Journal of Fungi

16 pages, 3130 KiB

Open AccessArticle

Ozone Treatment Inhibited the Blue Mold Development and Maintained the Main Active Ingredient Content in Radix astragali Infected by Penicillium polonicum Through Activating Reactive Oxygen Species Metabolism

by Jihui Xi, Qili Liu, Qingru Zhang, Zhiguang Liu, Huali Xue and Yuqin Feng

J. Fungi 2025, 11(6), 402; https://doi.org/10.3390/jof11060402 - 23 May 2025

Abstract

Radix astragali is a homologous plant of medicine and food with a variety of health benefits. However, our previous study showed that blue mold, caused by Penicillium polonicum, is the most important postharvest disease of fresh R. astragali during storage. Ozone, as [...] Read more.

Radix astragali is a homologous plant of medicine and food with a variety of health benefits. However, our previous study showed that blue mold, caused by Penicillium polonicum, is the most important postharvest disease of fresh R. astragali during storage. Ozone, as a strong oxidizing agent, can effectively control the occurrence of postharvest diseases in fruits and vegetables. Nevertheless, there are few research studies on the effect of ozone-treated fresh Chinese traditional medicine. In this study, we investigated the effect of ozone gas on the postharvest blue mold development, mycotoxin accumulation, and main active component contents in fresh R. astragali infected by P. polonicum, and analyzed the possible action mechanism on ROS metabolism. The result indicates that ozone application significantly inhibited the development of postharvest blue mold caused by P. polonicum infection, reduced the disease incidence, disease index, and weight loss rate, maintained the main active ingredients in fresh R. astragali by activating ROS metabolism, enhanced the antioxidant enzymatic activity, thus avoiding oxidative damage caused by excessive ROS accumulation, and maintained the integrity of the cell membrane, ultimately controlling the occurrence of blue mold of R. astragali. Moreover, ozone treatment also maintained the contents of the main active ingredients in R. astragali before 14 d during P. polonicum infection. In addition, the amount of active ingredients of astragaloside I, calycosin-7-glucoside, and ononin in the ozone-treated group was higher than that in the control group during the storage period. We speculate that, under the action of ozone, astragaloside IV was converted into astragaloside II by oxidative modification and astragaloside II was further oxidized to astragaloside I, resulting in the accumulation of astragaloside I. Similarity, the hydrogen atoms (-H) on the benzene ring in formononetin were oxidized to phenolic hydroxyl groups (-OH) to generate calycosin, which was further converted into calycosin-7-glucoside, resulting in calycosin-7-glucoside accumulation. This study will provide the theoretical basis for ozone commercial application to control the occurrence of postharvest diseases of R. astragali. Full article

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

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16 pages, 1679 KiB

Open AccessArticle

Whole-Genome Sequencing and Comparative Genomic Analysis of Three Clinical Bloodstream Infection Isolates of Trichosporon austroamericanum

by Takanori Horiguchi, Takashi Umeyama, Hiroko Tomuro, Amato Otani, Takayuki Shinohara, Masahiro Abe, Shogo Takatsuka, Ken Miyazawa, Minoru Nagi, Yasunori Muraosa, Yasutaka Hoshino, Takashi Sakoh, Hideki Araoka, Naoyuki Uchida, Tomoyoshi Kaneko, Yuko Nagano, Hiroki Tsukada, Taiga Miyazaki and Yoshitsugu Miyazaki

J. Fungi 2025, 11(5), 401; https://doi.org/10.3390/jof11050401 - 21 May 2025

Abstract

Trichosporon austroamericanum is a recently described yeast species related to Trichosporon inkin and exclusively isolated from clinical specimens. However, its genomic features and pathogenic potential remain poorly understood. In this study, we performed whole-genome sequencing on three blood-derived isolates from patients with invasive [...] Read more.

Trichosporon austroamericanum is a recently described yeast species related to Trichosporon inkin and exclusively isolated from clinical specimens. However, its genomic features and pathogenic potential remain poorly understood. In this study, we performed whole-genome sequencing on three blood-derived isolates from patients with invasive fungal infections and comparative analyses with 13 related Trichosporon species. The three isolates yielded high-quality assemblies of 9–10 scaffolds (~21 Mb), facilitating reliable comparisons. While most species had comparable genome sizes, Trichosporon ovoides, Trichosporon coremiiforme, and Cutaneotrichosporon mucoides displayed large, fragmented genomes, suggestive of polyploidy. ANI analysis and phylogenetic trees based on ANI and single-copy orthologs supported the classification of T. austroamericanum as a distinct clade with moderate intraspecific divergence. Using the Galleria mellonella, a model for fungal pathogenicity, all T. austroamericanum strains reduced larval survival, and NIIDF 0077300 exhibited virulence comparable to T. asahii and greater than T. inkin. To explore the gene-level differences associated with pathogenicity, we performed ortholog analysis based on single-copy genes. This revealed a unique Zn(II)₂Cys₆-type transcription factor gene (OG0010545) present only in NIIDF 0077300 and T. asahii. These findings highlight the genomic diversity and infection-associated traits of T. austroamericanum, providing a framework for future functional studies. Full article

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

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20 pages, 860 KiB

Open AccessArticle

The Impact of Epidemiological Trends and Guideline Adherence on Candidemia-Associated Mortality: A 14-Year Study in Northeastern Italy

by Fabiana Dellai, Alberto Pagotto, Francesco Sbrana, Andrea Ripoli, Giacomo Danieli, Alberto Colombo, Denise D’Elia, Monica Geminiani, Simone Giuliano, Assunta Sartor and Carlo Tascini

J. Fungi 2025, 11(5), 400; https://doi.org/10.3390/jof11050400 - 21 May 2025

Abstract

Invasive candidiasis represents a major global health concern, with incidence and mortality rates expected to rise due to medical advancements and unavoidable risk factors. This retrospective, multicentric study was conducted in eight hospitals in a northeastern Italian region, enrolling adult patients diagnosed with [...] Read more.

