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Journal of Fungi

Journal of Fungi is an international, peer-reviewed, open access journal of mycology published monthly online by MDPI. The Medical Mycological Society of the Americas (MMSA) and Spanish Phytopathological Society (SEF) are affiliated with the Journal of Fungi, and their members receive discounts on the article processing charges.

Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, CAPlus / SciFinder, AGRIS, and other databases.
Journal Rank: JCR - Q1 (Mycology) / CiteScore - Q1 (Ecology, Evolution, Behavior and Systematics)
Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 19 days after submission; acceptance to publication is undertaken in 2.8 days (median values for papers published in this journal in the second half of 2025).
Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.

Impact Factor: 4.0 (2024); 5-Year Impact Factor: 4.5 (2024)

Imprint Information Journal Flyer Open Access ISSN: 2309-608X

Latest Articles

27 pages, 5092 KB

Open AccessArticle

Cladobotryum rhodochroum sp. nov. (Hypocreales, Ascomycota): A New Fungicolous Species Revealed by Morphology, Phylogeny, and Comparative Genomics

by Anastasia C. Christinaki, Dimitrios Floudas, Antonis I. Myridakis, Zacharoula Gonou-Zagou and Vassili N. Kouvelis

J. Fungi 2026, 12(2), 117; https://doi.org/10.3390/jof12020117 - 6 Feb 2026

Species of the ascomycetous genus Cladobotryum (Hypocreales, Hypocreaceae) are ecologically and economically important mycoparasites that cause cobweb disease in cultivated and wild mushrooms. Despite their significance as fungal pathogens and producers of bioactive metabolites, the taxonomy of Cladobotryum remains unresolved due to extensive [...] Read more.

Species of the ascomycetous genus Cladobotryum (Hypocreales, Hypocreaceae) are ecologically and economically important mycoparasites that cause cobweb disease in cultivated and wild mushrooms. Despite their significance as fungal pathogens and producers of bioactive metabolites, the taxonomy of Cladobotryum remains unresolved due to extensive morphological plasticity, complex teleomorph–anamorph connections, and the presence of cryptic species. This study employs an integrative approach combining micro- and macromorphological characterization, multi-locus phylogeny (ITS, rpb2, and tef-1a), and comparative genomics to clarify the taxonomic position of the Greek isolate Cladobotryum sp. ATHUM 6904, previously designated as an unclassified red-pigmented (URP) strain. Phylogenetic analyses demonstrated that URP strains form a distinct, well-supported clade closely related to C. tenue and C. rubrobrunnescens, yet genetically and morphologically distinct from both. Comparative genomic analyses of isolate ATHUM 6904 and the ex-type strains of C. tenue and C. rubrobrunnescens revealed pronounced divergence in transposable element content, mitochondrial genome architecture, gene order, orthologous gene composition, secondary metabolite biosynthetic potential, and overall genomic distance. Micro- and macromorphological comparisons further supported the differentiation of isolate ATHUM 6904 from both reference species. Based on the combined molecular, morphological, and genomic evidence, the Greek isolate ATHUM 6904 is described as a novel species, Cladobotryum rhodochroum sp. nov. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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13 pages, 1565 KB

Open AccessArticle

Functional Annotation Workflow for Fungal Transcriptomes

by Nagisa Morihara and Hidemasa Bono

J. Fungi 2026, 12(2), 116; https://doi.org/10.3390/jof12020116 - 6 Feb 2026

Although RNA sequencing (RNA-seq) enables rapid transcriptome profiling, functional annotation of fungal transcriptomes remains challenging. Existing tools prioritize broad taxonomic coverage, and reference genomes are scarce for non-model species. This study aimed to develop a fungal-specific functional annotation workflow to support rapid and [...] Read more.

Although RNA sequencing (RNA-seq) enables rapid transcriptome profiling, functional annotation of fungal transcriptomes remains challenging. Existing tools prioritize broad taxonomic coverage, and reference genomes are scarce for non-model species. This study aimed to develop a fungal-specific functional annotation workflow to support rapid and accurate functional analyses downstream of RNA-seq, independent of reference genome availability. To evaluate the workflow, RNA-seq data from 57 samples of Lentinula edodes strain H600 (shiitake mushroom) were retrieved, along with full-length transcript sequencing (Iso-Seq) data and corresponding RNA-seq data from 20 samples of Phakopsora pachyrhizi (Asian soybean rust) from public databases. The workflow successfully annotated over 96% of protein-coding transcripts and demonstrated applicability to Iso-Seq data. Functional enrichment analyses revealed higher-resolution functional detection than existing annotation tools. Furthermore, integrating homology searches against fungal-specific databases with expression pattern-based annotations highlighted the workflow’s utility for target identification in genome editing and other applications. Overall, the results of this study highlight the potential of the developed workflow in facilitating the discovery of functionally important transcripts and their translation into biotechnological applications. Full article

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

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16 pages, 5794 KB

Open AccessArticle

Comparative Phosphoproteomics of Two Flammulina filiformis Cultivars with Differential Postharvest Browning Susceptibility

by Yu Fu, Xiaojing Guo, Xiaolan He, Bo Wang, Weihong Peng and Yang Yu

J. Fungi 2026, 12(2), 115; https://doi.org/10.3390/jof12020115 - 5 Feb 2026

Protein phosphorylation modification plays a role in cells’ response to oxidative stress, a key factor leading to postharvest browning of Flammulina filiformis. However, the molecular mechanism by which protein phosphorylation contributes to postharvest browning of F. filiformis remains unclear. This study aimed [...] Read more.

