aaubp3, Aaubp4, Aaubp6, Aaubp14, and Aaubp15) regulated mycelial growth. Aaubp14 deletion abolished sporulation, while mutations of Aaubp3, Aaubp4, Aaubp6, Aaubp8, and Aaubp15 altered conidial morphology. qRT-PCR demonstrated distinct host-induced expression patterns among Aaubp genes. Pathogenicity tests showed that ΔAaubp6, ΔAaubp14, and ΔAaubp15 mutants failed to produce lesions on Citrus reticulata cv. Hongjv leaves. Moreover, Aaubp14 deletion significantly suppressed ACT biosynthesis gene expression and blocked ACT production. Comparative proteomics showed Aaubp14 regulates ACT biosynthesis by modulating protein ubiquitination in metabolic pathways and controls pathogenicity via a complex network. Our findings elucidate Aaubp gene function in development and pathogenicity, particularly the Aaubp14-mediated regulation mechanism, providing insights into ubiquitination-mediated pathogenicity in phytopathogenic fungi. Full article

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

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Graphical abstract

25 pages, 4815 KiB

Open AccessArticle

Six Novel Species of Distoseptispora (Distoseptisporaceae, Distoseptisporales) and Helminthosporium (Massarinaceae, Pleosporales) Isolated from Terrestrial Habitats in Southern China

by Ming-Gen Liao, Xing-Xing Luo, Ji-Wen Xia, Ya-Fen Hu, Xiu-Guo Zhang, Lian-Hu Zhang, Xian-Peng Zhang, Zhao-Huan Xu and Jian Ma

J. Fungi 2025, 11(7), 494; https://doi.org/10.3390/jof11070494 - 29 Jun 2025

Abstract

Saprobic hyphomycetous fungi exhibit high colonization density and diversity on rotting woody plant material. During our continuing mycological research in the forest ecosystem of Jiangxi, Fujian and Zhejiang provinces, China, several Distoseptispora-like and Helminthosporium-like strains were isolated from unidentified dead branches [...] Read more.

Saprobic hyphomycetous fungi exhibit high colonization density and diversity on rotting woody plant material. During our continuing mycological research in the forest ecosystem of Jiangxi, Fujian and Zhejiang provinces, China, several Distoseptispora-like and Helminthosporium-like strains were isolated from unidentified dead branches in terrestrial habitats. Based on morphological comparisons and multi-locus phylogenetic analyses using maximum-likelihood (ML) and Bayesian inference (BI), six novel species of Distoseptispora (D. terrestris, D. wuyishanensis, D. zhejiangensis) and Helminthosporium (H. ganzhouense, H. jiangxiense, H. saprophyticum) were introduced, and one known species, H. velutinum was reported. The species diversity within Distoseptispora and Helminthosporium was supplemented in this study. Full article

(This article belongs to the Special Issue Plant Pathogenic Fungi: Taxonomy, Phylogeny and Morphology，2nd Edition)

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17 pages, 1421 KiB

Open AccessArticle

Assessing Venturia inaequalis Response to Common Fungicides in Morocco

by Safae Gouit, Safae Chiadmi, Khadija Goura, Ikram Legrifi, Moussa El Jarroudi, Zineb Belabess, Abdessalem Tahiri, Abderrahim Lazraq, Mohammed Baala and Rachid Lahlali

J. Fungi 2025, 11(7), 493; https://doi.org/10.3390/jof11070493 - 29 Jun 2025

Abstract

Apple scab, caused by Venturia inaequalis, remains a major challenge for apple production in Morocco, where disease management heavily depends on fungicide applications. However, increasing reports of resistance have raised concerns about the long-term efficacy of commonly used products and the economic [...] Read more.

Apple scab, caused by Venturia inaequalis, remains a major challenge for apple production in Morocco, where disease management heavily depends on fungicide applications. However, increasing reports of resistance have raised concerns about the long-term efficacy of commonly used products and the economic sustainability of apple orchards. In this study, we evaluated the sensitivity of five V. inaequalis isolates from the Fes-Meknes region, a key apple-producing area in Morocco, to three fungicides: difenoconazole, trifloxystrobin, and thiophanate-methyl. The identity of the isolates was confirmed based on both morphological characteristics and by molecular analysis of the ITS region. In vitro and in vivo assays revealed significant differences in isolate responses. Difenoconazole consistently showed the highest efficacy, with EC₅₀ values ranging from 0.05 to 1.46 µg/mL, and preventive applications reducing disease severity by up to 85.8% at 10 µg/mL. In contrast, trifloxystrobin and thiophanate-methyl exhibited much higher EC₅₀ values (2.94–29.62 µg/mL and 14.84–1237.20 µg/mL, respectively), indicating widespread resistance, particularly to thiophanate-methyl, whose curative and preventive efficacy rarely exceeded 44%. Preventive treatments were significantly more effective than curative applications for all fungicides tested. These findings highlight the urgent need to revise apple scab management strategies in Morocco, including the rotation of fungicides with different modes of action and the integration of non-chemical approaches. Broader sensitivity monitoring and the use of molecular diagnostics are recommended to better inform sustainable disease control programs. Full article

