Journal of Fungi

18 pages, 10466 KB

Open AccessArticle

Morphology and Comparative Transcriptome Analysis of Resistant and Susceptible Bitter Gourd (Momordica charantia L.) Reveals the Molecular Response Related to Powdery Mildew Resistance

by Lei Xia, Kai Wang, Feng Guan, Bo Shi, Xuetong Yang, Yuanyuan Xie, Xinjian Wan and Jingyun Zhang

J. Fungi 2026, 12(1), 80; https://doi.org/10.3390/jof12010080 - 22 Jan 2026

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Abstract

Powdery mildew (PM) is a major disease affecting bitter gourd cultivation, and resolving the molecular regulatory mechanisms underlying PM resistance is important for bitter gourd molecular breeding for resistance. In this study, morphological and molecular methods were used to identify the PM pathogen [...] Read more.

Powdery mildew (PM) is a major disease affecting bitter gourd cultivation, and resolving the molecular regulatory mechanisms underlying PM resistance is important for bitter gourd molecular breeding for resistance. In this study, morphological and molecular methods were used to identify the PM pathogen in bitter gourd, and comparative transcriptome analysis was performed on leaves of the resistant cultivar R and the susceptible cultivar S after PM infection. The morphological and molecular identification results showed that the PM pathogen in bitter gourd was Podosphaera xanthii. Scanning electron microscopy results revealed that the P. xanthii exhibited distinct growth patterns in the R and S after P. xanthii infection. Compared to the S, the R exhibited 3966, 2729, 5891, and 3878 differentially expressed genes (DEGs) at 0, 2, 3, and 4 days after P. xanthii infection, respectively. KEGG enrichment analysis showed that DEGs were primarily enriched in plant–pathogen interactions, MAPK signaling pathway plants, and plant hormone signal transduction pathways. Transcription factor (TF) analysis of differentially expressed genes revealed that MYB, bHLH, and ERF family members could be involved in the defense process against the P. xanthii infection. Moreover, the analysis of the MLO genes revealed that Moc10g30350.1 could be involved in regulating PM resistance. These findings could enrich the molecular theoretical basis for resistance to PM, and provide new insights for the molecular breeding process of bitter gourd resistance to PM. Full article

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

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15 pages, 2501 KB

Open AccessArticle

Development of a Field-Deployable Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Erysiphe corylacearum in Hazelnut

by Marta Maria Barone, Marco Moizio, Ravish Choudhary, Chiara D’Errico, Vojislav Trkulja, Livio Torta, Salvatore Davino and Slavica Matić

J. Fungi 2026, 12(1), 79; https://doi.org/10.3390/jof12010079 - 22 Jan 2026

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Abstract

Erysiphe corylacearum, the causal agent of powdery mildew in hazelnut (Corylus avellana L.), has become an emerging pathogen of concern in Italian hazelnut production requiring rapid and accurate detection to support timely disease management and phytosanitary measures. We developed and validated [...] Read more.

Erysiphe corylacearum, the causal agent of powdery mildew in hazelnut (Corylus avellana L.), has become an emerging pathogen of concern in Italian hazelnut production requiring rapid and accurate detection to support timely disease management and phytosanitary measures. We developed and validated a field-deployable loop-mediated isothermal amplification (LAMP) assay for the specific detection of E. corylacearum and evaluated three primer sets targeting the Internal Transcribed Spacer (ITS) region, RNA polymerase II second largest subunit (rpb2), and glutamine synthetase (GS) genes; the GS-targeting Ecg set showed the highest sensitivity and specificity. The assay was shown to be sensitive down to 200 fg of fungal DNA, efficiently detected E. corylacearum from diluted crude leaf extracts, and produced results within half an hour, allowing the detection of latent infections before visible symptoms emerged. On-site validation with a portable LAMP instrument showed the assay’s suitability for field-deployable diagnosis and early-warning applications in hazelnut orchards. 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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35 pages, 21047 KB

Open AccessArticle

Morphological and Phylogenetic Evidence Reveal Nine New Species of Russula (Russulaceae, Russulales) from Shanxi Province, North China

by Hao-Yu Fu, Jia-He Li, Hui-Min Ji, Ning Mao, Ting Li and Li Fan

J. Fungi 2026, 12(1), 78; https://doi.org/10.3390/jof12010078 - 22 Jan 2026

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Abstract

Shanxi Province, located in northern China, characterized by a warm-temperate monsoon climate, complex mountainous topography, and vegetation dominated by trees of Fagaceae and Pinaceae, provides diverse habitats for Russula diversity. Recent investigations on macrofungi in this region revealed nine new Russula species based [...] Read more.

Shanxi Province, located in northern China, characterized by a warm-temperate monsoon climate, complex mountainous topography, and vegetation dominated by trees of Fagaceae and Pinaceae, provides diverse habitats for Russula diversity. Recent investigations on macrofungi in this region revealed nine new Russula species based on integrated morphological and multi-locus phylogenetic analyses (ITS, nrLSU, rpb2, tef1), which are described and illustrated in this paper. These new taxa are classified into three subgenera of Russula: one species of subgen. Brevipes, four of subgen. Heterophyllidia, four of subgen. Russula. This work enhances the understanding of Russula resources in China’s temperate zone. Full article

(This article belongs to the Special Issue Diversity, Phylogeny and Ecology of Forest Fungi, 2nd Edition)

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21 pages, 949 KB

Open AccessArticle

Antimicrobial Activity of Submerged Cultures of Endophytic Fungi Isolated from Three Chilean Nothofagus Species

by Héctor Valenzuela, Daniella Aqueveque-Jara, Mauricio Sanz, Margarita Ocampo, Karem Henríquez-Aedo, Mario Aranda and Pedro Aqueveque

J. Fungi 2026, 12(1), 77; https://doi.org/10.3390/jof12010077 - 21 Jan 2026

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Abstract

Endophyte fungi (EF) are considered a new and valuable reservoir of bioactive molecules of biotechnological interest for pharmacy, agricultural and forestry industries. In this study, thirty EFs, isolated from three Chilean Nothofagus species (N. alpina, N. dombeyi, N. oblicua) [...] Read more.

Endophyte fungi (EF) are considered a new and valuable reservoir of bioactive molecules of biotechnological interest for pharmacy, agricultural and forestry industries. In this study, thirty EFs, isolated from three Chilean Nothofagus species (N. alpina, N. dombeyi, N. oblicua) were identified and cultured in submerged liquid fermentations aimed at searching for natural active substances. The extracts obtained were evaluated against pathogenic bacteria and fungi. Sixteen extracts (53.3%) presented antibacterial and fourteen (46.6%) presented antifungal activities in different intensities. Extracts from isolates Coryneum sp.-72 and P. cinnamomea-78 exhibited the highest antimicrobial activity. Using bioautography, the compounds responsible for the antimicrobial activity exhibited by Coryneum sp.-72 and P. cinnamomea-78 were detected and characterized. Coryneum sp.-72 showed bactericidal properties at 200 μg/mL and bacteriostatic effects at 50 μg/mL against B. cereus, B. subtilis, L. monocytogenes and S. aureus. MIC values indicated that P. cinnamomea-78 exhibited a strong fungistatic and fungicidal effect against B. cinerea and C. gloesporioides at 10–50 μg/mL. Isolates were grouped in the following order: Botryosphaeriales, Diaporthales, Eurotiales, Helotiales, Hypocreales, Pleosporales, Magnaporthales, Sordariales and Polyporales. EF isolated, identified and evaluated constitute the first report for Chilean Nothofagus genus. Full article

(This article belongs to the Special Issue Bioactive Secondary Metabolites from Fungi)

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21 pages, 3151 KB

Open AccessArticle

Genomic Insights into Candidozyma auris Clade II: Comparative Phylogenomics and Structural Validation of Fluconazole Resistance Mechanisms

by Sanghak Lee, Kei-Anne Garcia Baritugo, Han-Soo Kim, Hyeyoung Lee, Sook Won Ryu, Soo-Young Kim, Chae Hoon Lee, Young Ree Kim, Jeong Hwan Shin, Jayoung Kim and Gi-Ho Sung

J. Fungi 2026, 12(1), 76; https://doi.org/10.3390/jof12010076 - 20 Jan 2026

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Abstract

Candidozyma auris (formerly Candida auris) is an emerging multidrug-resistant fungal pathogen with confirmed cases in over 30 countries. Although whole-genome sequencing (WGS) analysis defined distinct clades during characterization of underlying genetic mechanism behind multidrug resistance, Clade II remains under-evaluated. In this study, [...] Read more.

