Journal of Fungi

16 pages, 1191 KB

Open AccessArticle

First Report of Candida auris Candidemia in Portugal: Genomic Characterisation and Antifungal Resistance-Associated Genes Analysis

by Isabel M. Miranda, Micael F. M. Gonçalves, Dolores Pinheiro, Sandra Hilário, José Artur Paiva, João Tiago Guimarães and Sofia Costa de Oliveira

J. Fungi 2025, 11(10), 716; https://doi.org/10.3390/jof11100716 - 3 Oct 2025

Abstract

Candida auris has emerged as a global public health threat due to its high mortality rates, multidrug resistance, and rapid transmission in healthcare settings. This study reports the first documented cases of C. auris candidemia in Portugal, comprising eight isolates from candidemia and [...] Read more.

Candida auris has emerged as a global public health threat due to its high mortality rates, multidrug resistance, and rapid transmission in healthcare settings. This study reports the first documented cases of C. auris candidemia in Portugal, comprising eight isolates from candidemia and colonised patients admitted to a major hospital in northern Portugal in 2023. Whole-genome sequencing (WGS) was performed to determine the phylogenetic relationships of the isolates, which were classified as belonging to Clade I. Genome sequencing also enabled the detection of missense mutations in antifungal resistance genes, which were correlated with antifungal susceptibility profiles determined according to EUCAST (European Committee on Antimicrobial Susceptibility Test) protocols and guidelines. All isolates exhibited resistance to fluconazole and amphotericin B according to the recently established EUCAST epidemiological cut-offs (ECOFFs). Most of the isolates showed a resistant phenotype to anidulafungin and micafungin. All isolates were resistant to caspofungin. Missense mutations identified included Y132F in ERG11, E709D in CDR1, A583S in TAC1b, K52N and E1464K in SNQ2, K74E in CIS2, M192I in ERG4, a novel mutation S237T in CRZ1, and variants in GCN5, a gene involved in chromatin remodelling and stress-response regulation. Identifying known and novel mutations highlights the evolution of antifungal resistance mechanisms in C. auris. These findings underscore the need for further research to understand C. auris resistance pathways and to guide effective clinical management strategies. Full article

(This article belongs to the Collection Invasive Candidiasis)

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7 pages, 894 KB

Open AccessCommentary

Advancing Peptide-Based Vaccines Against Candida: A Comparative Perspective on Liposomal and Synthetic Formulations

by Hong Xin

J. Fungi 2025, 11(10), 715; https://doi.org/10.3390/jof11100715 - 2 Oct 2025

Abstract

The growing threat of multidrug-resistant fungal pathogens, especially Candida auris, has underscored the need for effective antifungal vaccines. This commentary highlights recent advances in peptide-based vaccination using the SNAP (Spontaneous Nanoliposome Antigen Presentation) platform, focusing on the FM-SNAP vaccine, a bivalent liposomal [...] Read more.

The growing threat of multidrug-resistant fungal pathogens, especially Candida auris, has underscored the need for effective antifungal vaccines. This commentary highlights recent advances in peptide-based vaccination using the SNAP (Spontaneous Nanoliposome Antigen Presentation) platform, focusing on the FM-SNAP vaccine, a bivalent liposomal formulation targeting the surface-expressed peptides fructose bisphosphate aldolase (Fba) and methionine synthase (Met6). Compared to earlier constructs such as MP12, FM-SNAP achieves superior immunogenicity and long-lasting protection at lower antigen doses. It elicits balanced Th1/Th2 cytokine responses and demonstrates durable efficacy in both immunocompetent and complement-deficient mouse models. The platform’s compatibility with clinically approved adjuvants (MPLA and QS-21), modular peptide design, and potential for multi-pathogen applications underscores its translational promise. FM-SNAP exemplifies a next-generation vaccine strategy that is both scalable and adaptable for high-risk immunocompromised populations. Full article

(This article belongs to the Special Issue Bioinformatics and Current Techniques in Medical Mycology: Combining Laboratory and Clinical Viewpoints)

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22 pages, 6066 KB

Open AccessArticle

Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Trichoderma longibrachiatum T6 Strain: Insights into Biocontrol of Heterodera avenae

by Cizhong Duan, Jia Liu, Shuwu Zhang and Bingliang Xu

J. Fungi 2025, 11(10), 714; https://doi.org/10.3390/jof11100714 - 1 Oct 2025

Abstract

The cereal cyst nematode, Heterodera avena, is responsible for substantial economic losses in the global production of wheat, barley, and other cereal crops. Extracellular enzymes, particularly those from the glycoside hydrolase 18 (GH18) family, such as chitinases secreted by Trichoderma spp., play [...] Read more.