(This article belongs to the Special Issue Innovative Insights and Challenges in Managing Fungal Diseases in Crops: Toward Sustainable Agricultural Practices)

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17 pages, 796 KiB

Open AccessArticle

Silent Allies: Endophytic Entomopathogenic Fungi Promote Biological Control and Reduce Spittlebug Mahanarva spectabilis Distant, 1909 (Hemiptera: Cercopidae)

by Michelle O. Campagnani, Luís Augusto Calsavara, Charles Martins de Oliveira and Alexander Machado Auad

J. Fungi 2025, 11(7), 492; https://doi.org/10.3390/jof11070492 - 27 Jun 2025

Abstract

Urochloa ruziziensis (R. Germ. and C.M. Evrard) Crins (synonym Brachiaria ruziziensis) Poales: Poaceae) pastures are often attacked by spittlebugs, compromising their biomass for livestock usage. A sustainable control method involves the use of entomopathogenic fungi. Therefore, the objective of this study was [...] Read more.

Urochloa ruziziensis (R. Germ. and C.M. Evrard) Crins (synonym Brachiaria ruziziensis) Poales: Poaceae) pastures are often attacked by spittlebugs, compromising their biomass for livestock usage. A sustainable control method involves the use of entomopathogenic fungi. Therefore, the objective of this study was to evaluate the efficacy of controlling Mahanarva spectabilis Distant, 1909 (Hemiptera: Cercopidae), in greenhouse and field conditions via endophytic entomopathogenic fungi. In the greenhouse, the mortality of nymphs and adults was 100%, and more than 53% of the nymphs and 59% of the adults that fed on plants inoculated with Fusarium multiceps and Metarhizium anisopliae presented with these fungi in their cadavers. In the field, more than 45% of the insect cadavers that had fed on plants grown from fungus-treated seeds were found to contain the fungi. F. multiceps was found to be endophytic in more than 60% of the plants up to 90 days after seed treatment, and M. anisopliae was found in more than 70% of the plants up to 120 days after treatment. The damage scores of the control plants, both in the greenhouse and in the field, were greater than those of the plants inoculated with the fungi. F. multiceps and M. anisopliae in the endophytic pathway of U. ruziziensis are therefore efficient at controlling spittlebugs. Full article

(This article belongs to the Special Issue Pathogenic Mechanisms and Biological Control in Entomopathogenic Fungi)

16 pages, 4084 KiB

Open AccessArticle

Exploring the Characteristics of Atoxigenic Aspergillus flavus Isolates and Their Biocontrol Impact on Soil Fungal Communities

by Yanyan Zhang, Wanning Wang, Chenggui Piao, Wenjin Li, Peter J. Cotty, Shihua Shan, Usman Rasheed, Quirico Migheli and Qing Kong

J. Fungi 2025, 11(7), 491; https://doi.org/10.3390/jof11070491 - 27 Jun 2025

Abstract

Aspergillus flavus can produce aflatoxins, posing a threat of contamination to peanuts. To mitigate this issue, the use of biocontrol isolates, which do not produce aflatoxins (AF⁻), has been considered to reduce aflatoxin levels. In this study, we evaluated five different [...] Read more.

Aspergillus flavus can produce aflatoxins, posing a threat of contamination to peanuts. To mitigate this issue, the use of biocontrol isolates, which do not produce aflatoxins (AF⁻), has been considered to reduce aflatoxin levels. In this study, we evaluated five different AF⁻ isolates belonging to different vegetative compatibility groups, all of which exhibited varying degrees of deletion in aflatoxin biosynthesis gene clusters. One isolate that exhibited poor competitive ability against toxigenic A. flavus was eliminated, and the remaining four isolates were formulated as biocontrol agents and applied to a peanut field in Tai’an, Shandong, as a combination. Three months after application, the soil aflatoxin content was reduced from 0.62 ± 0.01 to 0.19 ± 0.03 μg/kg (inhibition rate: 69.35%). Among filamentous fungi in the soil, the proportion of AF⁻ isolates increased from 0% to 4.33%. Using SSR-specific primers, the microbial agents were recovered. We discovered that among the four AF⁻ isolates, CA04 had a lower colonization rate compared to the other three (only 12.00% of the total AF⁻ population), suggesting that the absence of sclerotia may result in poor reversibility and weaker dispersal ability. We utilized Illumina sequencing to investigate the changes in soil fungal ecology. The results showed a reduction in the population density of harmful fungi, such as Fusarium spp. (66.18%) and Plectosphaerella spp. (79.90%), but an increase in the density of Nothopassalora personata. This is the first study on the dispersal distance and soil fungal community structure following the application of AF⁻ agents in peanut fields in China. Full article