Candidozyma auris (formerly Candida auris) is an emerging multidrug-resistant fungal pathogen with confirmed cases in over 30 countries. Although whole-genome sequencing (WGS) analysis defined distinct clades during characterization of underlying genetic mechanism behind multidrug resistance, Clade II remains under-evaluated. In this study, a three-level comparative genomic strategy (Global, Clade, Phenotype) was employed by integration of unbiased genome-wide comparative SNP screening (GATK v4.1.9.0), targeted BLAST profiling (BLAST+ v2.17.0), and in silico protein analysis (ColabFold v1.5.5; DynaMut2 v2.0) for systematic evaluation of mechanisms of antifungal resistance in thirty-nine Clade II C. auris clinical isolates and fourteen reference strains. Global and clade-level analyses confirmed that all the clinical isolates belong to Clade II, according to phylogenetic clustering and mating type locus (MTL) conservation. At the phenotype level, a distinct subclade of fluconazole-resistant mutants was identified to have a heterogenous network of mutations in seven key enzymes associated with cell membrane dynamics and the metabolic stress response. Among these, four core mutations (TAC1B, CAN2, NIC96, PMA1) were confirmed as functional drivers based on strict criteria during multitier in silico protein analysis: cross-species conservation, surface exposure, active site proximity, thermodynamic stability, and protein interface interaction. On the other hand, three high-level fluconazole-resistant clinical isolates (≥128 μg/mL) that lacked these functional drivers were subjected to comprehensive subtractive genomic profiling analysis. The absence of coding mutations in validated resistance drivers, yeast orthologs, and convergent variants suggests that there is an alternative novel non-coding or regulatory mechanism behind fluconazole resistance. These findings highlight Clade II’s evolutionary divergence into two distinct trajectories towards the development of a high level of fluconazole resistance: canonical protein alteration versus regulatory modulation. Full article

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

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20 pages, 2842 KB

Open AccessArticle

Comparative Mitogenomics Reveals Intron Dynamics and Mitochondrial Gene Expression Shifts in Domesticated and Wild Pleurotus ostreatus

by Gumer Pérez, Idoia Jiménez, Edurne Garde, Lucía Ramírez and Antonio G. Pisabarro

J. Fungi 2026, 12(1), 75; https://doi.org/10.3390/jof12010075 - 20 Jan 2026

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Abstract

Mitochondrial genomes play a central role in fungal physiology and adaptation, yet their evolutionary dynamics during domestication remain poorly understood. Here, we performed a comparative mitogenomic and gene-expression analysis of three Pleurotus ostreatus dikaryotic strains differing in origin and degree of adaptation to [...] Read more.

Mitochondrial genomes play a central role in fungal physiology and adaptation, yet their evolutionary dynamics during domestication remain poorly understood. Here, we performed a comparative mitogenomic and gene-expression analysis of three Pleurotus ostreatus dikaryotic strains differing in origin and degree of adaptation to laboratory conditions: the long-term commercial strain dkN001, the laboratory-maintained wild isolate dkF515, and the recently collected wild strain dkN009. High-throughput Illumina sequencing enabled complete assembly of circular mitochondrial genomes, revealing substantial size variation among strains, where the dkN001 strain exhibited the second smallest mitogenome reported for the genus Pleurotus. Comparative analyses showed >99% sequence identity between wild isolates and ~95% identity relative to the commercial strain. Variations in genome size among strains were associated with intron dynamics in the cox1 and rnl genes, as well as intron loss predominantly in the commercial strain dkN001, consistent with mitochondrial genome streamlining during domestication. Expression profiling of mitochondrial protein-coding genes (PCGs) under multiple culture conditions revealed conserved transcriptional responses in dkN001 and dkF515 that contrasted sharply with those of dkN009. The differences observed, which affected components of the electron transport chain, suggested shifts in energy metabolism associated with long-term laboratory maintenance. Therefore, our results demonstrate that domestication in P. ostreatus involves both structural remodelling of the mitogenome and changes in regulation of mitochondrial PCGs, highlighting the importance of mitonuclear interactions in fungal adaptation to controlled environments. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)

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18 pages, 5948 KB

Open AccessArticle

Root and Leaf-Specific Metabolic Responses of Ryegrass to Arbuscular Mycorrhizal Fungi Under Cadmium Stress

by Dapeng Jin, Lingyu Xin, Panpan Tu, Huiping Song, Yan Zou, Zhiwei Bian and Zhengjun Feng

J. Fungi 2026, 12(1), 74; https://doi.org/10.3390/jof12010074 - 19 Jan 2026

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Abstract

Cadmium (Cd) drastically inhibits plant growth and metabolism, whereas arbuscular mycorrhizal (AM) fungi can enhance plant Cd tolerance through metabolic regulation. To clarify tissue-specific responses, we conducted a pot experiment combined with GC-MS to examine how AM fungi influence root and leaf metabolism [...] Read more.

Cadmium (Cd) drastically inhibits plant growth and metabolism, whereas arbuscular mycorrhizal (AM) fungi can enhance plant Cd tolerance through metabolic regulation. To clarify tissue-specific responses, we conducted a pot experiment combined with GC-MS to examine how AM fungi influence root and leaf metabolism of ryegrass (Lolium perenne L.) under different Cd levels. Root and leaf metabolomes diverged substantially in composition and function. In total, 83 metabolites were identified in roots, mainly phenolics, amines, and sugars associated with carbon–nitrogen metabolism and stress-defense pathways, whereas 75 metabolites were identified in leaves, largely related to photosynthetic metabolism. Roots were more sensitive to Cd, showing significant metabolic alterations at Cd ≥ 5 mg·kg⁻¹, including disruption of galactose metabolism, while leaves exhibited notable changes only at Cd ≥ 100 mg·kg⁻¹, with suppression of citrate, L-aspartate, and starch and sucrose metabolism. AM fungi modulated plant metabolism more strongly under Cd stress. Specifically, AM fungi restored Cd-suppressed galactose and glyoxylate/dicarboxylate metabolism in roots, enhanced starch and sucrose metabolism and amino acid pathways in leaves, and increased stress-related amino acids and organic acids in both tissues. Overall, AM fungi substantially alleviated Cd-induced metabolic inhibition, particularly at Cd ≥ 50 mg·kg⁻¹, providing mechanistic insight into AM-enhanced Cd tolerance and supporting the application of AM symbiosis in remediation of Cd-contaminated soils. Full article

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

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16 pages, 6066 KB

Open AccessArticle

Validation and Improvement of a Rapid, CRISPR-Cas-Free RPA-PCRD Strip Assay for On-Site Genomic Surveillance and Quarantine of Wheat Blast

by Dipali Rani Gupta, Shamfin Hossain Kasfy, Julfikar Ali, Farin Tasnova Hia, M. Nazmul Hoque, Mahfuz Rahman and Tofazzal Islam

J. Fungi 2026, 12(1), 73; https://doi.org/10.3390/jof12010073 - 18 Jan 2026

Viewed by 1116

Abstract

As an emerging threat to global food security, wheat blast necessitates the development of a rapid and field-deployable detection system to facilitate early diagnosis, enable effective management, and prevent its further spread to new regions. In this study, we aimed to validate and [...] Read more.