Invasive candidiasis represents a major global health concern, with incidence and mortality rates expected to rise due to medical advancements and unavoidable risk factors. This retrospective, multicentric study was conducted in eight hospitals in a northeastern Italian region, enrolling adult patients diagnosed with candidemia from 1 January 2018 to 31 December 2022. Epidemiological trends and clinical characteristics were analyzed and compared to those from a prior regional study (2009–2011), allowing a fourteen-year comparative evaluation. A shift in species distribution was observed, with a decline in Candida albicans (from 65.7% to 57.8%) and a rise in non-albicans species, particularly the Candida parapsilosis complex (from 16.1% to 18.2%). Guideline adherence was assessed applying the EQUAL Candida score; scores ≥ than 11.5 were independently associated with improved in-hospital survival (HR 3.51, p < 0.001). Among individual score components, empiric echinocandin therapy and central venous catheter removal correlated with better outcomes. Centers with routine infectious disease (ID) consultations showed higher survival and adherence, reinforcing the value of specialist involvement. These findings support local epidemiological and management practice surveillance program adoption to address context-specific gaps, promote the adoption of best practices in Candida BSI management—as expanded ID specialist consultations and education programs—and, ultimately, reduce candidemia-related mortality rates. Full article

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

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14 pages, 2745 KiB

Open AccessArticle

Genomic Insights into Neofusicoccum laricinum: The Pathogen Behind Chinese Larch Shoot Blight

by Jialiang Pan, Zhijun Yu, Wenhao Dai, Chunhe Lv, Yifan Chen, Hong Sun, Jie Chen and Junxin Gao

J. Fungi 2025, 11(5), 399; https://doi.org/10.3390/jof11050399 - 21 May 2025

Abstract

Larch shoot blight, caused by the fungus Neofusicoccum laricinum, threatens larch (Larix spp.) forests across northeastern China, jeopardizing both timber productivity and ecological stability. This study aimed to investigate the genomic diversity, population structure, and potential adaptive mechanisms of N. laricinum [...] Read more.

Larch shoot blight, caused by the fungus Neofusicoccum laricinum, threatens larch (Larix spp.) forests across northeastern China, jeopardizing both timber productivity and ecological stability. This study aimed to investigate the genomic diversity, population structure, and potential adaptive mechanisms of N. laricinum across contrasting climatic regions. To achieve this, we conducted whole-genome resequencing of 23 N. laricinum isolates collected from three major provinces—Heilongjiang, Inner Mongolia, and Jilin—that represent distinct climatic zones ranging from cold-temperate to relatively warmer regions. We identified ~219.1 K genetic variants, offering a detailed portrait of the pathogen’s genomic diversity. Population structure analyses, including principal component analysis and phylogenetic tree, revealed clear genetic differentiation aligning with geographic origin and climate. Functional annotation (GO and KEGG) highlighted enrichment in metabolic, stress-response, and membrane transport pathways, suggesting potential adaptation to varied temperature regimes and environmental pressures. Moreover, region-specific variants—particularly missense and stop-gain mutations—were linked to genes involved in ATP binding, oxidoreductase activity, and cell division, underscoring the fungus’s capacity for rapid adaptation. Collectively, these findings fill a critical gap in the population genetics of N. laricinum and lay a foundation for future disease management strategies to larch shoot blight under changing climatic conditions. 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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14 pages, 2383 KiB

Open AccessArticle

Myricetin Exerts Antibiofilm Effects on Candida albicans by Targeting the RAS1/cAMP/EFG1 Pathway and Disruption of the Hyphal Network

by Melda Meral Ocal, Merve Aydin, Esra Sumlu, Emine Nedime Korucu and Ali Ozturk

J. Fungi 2025, 11(5), 398; https://doi.org/10.3390/jof11050398 - 21 May 2025

Abstract

Increasing antifungal resistance and side effects of existing drugs demand alternative approaches for treating Candida (C.) infections. This study aimed to comprehensively evaluate the antifungal efficacy of myricetin (MYR), a natural flavonoid, against both fluconazole (FLC)-resistant and susceptible clinical Candida strains, [...] Read more.