12 pages, 1229 KiB

Open AccessArticle

Methodology for Extracting High-Molecular-Weight DNA from Field Collections of Macrofungi

by Leigh A. Burgoyne, Andy R. Nilsen, Teresa Lebel, Pamela S. Catcheside, Tom W. May, David Orlovich, Alan Kuo, Anna Lipzen, Kurt Labutti, Robert Riley, William Andreopoulos, Maxim Koriabine, Mi Yan, Vivian Ng, Igor V. Grigoriev and David E. A. Catcheside

J. Fungi 2025, 11(7), 490; https://doi.org/10.3390/jof11070490 - 27 Jun 2025

Abstract

Many macrofungi are impractical or impossible to culture. Consequently, DNA for long-read sequencing required for the assembly of high-quality genomes must be isolated from samples taken from the environment. Collection is often in remote locations, limiting the options for stabilising samples to methods [...] Read more.

Many macrofungi are impractical or impossible to culture. Consequently, DNA for long-read sequencing required for the assembly of high-quality genomes must be isolated from samples taken from the environment. Collection is often in remote locations, limiting the options for stabilising samples to methods that do not require refrigeration. Fungi contain species-specific arrays of metabolites that may complicate purification techniques and call for judgement to be made to apply appropriate modifications to the DNA extraction protocol in specific cases. The protocols and commentary we describe are informed by the preparation of DNA from a range of Australasian ectomycorrhizal and saprotrophic macrofungi. We collect samples into isopropanol at ambient temperature and employ a strategy of chromatin isolation followed by the sequential removal of unwanted molecular components to purify DNA. Full article

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24 pages, 45979 KiB

Open AccessArticle

Additions to Macgarvieomyces in Iran: Morphological and Phylogenetic Analyses Reveal Six New Species

by Abdollah Ahmadpour, Youbert Ghosta, Fatemeh Alavi, Zahra Alavi, Esmaeil Hashemlou, Jaturong Kumla, Samantha C. Karunarathna and Nakarin Suwannarach

J. Fungi 2025, 11(7), 489; https://doi.org/10.3390/jof11070489 - 27 Jun 2025

Abstract

The genus Macgarvieomyces (Magnaporthales, Sordariomycetes, Ascomycota) currently includes three species, which are associated with leaf spots on plants belonging to the Cyperaceae and Juncaceae families and are known only in Europe and New Zealand. During a comprehensive survey conducted [...] Read more.

The genus Macgarvieomyces (Magnaporthales, Sordariomycetes, Ascomycota) currently includes three species, which are associated with leaf spots on plants belonging to the Cyperaceae and Juncaceae families and are known only in Europe and New Zealand. During a comprehensive survey conducted between 2020 and 2022 targeting host plants from these families across various regions of Iran, six novel species of Macgarvieomyces—M. caspica, M. cyperi, M. junci-acuti, M. juncigenus, M. salkadehensis, and M. schoeni—were uncovered. These species were identified based on detailed morphological characterizations and multi-locus phylogenetic analyses using ITS-rDNA, RPB1, ACT, and CAL gene regions. This study provides thorough descriptions and illustrations of the new taxa, including information on their morphology, ecological preferences, and geographic distribution. The phylogenetic relationships among the species are also discussed. This work significantly enhances the known diversity of Macgarvieomyces associated with Cyperaceae and Juncaceae, expands their geographic distribution, and underscores the value of integrating morphological and molecular data in fungal taxonomy; accordingly, the findings of this study lay the groundwork for future ecological and evolutionary studies of this genus. Full article

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

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16 pages, 2599 KiB

Open AccessArticle

Synergistic Effects of Rhizophagus irregularis and Trichoderma harzianum Co-Inoculation on Enhancing Drought Tolerance and Secondary Metabolite Production in Licorice (Glycyrrhiza uralensis)

by Kangxu Zhang, Mengyao Sun, Haiyan Feng, Xia Wei, Wei Xie, Wei Fu, Lanping Guo, Xin Zhang, Zhipeng Hao and Baodong Chen

J. Fungi 2025, 11(7), 488; https://doi.org/10.3390/jof11070488 - 27 Jun 2025

Abstract

Drought stress significantly hinders the cultivation of medicinal plants such as licorice (Glycyrrhiza uralensis), valued for its bioactive compounds, glycyrrhizin, and liquiritin. This study aims to investigate how co-inoculation with arbuscular mycorrhizal fungus Rhizophagus irregularis and Trichoderma harzianum can enhance licorice [...] Read more.