As an emerging threat to global food security, wheat blast necessitates the development of a rapid and field-deployable detection system to facilitate early diagnosis, enable effective management, and prevent its further spread to new regions. In this study, we aimed to validate and improve a Recombinase Polymerase Amplification coupled with PCRD lateral flow detection (RPA-PCRD strip assay) kit for the rapid and specific identification of Magnaporthe oryzae pathotype Triticum (MoT) in field samples. The assay demonstrated exceptional sensitivity, detecting as low as 10 pg/µL of target DNA, and exhibited no cross-reactivity with M. oryzae Oryzae (MoO) isolates and other major fungal phytopathogens under the genera of Fusarium, Bipolaris, Colletotrichum, and Botrydiplodia. The method successfully detected MoT in wheat leaves as early as 4 days post-infection (DPI), and in infected spikes, seeds, and alternate hosts. Furthermore, by combining a simplified polyethylene glycol-NaOH method for extracting DNA from plant samples, the entire RPA-PCRD strip assay enabled the detection of MoT within 30 min with no specialized equipment and high technical skills at ambient temperature (37–39 °C). When applied to field samples, it successfully detected MoT in naturally infected diseased wheat plants from seven different fields in a wheat blast hotspot district, Meherpur, Bangladesh. Training 52 diverse stakeholders validated the kit’s field readiness, with 88% of trainees endorsing its user-friendly design. This method offers a practical, low-cost, and portable point-of-care diagnostic tool suitable for on-site genomic surveillance, integrated management, seed health testing, and quarantine screening of wheat blast in resource-limited settings. Furthermore, the RPA-PCRD platform serves as an early warning modular diagnostic template that can be readily adapted to detect a wide array of phytopathogens by integrating target-specific genomic primers. Full article

(This article belongs to the Special Issue Integrated Management of Plant Fungal Diseases—2nd Edition)

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18 pages, 1807 KB

Open AccessArticle

A One Health Perspective on Aspergillus fumigatus in Brazilian Dry Foods: High Genetic Diversity and Azole Susceptibility

by Maria Clara Shiroma Buri, Katherin Castro-Ríos, Arla Daniela Ramalho da Cruz, Thais Moreira Claudio and Paulo Cezar Ceresini

J. Fungi 2026, 12(1), 72; https://doi.org/10.3390/jof12010072 - 16 Jan 2026

Viewed by 435

Abstract

Aspergillus fumigatus, a saprophytic fungus, causes aspergillosis, primarily affecting the immunocompromised. The efficacy of triazole antifungals is compromised by resistance that has developed both clinically and environmentally. Widespread agricultural use of similar triazole fungicides selects for resistant genotypes, leading to potential food [...] Read more.

Aspergillus fumigatus, a saprophytic fungus, causes aspergillosis, primarily affecting the immunocompromised. The efficacy of triazole antifungals is compromised by resistance that has developed both clinically and environmentally. Widespread agricultural use of similar triazole fungicides selects for resistant genotypes, leading to potential food contamination and compromising treatment. This study assessed the presence of azole-resistant A. fumigatus in minimally processed food items commonly consumed in Brazil. A total of 25 commercial samples, including black pepper, yerba mate, and green coffee beans, were collected from different regions. Forty-two A. fumigatus isolates were recovered and screened for susceptibility to agricultural and clinical triazoles by determining EC₅₀ values for tebuconazole (0.04–0.7 µg/mL), itraconazole (0.06–0.5 µg/mL), and voriconazole (0.07–0.15 µg/mL). Sequence analysis of the CYP51A gene revealed the presence of M172V mutation, none of which are associated with resistance. Microsatellite genotyping indicated high genotypic diversity and genetic relatedness among isolates from different food sources. Although no azole-resistant phenotypes were identified, the consistent recovery of A. fumigatus from products not directly exposed to azole fungicides highlights the need for continued surveillance. Agricultural environments remain critical hotspots for the emergence and dissemination of resistance, reinforcing the importance of integrated One Health strategies in antifungal resistance monitoring. Full article

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

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18 pages, 4983 KB

Open AccessArticle

Genome-Wide Identification of Histone Acetyltransferases in Fusarium oxysporum and Their Response to Panax notoginseng Notoginsenosides

by Yun-Ju Hong, Hong-Xin Liao, Jin-Rui Wen, Huan-Qi Cun, Hong-Mei Shi, Zhang-Feng Hu, Fu-Rong Xu, Sulukkana Noiprasert, Kanyaphat Apiwongsrichai, Xiao-Yun Liu and Xian Dong

J. Fungi 2026, 12(1), 71; https://doi.org/10.3390/jof12010071 - 16 Jan 2026

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Abstract

Panax notoginseng, a high-value medicinal crop, suffers substantial yield losses due to Fusarium oxysporum-mediated root rot, for which no molecularly defined control targets are currently available. Histone acetyltransferases (HATs) serve as crucial epigenetic regulators of fungal development and stress responses; however, [...] Read more.

Panax notoginseng, a high-value medicinal crop, suffers substantial yield losses due to Fusarium oxysporum-mediated root rot, for which no molecularly defined control targets are currently available. Histone acetyltransferases (HATs) serve as crucial epigenetic regulators of fungal development and stress responses; however, their functional roles in F. oxysporum remain largely unexplored. In this study, we systematically identified six FoHAT genes via genome-wide analysis and classified them into evolutionarily conserved subfamilies through phylogenetic comparison with orthologs from Saccharomyces cerevisiae, Homo sapiens, and Arabidopsis thaliana. Structural analyses revealed distinct motif compositions and domain architectures among FoHAT members, while promoter cis-element profiling suggested potential subfunctionalization via stress-responsive regulatory mechanisms. Functional investigations demonstrated that major notoginsenosides present in P. notoginseng root exudates—R₁, Rg₁, Rg₂, Re, and Rd—dynamically influenced both spore germination and FoHAT expression profiles. Intriguingly, each notoginsenoside exerted concentration-dependent non-linear effects on spore germination, either inhibiting or promoting the process. Concurrently, notoginsenoside exposure triggered compensatory transcriptional responses, most notably a rebound in Fo-Hat1_N expression from 9% to 112% under Rd treatment. This work establishes an initial epigenetic framework for combating Fusarium root rot in medicinal plants and offers a foundation for developing HAT-targeted small-molecule inhibitors. Full article

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

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40 pages, 2989 KB

Open AccessSystematic Review

The Genus Leccinum: Global Advances in Taxonomy, Ecology, Nutritional Value, and Environmental Significance

by Ruben Budau, Simona Ioana Vicas, Mariana Florica Bei, Danut Aurel Dejeu, Lucian Dinca and Danut Chira

J. Fungi 2026, 12(1), 70; https://doi.org/10.3390/jof12010070 - 16 Jan 2026

Viewed by 632

Abstract

Leccinum is an ecologically significant and taxonomically complex genus of ectomycorrhizal fungi widely distributed across boreal, temperate, Mediterranean, and selected tropical regions. Despite its ecological, nutritional, and applied importance, no comprehensive review has previously synthesized global knowledge on this genus. This work provides [...] Read more.

Leccinum is an ecologically significant and taxonomically complex genus of ectomycorrhizal fungi widely distributed across boreal, temperate, Mediterranean, and selected tropical regions. Despite its ecological, nutritional, and applied importance, no comprehensive review has previously synthesized global knowledge on this genus. This work provides the first integrative assessment of Leccinum research, combining a bibliometric analysis of 293 peer-reviewed publications with an in-depth qualitative synthesis of ecological, biochemical, and environmental findings. Bibliometric results show increasing scientific attention since the mid-20th century, with major contributions from Europe, Asia, and North America, and dominant research themes spanning taxonomy, ecology, chemistry, and environmental sciences. The literature review highlights substantial advances in phylogenetic understanding, species diversity, and host specificity. Leccinum forms ectomycorrhizal associations with over 60 woody host genera, underscoring its functional importance in forest ecosystems. Nutritionally, Leccinum species are rich in proteins, carbohydrates, minerals, bioactive polysaccharides, phenolic compounds, and umami-related peptides, with demonstrated antioxidant, immunomodulatory, and antitumor activities. At the same time, the genus exhibits notable bioaccumulation capacity for heavy metals (particularly Hg, Cd, and Pb) and radionuclides, making it both a valuable food source and a sensitive environmental bioindicator. Applications in biotechnology, environmental remediation, forest restoration, and functional food development are emerging but remain insufficiently explored. Identified research gaps include the need for global-scale phylogenomic frameworks, expanded geographic sampling, standardized biochemical analyses, and deeper investigation into physiological mechanisms and applied uses. This review provides the first holistic synthesis of Leccinum, offering an integrated perspective on its taxonomy, ecology, nutritional composition, environmental significance, and practical applications. The findings serve as a foundation for future mycological, ecological, and biotechnological research on this diverse and understudied fungal genus. Full article