Increasing antifungal resistance and side effects of existing drugs demand alternative approaches for treating Candida (C.) infections. This study aimed to comprehensively evaluate the antifungal efficacy of myricetin (MYR), a natural flavonoid, against both fluconazole (FLC)-resistant and susceptible clinical Candida strains, with a particular focus on its inhibitory effects on C. albicans biofilms. Antifungal susceptibility was evaluated on Candida spp. by the broth microdilution method, and the impact of myricetin on C. albicans biofilms was determined using the Cell Counting Kit-8 (CCK-8) assay. To understand the molecular mechanisms underlying the antibiofilm properties of myricetin, expression analysis of genes in the RAS1/cAMP/EFG1 pathway (ALS3, HWP1, ECE1, UME6, HGC1) and cAMP-dependent protein kinase regulation (RAS1, CYR1, EFG1) involved in the transition from yeast to hyphae was performed. Field emission scanning electron microscopy (FESEM) was used to study the ultrastructural changes and morphological dynamics of Candida biofilms after exposure to MYR and FLC. The in vivo toxicity of myricetin was evaluated by survival analysis using the Galleria mellonella model. Myricetin significantly suppressed key genes related to hyphae development (RAS1, CYR1, EFG1, UME6, and HGC1) and adhesion (ALS3 and HWP1) in both clinical and reference Candida strains at a concentration of 640 µg/mL. FESEM analysis revealed that myricetin inhibited hyphae growth and elongation in C. albicans. This study highlights the promising antibiofilm potential of myricetin through a significant inhibition of biofilm formation and hyphal morphogenesis. Full article

(This article belongs to the Special Issue Alternative Therapeutic Approaches of Candida Infections, 4th Edition)

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13 pages, 5005 KiB

Open AccessArticle

FGSE02, a Novel Secreted Protein in Fusarium graminearum FG-12, Leads to Cell Death in Plant Tissues and Modulates Fungal Virulence

by Zhigang Hao, Lei Pan, Jiaqing Xu, Chengxuan Yu, Jianqiang Li and Laixin Luo

J. Fungi 2025, 11(5), 397; https://doi.org/10.3390/jof11050397 - 21 May 2025

Abstract

Fungal phytopathogens employ effector proteins and secondary metabolites to subvert host immunity. Effector proteins have attracted widespread interest in infection, especially for unknown, unreported genes. However, the type of protein remains much less explored. Here, we combined transcriptome analysis and functional validation to [...] Read more.

Fungal phytopathogens employ effector proteins and secondary metabolites to subvert host immunity. Effector proteins have attracted widespread interest in infection, especially for unknown, unreported genes. However, the type of protein remains much less explored. Here, we combined transcriptome analysis and functional validation to identify virulence-associated genes in Fusarium graminearum during fungi infection. A unique secreted protein, FGSE02, was significantly upregulated in the early infection stage. Proteomic characterization revealed that the protein contains a functional signal peptide but lacks known domains. The transient expression of FGSE02 in Nicotiana benthamiana induced rapid cell death, while gene knockout stains reduced fungal virulence without affecting growth. Our findings highlight FGSE02 as a key virulence factor, offering potential targets for disease control. Taken together, the results of this study identify a pathogenic factor and provide new insights into the development of green pesticides. 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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23 pages, 4096 KiB

Open AccessArticle

Act1 out of Action: Identifying Reliable Reference Genes in Trichoderma reesei for Gene Expression Analysis

by Caroline Danner, Yuriy Karpenko, Robert L. Mach and Astrid R. Mach-Aigner

J. Fungi 2025, 11(5), 396; https://doi.org/10.3390/jof11050396 - 21 May 2025

Abstract

Trichoderma reesei is a well-established industrial enzyme producer and has been the subject of extensive research for various applications. The basis of many research studies is the analysis of gene expression, specifically with RT-qPCR, which requires stable reference genes for normalization to yield [...] Read more.

Trichoderma reesei is a well-established industrial enzyme producer and has been the subject of extensive research for various applications. The basis of many research studies is the analysis of gene expression, specifically with RT-qPCR, which requires stable reference genes for normalization to yield reliable results. Yet the commonly used reference genes, act1 and sar1, were initially chosen based on reports from the literature rather than systematic validation, raising concerns about their stability. Thus, properly evaluated reference genes for T. reesei are lacking. In this study, five potentially new reference genes were identified by analyzing publicly available transcriptome datasets of the T. reesei strains QM6a and Rut-C30. Their expression stability was then evaluated under relevant cultivation conditions using RT-qPCR and analyzed with RefFinder. The two most stable candidate reference genes were further validated by normalizing the expression of the well-characterized gene cbh1 and comparing the results to those obtained using act1 and sar1. Additionally, act1 and sar1 were normalized against the new reference genes to assess the variability in their expression. All five new reference genes exhibited a more stable expression than act1 and sar1. Both in silico and RT-qPCR analysis ranked the so far uncharacterized gene, bzp1, as the most stable. Further, we found that act1 and sar1 have strain- and condition-dependent expression variability, suggesting that they are unsuitable as universal reference genes in T. reesei. Based on these results, we propose to use the combination of bzp1 and tpc1 for the normalization in RT-qPCR analysis instead of act1 and sar1. Full article

(This article belongs to the Special Issue Trichoderma in Action)

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23 pages, 5251 KiB

Open AccessArticle

Genomic Sequencing and Characterization of Two Auricularia Species from the Qinling Region: Insights into Evolutionary Dynamics and Secondary Metabolite Potential

by Jianzhao Qi, Shijie Kang, Ming Zhang, Shen Qi, Yulai Li, Khassanov Vadim, Shuangtian Du and Minglei Li

J. Fungi 2025, 11(5), 395; https://doi.org/10.3390/jof11050395 - 20 May 2025

Abstract

Auricularia mushrooms, common bulk edible fungi, have considerable culinary and medicinal value. The Qinling region, represented by Zhashui County, is the main production area of Auricularia mushrooms in China. In this study, two wild Auricularia strains, M12 and M13, selected from the Qinling [...] Read more.