Drought stress significantly hinders the cultivation of medicinal plants such as licorice (Glycyrrhiza uralensis), valued for its bioactive compounds, glycyrrhizin, and liquiritin. This study aims to investigate how co-inoculation with arbuscular mycorrhizal fungus Rhizophagus irregularis and Trichoderma harzianum can enhance licorice drought tolerance and secondary metabolite production, providing insights for sustainable agriculture in arid regions. The results demonstrate that inoculation with R. irregularis significantly improved biomass, drought stress tolerance, and increased glycyrrhizin and liquiritin concentrations by 29.9% and 3.3-fold, respectively, particularly under drought conditions. Co-inoculation with T. harzianum further boosted glycyrrhizin yield by 93.7%, indicating a synergistic relationship between the two microbes. The expression of key biosynthetic genes, including squalene synthase (SQS1) for glycyrrhizin and chalcone synthase (CHS) for liquiritin, was significantly upregulated, enhancing water use efficiency and the biosynthesis of secondary metabolites. Nutrient analysis showed improved phosphorus uptake, alongside reduced root carbon and nitrogen concentrations, leading to greater nutrient utilization efficiency. These findings suggest that co-inoculating R. irregularis and T. harzianum is a promising approach to improving licorice growth and medicinal quality under drought stress, with broad applications for sustainable crop management. Full article

(This article belongs to the Special Issue New Insights into Arbuscular Mycorrhizal Fungi)

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15 pages, 7294 KiB

Open AccessArticle

Evolutionary Dynamics and Functional Bifurcation of the C2H2 Gene Family in Basidiomycota

by Chao Duan and Jie Yang

J. Fungi 2025, 11(7), 487; https://doi.org/10.3390/jof11070487 - 27 Jun 2025

Abstract

This study performed a phylogenomic analysis of the C2H2 gene family across 30 Basidiomycota species, identifying 1032 genes distributed across six evolutionary clades (Groups I–VI). Functional diversification and lineage-specific expansions were observed: Group II (37.1%) formed a conserved core, while wood decayers (e.g., [...] Read more.

This study performed a phylogenomic analysis of the C2H2 gene family across 30 Basidiomycota species, identifying 1032 genes distributed across six evolutionary clades (Groups I–VI). Functional diversification and lineage-specific expansions were observed: Group II (37.1%) formed a conserved core, while wood decayers (e.g., Schizophyllum commune) and edible fungi (e.g., Pleurotus ostreatus) exhibited clade-specific expansions in Groups III and V, respectively. Physicochemical profiling revealed an acidic bias in Agaricomycotina proteins (pI 4.3–5.8) compared to alkaline trends in pathogens (Ustilaginomycotina/Pucciniomycotina; pI 8.3–8.6). Comparative genomics indicated that saprotrophs retained long genes (12.4 kb) with abundant introns (mean = 6.2/gene), whereas pathogens exhibited genomic streamlining (introns ≤ 2). Synteny network analysis revealed high ancestral conservation in core clusters (Cluster_1–2: 58% homologs) under strong purifying selection (Ka/Ks = 0.18–0.22), while peripheral clusters (Cluster_Mini) approached neutral evolution (Ka/Ks = 0.73). This study reveals stage-specific expression dynamics of 17 C2H2 zinc finger genes in Sarcomyxa edulis, highlighting their roles in coordinating developmental transitions (e.g., SeC2H2_1 in low-temperature adaptation, SeC2H2_7/12 in primordia initiation, and SeC2H2_8/9/13 in fruiting body maturation) through temporally partitioned regulatory programs, providing insights into fungal morphogenesis and stress-responsive adaptation. These findings underscore the dual role of C2H2 genes in sustaining conserved regulatory networks and facilitating ecological adaptation, providing new insights into fungal genome evolution. Full article

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13 pages, 342 KiB

Open AccessSystematic Review

A Distinct Clinical Entity of Invasive Cardiac Aspergillosis: Not the Heart Valves This Time

by Zaid Al Khouri, Hunter Smeltzer, Anood Al Qura’an, Mohammad H. Khan and Alexandre E. Malek

J. Fungi 2025, 11(7), 486; https://doi.org/10.3390/jof11070486 - 26 Jun 2025

Abstract

Invasive aspergillosis (IA) is a life-threatening infection that mainly affects immunocompromised hosts. Cardiac involvement is rare but can be the sole presentation of IA. It is associated with a high mortality rate and mostly occurs in patients with pre-existing cardiac disease. It can [...] Read more.