The cereal cyst nematode, Heterodera avena, is responsible for substantial economic losses in the global production of wheat, barley, and other cereal crops. Extracellular enzymes, particularly those from the glycoside hydrolase 18 (GH18) family, such as chitinases secreted by Trichoderma spp., play a crucial role in nematode control. However, the genome-wide analysis of Trichoderma longibrachiatum T6 (T6) GH18 family genes in controlling of H. avenae remains unexplored. Through phylogenetic analysis and bioinformatics tools, we identified and conducted a detailed analysis of 18 GH18 genes distributed across 13 chromosomes. The analysis encompassed gene structure, evolutionary development, protein characteristics, and gene expression profiles following T6 parasitism on H. avenae, as determined by RT-qPCR. Our results indicate that 18 GH18 members in T6 were clustered into three major groups (A, B, and C), which comprise seven subgroups. Each subgroup exhibits highly conserved catalytic domains, motifs, and gene structures, while the cis-acting elements demonstrate extensive responsiveness to hormones, stress-related signals, and light. These members are significantly enriched in the chitin catabolic process, extracellular region, and chitinase activity (GO functional enrichment), and they are involved in amino sugar and nucleotide sugar metabolism (KEGG pathway enrichment). Additionally, 13 members formed an interaction network, enhancing chitin degradation efficiency through synergistic effects. Interestingly, 18 members of the GH18 family genes were expressed after T6 parasitism on H. avenae cysts. Notably, GH18-3 (Group B) and GH18-16 (Group A) were significantly upregulated, with average increases of 3.21-fold and 3.10-fold, respectively, from 12 to 96 h after parasitism while compared to the control group. Meanwhile, we found that the GH18-3 and GH18-16 proteins exhibit the highest homology with key enzymes responsible for antifungal activity in T. harzianum, demonstrating dual biocontrol potential in both antifungal activity and nematode control. Overall, these results indicate that the GH18 family has undergone functional diversification during evolution, with each member assuming specific biological roles in T6 effect on nematodes. This study provides a theoretical foundation for identifying novel nematicidal genes from T6 and cultivating highly efficient biocontrol strains through transgenic engineering, which holds significant practical implications for advancing the biocontrol of plant-parasitic nematodes (PPNs). Full article

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

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16 pages, 616 KB

Open AccessSystematic Review

Pediatric Coccidioidal Meningitis: A Systematic Review and Proportional Synthesis of Cases Reported in the Fluconazole Era (2000–2025)

by Maria F. De la Cerda-Vargas, Pedro Navarro-Dominguez, Elizabeth Meza-Mata, Melisa A. Muñoz-Hernandez, Fany Karina Segura-Lopez, Marisela Del Rocio Gonzalez-Martinez, Hector A. Delgado-Aguirre, Sergio Valente Flores-Miranda, David de Jesús Mercado-Rubio, Yair O. Adame-Martínez, Geovanni A. Valadez-Altamira and Jose Antonio Candelas-Rangel

J. Fungi 2025, 11(10), 713; https://doi.org/10.3390/jof11100713 - 1 Oct 2025

Abstract

Coccidioidal meningitis (CM) is a rare but life-threatening complication of disseminated coccidioidomycosis, occurring in ~16% of cases, particularly among children in endemic regions such as the southwestern US and northern Mexico. Without timely diagnosis and antifungal therapy, pediatric CM is almost universally fatal [...] Read more.

Coccidioidal meningitis (CM) is a rare but life-threatening complication of disseminated coccidioidomycosis, occurring in ~16% of cases, particularly among children in endemic regions such as the southwestern US and northern Mexico. Without timely diagnosis and antifungal therapy, pediatric CM is almost universally fatal within the first year. Hydrocephalus develops in up to 50% of cases. In 2000, Galgiani et al. established fluconazole as first-line therapy for CM. Subsequent guidelines refined management but did not specifically address pediatric patients (>1 month–≤19 years). No studies in the fluconazole era have systematically evaluated risk factors for complications in this population. We therefore conducted a systematic review and proportional synthesis of pediatric CM cases, focusing on CNS complications and outcomes. PubMed/MEDLINE, Embase (Ovid), and Web of Science were systematically searched (2000–2025). PROSPERO registration ID (1130290). Inclusion criteria encompassed epidemiological studies, case series, and case reports that described at least one pediatric case of CM or CNS involvement, confirmed by diagnostic methods. Cases in adults, neonates (<1 month), congenital infections, teratogenicity studies, reviews, or incomplete reports were excluded. Only cases with complete individual data (n = 48) were included. Methodological rigor was ensured using JBI Critical Appraisal Tools. Of 1089 studies, 31 met the inclusion criteria, representing 3874 pediatric cases. CM/CNS involvement was confirmed in 165 cases (4.25%; 95% CI: 3.6–4.9%), with hydrocephalus in 62 (37.5%). Among 48 case reports with complete data, fluconazole was first-line therapy in 65%. Serum CF titers ≥ 1:16 were associated with hydrocephalus plus stroke (p = 0.027) and independently predicted adverse outcomes (relapse/death; OR = 4.5, p = 0.037), whereas lifelong azole therapy was associated with improved outcomes (overall survival mean, 82 vs. 32 months; p = 0.002). Pediatric CM remains highly lethal, with hydrocephalus a frequent and severe complication. High serum CF titers (≥1:16) predict poor outcomes, emphasizing the urgent need for standardized, pediatric-specific diagnosis and management guidelines. Full article

(This article belongs to the Special Issue Pediatric Fungal Infections, 2nd Edition)

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26 pages, 2123 KB

Open AccessReview

Cochlioquinones 1968–2024: Chemistry, Biosynthesis, and Biological Activities with Future Perspectives

by Huiqi Fang, Qi Li, Lin Chen and Gang Ding

J. Fungi 2025, 11(10), 712; https://doi.org/10.3390/jof11100712 - 30 Sep 2025

Abstract

Cochlioquinones are a member of meroterpenoids possessing a core 6/6/6/6 tetracyclic ring system, which originate from the polyketide-terpenoid hybrid biosynthesis. Up to date, there are eighty-one analogues with diverse post-modifications isolated from different fungi, most of which exhibit different biological activities, such as [...] Read more.