Auricularia mushrooms, common bulk edible fungi, have considerable culinary and medicinal value. The Qinling region, represented by Zhashui County, is the main production area of Auricularia mushrooms in China. In this study, two wild Auricularia strains, M12 and M13, selected from the Qinling region for their desirable horticultural traits after domestication, were sequenced and characterized. Sequencing assembly results based on Illumina NovaSeq and PacBio Sequel II HiFi showed that the M12 genome was 56.04 Mbp in size, with 2.58% heterozygosity and 14.13% repetitive sequences, and was anchored on 12 chromosomes using HI-C technology. In contrast, the M13 genome was 52.10 Mbp, showed 2.34% heterozygosity, 13.89% repetitive sequences, and was assembled into 12 scaffolds. Collinearity analysis revealed extensive homologous regions between the M12 and M13 genomes. Phylogenetic analysis suggested that the divergence between M12 and M13 occurred approximately 4.575 million years ago (MYAs), while their divergence from Auricularia subglabra TFB-10046 SS5 occurred approximately 33.537 MYAs. Analyses of CYP450, carbohydrate-active enzymes (CAZymes), and gene family expansion/contraction revealed distinct genomic features between the two strains. SSR and LTR insertion time analyses revealed the genome dynamics of the two strains during their evolution. Analysis of secondary metabolite-associated biosynthetic gene clusters (BGCs) provides powerful clues to understand the origin of bioactive compounds in the Auricularia mushroom. This work represents the first genome sequencing of the Auricularia species derived from the Qinling region. These results not only enriched our understanding of the Auricularia genome but also provided an important genomic resource and theoretical basis for the subsequent genetic breeding, functional gene mining, and development of medicinal components of Auricularia species. Full article

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

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15 pages, 2510 KiB

Open AccessArticle

Phenotypic and Molecular Characterization of Multidrug-Resistant Clinical Isolates of the Candidozyma haemuli Species Complex (Formerly Candida haemulonii Species Complex) from the Brazilian Amazon Reveals the First Case of Candidozyma pseudohaemuli in Brazil

by Sérgio Lobato França, Rodrigo Santos de Oliveira, Gabriel Silas Marinho Sousa, Sarah Rodrigues de Sá, Walber da Silva Nogueira, Elaine Patrícia Tavares do Espírito Santo, Daniel dos Santos Caldas and Silvia Helena Marques da Silva

J. Fungi 2025, 11(5), 394; https://doi.org/10.3390/jof11050394 - 20 May 2025

Abstract

This study included 24 isolates of the Candidozyma haemuli species complex from patients in the Brazilian Amazon between 2021 and 2024. These isolates were identified by sequencing as C. duobushaemuli (54.2%), C. haemuli sensu stricto (29.2%), C. haemuli var. vulneris (12.5%), and C. [...] Read more.

This study included 24 isolates of the Candidozyma haemuli species complex from patients in the Brazilian Amazon between 2021 and 2024. These isolates were identified by sequencing as C. duobushaemuli (54.2%), C. haemuli sensu stricto (29.2%), C. haemuli var. vulneris (12.5%), and C. pseudohaemuli (4.2%). The finding of C. pseudohaemuli represents the first case reported in Brazil. Haplotype and phylogenetic analysis of these species, along with other isolates from Brazil, revealed low intraspecific genetic diversity. Resistance to at least one antifungal was observed in 83.3% of isolates, with multidrug resistance in 58.3%, including one isolate resistant to all tested antifungals. The isolates demonstrated active biofilm production, lytic enzyme activity, and thermotolerance. Notably, one C. duobushaemuli isolate exhibited tolerance to 42 °C, a phenotype not previously described. It is crucial for Brazil and other countries to recognize the emergence of these species as a public health threat and to take proactive measures to prevent outbreaks. Full article

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20 pages, 1812 KiB

Open AccessSystematic Review

Pine Forest Plantations in the Neotropics: Challenges and Potential Use of Ectomycorrhizal Fungi and Bacteria as Inoculants

by Yajaira Baeza-Guzmán, Sara Lucía Camargo-Ricalde, Dora Trejo-Aguilar and Noé Manuel Montaño

J. Fungi 2025, 11(5), 393; https://doi.org/10.3390/jof11050393 - 20 May 2025

Abstract

Forest plantations in the Neotropics aim to alleviate pressure on primary forests. This study synthesizes knowledge on pine species used in these plantations, emphasizing the challenges and potential of ectomycorrhizal fungi and bacteria as inoculants. An analysis of 98 articles identifies 23 pine [...] Read more.