Invasive aspergillosis (IA) is a life-threatening infection that mainly affects immunocompromised hosts. Cardiac involvement is rare but can be the sole presentation of IA. It is associated with a high mortality rate and mostly occurs in patients with pre-existing cardiac disease. It can also be seen in immunocompetent patients with a structurally normal heart. The reported cases of cardiac involvement are usually due to infectious endocarditis (IE) caused by Aspergillus species (most commonly Aspergillus fumigatus). However, there is limited data on non-valvular cardiac aspergillosis (NVCA). We reviewed 67 cases of NVCA published between 1950–2024 and reported an additional case from our institution involving a 48-year-old female with kyphoscoliosis diagnosed with Aspergillus pericarditis. Full article

(This article belongs to the Special Issue Fungal Infections: New Challenges and Opportunities, 3rd Edition)

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14 pages, 2702 KiB

Open AccessArticle

Host-Adaptive Divergence Shapes the Genetic Architecture of Magnaporthe oryzae in Southern China’s Rice Agroecosystems

by Xin Liu, Jun Fu, Zhao Deng, Xinwei Chen, Xiaochun Hu, Zhouyi Tu, Qiuyi Wang, Yuxuan Zhu, Pengcheng Chen, Zhenan Bai, Tiangang Liu, Xuanwen Zhang, Peng Qin, Kai Wang, Nan Jiang and Yuanzhu Yang

J. Fungi 2025, 11(7), 485; https://doi.org/10.3390/jof11070485 - 26 Jun 2025

Abstract

Rice blast disease, caused by the ascomycete fungus Magnaporthe oryzae (syn. Pyricularia oryzae), poses a severe threat to global rice production. Southern China, a major rice-growing region characterized by diverse agroecological conditions, faces substantial challenges from blast disease, yet our understanding of [...] Read more.

Rice blast disease, caused by the ascomycete fungus Magnaporthe oryzae (syn. Pyricularia oryzae), poses a severe threat to global rice production. Southern China, a major rice-growing region characterized by diverse agroecological conditions, faces substantial challenges from blast disease, yet our understanding of the genetic structure of M. oryzae populations in this region remains limited. Here, we analyzed 885 M. oryzae strains from 18 nurseries across four rice ecological regions in Southern China using a panel of genome-wide SNP markers. Phylogenetic and principal component analyses revealed three distinct clonal lineages: lineage I (58.19%), lineage II (21.36%), and lineage III (20.45%). Lineage I exhibited a broader geographic distribution compared to the other two lineages. Host-adapted divergence was observed across rice subspecies, with lineage III predominantly associated with japonica growing-regions, while lineages I and II mainly colonized indica rice-growing regions. Genetic diversity exhibited significant spatial heterogeneity, with the nucleotide diversity (π) ranging from 0.17 in South China to 0.32 in the Middle–Lower Yangtze River region, reflecting differential cropping systems. The predominantly negative Tajima’s D values across populations suggested recent expansion or selective sweeps, likely driven by host resistance pressures. High genetic differentiation between lineage I and other lineages contrasted with low divergence between lineages II and III, indicating distinct evolutionary trajectories. Furthermore, an uneven distribution of mating types among three genetic lineages was observed, suggesting limited sexual recombination within clonal lineages. The information obtained in this study may be beneficial in devising suitable strategies to control rice blast disease in Southern China. Full article

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17 pages, 1988 KiB

Open AccessArticle

Transcriptomic Profiling of Thermotolerant Sarcomyxa edulis PQ650759 Reveals the Key Genes and Pathways During Fruiting Body Formation

by Zitong Liu, Minglei Li, Hongyu Ma, Fei Wang, Lei Shi, Jinhe Wang, Chunge Sheng, Peng Zhang, Haiyang Yu, Jing Zhao and Yanfeng Wang

J. Fungi 2025, 11(7), 484; https://doi.org/10.3390/jof11070484 - 26 Jun 2025

Abstract

Sarcomyxa edulis is a characteristic low-temperature, edible mushroom in Northeast China. It has a delicious taste and rich nutritional and medicinal value. S. edulis can undergo explosive fruiting, neat fruiting, and unified harvesting, making it suitable for factory production. The molecular mechanisms underlying [...] Read more.