(This article belongs to the Special Issue Research Progress on Edible Fungi)

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19 pages, 6613 KB

Open AccessArticle

Identification and Multigene Phylogenetic Analysis Reveal Alternaria as the Primary Pathogen Causing European Plum (Prunus domestica) Brown Spot in Xinjiang, China

by Shuaishuai Sha, Qiuyan Han, Hongyue Li, Wenwen Gao, Jiyuan Ma, Lingkai Xu, Canpeng Fu and Pan Xie

J. Fungi 2026, 12(1), 69; https://doi.org/10.3390/jof12010069 - 15 Jan 2026

Viewed by 356

Abstract

European plum (Prunus domestica) orchards in the Kashi region, Xinjiang, China, suffer from fruit brown spot disease. The disease typically appears as red spots on the fruit surface that expand into brown necrotic lesions; affected fruit flesh can shrink, and fruits [...] Read more.

European plum (Prunus domestica) orchards in the Kashi region, Xinjiang, China, suffer from fruit brown spot disease. The disease typically appears as red spots on the fruit surface that expand into brown necrotic lesions; affected fruit flesh can shrink, and fruits can harden and drop. We isolate and identify pathogens associated with this disease in this plum from five Kashi counties. Of 210 fungal isolates obtained through standard tissue isolation, Alternaria accounted for 84.8%, with the remainder comprising species of Aspergillus (9.5%), Diplodia (3.3%), and Neoscytalidium (2.4%). Using PCR amplification and sequencing of five loci, pathogens were identified using multi-gene phylogenetic analyses, combined with observations of colony and spore morphology. Multi-locus sequences of Alternaria isolates were highly homologous to those of the Alternaria alternata type strain, and we refer them to an A. alternata species complex. Pathogenicity tests confirm that Alternaria isolates reproduce brown spot symptoms on European plum fruits. By demonstrating that Alternaria is the primary pathogen causing brown spot disease in European plum in Xinjiang, we clarify both the fungal species composition and taxonomic placement of the dominant pathogen associated with this disease. Full article

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

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14 pages, 3406 KB

Open AccessArticle

Wheat SWI3B Subunit of SWI/SNF Chromatin Remodeling Complex Governs Powdery Mildew Susceptibility by Suppressing Salicylic Acid Biosynthesis

by Wanzhen Chen, Yixian Fu, Mengdi Zhang, Wenrui Zhao, Pengfei Zhi and Cheng Chang

J. Fungi 2026, 12(1), 68; https://doi.org/10.3390/jof12010068 - 14 Jan 2026

Viewed by 348

Abstract

The fungal pathogen Blumeria graminis forma specialis tritici (B.g. tritici) infects bread wheat (Triticum aestivum L.) to cause wheat powdery mildew disease. Elucidating the molecular mechanism underlying wheat susceptibility to the pathogenic fungus B.g. tritici could facilitate wheat genetic improvement. [...] Read more.

The fungal pathogen Blumeria graminis forma specialis tritici (B.g. tritici) infects bread wheat (Triticum aestivum L.) to cause wheat powdery mildew disease. Elucidating the molecular mechanism underlying wheat susceptibility to the pathogenic fungus B.g. tritici could facilitate wheat genetic improvement. In this study, we identified the wheat TaSWI3B gene as a novel Susceptibility gene positively regulating wheat susceptibility to B.g. tritici. The TaSWI3B gene encodes the SWI3B subunit of the SWI/SNF chromatin remodeling complex. The overexpression of the TaSWI3B gene enhances wheat powdery mildew susceptibility, whereas TaSWI3B silencing results in attenuated wheat powdery mildew susceptibility. Importantly, we found that TaSWI3B could be enriched at the promoter regions of the salicylic acid (SA) biosynthesis activator gene TaSARD1, facilitating nucleosome occupancy and thereby suppressing TaSARD1 transcription and inhibiting SA biosynthesis. Silencing of TaSARD1 and TaICS1 encoding a key enzyme in SA biosynthesis could attenuate the SA biosynthesis and powdery mildew resistance potentiated by knockdown of TaSWI3B expression. Collectively, these results suggest that the SWI3B subunit of the wheat SWI/SNF chromatin remodeling complex negatively regulates SA biosynthesis by suppressing TaSARD1 transcription at the epigenetic level and thus facilitates wheat powdery mildew susceptibility. Full article

(This article belongs to the Special Issue Plant Fungal Pathogenesis 2025)

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20 pages, 1015 KB

Open AccessArticle

Cryptococcosis in Colombia: Analysis of Data from Laboratory-Based Surveillance 2017–2024

by Jairo Lizarazo, Clara Inés Agudelo, Patricia Escandón and Elizabeth Castañeda

J. Fungi 2026, 12(1), 67; https://doi.org/10.3390/jof12010067 - 14 Jan 2026

Viewed by 361

Abstract

Since 1997, a laboratory-based survey on cryptococcosis has been conducted in Colombia. We present the results for the period 2017–2024. A total of 891 surveys were received. The overall incidence was 0.22 cases per 100,000 people. Among those living with HIV, the incidence [...] Read more.

Since 1997, a laboratory-based survey on cryptococcosis has been conducted in Colombia. We present the results for the period 2017–2024. A total of 891 surveys were received. The overall incidence was 0.22 cases per 100,000 people. Among those living with HIV, the incidence was 38, and among HIV-negative people, it was 0.08. Cryptococcosis demonstrated a higher prevalence among men than women (3.2:1). Among patients living with Human Immunodeficiency Virus (HIV), the condition primarily affected younger adults (26–40 years). In contrast, among HIV-negative people, it was mostly observed in older adults (≥60 years). HIV infection was the most significant risk factor (63%), but another cause of immunosuppression was identified in 21.2% cases. Neurocryptococcosis was the most common form of presentation (62.2%), followed by disseminated cryptococcosis (31.1%). The diagnosis was confirmed by culture in 99.4% of patients; the most important sample was cerebrospinal fluid (67.3%), followed by blood (35.4%). Cryptococcus neoformans was identified in 93.1% of cases, and Cryptococcus gatti in 6.9%. Predominant molecular patterns were VNI (92.4%) and VGII (45.3%). The epidemiology of cryptococcosis in Colombia is changing, with a progressive decrease in HIV coinfection and an increase in other immunosuppressive conditions in older people. This study highlights the importance of cryptococcosis in Colombia and the need to report it in order to improve knowledge and thereby promote the quality of diagnosis and the opportunity for more effective treatment. Full article

(This article belongs to the Special Issue Clinical and Epidemiological Study of Mycoses)

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23 pages, 4533 KB

Open AccessArticle

Environmental Filtering Drives Microbial Community Shifts and Functional Niche Differentiation of Fungi in Waterlogged and Dried Archeological Bamboo Slips

by Liwen Zhong, Weijun Li, Guoming Gao, Yu Wang, Cen Wang and Jiao Pan

J. Fungi 2026, 12(1), 66; https://doi.org/10.3390/jof12010066 - 14 Jan 2026

Viewed by 403

Abstract

Changes in preservation conditions act as an important environmental filter driving shifts in microbial communities. However, the precise identities, functional traits, and ecological mechanisms of the dominant agents driving stage-specific deterioration remain insufficiently characterized. This study investigated microbial communities and dominant fungal degraders [...] Read more.