Forest plantations in the Neotropics aim to alleviate pressure on primary forests. This study synthesizes knowledge on pine species used in these plantations, emphasizing the challenges and potential of ectomycorrhizal fungi and bacteria as inoculants. An analysis of 98 articles identifies 23 pine species in Mexico and Central America and about 16 fast-growing species in South America. While pine plantations provide a habitat for generalist species, they reduce the richness of specialist species. Ectomycorrhizal fungi and bacterial diversity in plantations with introduced pines is up to 20% lower compared to native ecosystems. Suillus and Hebeloma are commonly used as mycorrhizal inoculants for Neotropical and introduced species, including Pinus ponderosa and Pinus radiata in South America. Commercial inoculants predominantly feature the fungal species Pisolithus tinctorius, alongside bacterial genera such as Bacillus, Cohnella, and Pseudomonas. This study emphasizes the importance of leveraging native microbial communities and their synergistic interactions with ECM fungi and bacteria to enhance seedling growth and quality. Such a combined approach can improve plantation survival, boost resilience to environmental stressors, and promote long-term productivity. These findings underscore the need to incorporate native fungi and bacteria into inoculant strategies, advancing sustainable forestry practices and ecosystem adaptation in the Neotropics. Full article

(This article belongs to the Special Issue Mycological Research in Mexico)

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22 pages, 7024 KiB

Open AccessArticle

Isolation and Identification of Colletotrichum nymphaeae as a Causal Agent of Leaf Spot on Rhododendron hybridum Ker Gawl and Its Effects on the Ultrastructure of Host Plants

by Yajiao Sun, Yunjing Tian, Jian Liu, Huali Li, Junjia Lu, Mengyao Wang and Shuwen Liu

J. Fungi 2025, 11(5), 392; https://doi.org/10.3390/jof11050392 - 19 May 2025

Abstract

Rhododendron hybridum Ker Gawl, a widely cultivated horticultural species in China, is highly valued for its ornamental and medicinal properties. However, with the expansion of its cultivation, leaf spot disease has become more prevalent, significantly affecting the ornamental value of R. hybridum Ker [...] Read more.

Rhododendron hybridum Ker Gawl, a widely cultivated horticultural species in China, is highly valued for its ornamental and medicinal properties. However, with the expansion of its cultivation, leaf spot disease has become more prevalent, significantly affecting the ornamental value of R. hybridum Ker Gawl. In this study, R. hybridum Ker Gawl from the Kunming area was selected as the experimental material. The tissue isolation method was employed in this study to isolate pathogenic strains. The biological characteristics of the pathogens were determined using the mycelial growth rate method. The pathogens’ influence on the host plant’s ultrastructure was investigated using transmission electron microscopy (TEM). Colletotrichum nymphaeae was identified as the pathogen implicated in the development of leaf spot disease in R. hybridum Ker Gawl across three regions in Kunming City through the integration of morphological traits and phylogenetic analyses of multiple genes (ITS, ACT, GAPDH, HIS3, CHS1, and TUB2). Its mycelial growth is most effective at a temperature of 25 °C. pH and light have relatively minor effects on the growth of mycelium. The preferred carbon and nitrogen sources were identified as mannitol and yeast extract, respectively. Additionally, TEM observations revealed significant damage to the cell structure of R. hybridum Ker Gawl leaves infected by the pathogen. The cell walls were dissolved, the number of chloroplasts decreased markedly, starch granules within chloroplasts were largely absent, and the number of osmiophilic granules increased. This is the first report of leaf spot disease in R. hybridum Ker Gawl caused by C. nymphaeae. The results of this study provide valuable insights for future research on the prevention and control of this disease. Full article

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18 pages, 7007 KiB

Open AccessArticle

by Thilini Weerasinghe, Josh Li, Xuanye Chen, Jiayang Gao, Lei Tian, Yan Xu, Yihan Gong, Weijie Huang, Yuelin Zhang, Liwen Jiang and Xin Li

J. Fungi 2025, 11(5), 391; https://doi.org/10.3390/jof11050391 - 19 May 2025

Abstract

Sclerotinia sclerotiorum is a devastating fungal pathogen that can colonize numerous crops. Despite its economic importance, the regulation of its development and pathogenicity remains poorly understood. From a forward genetic screen in S. sclerotiorum, six UV mutants were identified with loss-of-function mutations [...] Read more.

Sclerotinia sclerotiorum is a devastating fungal pathogen that can colonize numerous crops. Despite its economic importance, the regulation of its development and pathogenicity remains poorly understood. From a forward genetic screen in S. sclerotiorum, six UV mutants were identified with loss-of-function mutations in SsATG1, SsATG2, SsATG4, SsATG5, SsATG9, and SsATG26. Functional validation through gene knockouts revealed that each ATG is essential for sclerotia formation, although the morphology of appressoria was not significantly altered in the mutants. Different levels of virulence attenuation were observed among these mutants. Autophagy, monitored using GFP-ATG8, showed dynamic activities during sclerotia development. These findings suggest that macroautophagy and pexophagy contribute to sclerotia maturation and virulence processes. Future work will reveal how autophagy controls target organelle or protein turnover to regulate these processes. Full article

(This article belongs to the Special Issue Current Research in Soil Borne Plant Pathogens)

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14 pages, 2135 KiB

Open AccessArticle

Neocotylidia gen. nov. (Hymenochaetales, Basidiomycota) Segregated from Cotylidia Based on Morphological, Phylogenetic, and Ecological Evidence

by Jinxin Ma, Yizhe Zhang, Jiaqi Liang, Yue Li, Heng Zhao, Zhirui Shang, Jing Si and Haijiao Li

J. Fungi 2025, 11(5), 390; https://doi.org/10.3390/jof11050390 - 19 May 2025

Abstract

Taxonomic and phylogenetic studies of Cotylidia (Hymenochaetales, Basidiomycota) were performed. A phylogenetic estimate based on six genetic markers revealed that Cotylidia in the current sense includes species belonging to three distantly related clades in the Hymenochaetales. Based on morphology, phylogeny, and ecological habitat, [...] Read more.