Sarcomyxa edulis is a characteristic low-temperature, edible mushroom in Northeast China. It has a delicious taste and rich nutritional and medicinal value. S. edulis can undergo explosive fruiting, neat fruiting, and unified harvesting, making it suitable for factory production. The molecular mechanisms underlying fruiting body development in S. edulis remain poorly understood. This study employed transcriptome analysis to compare the post-ripening mycelium (NPM) and primordial fruiting bodies (PRMs) of the thermostable S. edulis strain PQ650759, which uniquely forms primordia under constant temperature. A total of 4862 differentially expressed genes (DEGs) (|log2(fold change)| ≥ 1) were identified and found to be predominantly enriched in biological processes such as cell wall organization, DNA replication, and carbohydrate metabolism. KEGG pathway analysis revealed significant enrichment in 20 metabolic pathways, including mismatch repair, yeast cell cycle, and starch/sucrose metabolism. Ten candidate genes (e.g., SKP1, MRE11, GPI) linked to cell cycle regulation, DNA repair, and energy metabolism were randomly selected and prioritized for functional analysis. Quantitative PCR validation confirmed the reliability of transcriptome data, with expression trends consistent across both methods. Our findings provide critical insights into the molecular regulation of fruiting body development in S. edulis and establish a foundation for future mechanistic studies and strain optimization in industrial cultivation. Full article

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

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10 pages, 380 KiB

Open AccessArticle

Microbiological Relevance of Candida in Urine Cultures

by Leticia Castellano-Sánchez, Antonio Rosales-Castillo, Raquel Marcos-Rodríguez, María Carmen Olvera-Porcel, José María Navarro-Marí and José Gutiérrez-Fernández

J. Fungi 2025, 11(7), 483; https://doi.org/10.3390/jof11070483 - 26 Jun 2025

Abstract

The presence of Candida spp. in urine has traditionally been considered to be a colonization; however, in certain clinical circumstances, such as in critically ill patients, immunocompromised individuals, or those with chronic diseases, it gains greater relevance due to the possibility of active [...] Read more.

The presence of Candida spp. in urine has traditionally been considered to be a colonization; however, in certain clinical circumstances, such as in critically ill patients, immunocompromised individuals, or those with chronic diseases, it gains greater relevance due to the possibility of active infection and complications. The aim of this study was to characterize the epidemiology (incidence, species distribution, demographic characteristics, and origin) of Candida spp. isolates in urine through a retrospective cross-sectional analysis of urine culture isolates from clinical samples between January 2016 and December 2023. Out of a total of 111,656 urine cultures, Candida spp. was isolated at 2.72% (n = 3037). The most frequently isolated species was Candida albicans (54.25%; 1646/3037), followed by Nakaseomyces glabrata (22.78%; 692/3037) and Candida tropicalis (10.2%; 311/3037). Advanced age (>70 years), male sex, presence of a urinary catheter, and origin from intensive care units, oncology, or surgical services were variables associated with a higher risk of candiduria, highlighting the relevance of candiduria in the presence of such clinical scenarios. Full article

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26 pages, 5541 KiB

Open AccessArticle

Disentangling a Complex of Violet, Endangered Species of Clavaria Subsumed Under the Misapplied Name Clavaria zollingeri Lév. (Clavariaceae, Fungi)

by Ibai Olariaga, Luis A. Parra, Thomas Læssøe, Juan Manuel Velasco, Ivona Kautmanova, Åsa Kruys and Isabel Salcedo

J. Fungi 2025, 11(7), 482; https://doi.org/10.3390/jof11070482 - 26 Jun 2025

Abstract

The name Clavaria zollingeri Lév. is currently applied to striking violet species producing branched basidiomata and lacking clamp connections, two typical characteristics of the genus Clavaria Pers. Interestingly, as currently interpreted, C. zollingeri has been globally assessed as Vulnerable by the IUCN and [...] Read more.

The name Clavaria zollingeri Lév. is currently applied to striking violet species producing branched basidiomata and lacking clamp connections, two typical characteristics of the genus Clavaria Pers. Interestingly, as currently interpreted, C. zollingeri has been globally assessed as Vulnerable by the IUCN and is red-listed in several European countries. However, the type material of C. zollingeri, examined here, possesses clamp connections and should be referred to the genus Clavulinopsis Van Overeem. Thus, the name C. zollingeri is being misapplied. Based on the taxonomic revision of the specimens, along with morphological and molecular studies of the nrDNA ITS-LSU regions, three species differing in spore characters, basidial size and distribution are recognized. After our nomenclatural revision we conclude that one of the species should be named Clavaria amethystina (Holmsk.) Bull., characterized by ellipsoid spores and distribution in the Northern Hemisphere; the second C. lilacina Jungh., with subglobose spores and present in Eastern Asia and Oceania; whereas the third, also with subglobose spores and distributed in Europe and North America, is newly described as C. violaceopulchra. Clavaria orientalis is proposed to be a later synonym of C. lilacina. Nine type specimens were examined, the name C. amethystina is typified and the combination of C. zollingeri in Clavulinopsis is proposed. Full article