Cochlioquinones are a member of meroterpenoids possessing a core 6/6/6/6 tetracyclic ring system, which originate from the polyketide-terpenoid hybrid biosynthesis. Up to date, there are eighty-one analogues with diverse post-modifications isolated from different fungi, most of which exhibit different biological activities, such as phytotoxic, antibacterial, cytotoxic, and immunosuppressive effects. Structurally, cochlioquinones can be mainly categorized into two classes: benzoquinone-type and phenol-type cochlioquinones, respectively. In this review, chemistry and biology of cochlioquinones including the structures, NMR and MS features, bioactivities, and biosynthesis from 1968 to 2024 are systematically summarized, which might provide insights into the exploration and utilization of this group of meroterpenoids in the agricultural or pharmaceutical industry. Full article

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

25 pages, 3326 KB

Open AccessArticle

Analysis of Amino Acid and Derivative Diversity and Antioxidant Capacity in Ophiocordyceps sinensis and Its Substitutes

by Haoxu Tang, Bing Jia, Chuyu Tang, Chao Feng, Yuling Li and Xiuzhang Li

J. Fungi 2025, 11(10), 711; https://doi.org/10.3390/jof11100711 - 30 Sep 2025

Abstract

In this study, we used liquid chromatography–tandem mass spectrometry (LC-MS/MS) combined with multivariate statistical analysis to conduct comprehensive qualitative and quantitative profiling of amino acids and their derivatives in wild Ophiocordyceps sinensis (O. sinensis) samples from Naqu (NQ) and Xiaojin (XJ), [...] Read more.

In this study, we used liquid chromatography–tandem mass spectrometry (LC-MS/MS) combined with multivariate statistical analysis to conduct comprehensive qualitative and quantitative profiling of amino acids and their derivatives in wild Ophiocordyceps sinensis (O. sinensis) samples from Naqu (NQ) and Xiaojin (XJ), cultivated O. sinensis (RG), and Bailing Capsules (BL). The objective was to systematically characterize amino acid metabolism and assess its correlation with antioxidant functionality. A total of 82 amino acids and their derivatives were identified. XJ had the highest essential amino acids, while BL had significantly lower content (except lysine) (p < 0.05). Antioxidant assays revealed that NQ and XJ samples exhibited superior antioxidant activity in 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonate) (ABTS), 2,2-diphenyl-1-picrylhydrazyl (DPPH), and ferric ion reducing antioxidant power (FRAP) assays, and this activity showed a correlation to the contents of bioactive components such as total phenols (TPS), total polysaccharide (TPE), and total flavonoids (TF). Further pathway analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) suggested that arginine and proline metabolism, aromatic amino acid biosynthesis, and tryptophan metabolism may be critical pathways that could underpin regional differences in O. sinensis quality, while variation in tyrosine metabolism may account for differences in antioxidant activity. This study provides a systematic comparison of amino acid profiles and antioxidant capacities across O. sinensis and its substitutes, offering a robust theoretical foundation for the development and functional evaluation of these bioresources. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

18 pages, 2398 KB

Open AccessArticle

Genome Analysis of Alternaria alstroemeriae L6 Associated with Black Spot of Strawberry: Secondary Metabolite Biosynthesis and Virulence

by Li Zhang, Boyuan Zhang, Lizhu Shao, Miaomiao Yang, Xueling Zhao, Ziyu Wang, Yingjun Zhang, Yuting Li, Yating Wang, Yuansen Hu and Peng Li

J. Fungi 2025, 11(10), 710; https://doi.org/10.3390/jof11100710 - 30 Sep 2025

Abstract

A pathogenic fungus was isolated from the leaves of strawberry black spot in Zhengzhou China. Based on morphological and phylogenetic analysis, the isolate was identified as Alternaria alstroemeriae. Hybrid sequencing and assembly yielded a high-quality 38.7 Mb genome with 12,781 predicted genes [...] Read more.

A pathogenic fungus was isolated from the leaves of strawberry black spot in Zhengzhou China. Based on morphological and phylogenetic analysis, the isolate was identified as Alternaria alstroemeriae. Hybrid sequencing and assembly yielded a high-quality 38.7 Mb genome with 12,781 predicted genes and 99.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness. Functional annotation revealed enrichment in carbohydrate metabolism, secondary metabolite biosynthesis, and virulence-associated genes. Strain L6 harbored 45 biosynthetic gene clusters(BGCs), including 12 clusters for terpenes, 7 for non-ribosomal peptide synthetases, and 7 for polyketide synthases. Six BGCs showed high similarity to known pathways producing alternariol (phytotoxic/mycotoxic compound), alternapyrone (phytotoxin), choline (osmoprotectant), terpestacin (anti-angiogenic agent), clavaric acid (anticancer terpenoid), and betaenone derivatives (phytotoxins). CAZyme analysis identified 596 carbohydrate-active enzymes, aligning with L6’s biotrophic lifestyle. Additionally, 996 secreted proteins were predicted, of which five candidate effectors contained the conserved RxLx [EDQ] host-targeting motif, suggesting potential roles in virulence. This genome resource highlights L6’s exceptional secondary metabolites (SMs) diversity, featuring both plant-pathogenic toxins and pharmacologically valuable compounds, indicating that this endophytic fungus is a potential producer of metabolites meriting further exploration and development. Full article