Changes in preservation conditions act as an important environmental filter driving shifts in microbial communities. However, the precise identities, functional traits, and ecological mechanisms of the dominant agents driving stage-specific deterioration remain insufficiently characterized. This study investigated microbial communities and dominant fungal degraders in waterlogged versus dried bamboo slips using amplicon sequencing, multivariate statistics, and microbial isolation. Results revealed compositionally distinct communities, with dried slips sharing only a small proportion of operational taxonomic units (OTUs) with waterlogged slips, while indicating the persistence of a subset of taxa across preservation states. A key discovery was the dominance of Fonsecaea minima (92% relative abundance) at the water-solid-air interface of partially submerged slips. Scanning electron microscopy (SEM) and pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) indicate that this fungus forms melanin-rich, biofilm-like surface structures, suggesting enhanced surface colonization and stress resistance. In contrast, the fungal community isolated from dried slips was characterized by Apiospora saccharicola associated with detectable xylanase activity. Meanwhile, the xerophilic species Xerogeomyces pulvereus dominated (99% relative abundance) the storage box environment. Together, these results demonstrate that preservation niches select for fungi with distinct functional traits, highlighting the importance of stage-specific preservation strategies that consider functional traits rather than taxonomic identity alone. Full article

(This article belongs to the Special Issue Mycological Research in Cultural Heritage Protection)

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23 pages, 3378 KB

Open AccessArticle

Fungal Endophyte Comprehensively Orchestrates Nodulation and Nitrogen Utilization of Legume Crop (Arachis hypogaea L.)

by Xing-Guang Xie, Hui-Jun Jiang, Kai Sun, Yuan-Yuan Zhao, Xiao-Gang Li, Ting Han, Yan Chen and Chuan-Chao Dai

J. Fungi 2026, 12(1), 65; https://doi.org/10.3390/jof12010065 - 13 Jan 2026

Viewed by 348

Abstract

(1) Background: Improving nitrogen use efficiency in peanuts is essential for achieving a high yield with reduced nitrogen fertilizer input. This study investigates the role of the fungal endophyte Phomopsis liquidambaris in regulating nitrogen utilization throughout the entire growth cycle of peanuts. (2) [...] Read more.

(1) Background: Improving nitrogen use efficiency in peanuts is essential for achieving a high yield with reduced nitrogen fertilizer input. This study investigates the role of the fungal endophyte Phomopsis liquidambaris in regulating nitrogen utilization throughout the entire growth cycle of peanuts. (2) Methods: Field pot experiments and a two-year plot trial were conducted. The effects of Ph. liquidambaris colonization on the rhizosphere microbial community, soil nitrogen forms, and peanut physiology were analyzed. (3) Results: Colonization by Ph. liquidambaris significantly suppressed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the rhizosphere at the seedling stage. This led to a transient decrease in nitrate and an increase in ammonium availability, which enhanced nodulation-related physiological responses. Concurrently, the peanut-specific rhizobium Bradyrhizobium sp. was enriched in the rhizosphere, and the root exudates induced by the fungus further stimulated nodulation activity. These early-stage effects promoted the establishment of peanut–Bradyrhizobium symbiosis. During the mid-to-late growth stages, the fungus positively reshaped the composition of key functional microbial groups (including diazotrophs, AOA, and AOB), thereby increasing rhizosphere nitrogen availability. (4) Conclusions: Under low nitrogen fertilization, inoculation with Ph. liquidambaris maintained yield stability in long-term monocropped peanuts by enhancing early nodulation and late-stage rhizosphere nitrogen availability. This study provides a promising microbe-based strategy to support sustainable legume production with reduced nitrogen fertilizer application. Full article

(This article belongs to the Special Issue Plant Symbiotic Fungi)

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22 pages, 1609 KB

Open AccessReview

An Overview of the Alternaria Genus: Ecology, Pathogenicity and Importance for Agriculture and Human Health

by Stanislava A. Vinogradova, Konstantin V. Kiselev and Andrey R. Suprun

J. Fungi 2026, 12(1), 64; https://doi.org/10.3390/jof12010064 - 13 Jan 2026

Viewed by 585

Abstract

Alternaria is a widespread genus and a diverse taxonomic group of fungi, whose members exhibit a wide range of ecological roles, from endophytes and saprophytes to potent plant pathogens, and in some cases, to opportunistic pathogens or allergens affecting humans. Their high adaptability [...] Read more.

Alternaria is a widespread genus and a diverse taxonomic group of fungi, whose members exhibit a wide range of ecological roles, from endophytes and saprophytes to potent plant pathogens, and in some cases, to opportunistic pathogens or allergens affecting humans. Their high adaptability to various environmental conditions determines their widespread distribution and resilience. A key feature of the genus Alternaria is its substantial species diversity. According to the Species Fungorum database, it currently comprises 792 registered species, which are grouped into 29 sections. It should be noted that this number reflects the current state of taxonomic classification and is subject to ongoing revision. The ecological role of representatives of this genus is particularly relevant in the context of agriculture, as many species are pathogens and causative agents of Alternaria leaf spot in important agricultural plants such as tomatoes, potatoes, apples, wheat, and others. This disease causes significant economic losses. At the same time, some strains demonstrate potential for use in biotechnology due to their ability to produce biologically active metabolites. This review examines the taxonomy, morphological characteristics, ecological role, pathogenicity, and control methods of fungi of the genus Alternaria, as well as their biotechnological potential. Full article

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

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20 pages, 4224 KB

Open AccessArticle

Genome and Comparative Transcriptome Analysis of Growth and Developmental Changes in the Pileus of the Cyclocybe chaxingu

by Liyuan Luo, Shiqi Wan, Yuling Zhou, Chezhao Wang, Chunyan Yang, Wenqi Huang, Ling Chen, Zhiting Yu, Sihan Li, Xiaolong Chai and Xinrui Liu

J. Fungi 2026, 12(1), 63; https://doi.org/10.3390/jof12010063 - 13 Jan 2026

Viewed by 381

Abstract

Cyclocybe chaxingu is a well-known edible fungus in China, in which pileus size and color are key traits determining its commercial value. However, the molecular genetic mechanisms underlying the morphological development of its pileus remains limited at present. To address this, our study [...] Read more.

Cyclocybe chaxingu is a well-known edible fungus in China, in which pileus size and color are key traits determining its commercial value. However, the molecular genetic mechanisms underlying the morphological development of its pileus remains limited at present. To address this, our study first completed the high-quality genome assembly of the monokaryotic strain Ag.c0002-1 of albino C. chaxingu, anchoring it to 13 chromosomes via Hi-C technology. The final genome size was 51.7 Mb with a GC content of 51.06%, and 11,332 protein-coding genes were annotated. Phenotypic observations and comparative transcriptome analyses were then conducted on the pilei of the brown cultivar Ag.c0067 and the white cultivar Ag.c0002 at the primordium, elongation, and mature stages. Phenotypic analysis revealed continuous pileus expansion accompanied by progressive color lightening in both cultivars during development. Comparative transcriptomic analyses revealed significant differences in gene expression patterns between the two cultivars across developmental stages. KEGG enrichment analysis indicated that pileus expansion is closely associated with pathways related to DNA replication, cell cycle of yeast, carbon metabolism, and carbohydrate digestion and absorption. Among these, differentially expressed genes involved in cell division tended to be downregulated, whereas genes associated with energy metabolism and substance transport were upregulated, providing the necessary energy and material support for pileus growth. Changes in pileus pigmentation were primarily associated with tyrosine metabolism, betalain biosynthesis, tryptophan metabolism, and melanogenesis pathways. Notably, the downregulation of tyrosinase genes and the upregulation of glutathione S-transferase genes during development may represent major molecular mechanisms underlying pileus color lightening. Overall, this study provides important insights into the molecular mechanisms regulating pileus development and pigmentation in C. chaxingu, while also offering valuable theoretical support for genetic analysis of basidiomycete morphogenesis and the molecular breeding of edible mushrooms. Full article

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

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20 pages, 41314 KB

Open AccessArticle

Diversity, Pathogenicity, and Biological Characteristics of Root Rot Pathogens from Lycium barbarum L. in Qinghai Province, China

by Yongbao Zhao, Lingshan Wang, Kaifu Zheng, Chengwen Zheng, Lijie Liu and Hexing Qi

J. Fungi 2026, 12(1), 62; https://doi.org/10.3390/jof12010062 - 13 Jan 2026

Viewed by 458

Abstract

Lycium barbarum L. is an important economic crop in Qinghai province, China. However, root rot seriously reduces the economic results of L. barbarum. Here, we collected the diseased L. barbarum roots from Nuomuhong Farm of Haixi Mongolian and Tibetan Autonomous Prefecture, Qinghai [...] Read more.