(This article belongs to the Special Issue Fungal Diversity in Europe, 3rd Edition)

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15 pages, 868 KiB

Open AccessArticle

Comparative Genomics Reveals Ancient and Unique Pathogenicity Features in Australian Fusarium oxysporum f. sp. vasinfectum

by Angel David Popa-Baez, Linda J. Smith, Warwick N. Stiller, Melanie Soliveres, Gunjan Pandey, Christopher A. Saski, Don C. Jones and Iain W. Wilson

J. Fungi 2025, 11(7), 481; https://doi.org/10.3390/jof11070481 - 25 Jun 2025

Abstract

Fusarium oxysporum f. sp. vasinfectum (Fov) is a devastating cotton pathogen. Australian Fov strains are distinguished by their ability to infect plants without nematode interaction and are genetically distinct from global Fov, classified into two vegetative compatibility groups (VCG-01111 and [...] Read more.

Fusarium oxysporum f. sp. vasinfectum (Fov) is a devastating cotton pathogen. Australian Fov strains are distinguished by their ability to infect plants without nematode interaction and are genetically distinct from global Fov, classified into two vegetative compatibility groups (VCG-01111 and VCG-01112). Here, we present chromosome-level genome assemblies of a historical isolate for each Australian Fov VCG. The end-to-end gapless genome assemblies demonstrate high contiguity and completeness, with 97.7% BUSCO completeness for both isolates. Phylogenetic analysis indicates that the Australian Fov lineages diverged from other known Fov genomes over 3.6 million years ago, while VCG-01111 and VCG-01112 separated approximately 1.1 million years ago. Comparative genomics analysis identified four accessory chromosomes unique to the Australian isolates. Functional annotations revealed 14,495 and 15,342 genes in VCG-01111 and VCG-01112, respectively, with accessory chromosomes containing significantly fewer genes than core chromosomes. Ortholog analysis uncovered unique gene clusters enriched in key metabolic pathways, pathogenicity, and cell division processes. Additionally, we identified several novel lineage-specific peptides unique to each Australian isolate. This comprehensive genomic characterization provides the first insights into the unique evolutionary history of Australian Fov, distinguishing them from global Fov races. Our findings lay the foundation for understanding the genetic factors underlying their exceptional virulence, which makes Australian Fov among the most aggressive cotton pathogens worldwide. Full article

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

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16 pages, 425 KiB

Open AccessArticle

Current Challenges in the Treatment of Invasive Aspergillosis in Geriatric Patients

by Sara Fueyo Álvarez, Elena Valle Calonge, Julieth Andrea Caballero Velasquez, Alba Magaly Revelo Rueda, Pablo Enrique Solla Suarez, Eva María López Álvarez, Mercedes Rodriguez Perez and María Teresa Peláez García de la Rasilla

J. Fungi 2025, 11(7), 480; https://doi.org/10.3390/jof11070480 - 25 Jun 2025

Abstract

Background: Invasive aspergillosis (IA) is a severe fungal infection increasingly affecting elderly patients with chronic respiratory diseases and prolonged corticosteroid use. Methods: We evaluated clinical, biochemical, and fungal biomarkers in 45 patients over 80 years diagnosed with IA and hospitalized in a Spanish [...] Read more.

Background: Invasive aspergillosis (IA) is a severe fungal infection increasingly affecting elderly patients with chronic respiratory diseases and prolonged corticosteroid use. Methods: We evaluated clinical, biochemical, and fungal biomarkers in 45 patients over 80 years diagnosed with IA and hospitalized in a Spanish Acute Geriatric Unit. Patients received either voriconazole or isavuconazole. Mortality rates and associated risk factors were analyzed. Results: Overall mortality was 35.61%. Significant mortality risk factors included leukocytosis (p = 0.0371), neutrophilia (p = 0.0144), and lymphopenia (p = 0.0274). Deceased patients had longer hospital stays (26.6 vs. 16.8 days; p = 0.00353). Voriconazole treatment was associated with higher 30-day mortality (61.5% vs. 19.2%; p = 0.0001) and a higher incidence of adverse effects (60% vs. 5%; p = 0.0003) compared to isavuconazole. Voriconazole also showed greater pharmacokinetic variability, with 76.9% of cases outside the therapeutic range. Conclusions: Voriconazole may not be optimal for IA treatment in patients over 80 years. Isavuconazole demonstrated a more favorable safety and efficacy profile. Personalized therapeutic strategies and a multidisciplinary approach are essential to improve clinical outcomes and quality of life in this vulnerable population. Full article