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13 pages, 4462 KB

Open AccessArticle

Application and Mechanism of Action of Carvacrol Against Aspergillus niger Causing Postharvest Rot of Garlic Scapes (Allium sativum L.)

by Pei Li, Wenqing Wu, Can He, Boxi Tan, Shijing Tang and Lu Yu

J. Fungi 2025, 11(10), 709; https://doi.org/10.3390/jof11100709 - 30 Sep 2025

Abstract

During prolonged storage of garlic scapes (Allium sativum L.), the proliferation of microorganisms, particularly fungi, frequently results in postharvest rot, which negatively impacts both product quality and market value. Carvacrol, a promising natural food preservative, exhibits broad-spectrum bioactivity against various microorganisms. In [...] Read more.

During prolonged storage of garlic scapes (Allium sativum L.), the proliferation of microorganisms, particularly fungi, frequently results in postharvest rot, which negatively impacts both product quality and market value. Carvacrol, a promising natural food preservative, exhibits broad-spectrum bioactivity against various microorganisms. In this study, a specific pathogenic fungal strain causing postharvest rot in garlic scapes, designated as HQ, was initially isolated from symptomatic garlic scapes. Based on a combination of physiological characteristics and molecular identification techniques, the HQ strain was identified as Aspergillus niger. Our findings further demonstrated that carvacrol exhibits significant in vitro inhibitory effects against Aspergillus niger with an EC₅₀ value of 75.99 μg/L. Moreover, scanning electron microscopy (SEM) observations revealed that carvacrol induces irreversible morphological and structural changes in the hyphae, resulting in deformation and rupture. Additionally, integrated transcriptomic and proteomic analyses indicated that carvacrol primarily targets the cell wall integrity (CWI) signaling pathway within the mitogen-activated protein kinase (MAPK) signaling pathway in Aspergillus niger, thereby compromising cell membrane integrity and stability, which ultimately suppresses fungal growth and proliferation. Full article

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

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9 pages, 741 KB

Open AccessBrief Report

Dual-Emission FRET-PCR Outperforms SYBR Green and EvaGreen for Accurate Discrimination of Primary Canine Dermatophytes: Microsporum canis, Nannizzia gypsea, and Trichophyton mentagrophytes

by Nneka Vivian Iduu, Rae Kantzler, Donna Raiford, Brenda Bixler, Kelly Chenoweth and Chengming Wang

J. Fungi 2025, 11(10), 708; https://doi.org/10.3390/jof11100708 - 30 Sep 2025

Abstract

Conventional diagnosis of dermatophytosis relies on fungal culture and microscopic examination, methods that are often time-consuming and lack sensitivity. This study aimed to develop and compare real-time PCR assays for the simultaneous detection and differentiation of three major dermatophytes in dogs: Microsporum canis [...] Read more.

Conventional diagnosis of dermatophytosis relies on fungal culture and microscopic examination, methods that are often time-consuming and lack sensitivity. This study aimed to develop and compare real-time PCR assays for the simultaneous detection and differentiation of three major dermatophytes in dogs: Microsporum canis, Nannizzia gypsea, and Trichophyton mentagrophytes. Three qPCR platforms targeting the chitin synthase 1 (CHS1) gene—SYBR Green, EvaGreen, and dual-emission fluorescence resonance energy transfer (FRET)—were evaluated. The FRET assay demonstrated the highest performance, achieving a detection limit of a single gene copy per reaction and producing distinct melting profiles that enabled accurate species discrimination (M. canis ~56.1 °C, N. gypsea ~53.0 °C, T. mentagrophytes ~51.8 °C). In contrast, SYBR Green and EvaGreen assays showed reduced sensitivity and cross-reactivity with non-target fungi. All assays were validated using three ATCC reference strains, ten clinical isolates of the target dermatophytes, and nine additional fungal species, including Nocardia, Aspergillus, Fusarium, Sporothrix, and Candida. Overall, FRET-qPCR exhibited a 100% specificity and a detection limit of one copy of target gene per reaction, offering a rapid, reliable tool for accurate diagnosis and molecular surveillance of dermatophytosis in companion animals. Full article

(This article belongs to the Special Issue Dermatophytes and Cutaneous Fungal Infections)

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15 pages, 3145 KB

Open AccessArticle

ABA and Ethylene Mediates Tomato Root Development Modulation During Endophytic Fungal Interaction

by Maria Feka, Bilge Chousein, Olga Tsiouri and Kalliope K. Papadopoulou

J. Fungi 2025, 11(10), 707; https://doi.org/10.3390/jof11100707 - 30 Sep 2025

Abstract

The early stages of plant–microbe interaction are critical for establishing beneficial symbioses. We investigated how the endophytic fungus Fusarium solani strain FsK modulates tomato (Solanum lycopersicum) development and hormone pathways during in vitro co-cultivation. Seedlings were sampled at three early interaction [...] Read more.