Taxonomic and phylogenetic studies of Cotylidia (Hymenochaetales, Basidiomycota) were performed. A phylogenetic estimate based on six genetic markers revealed that Cotylidia in the current sense includes species belonging to three distantly related clades in the Hymenochaetales. Based on morphology, phylogeny, and ecological habitat, the name Cotylidia s.s. is proposed for the first clade, including the type species C. undulata and C. carpatica. Neocotylidia gen. nov. is proposed for the second clade, which includes N. diaphana, N. fibrae, the new species N. bambusicola, and two accessions recorded as Cotylidia aurantiaca var. alba and C. aurantiaca. Contrary to the findings in earlier studies, C. pannosa demonstrated a weak grouping affinity with Globulicium hiemale, Hastodontia hastata, Atheloderma mirabile, Tsugacorticium kenaicum, Lawrynomyces capitatus, and Lyoathelia laxa. The morphological characteristics of Cotylidia s.s. are restricted to species with hymenial cystidia, pileocystidia, and caulocystidia, as well as a muscicolous habitat. Neocotylidia species differ from Cotylidia s.s. in the lack of pileocystidia and caulocystidia and substrate preference for soil or wood. Illustrated descriptions of the new species and genus, as well as an identification key to the worldwide species of Cotylidia s.l. are provided. Full article

(This article belongs to the Special Issue Taxonomy, Systematics and Evolution of Forestry Fungi, 2nd Edition)

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21 pages, 4432 KiB

Open AccessArticle

Soil Fungal Diversity, Community Structure, and Network Stability in the Southwestern Tibetan Plateau

by Shiqi Zhang, Zhenjiao Cao, Siyi Liu, Zhipeng Hao, Xin Zhang, Guoxin Sun, Yuan Ge, Limei Zhang and Baodong Chen

J. Fungi 2025, 11(5), 389; https://doi.org/10.3390/jof11050389 - 19 May 2025

Abstract

Despite substantial research on how environmental factors affect fungal diversity, the mechanisms shaping regional-scale diversity patterns remain poorly understood. This study employed ITS high-throughput sequencing to evaluate soil fungal diversity, community composition, and co-occurrence networks across alpine meadows, desert steppes, and alpine shrublands [...] Read more.

Despite substantial research on how environmental factors affect fungal diversity, the mechanisms shaping regional-scale diversity patterns remain poorly understood. This study employed ITS high-throughput sequencing to evaluate soil fungal diversity, community composition, and co-occurrence networks across alpine meadows, desert steppes, and alpine shrublands in the southwestern Tibetan Plateau. We found significantly higher fungal α-diversity in alpine meadows and desert steppes than in alpine shrublands. Random forest and CAP analyses identified the mean annual temperature (MAT) and normalized difference vegetation index (NDVI) as major ecological drivers. Mantel tests revealed that soil physicochemical properties explained more variation than climate, indicating an indirect climatic influence via soil characteristics. Distance–decay relationships suggested that environmental heterogeneity and species interactions drive community isolation. Structural equation modeling confirmed that the MAT and NDVI regulate soil pH and carbon/nitrogen availability, thereby influencing fungal richness. The highly modular fungal co-occurrence network depended on key nodes for connectivity. Vegetation coverage correlated positively with network structure, while soil pH strongly affected network stability. Spatial heterogeneity constrained stability and diversity through resource distribution and niche segregation, whereas stable networks concentrated resources among dominant species. These findings enhance our understanding of fungal assemblage processes at a regional scale, providing a scientific basis for the management of soil fungal resources in plateau ecosystems. Full article

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

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20 pages, 3840 KiB

Open AccessArticle

Vacuolar Proteases of Candida auris from Clades III and IV and Their Relationship with Autophagy

by Daniel Clark-Flores, Alvaro Vidal-Montiel, Ricardo Mondragón-Flores, Eulogio Valentín-Gómez, César Hernández-Rodríguez, Margarita Juárez-Montiel and Lourdes Villa-Tanaca

J. Fungi 2025, 11(5), 388; https://doi.org/10.3390/jof11050388 - 18 May 2025

Abstract

Candida auris is a multidrug-resistant pathogen with a high mortality rate and widespread distribution. Additionally, it can persist on inert surfaces for extended periods, facilitating its transmissibility in hospital settings. Autophagy is a crucial cellular mechanism that enables fungal survival under adverse conditions. [...] Read more.