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

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16 pages, 2357 KiB

Open AccessArticle

Dynamics of Nutrient Components and Microbial Communities in Substrates During the Development of the Fruiting Bodies of Volvariella volvacea

by Le Wang, Qin Dong, Qian Guo, Lei Zha, Lin Yang, Changxia Yu and Yan Zhao

J. Fungi 2025, 11(7), 479; https://doi.org/10.3390/jof11070479 - 24 Jun 2025

Abstract

Cotton waste, a growth medium for Volvariella volvacea, has significant commercial and nutritional value. Under controlled environmental conditions, substrate nutrient composition and microorganisms affect the growth of V. volvacea. In this study, the changes in the nutrient content of the substrate [...] Read more.

Cotton waste, a growth medium for Volvariella volvacea, has significant commercial and nutritional value. Under controlled environmental conditions, substrate nutrient composition and microorganisms affect the growth of V. volvacea. In this study, the changes in the nutrient content of the substrate at different stages of fruiting body development were compared based on an 86% waste cotton substrate, and microbial diversity was studied via 16S rRNA analysis. The results indicated that there were significant differences in nutrient content in the substrate at different stages of fruiting body development. The total contents of carbon, nitrogen, and phosphorus initially increased but then decreased due to nutrient absorption and utilization by V. volvacea. It was also found that large amounts of organic nitrogen decomposed into more readily utilizable inorganic nitrogen. The nutritional content and microbial community structure of the substrate during the egg stage significantly differed from those during the other four stages, making the egg stage the most critical period in cultivation. Through correlation analysis between nutrient content and microbial differences, it was found that differential microbial taxa (Beijerinckiaceae, Burkholderiales, Chitinophaga jiangningensis, etc.) with nitrogen fixation, denitrification, and cellulose decomposition functions were significantly related to carbon- and nitrogen-related indicators such as nitrate nitrogen, microbial biomass carbon, and alkali-hydrolyzed nitrogen. These microorganisms play important roles in determining the variation in the nutritional profile of the substrate. This study provides a theoretical basis for promoting the absorption and utilization of nutrients by V. volvacea by altering the structure of the microbial community of the growth substrate. Full article

(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)

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25 pages, 9272 KiB

Open AccessArticle

Monitoring of Fungal Diversity and Microclimate in Nine Different Museum Depots

by Katharina Derksen, Peter Brimblecombe, Guadalupe Piñar, Monika Waldherr, Alexandra Bettina Graf, Pascal Querner and Katja Sterflinger

J. Fungi 2025, 11(7), 478; https://doi.org/10.3390/jof11070478 - 24 Jun 2025

Abstract

Within museum depots, the largest part of all heritage collections is stored. Often, the preservation of highly sensitive objects is an ongoing challenge, as the materials are constantly subjected to and influenced by ever-present environmental factors—above all the surrounding climate and other physicochemical [...] Read more.

Within museum depots, the largest part of all heritage collections is stored. Often, the preservation of highly sensitive objects is an ongoing challenge, as the materials are constantly subjected to and influenced by ever-present environmental factors—above all the surrounding climate and other physicochemical processes. Biological degradation is also a major risk for collections. Fungal infestation poses a particular threat, in many regions increasingly the result of climate change. Models for damage prediction and risk assessment are still underdeveloped and require a more substantial database. Approaching this need, nine museum depots and archives were selected in this study. Two years of monitoring the indoor microclimate with thermohygrometric sensors, investigating fungal abundance and diversity through culture-dependent and -independent (metagenomics) approaches, and the collection of relevant additional information resulted in a vast amount of diverse data. The main fungal genera identified through cultivation were Cladosporium, Penicillium, Aspergillus, Alternaria and Epicoccum. The cultivation-independent approach identified Aspergillus, Pyronema, Penicillium, Xenodidymella and Blumeria as the main taxa. Data analyses indicated that key drivers involved in similarities, patterns and differences between the locations were their geographic location, immediate outdoor surroundings and indoor (micro)climatic fluctuations. The study also sheds light on a possible shift in focus when developing strategies for preventing mold growth in collection depots beyond the prevailing path of tightest possible climate control. Full article

(This article belongs to the Special Issue Diversity of Microscopic Fungi)

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