The early stages of plant–microbe interaction are critical for establishing beneficial symbioses. We investigated how the endophytic fungus Fusarium solani strain FsK modulates tomato (Solanum lycopersicum) development and hormone pathways during in vitro co-cultivation. Seedlings were sampled at three early interaction stages (pre-contact, T1; initial contact, T2, 3 days post-contact, T3). Root traits and root and leaf transcripts for abscisic acid (ABA) and ethylene (ET) pathways were quantified, alongside fungal ET-biosynthesis genes. FsK altered root system architecture, increasing root area, lateral root number, root-hair length, and fresh biomass. These morphological changes coincided with tissue- and time-specific shifts. In leaves, FsK broadly affected ABA biosynthetic and homeostasis genes (ZEP1, NCED1, ABA2, AAO1, ABA-GT, BG1), indicating reduced de novo synthesis with enhanced deconjugation of stored ABA. ET biosynthesis was curtailed in leaves via down-regulation of ACC oxidase (ACO1–3), with isoform-specific changes in ACC synthase (ACS). The ET receptor ETR1 was transiently expressed early (T1–T2). FsK itself showed staged activation of fungal ET-biosynthesis genes. These results reveal coordinated fungal–plant hormone control at the transcriptional level that promotes root development during early interaction and support FsK’s potential as a biostimulant. Full article

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

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16 pages, 1912 KB

Open AccessArticle

Some Like It Rock ‘N’ Cold: Speleomycology of Ravništarka Cave (Serbia)

by Miloš Stupar, Željko Savković, Marija Pećić, Dragana Jerinkić, Olga Jakovljević and Slađana Popović

J. Fungi 2025, 11(10), 706; https://doi.org/10.3390/jof11100706 - 29 Sep 2025

Abstract

Caves and other subterranean ecosystems are characterized by stable, low temperatures, high humidity, and limited nutrient input, creating unique environments for extremophilic microorganisms. Among them, fungi play key roles in organic matter degradation, mineral interactions, and biogeochemical cycling, yet the diversity and adaptations [...] Read more.

Caves and other subterranean ecosystems are characterized by stable, low temperatures, high humidity, and limited nutrient input, creating unique environments for extremophilic microorganisms. Among them, fungi play key roles in organic matter degradation, mineral interactions, and biogeochemical cycling, yet the diversity and adaptations of cold-adapted fungi in cave habitats remain insufficiently explored. This study investigated psychrophilic and psychrotolerant fungi inhabiting the stone surfaces of Ravništarka Cave in Eastern Serbia. Biofilm samples were collected from nine sites and analyzed using culture-based isolation on both nutrient-rich and diluted media, followed by incubation at 10 °C, 25 °C, and 37 °C. Fungal identification combined morphological characteristics with molecular analyses of the ITS region and BenA gene, while ecological roles were assigned using FUNGuild. A total of 41 fungal species were documented, spanning Ascomycota (53.1%), Basidiomycota (43.7%), and Mortierellomycota (3.1%) phyla. The genus Penicillium exhibited the greatest species richness, with 14 taxa documented, including P. chrysogenum, P. glandicola, and P. solitum, all previously associated with cold or oligotrophic environments. The psychrotolerant species Mortierella alpina was the only representative of Mortierellomycota. Ecological guild assignment revealed fungi functioning at different trophic levels, highlighting their multifunctional ecological roles in extreme subterranean habitats. Full article

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

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17 pages, 4865 KB

Open AccessArticle

Biocontrol Efficiency of Leuconostoc mesenteroides GY-2 Against Postharvest Black Rot Caused by Alternaria alternata and the Mechanisms of Action

by Pengbo Dai, Bing Li, Yanan Li, Li Wang, Tongle Hu, Yanan Wang, Xianglong Meng, Bo Li, Keqiang Cao, Shutong Wang and Manli Sun

J. Fungi 2025, 11(10), 705; https://doi.org/10.3390/jof11100705 - 29 Sep 2025

Abstract

Apple black rot, a destructive postharvest disease caused by Alternaria alternata, poses significant economic threats during fruit storage and transportation. However, effective biocontrol bacteria to manage this disease remain limited. In this study, Leuconostoc mesenteroides strain GY-2, isolated from healthy apple fruit [...] Read more.

Apple black rot, a destructive postharvest disease caused by Alternaria alternata, poses significant economic threats during fruit storage and transportation. However, effective biocontrol bacteria to manage this disease remain limited. In this study, Leuconostoc mesenteroides strain GY-2, isolated from healthy apple fruit surfaces, had a remarkable biocontrol ability on apple black rot. While GY-2 exhibited no direct inhibitory effects in confrontation assays, volatile organic compounds (VOCs) emitted by the strain suppressed colony diameter of A. alternata by 70.8% in dual plate assays, indicating potent fungistatic activity. Notably, these VOCs produced by L. mesenteroides displayed broad-spectrum antifungal properties against multiple apple fungal pathogens. Microscopic analysis revealed that VOC exposure induced structural anomalies in A. alternata hyphae, including surface perforations and protoplast leakage, suggesting membrane integrity disruption. The VOCs produced by strain GY-2 were identified; four compounds had antifungal activities, among them, isoamylol exhibited the highest antifungal activity. Applying bacterial suspensions of strain GY-2 on apple fruit significantly reduced 91.4% of lesion areas of black rot. The strain exhibited robust colonization capacity on fruit surfaces, maintaining viable populations for over 15 days post-application, guaranteeing a sustained disease prevention. Furthermore, GY-2 treatment enhanced systemic resistance in apple fruit, as evidenced by upregulated antioxidant enzymes and defense-related enzymes. Importantly, application of GY-2 did not adversely affect key parameters of fruit quality, including firmness, soluble solids content, or acidity. These findings showed that the bacterial L. mesenteroides GY-2 was a promising biocontrol agent for managing postharvest black rot of apple fruit. Full article