Candida auris is a multidrug-resistant pathogen with a high mortality rate and widespread distribution. Additionally, it can persist on inert surfaces for extended periods, facilitating its transmissibility in hospital settings. Autophagy is a crucial cellular mechanism that enables fungal survival under adverse conditions. A fundamental part of this process is mediated by vacuolar proteases, which play an essential role in the degradation and recycling of cellular components. The present work explores the relationship between C. auris vacuolar peptidases and autophagy, aiming to establish a precedent for understanding the survival mechanisms of this emerging fungus. Thus, eight genes encoding putative vacuolar peptidases in the C. auris genomes were identified: PEP4, PRB1, PRC1, ATG42, CPS, LAP4, APE3, and DAP2. Analysis of the protein domains and their phylogenetic relationships suggests that these enzymes are orthologs of Saccharomyces cerevisiae vacuolar peptidases. Notably, both vacuolar protease gene expression and the proteolytic activity of cell-free extracts increased under nutritional stress and rapamycin. An increase in the expression of the ATG8 gene and the presence of autophagic bodies were also observed. These results suggest that proteases could play a role in yeast autophagy and survival during starvation conditions. Full article

(This article belongs to the Special Issue Candidiasis: Changes and Challenges in Its Epidemiology, Pathogenesis, Diagnosis, Treatment and Prevention)

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20 pages, 34946 KiB

Open AccessArticle

Feasibility of Bamboo Sawdust as Sustainable Alternative Substrate for Auricularia heimuer Cultivation

by Ya-Hui Wang, Cong-Sheng Yan, Yong-Jin Deng, Zheng-Fu Zhu, Hua-An Sun, Hui-Ping Li, Hong-Yuan Zhao and Guo-Qing Li

J. Fungi 2025, 11(5), 387; https://doi.org/10.3390/jof11050387 - 17 May 2025

Abstract

With the increasing scarcity of traditional hardwood sawdust resources, developing sustainable substrates for edible fungi cultivation has become an urgent industrial priority. This study systematically evaluated the effects of bamboo sawdust substitutions (20%, 30%, 40%, and 50%) on mycelial growth, fruiting body development, [...] Read more.

With the increasing scarcity of traditional hardwood sawdust resources, developing sustainable substrates for edible fungi cultivation has become an urgent industrial priority. This study systematically evaluated the effects of bamboo sawdust substitutions (20%, 30%, 40%, and 50%) on mycelial growth, fruiting body development, and nutritional quality of Auricularia heimuer, while elucidating the underlying molecular mechanisms through transcriptome sequencing. The results demonstrated that bamboo substitution of ≤30% maintained normal mycelial growth and fruiting body differentiation, with 20% and 30% substitutions increasing yields by 5.30% and 3.70%, respectively, compared to the control. However, 50% substitution significantly reduced yield by 9.49%. Nutritional analysis revealed that 20–40% bamboo substitution significantly enhanced the contents of crude protein, polysaccharides, and essential minerals (calcium, iron, and selenium) in fruiting bodies. Transcriptome analysis identified upregulation of glycosyl hydrolase family genes and downregulation of redox-related genes with increasing bamboo proportions. Biochemical assays confirmed these findings, showing decreased oxidative substances and increased reductive compounds in mycelia grown with high bamboo content, which indicate disrupted cellular redox homeostasis. This study provides both a practical solution to alleviate the “edible mushrooms derived from lignicolous fungi–forest conflict” and fundamental insights into fungal adaptation mechanisms to non-wood substrates, thus establishing a theoretical foundation for the valorization of agricultural and forestry wastes. Full article

(This article belongs to the Special Issue Fungi in Sustainable Applications and the Circular Economy: A Themed Issue Dedicated to Academician Yu Li)

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19 pages, 11989 KiB

Open AccessArticle

PEG-Mediated Protoplast Transformation of Penicillium sclerotiorum (scaumcx01): Metabolomic Shifts and Root Colonization Dynamics

by Israt Jahan, Qilin Yang, Zijun Guan, Yihan Wang, Ping Li and Yan Jian

J. Fungi 2025, 11(5), 386; https://doi.org/10.3390/jof11050386 - 17 May 2025

Abstract

Protoplast-based transformation is a vital tool for genetic studies in fungi, yet no protoplast method existed for P. sclerotiorum-scaumcx01 before this study. Here, we optimized protoplast isolation, regeneration, and transformation efficiency. The highest protoplast yield (6.72 × 10⁶ cells/mL) was obtained [...] Read more.

Protoplast-based transformation is a vital tool for genetic studies in fungi, yet no protoplast method existed for P. sclerotiorum-scaumcx01 before this study. Here, we optimized protoplast isolation, regeneration, and transformation efficiency. The highest protoplast yield (6.72 × 10⁶ cells/mL) was obtained from liquid mycelium after 12 h of enzymatic digestion at 28 °C using Lysing Enzymes, Yatalase, cellulase, and pectinase. Among osmotic stabilizers, 1 M MgSO₄ yielded the most viable protoplasts. Regeneration occurred via direct mycelial outgrowth and new protoplast formation, with a 1.02% regeneration rate. PEG-mediated transformation with a hygromycin resistance gene and GFP tagging resulted in stable GFP expression in fungal spores and mycelium over five generations. LC/MS-based metabolomic analysis revealed significant changes in glycerophospholipid metabolism, indicating lipid-related dynamics influenced by GFP tagging. Microscopy confirmed successful colonization of tomato roots by GFP-tagged scaumcx01, with GFP fluorescence observed in cortical tissues. Enzymatic (cellulase) seed pretreatment enhanced fungal colonization by modifying root surface properties, promoting plant–fungal interaction. This study establishes an efficient protoplast transformation system, reveals the metabolic impacts of genetic modifications, and demonstrates the potential of enzymatic seed treatment for enhancing plant–fungal interactions. Full article