Lycium barbarum L. is an important economic crop in Qinghai province, China. However, root rot seriously reduces the economic results of L. barbarum. Here, we collected the diseased L. barbarum roots from Nuomuhong Farm of Haixi Mongolian and Tibetan Autonomous Prefecture, Qinghai Province, China, to clarify the diversity, pathogenicity, and biological characteristics of its root rot pathogens. A total of 125 isolates were collected, and based on morphological characteristics and rDNA ITS, TEF-1α, and RPB2 genes sequence analysis, they were identified as Fusarium equiseti, F. avenaceum, F. solani, F. citri, F. acuminatum, F. culmorum, F. sambucinum, F. incarnatum, F. oxysporum, F. tricinctum, Microdochium bolleyi, and Clonostachys rosea. These fungi were used to inoculate the roots of 1-year-old L. barbarum seedlings using scratching and root-irrigation inoculation methods, and all isolates caused root rot. This is the first report that M. bolleyi, F. avenaceum, and F. citri caused root rot in L. barbarum. And the best media, the lethal temperatures, and the optimum carbon sources and nitrogen sources of the 12 pathogen species were determined in this study. Moreover, our findings provide a theoretical foundation for root rot management in the future. Full article

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

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19 pages, 606 KB

Open AccessReview

Genetic Manipulation in Sporothrix Species: Molecular Tools, Challenges, and Applications

by Mafalda Barros, Matheus Tavares, Ricardo Silvestre, Roberta Peres da Silva and Fernando Rodrigues

J. Fungi 2026, 12(1), 61; https://doi.org/10.3390/jof12010061 - 13 Jan 2026

Viewed by 348

Abstract

Sporothrix species are thermally dimorphic fungi responsible for sporotrichosis, a globally prevalent subcutaneous mycosis and an emerging zoonotic threat, particularly in South America. The high virulence of Sporothrix brasiliensis and its efficient transmission from cats to humans have intensified recent outbreaks, underscoring the [...] Read more.

Sporothrix species are thermally dimorphic fungi responsible for sporotrichosis, a globally prevalent subcutaneous mycosis and an emerging zoonotic threat, particularly in South America. The high virulence of Sporothrix brasiliensis and its efficient transmission from cats to humans have intensified recent outbreaks, underscoring the importance of understanding the pathogenic mechanisms. While several putative virulence factors have been identified, such as melanin production, cell wall remodeling, extracellular vesicles, and thermotolerance, functional studies remain hampered by limited molecular tools. Recent advances, including random mutagenesis, protoplast-mediated transformation, Agrobacterium tumefaciens-mediated transformation, RNA interference and CRISPR/Cas9-based genome editing, are changing this landscape. These methods have enabled the functional validation of key virulence factors and the investigation of gene function in both environmental and clinical strains. In this review, we summarize the genetic toolbox available for Sporothrix, outline current challenges, and discuss how these strategies are reshaping the study of fungal virulence and host–pathogen interactions. Full article

(This article belongs to the Special Issue Advances in Fungal Genetic Manipulation: From Conventional Systems to Historically Intractable Fungi)

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14 pages, 1295 KB

Open AccessArticle

Advancing the Identification of Risk Factors for Invasive Fungal Disease in Children with Cancer

by Marlon Barraza, Romina Valenzuela, Valentina Gutiérrez, Claudia Greppi, Ana M. Álvarez, Jaime Cerda and María Elena Santolaya

J. Fungi 2026, 12(1), 60; https://doi.org/10.3390/jof12010060 - 13 Jan 2026

Viewed by 438

Abstract

Invasive fungal disease (IFD) is one of the leading causes of morbidity and mortality in immunocompromised pediatric patients. This is a multicenter prospective cohort study with a nested retrospective analysis aimed at identifying risk factors for IFD in immunocompromised children with cancer and [...] Read more.

Invasive fungal disease (IFD) is one of the leading causes of morbidity and mortality in immunocompromised pediatric patients. This is a multicenter prospective cohort study with a nested retrospective analysis aimed at identifying risk factors for IFD in immunocompromised children with cancer and episodes of persistent high-risk febrile neutropenia (HRFN). One hundred and seventy-four episodes of persistent HRFN were analyzed, of which 34 (19.5%) were confirmed as IFD, 52.9% were caused by filamentous fungi, and 47.1% by yeasts. Logistic regression and survival analyses identified the following significant risk factors for IFD: male sex (OR 4.04), adolescence (OR 4.65), C-reactive protein ≥ 90 mg/L at admission (OR 3.13), and transfer to a critical care unit (OR 10.73). The predictive model demonstrated strong discriminatory capacity (AUC 0.84), with 79.4% sensitivity and 82.1% specificity. These findings highlight that adolescents, particularly males with severe clinical conditions and elevated inflammatory markers, are at the highest risk for IFD during episodes of HRFN. The proposed risk factor-based model may support early risk stratification and guide targeted antifungal prophylaxis or therapy, potentially improving outcomes in this population. Validation an external cohort is required to confirm these results and optimize clinical applicability. Full article

(This article belongs to the Special Issue Advances in Pediatric Fungal Infections: Diagnosis, Treatment, and Emerging Challenges)

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21 pages, 860 KB

Open AccessReview

Early Antifungal Treatment in Immunocompromised Patients, Including Hematological and Critically Ill Patients

by Galina Klyasova, Galina Solopova, Jehad Abdalla, Marina Popova, Muhlis Cem Ar, Murat Sungur, Riad El Fakih, Reem S. Almaghrabi and Murat Akova

J. Fungi 2026, 12(1), 59; https://doi.org/10.3390/jof12010059 - 13 Jan 2026

Viewed by 649

Abstract

(1) Background: Invasive fungal diseases (IFDs) represent significant challenges in clinical practice, particularly among immunocompromised individuals, leading to substantial morbidity and mortality. The present document aims to provide evidence-based consensus for the timely initiation of antifungal treatment, focusing on early empiric approaches among [...] Read more.

(1) Background: Invasive fungal diseases (IFDs) represent significant challenges in clinical practice, particularly among immunocompromised individuals, leading to substantial morbidity and mortality. The present document aims to provide evidence-based consensus for the timely initiation of antifungal treatment, focusing on early empiric approaches among immunocompromised patients. (2) Methods: A multidisciplinary expert panel of nine healthcare professionals (HCPs) reviewed the literature, including guidelines and consensus reports (2013–2023; PubMed, Scopus). The panel defined appropriate empiric antifungal approaches for invasive candidiasis, aspergillosis, and mucormycosis among hematological and critically ill patients. Consensus was defined as ≥75% agreement. (3) Results: A total of 47 statements were included. The experts recommend that early targeted antifungal therapy is critical for high-risk patients with suspected IFDs. Empiric therapy may be initiated before definitive diagnosis, considering the local fungal prevalence and the patient’s risk category. Close monitoring is essential, and switching between antifungal classes may be necessary for patients who experience deterioration or side effects. The transition from intravenous to oral therapy depends on the specific infection, the availability of therapeutic drug monitoring, and the patient’s progress. (4) Conclusions: Implementing this targeted, early approach may improve the outcomes of vulnerable patients with IFDs. Full article

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

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17 pages, 962 KB

Open AccessReview

The Medicinal Mushroom Ganoderma: A Review of Systematics, Phylogeny, and Metabolomic Insights

by Gideon Adotey, Abraham Quarcoo, Mohammed Ahmed Gedel, Paul Yerenkyi, Phyllis Otu, Abraham K. Anang, Laud K. N. Okine, Winfred S. K. Gbewonyo, John C. Holliday and Vincent C. Lombardi

J. Fungi 2026, 12(1), 58; https://doi.org/10.3390/jof12010058 - 12 Jan 2026

Viewed by 476

Abstract

Ganoderma is a genus of medically significant fungi, that is used in traditional medicine and is increasingly incorporated into modern nutraceuticals and pharmaceuticals. Accurate species identification and product standardization remain major challenges due to morphological plasticity and cryptic diversity. This review articulates current [...] Read more.