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

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16 pages, 8060 KB

Open AccessArticle

Endophytic Fungal Diversity in Carpesium lipskyi from the Gaoligong Mountains, Yunnan, China

by Hancaiyuan Zheng, Qun Liu, Yining Di, Tao Liu, Yu Su, Yuqin He, Juntong Chen, Jingyi Peng, Shiou Yih Lee, Inh Thkim Hoa, Xianhan Huang and Lufeng Liu

J. Fungi 2025, 11(10), 704; https://doi.org/10.3390/jof11100704 - 28 Sep 2025

Abstract

Endophytic fungi represent key microbial symbionts that colonize internal plant tissues without causing apparent disease, playing vital roles in host growth, stress resistance, and biosynthesis of bioactive compounds. Carpesium lipskyi C. Winkl., a medicinal plant endemic to the Gaoligong Mountains in Yunnan, remains [...] Read more.

Endophytic fungi represent key microbial symbionts that colonize internal plant tissues without causing apparent disease, playing vital roles in host growth, stress resistance, and biosynthesis of bioactive compounds. Carpesium lipskyi C. Winkl., a medicinal plant endemic to the Gaoligong Mountains in Yunnan, remains largely unexplored regarding its endophytic fungal composition. In this study, a total of 737 amplicon sequence variants (ASVs) were identified through high-throughput sequencing, spanning 9 phyla, 36 classes, 67 orders, 137 families, 206 genera, and 277 species. The dominant phyla were Ascomycota, Basidiomycota, and Glomeromycota. Alpha diversity in stems and leaves followed a unimodal distribution along the elevational gradient, in contrast to root endophytic communities, which showed no significant correlation with altitude. Peak diversity occurred at 2734 m, indicating a non-linear altitude-diversity relationship. Altitude, along with stable precipitation and temperature (2600–3210 m), significantly influenced fungal diversity. Medicinal fungi such as Cladosporium sp., Meyerozyma guilliermondii, Phialocephala fortinii, and Rhodotorula mucilaginosa were found in either roots or stems. This is the first comprehensive assessment of endophytic fungi in C. lipskyi from this region, providing a foundation for future ecological and pharmacological studies. Full article

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

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21 pages, 2038 KB

Open AccessArticle

Improving the Yield and Quality of Morchella spp. Using Agricultural Waste

by Jiawen Wang, Weiming Cai, Qunli Jin, Lijun Fan, Zier Guo and Weilin Feng

J. Fungi 2025, 11(10), 703; https://doi.org/10.3390/jof11100703 - 28 Sep 2025

Abstract

Morchella spp. is a type of valuable and rare edible fungi cultivated in soil. Optimization of the cultivation medium for Morchella spp. is key to obtaining high-efficiency production in an ecologically friendly manner. Recently, the sustainable resource utilization of agricultural waste has gathered [...] Read more.

Morchella spp. is a type of valuable and rare edible fungi cultivated in soil. Optimization of the cultivation medium for Morchella spp. is key to obtaining high-efficiency production in an ecologically friendly manner. Recently, the sustainable resource utilization of agricultural waste has gathered attention. Specifically, reusing tomato substrate, mushroom residues, and coconut shells can lower the production costs and reduce environmental pollution, demonstrating remarkable ecological and economic benefits. To determine the soil microbial communities of Morchella spp. using different culture medias and influencing factors, this study analysed the relative abundance of bacterial and fungal communities in natural soil, soil with 5% tomato substrate, soil with 5% mushroom residues, and soil with 5% coconut shells using Illumina NovaSeq high-throughput sequencing. In addition, intergroup differences, soil physiochemical properties, and product quality were also determined. Results demonstrated that agricultural waste consisting of mushroom residues, waste tomato substrate, and coconut shells can improve the efficiency of Morchella spp. cultivation. When considering yield and quality, mushroom residue achieved the highest yield (soil nutrient enrichment), followed by tomato substrate (water holding + grass carbon nutrient). All three types of agricultural waste promoted early fruiting, significantly increased polysaccharide, crude protein, and potassium content, and lowered crude fat and fibre. In regard to soil improvement, the addition of different materials optimized the soil’s physical structure (reducing volume weight and increasing water holding capacity) and chemical properties (enrichment of nitrogen, phosphorus, and potassium, regulating nitrogen and medium trace elements). For microbial regulation, the added materials significantly increased the abundance of beneficial bacteria (e.g., Actinomycetota, Gemmatimonadota and Devosia) and strengthened nitrogen’s fixation/nitration/decomposition functions. In the mushroom residue group, the abundance of Bacillaceae was positively related to yield. Moreover, it inhibited pathogenic fungi like Mortierella and Trichoderma, and lowered fungal diversity to decrease ecological competition. In summary, mushroom residues have nutrient releasing and microbial regulation advantages, while tomato substrate and coconut shells are new high-efficiency resources. These increase yield through the “physiochemical–microorganism” collaborative path. Future applications may include regulating the function of microorganisms and optimizing waste preprocessing technologies to achieve sustainability. Full article