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

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28 pages, 4056 KiB

Open AccessArticle

Morphological, Physiological, Biochemical, and Molecular Characterization of Fungal Species Associated with Papaya Rot in Cameroon

by Moussango Victor Davy, Voundi Olugu Steve, Tchabong Raymond Sammuel, Marie Ampères Bedine Boat, Ntah Ayong Moise, Anna Cazanevscaia Busuioc, Priscile Ebong Mbondi, Andreea Veronica Dediu Botezatu, Manz Koule Jules, Maria Daniela Ionica Mihaila, Rodica Mihaela Dinica and Sameza Modeste Lambert

J. Fungi 2025, 11(5), 385; https://doi.org/10.3390/jof11050385 - 17 May 2025

Abstract

Post-harvest decay of Carica papaya L. is the primary cause of deterioration in papaya quality and the low economic impact of this sector in Cameroon. Field surveys conducted by teams from the Ministry of Agriculture and Rural Development (MINADER) in Cameroon have primarily [...] Read more.

Post-harvest decay of Carica papaya L. is the primary cause of deterioration in papaya quality and the low economic impact of this sector in Cameroon. Field surveys conducted by teams from the Ministry of Agriculture and Rural Development (MINADER) in Cameroon have primarily associated these decays with fungal attacks. However, to date, no methodological analysis has been conducted on the identification of these fungal agents. To reduce post-harvest losses, rapid detection of diseases is crucial for the application of effective management strategies. This study sought to identify the fungal agents associated with post-harvest decay of papaya cv Sunrise solo in Cameroon and to determine their physiological and biochemical growth characteristics. Isolation and pathogenicity tests were performed according to Koch’s postulate. Molecular identification of isolates was achieved by amplification and sequencing of the ITS1 and ITS4 regions. Phylogenetic analysis was based on the substitution models corresponding to each fungal genus determined by jModeltest, according to the Akaike information criterion (AIC). Fungal explants of each identified species were subjected to variations in temperature, pH, water activity, and NaCl concentration. The ability to secrete hydrolytic enzymes was determined on specific media such as skimmed milk agar for protease, peptone agar for lipase, and carboxymethylcellulose for cellulase. These experiments allowed the identification of three fungi responsible for papaya fruit decay, namely Colletotrichum gloeosporioides, Fusarium equiseti, and Lasiodiplodia theobromae. All three pathogens had maximum mycelial growth at a temperature of 25 ± 2 °C, pH 6.5, NaCl concentration of 100 µM, and water activity (aw) equal to 0.98. The three fungal agents demonstrated a strong potential for secreting cellulases, lipases, and proteases, which they use as lytic enzymes to degrade papaya tissues. The relative enzymatic activity varied depending on the fungal pathogen as well as the type of enzyme secreted. This study is the first report of F. equiseti as a causal agent of papaya fruit decay in Cameroon. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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15 pages, 5980 KiB

Open AccessArticle

Prevalence of Neofusicoccum parvum Associated with Fruit Rot of Mango in South Italy and Its Biological Control Under Postharvest Conditions

by Laura Vecchio, Alessandro Vitale, Dalia Aiello, Chiara Di Pietro, Lucia Parafati and Giancarlo Polizzi

J. Fungi 2025, 11(5), 384; https://doi.org/10.3390/jof11050384 - 17 May 2025

Abstract

Botryosphaeriaceae species were recently found to be responsible for heavy mango crop losses worldwide. In 2020, mango fruit samples showing fruit decay symptoms were collected from Glenn, Kent, Irwin, Palmer, Brokaw 2, and Gomera 3 accessions in 4 orchards located in Sicily (Italy). [...] Read more.

Botryosphaeriaceae species were recently found to be responsible for heavy mango crop losses worldwide. In 2020, mango fruit samples showing fruit decay symptoms were collected from Glenn, Kent, Irwin, Palmer, Brokaw 2, and Gomera 3 accessions in 4 orchards located in Sicily (Italy). A molecular analysis of the ITS and tub2 regions performed on 41 representative isolates allowed for the identification of mainly Neofusicoccum parvum and occasionally Botryosphaeria dothidea (1/41) as the causal agents of fruit decay. Pathogenicity proofs were satisfied for both fungal pathogens. Ripe and unripe Gomera 3 mango fruits were used to compare the virulence among the N. parvum isolates. Postharvest experiments performed on Gomera 3 fruits and by using different biocontrol agents (BCAs) showed that the performance of treatments in reducing fruit decay depends on N. parvum virulence. The data show that unregistered Wickerhamomyces anomalus WA-2 and Pichia kluyveri PK-3, followed by the trade bioformulate Serenade™ (Bacillus amyloliquefaciens QST713), were the most effective in managing mango fruit rot. This paper shows, for the first time, the potential of different BCAs, including Trichoderma spp., for the controlling of postharvest decay caused by N. parvum on mango fruits. Full article

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

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