Ganoderma is a genus of medically significant fungi, that is used in traditional medicine and is increasingly incorporated into modern nutraceuticals and pharmaceuticals. Accurate species identification and product standardization remain major challenges due to morphological plasticity and cryptic diversity. This review articulates current advances in Ganoderma systematics, phylogenetics, and metabolomics, with an emphasis on molecular identification strategies and chemical profiling. Internal transcribed spacer (ITS) sequencing has substantially improved species delineation compared with morphology alone, but its resolving power is limited in closely related species complexes, necessitating complementary multilocus approaches. Advances in metabolomics, and LC-MS- and HPLC-based profiling of triterpenes and polysaccharides, have enhanced species discrimination, chemotaxonomic resolution, and quality control of commercial products. Integrating molecular barcoding with metabolomic fingerprints provides a more robust framework for classification, pharmacological evaluation, and standardization. This review also highlights significant geographic knowledge gaps, particularly in Africa, where molecular and metabolomic data remain scarce despite high species diversity. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom)

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17 pages, 3639 KB

Open AccessArticle

The AP-1 Sigma Subunit Gene PsAP1 Acts as a Key Pathogenicity Factor by Regulating Metabolic Reprogramming in Puccinia striiformis f. sp. tritici

by Beibei Liu, Jianing Wu, Guoshuai Zhang, Jianghua Chen, Guangkuo Li, Xintong Wang, W. G. Dilantha Fernando, Haifeng Gao and Yue Li

J. Fungi 2026, 12(1), 57; https://doi.org/10.3390/jof12010057 - 12 Jan 2026

Viewed by 308

Abstract

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a severe threat to global wheat production. The adaptor protein complex AP-1 plays a crucial role in vesicular trafficking, yet its function in rust fungi remains poorly understood. In this study, [...] Read more.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a severe threat to global wheat production. The adaptor protein complex AP-1 plays a crucial role in vesicular trafficking, yet its function in rust fungi remains poorly understood. In this study, a gene encoding an AP-1 σ subunit, designated PsAP1, was identified in Pst. The expression of PsAP1 was highly induced during the early infection stage. Heterologous expression of PsAP1 in a Fusarium graminearum mutant partially restored its pathogenic defects. Subcellular localization analysis revealed that PsAP1 localizes to the plasma membrane, cytoplasm, and nucleus. Silencing PsAP1 in wheat using Barley stripe mosaic virus-mediated host-induced gene silencing (BSMV-HIGS) significantly attenuated Pst pathogenicity, reducing hyphal growth by 6.7% (colony diameter), sporulation by 61.6% (lesion length), and pathogen biomass by 66%, along with enhanced accumulation of host reactive oxygen species. Transcriptomic analysis further demonstrated that silencing PsAP1 disrupted multiple pathways, including MAPK signaling, glutathione metabolism, and carbohydrate metabolism. These findings indicate that PsAP1 facilitates Pst infection by modulating vesicular trafficking, suppressing host immunity, and reprogramming host metabolism. This study provides novel insights into the pathogenic mechanisms of rust fungi and suggests a potential target for disease control. Full article

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

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17 pages, 4129 KB

Open AccessArticle

Development and Comparison of Visual Colorimetric Endpoint LAMP and Real-Time LAMP-SYBR Green I Assays for Alternaria alternata (Fr.) Keissl in European Plum

by Hongyue Li, Canpeng Fu, Pan Xie, Wenwen Gao, Zhiqiang Mu, Lingkai Xu, Qiuyan Han and Shuaishuai Sha

J. Fungi 2026, 12(1), 56; https://doi.org/10.3390/jof12010056 - 12 Jan 2026

Viewed by 389

Abstract

European plum (Prunus domestica L.) is widely cultivated worldwide, with China producing 6.8 million t annually (55% of the global total output). However, the Kashgar region of Xinjiang, China’s primary production area, has experienced outbreaks of brown spot disease caused by Alternaria [...] Read more.

European plum (Prunus domestica L.) is widely cultivated worldwide, with China producing 6.8 million t annually (55% of the global total output). However, the Kashgar region of Xinjiang, China’s primary production area, has experienced outbreaks of brown spot disease caused by Alternaria alternata (Fr.) Keissl. Outbreaks of this disease severely hinder both domestic and global development of the European plum industry. Because this pathogen has a strong latent infection capability during the early stages of disease development, its early detection is important. We develop two detection methods targeting the ITS sequence of A. alternata: LAMP-Cresol Red chromogenic visible endpoint detection and LAMP-SYBR Green I real-time fluorescent detection. Both methods demonstrate high specificity for A. alternata, enabling stable detection of the pathogen in various plant samples; detection limits reach the femtogram (fg) level, significantly surpassing conventional PCR detection capabilities. Development of these highly efficient and precise early detection methods provides a solid foundation for sustainable development of China as a global hub of the European plum industry, and contributes significantly to global disease prevention, control, and industrial stability for this crop. Full article

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

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16 pages, 413 KB

Open AccessReview

Diagnostic Biomarkers for Invasive Candidiasis: A Clinician-Oriented Review

by Sebastian George Smadu, Simona Camelia Tetradov, Luminita Ene, Corina Oprisan, Dragoș Ștefan Lazăr and Simin Aysel Florescu

J. Fungi 2026, 12(1), 55; https://doi.org/10.3390/jof12010055 - 12 Jan 2026

Viewed by 448

Abstract

Introduction: A group of approximately 15 Candida species are frequently found to be responsible for human invasive candidiasis, an infection that appears in patients with prolonged hospitalization, particularly in Intensive Care Units, and in immunosuppressed individuals. Given the considerable burden if not rapidly [...] Read more.

Introduction: A group of approximately 15 Candida species are frequently found to be responsible for human invasive candidiasis, an infection that appears in patients with prolonged hospitalization, particularly in Intensive Care Units, and in immunosuppressed individuals. Given the considerable burden if not rapidly treated, clinicians face diagnostic challenges in distinguishing infection. The objective of this narrative review is to summarize the clinically applicable biomarkers used for invasive candidiasis and to evaluate their performance and create a diagnostic algorithm for clinical practice. Methods: This narrative review was conducted by searching PubMed and Scopus for studies published between 1990 and 2025, using keywords related to invasive candidiasis and non-culture diagnostic biomarkers. Clinical guidelines and consensus documents from major infectious diseases societies were additionally reviewed to supplement. Results: Blood cultures, which are considered the “gold standard” for diagnosis, face important fallouts caused by the limited sensitivity of 50%. Polymerase Chain Reaction assays can identify Candida species at an early stage when compared to blood cultures, demonstrating high specificity that ranges between 91% and 98, due to their high cost, and the limitations regarding only the identification of certain species, their widespread use remains limited. Non-culture serological tests such as mannan, anti-mannan and 1-3-β-D-glucan can detect fungal cell wall components or antibodies directed towards them. These tests have the advantage of being performed directly from blood samples. Reported sensitivity and specificity are 83% and 86% for mannan/anti-mannan, and 73% and 80% for 1-3-β-D-glucan, respectively. They are used for early detection of candidemia in high-risk patients, including immunocompromised individuals. Conclusions: Our report suggests that the traditional “gold standard” for diagnosing invasive candidiasis can be improved by integrating and combining novel biomarkers in the diagnostic pathways, and, thus, potentially reducing the time spent for diagnosing and facilitating early treatment access. Full article

(This article belongs to the Special Issue Medical Mycology: Antifungal Resistance, Diagnosis, and Infection Control)

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16 pages, 2607 KB

Open AccessReview

Pleurotus ostreatus for Environmental Remediation and Sustainable Bioprocesses: An Evidence-Mapped Review of Research Gaps and Opportunities

by Luz Miryam Lozada-Martinez, Juan David Reyes-Duque, Yadira Marin-Hamburger and Ivan David Lozada-Martinez

J. Fungi 2026, 12(1), 54; https://doi.org/10.3390/jof12010054 - 12 Jan 2026

Viewed by 415

Abstract

Fungi have emerged as versatile biotechnological platforms for addressing environmental challenges with potential co-benefits for human health. Among them, Pleurotus ostreatus stands out for its ligninolytic enzyme systems (notably laccases), capacity to valorize lignocellulosic residues, and ability to form functional mycelial materials. We [...] Read more.