(This article belongs to the Special Issue Morchella: Innovative Mushrooms from Forests to Farms, Then to Our Tables)

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16 pages, 687 KB

Open AccessReview

Proteases from Pleurotus spp.: Properties, Production and Biotechnological Applications

by Adriane Toledo da Silva, Liliana Aguilar-Marcelino, Amanda do Carmo Alves, Débora Castro Toledo de Souza, Ana Carolina Silva, Jhennifer Cristina de Souza Alves, Yanick Leontino Langa, Elias Honorato Gomes and Filippe Elias de Freitas Soares

J. Fungi 2025, 11(10), 702; https://doi.org/10.3390/jof11100702 - 27 Sep 2025

Abstract

Proteases (EC 3.4) are hydrolytic enzymes widely used in biotechnological processes, representing about 60 to 70% of the global industrial enzyme market. Edible mushrooms of the genus Pleurotus stand out as excellent producers of these enzymes, in addition to exhibiting high nutritional value [...] Read more.

Proteases (EC 3.4) are hydrolytic enzymes widely used in biotechnological processes, representing about 60 to 70% of the global industrial enzyme market. Edible mushrooms of the genus Pleurotus stand out as excellent producers of these enzymes, in addition to exhibiting high nutritional value and medicinal properties. The proteases produced by these species exhibit broad adaptability to different experimental conditions, including variations in optimal pH and temperature, as well as distinct sensitivities to inhibitors. The production of these enzymes can be intensified by solid-state fermentation (SSF) using low-cost agro-industrial substrates, such as wheat bran, which favors sustainable applications aligned with the circular economy. Parameters such as carbon/nitrogen (C/N) ratio, medium pH, cultivation time, and inoculum age directly influence enzyme productivity. Proteases from Pleurotus spp. show high potential in the biochemical control of parasites such as Meloidogyne incognita, Haemonchus spp., Taenia solium, and Moniezia sp., catalyzing the degradation of the cuticle or eggshell. Other biotechnological applications include milk coagulation, thrombolytic therapies, keratin bioconversion, increased protein digestibility, and use as additives in the food, detergent, and pharmaceutical industries. Full article

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

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20 pages, 14020 KB

Open AccessArticle

Gapless near Telomer-to-Telomer Assembly of Neurospora intermedia, Aspergillus oryzae, and Trichoderma asperellum from Nanopore Simplex Reads

by Mikael Terp, Mark Nyitrai, Christian Enrico Rusbjerg-Weberskov, Teis E. Sondergaard and Mette Lübeck

J. Fungi 2025, 11(10), 701; https://doi.org/10.3390/jof11100701 - 27 Sep 2025

Abstract

Assembling high-quality fungal genomes, specifically telomere-to-telomere (T2T) gapless assemblies, often necessitates the integration of multiple sequencing platforms. This requirement poses a limitation on the number of fungal genomes that can feasibly be generated within a single project. Here, we demonstrate that haplotype-aware error [...] Read more.

Assembling high-quality fungal genomes, specifically telomere-to-telomere (T2T) gapless assemblies, often necessitates the integration of multiple sequencing platforms. This requirement poses a limitation on the number of fungal genomes that can feasibly be generated within a single project. Here, we demonstrate that haplotype-aware error correction (HERRO) of Oxford Nanopore simplex reads enables the generation of high-quality assemblies from a single sequencing platform. We present an automated Snakemake workflow that, without manual intervention, produced gapless genome assemblies for industrially relevant strains: Neurospora intermedia NRRL 2884, Trichoderma asperellum TA1, and Aspergillus oryzae CBS 466.91, each achieving complete BUSCO (Benchmarking Universal Single-Copy Orthologs) scores exceeding 98%. Among these, only the T. asperellum assembly yielded a fully telomere-to-telomere gapless genome, while the N. intermedia and A. oryzae assemblies were gapless but near-telomere-to-telomere. Manual curation was required for the mitochondrial genome assembly of N. intermedia. Full article

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

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15 pages, 4989 KB

Open AccessArticle

Production of Mycelium Mats for Textile Applications

by Reyes K. Romero-Cedillo, Efrén R. Robledo-Leal, Liliana Aguilar-Marcelino, Ma. de Lourdes Acosta-Urdapilleta and Maura Téllez-Téllez

J. Fungi 2025, 11(10), 700; https://doi.org/10.3390/jof11100700 - 26 Sep 2025

Abstract

A mycelium is a network of hyphae that possesses the ability to self-assemble and grow into various shapes, acting as a natural binder that minimises the need for intensive chemical and energy processes, making it an alternative capable of forming structures that may [...] Read more.

A mycelium is a network of hyphae that possesses the ability to self-assemble and grow into various shapes, acting as a natural binder that minimises the need for intensive chemical and energy processes, making it an alternative capable of forming structures that may eventually outperform traditional fibres such as animal leather and polyester. In this work, two mycelium mats were created, and their thickness, water absorption, coverage, and tear strength for the sewing process were determined. Fibre mats were grown in vitro or on a jute substrate. The mats were treated with salt, tannin or citric acid solutions, then air- or oven-dried. In general, the treatment that least modified the colour and appearance of the mycelium mats was citric acid, and when dried by airflow, the thickness averaged 1.4 mm. The highest tear strengths were 10.55 N/mm and 12.7 N/mm for the mycelium mats treated with citric acid without and with jute, respectively. A high percentage of water absorption was observed, reaching 267% (mycelium mats treated with tannins and dried at 65 °C) and 28% (mycelium mats treated with citric acid and air-dried). In general, all mycelium mats can be sewn, except for those treated with citric acid, which have a viscous texture and require slow sewing to prevent the mycelium from breaking. The Trametes fungus can be utilised in the production of mycelial materials, allowing for the optimisation of growth conditions to obtain mycelial mats that meet the requirements for use as an environmentally friendly alternative in the textile and related industries. Full article

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

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14 pages, 266 KB

Open AccessArticle

Clinical Features and Outcomes of Invasive Fusarium Infections from a Singaporean Centre: Is It Time to Redefine How We Assess Treatment Outcomes?

by Yvonne Fu Zi Chan, Benjamin Pei Zhi Cherng, Cherie Le Si Gan, Siew Yee Thien, Sophie Seine Xuan Tan, Hei Man Wong, Yen Ee Tan, Ai Ling Tan and Shimin Jasmine Chung

J. Fungi 2025, 11(10), 699; https://doi.org/10.3390/jof11100699 - 26 Sep 2025

Abstract

Invasive Fusarium infections pose a significant threat to immunocompromised patients and are characterised by high mortality rates. In this study, we examined 22 unique episodes of proven and probable Fusarium infections over a 14-year period at a tertiary hospital in Singapore. Cases were [...] Read more.

Invasive Fusarium infections pose a significant threat to immunocompromised patients and are characterised by high mortality rates. In this study, we examined 22 unique episodes of proven and probable Fusarium infections over a 14-year period at a tertiary hospital in Singapore. Cases were analysed from clinical, microbiological, and radiological perspectives. The most common risk factor for invasive Fusarium infections was hematologic malignancy. Fifty percent of patients achieved resolution of infection and were alive at the end of treatment. Conversely, the overall mortality was 50%, with 90% of deaths occurring within three months of the diagnosis of invasive fusariosis; associated risk factors include neutropenia, disseminated infection, and corticosteroid use. Although these deaths would be classified as treatment failures by established criteria; many (8/10; 80%) were due to causes not directly related to invasive fusariosis; such as progression of the underlying malignancy or another infection. We believe that it may be time to redefine how we assess treatment outcomes for invasive mould infections. Nevertheless; invasive fusariosis remains a formidable foe in the immunocompromised host. Early; aggressive treatment with appropriate adjunctive therapies; such as surgery; is crucial for controlling the infection and achieving the best outcomes. Full article

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

17 pages, 2361 KB

Open AccessBrief Report

Co-Treatment with Ritonavir or Sertraline Enhances Itraconazole Efficacy Against Azole-Resistant Trichophyton indotineae Isolates

by Anna Günther, Anke Burmester, Mario Fabri, Jörg Tittelbach and Cornelia Wiegand

J. Fungi 2025, 11(10), 698; https://doi.org/10.3390/jof11100698 - 25 Sep 2025

Abstract

The treatment of azole-resistant Trichophyton indotineae poses a significant challenge for clinicians worldwide. Resistance mechanisms include amino acid substitutions in the sterol 14-α demethylase gene Erg11B, as well as overexpression of Erg11B. Additionally, efflux mechanisms mediated by fungal transporter proteins contribute [...] Read more.

The treatment of azole-resistant Trichophyton indotineae poses a significant challenge for clinicians worldwide. Resistance mechanisms include amino acid substitutions in the sterol 14-α demethylase gene Erg11B, as well as overexpression of Erg11B. Additionally, efflux mechanisms mediated by fungal transporter proteins contribute to antifungal resistance. Therefore, the inhibition of fungal efflux transporters using known inhibitors could be a promising strategy to prevent treatment failure. The inhibitory effects of itraconazole in combination with various efflux pump inhibitors were evaluated. Co-treatment with quinine hydrochloride and itraconazole did not lead to a significant reduction in the inhibitory concentration (IC) values in T. indotineae isolates. In contrast, ritonavir lowered IC values by approximately 50% without affecting fungal growth when applied as monotherapy. The most pronounced effect was observed with sertraline, which demonstrated intrinsic antifungal activity at higher concentrations. When combined with itraconazole, sertraline reduced IC values to below 10% in both susceptible and resistant strains, enhancing itraconazole efficacy markedly. The increasing prevalence of antifungal resistance is a growing global health concern. These findings suggest that sertraline holds considerable potential as an adjunctive therapy for the treatment of dermatomycoses. Full article

(This article belongs to the Special Issue Advances in Human and Zoonotic Dermatophytoses)

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