Fungi have emerged as versatile biotechnological platforms for addressing environmental challenges with potential co-benefits for human health. Among them, Pleurotus ostreatus stands out for its ligninolytic enzyme systems (notably laccases), capacity to valorize lignocellulosic residues, and ability to form functional mycelial materials. We conducted an evidence-mapped review, based on a bibliometric analysis of the Scopus corpus (2001–2025; 2085 records), to characterize research fronts and practical opportunities in environmental remediation and sustainable bioprocesses involving P. ostreatus. The mapped literature shows sustained growth and global engagement, with prominent themes in: (a) oxidative transformation of phenolic compounds, dyes and polycyclic aromatic hydrocarbons; (b) biodegradation/bioconversion of agro-industrial residues into value-added products; and (c) development of bio-based materials and processes aligned with the circular bioeconomy. We synthesize how these strands translate to real-world contexts, reducing contaminant loads, closing nutrient loops, and enabling low-cost processes that may indirectly reduce exposure-related risks. Key translational gaps persist: standardization of environmental endpoints, scale-up from laboratory to field, performance in complex matrices, life-cycle impacts and cost, ecotoxicological safety, and long-term monitoring. A practical agenda was proposed that prioritizes field-scale demonstrations with harmonized protocols, integration of life-cycle assessment and cost metrics, data sharing, and One Health frameworks linking environmental gains with plausible health co-benefits. In conclusion, P. ostreatus is a tractable platform organism for sustainable remediation and bio-manufacturing. This evidence map clarifies where the field is mature and where focused effort can accelerate the impact of future research. Full article

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

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24 pages, 5513 KB

Open AccessArticle

The Compatibility of the Epichloë bromicola–Hordeum Association

by Jing Liu, Jiping Li, Tao Li, Zhengfeng Wang and Chunjie Li

J. Fungi 2026, 12(1), 53; https://doi.org/10.3390/jof12010053 - 11 Jan 2026

Viewed by 334

Abstract

Background: Artificial inoculation of Epichloë endophytes into elite forage germplasm aims to establish beneficial symbioses for developing high-yield, high-quality, and stress-tolerant cultivars, but host specificity of the fungi often causes compatibility issues in non-natural hosts. Methods: The E. bromicola isolated from native wild [...] Read more.

Background: Artificial inoculation of Epichloë endophytes into elite forage germplasm aims to establish beneficial symbioses for developing high-yield, high-quality, and stress-tolerant cultivars, but host specificity of the fungi often causes compatibility issues in non-natural hosts. Methods: The E. bromicola isolated from native wild barley was inoculated into cultivated wild barley (Hordeum brevisubulatum) and cultivated barley (Hordeum valgare), forming Hb+Eb and Hv+Eb. The NHb+Eb (native wild barley naturally infected with E. bromicola) served as a control. We analyzed fungal colonization patterns and symbiotic gene regulation to clarify the compatibility between E. bromicola and non-natural hosts. Results: Compared with NHb+Eb and Hb+Eb, E. bromicola in Hv+Eb showed obvious hyphal vacuolization. E. bromicola colonization altered host trichome morphology and induced stomatal closure. Correspondingly, expression of the siderophore biosynthesis gene sidN and the NADPH oxidase complex genes (NoxA, NoxB, NoxR, RacA) was significantly lower (p < 0.05) in Hv+Eb than in Hb+Eb and NHb+Eb. Conclusions: This study reveals that the incompatibility between cultivated barley and E. bromicola is characterized by altered hyphal morphology, which is linked to the downregulation of sidN and Nox. These findings provide a critical theoretical foundation for developing highly compatible cereal-Epichloë germplasms. Full article

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

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24 pages, 4743 KB

Open AccessArticle

Antifungal Potential of Diaporthe sp. Endophytes from Antillean Avocado Against Fusarium spp.: From Organic Extracts to In Silico Chitin Synthase Inhibition

by Angie T. Robayo-Medina, Katheryn Michell Camargo-Jimenez, Felipe Victoria-Muñoz, Wilman Delgado-Avila, Luis Enrique Cuca and Mónica Ávila-Murillo

J. Fungi 2026, 12(1), 52; https://doi.org/10.3390/jof12010052 - 11 Jan 2026

Viewed by 351

Abstract

Fungal endophytes have emerged as a promising source of bioactive compounds with potent antifungal properties for plant disease management. This study aimed to isolate and characterize fungal endophytes from Antillean avocado (Persea americana var. americana) trees in the Colombian Caribbean, capable [...] Read more.

Fungal endophytes have emerged as a promising source of bioactive compounds with potent antifungal properties for plant disease management. This study aimed to isolate and characterize fungal endophytes from Antillean avocado (Persea americana var. americana) trees in the Colombian Caribbean, capable of producing bio-fungicide metabolites against Fusarium solani and Fusarium equiseti. For this, dual culture assays, liquid-state fermentation of endophytic isolates, and metabolite extractions were conducted. From 88 isolates recovered from leaves and roots, those classified within the Diaporthe genus exhibited the most significant antifungal activity. Some of their organic extracts displayed median inhibitory concentrations (IC₅₀) approaching 200 μg/mL. To investigate the mechanism of action, in silico studies targeting chitin synthase (CS) were performed, including homology models of the pathogens’ CS generated using Robetta, followed by molecular docking with Vina and interaction fingerprint similarity analysis of 15 antifungal metabolites produced by Diaporthe species using PROLIF. A consensus scoring strategy identified diaporxanthone A (12) and diaporxanthone B (13) as the most promising candidates, achieving scores up to 0.73 against F. equiseti, comparable to the control Nikkomycin Z (0.82). These results suggest that Antillean avocado endophytes produce bioactive metabolites that may inhibit fungal cell wall synthesis, offering a sustainable alternative for disease management. Full article

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

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8 pages, 1057 KB

Open AccessCase Report

Zoonotic Sporotrichosis by Sporothrix brasiliensis in Chile: Evidence of Emerging Transmission Under a One Health Perspective

by Patricio Godoy-Martínez, Rodrigo Muñoz, Pamela Thomson, Diego Orlandi, Flavio Queiroz-Telles, Nicomedes Valenzuela-Lopez, María Paz Villanueva, Joselin Solís and Isabel Iturrieta-González

J. Fungi 2026, 12(1), 51; https://doi.org/10.3390/jof12010051 - 11 Jan 2026

Viewed by 804

Abstract

Sporotrichosis, the most common implantation mycosis worldwide, is caused by dimorphic fungi of several species of the genus Sporothrix. Sporothrix brasiliensis, the most virulent species, has emerged in Latin America as an epi-zoonotic pathogen linked to domestic cats, dogs and humans. [...] Read more.

Sporotrichosis, the most common implantation mycosis worldwide, is caused by dimorphic fungi of several species of the genus Sporothrix. Sporothrix brasiliensis, the most virulent species, has emerged in Latin America as an epi-zoonotic pathogen linked to domestic cats, dogs and humans. This report describes a confirmed human case of lymphocutaneous sporotrichosis caused by S. brasiliensis in Chile, associated with feline exposure in a veterinarian. Diagnosis was supported by morphological and molecular analyses of the internal transcribed spacer (ITS) and β-tubulin gene. The patient responded favorably to itraconazole therapy. This case highlights the growing relevance of S. brasiliensis in Chile and reinforces the need for integrated One Health surveillance strategies. Full article

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

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J. Fungi, Volume 12, Issue 1 (January 2026) – 80 articles

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