Protein phosphorylation modification plays a role in cells’ response to oxidative stress, a key factor leading to postharvest browning of Flammulina filiformis. However, the molecular mechanism by which protein phosphorylation contributes to postharvest browning of F. filiformis remains unclear. This study aimed to characterize the basal phosphoproteomic landscapes associated with variations in different browning phenotypes of F. filiformis. Using data-independent acquisition (DIA) mass spectrometry, we comprehensively profiled the phosphorylation dynamics in susceptible-to-browning (SB) and resistant-to-browning (RB) cultivars at harvest and after 24 h storage. We identified 84,244 phosphorylation sites on 4494 phosphoproteins, with the SB cultivar displaying more altered sites (21,195) than the RB (16,087). Functional enrichment analysis revealed that the differential phosphorylation was significantly implicated in kinases and energy metabolism pathways. Notably, the SB cultivar exhibited a more pronounced phosphorylation profile on key proteins involved in ATP synthesis and glycolysis. Protein–protein interaction (PPI) network analysis further indicated a kinase-mediated regulatory network targeting core energy metabolism components, including ATP synthase and 6-phosphofructokinase. This distinct phosphosignature in the SB cultivar correlated with its more severe browning phenotype and a sharper decline in ATP content during storage. Our findings suggest that divergent phosphorylation-mediated regulation of energy metabolism is strongly associated with the differential postharvest browning susceptibility between these two cultivars, providing a valuable molecular resource for future functional studies. Full article

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

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16 pages, 6172 KB

Open AccessArticle

Identification and Transcriptomic Analyses of Two Endophytic Fungi WDR2 and WDR5 from Wild Soybean Elucidates Mechanistic Aspects of Alkali Stress Tolerance

by Jiali Tian, Xuan Liu, Shixi Lu, Xuan Dong, Yujie Chen, Siqi Hou, Tianyu Lei, Xinyu Li, Ruixin Cao, Yue Su, Xiaodong Ding, Qiang Li and Jialei Xiao

J. Fungi 2026, 12(2), 114; https://doi.org/10.3390/jof12020114 - 5 Feb 2026

Soil alkalinization constitutes a significant abiotic stress factor that severely constrains global agricultural productivity. The application of alkali-tolerant endophytes represents a promising strategy for enhancing crop resilience. This study focused on the isolation and characterization of alkali-resistant endophytic fungi derived from wild soybean [...] Read more.

Soil alkalinization constitutes a significant abiotic stress factor that severely constrains global agricultural productivity. The application of alkali-tolerant endophytes represents a promising strategy for enhancing crop resilience. This study focused on the isolation and characterization of alkali-resistant endophytic fungi derived from wild soybean (Glycine soja), aiming to elucidate their potential in promoting host plant growth and to investigate their molecular responses to alkali stress. From an initial collection of 39 wild soybean endophytic fungal isolates, 12 strains demonstrated significant alkali tolerance, as evidenced by increased mycelial dry weight under both mild and intense alkali stress. Among these, two strains, designated WDR2 and WDR5, demonstrated particularly pronounced biomass enhancement and were taxonomically identified as Fusarium verticillioides through comprehensive morphological and molecular analyses. Subsequent inoculation assays conducted on maize (Zea mays) revealed that both fungal strains significantly alleviated the inhibitory effects of alkali stress on root system architecture. Comparative evaluations in soybean indicated that the growth-promoting effects of these endophytes were host-specific and varied according to fungal strain, stress intensity, and inoculation timing. Transcriptomic profiling via RNA-Seq under mild alkali stress identified 589 and 182 differentially expressed genes (DEGs) in WDR2 and WDR5, respectively, with only 43 DEGs shared between the two strains, indicating largely strain-specific transcriptional adaptations. Functional enrichment analysis revealed several shared mechanisms underlying alkaline adaptation in both fungi species, including the maintenance of ion homeostasis, remodeling of the cell wall, and regulation of protein complex assembly and oxidative stress responses. Moreover, distinct metabolic adaptations were identified: WDR2 exhibited significant enrichment in cellular integrity and modulation of membrane-related processes, as well as amino sugar and nucleotide sugar metabolism pathways. In contrast, WDR5 was enriched in phosphate ion transport and related transporter functions, glycerol kinase activity, and glycerolipid and glutathione metabolism. In summary, this study successfully identified two novel alkali-tolerant wild soybean endophytic fungi, WDR2 and WDR5. The results provide valuable insights into their divergent molecular adaptation strategies and highlight their potential application as bio-inoculants to enhance crop productivity in alkaline soils. Full article

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

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27 pages, 3196 KB

Open AccessReview

Fungal Sphingolipids: Biosynthesis Pathways, Structural Features and Biological Functions

by Zixin Xue, Liuxi Wang and Chunmei Du

J. Fungi 2026, 12(2), 113; https://doi.org/10.3390/jof12020113 - 5 Feb 2026

Sphingolipids are a class of amphipathic lipids characterized by a sphingoid base backbone, which can be classified into glycosphingolipids and sphingomyelins. They exhibit structural complexity and functional diversity, being widely distributed in eukaryotes and some bacterial species. Sphingolipids are important regulators of signal [...] Read more.

Sphingolipids are a class of amphipathic lipids characterized by a sphingoid base backbone, which can be classified into glycosphingolipids and sphingomyelins. They exhibit structural complexity and functional diversity, being widely distributed in eukaryotes and some bacterial species. Sphingolipids are important regulators of signal transduction and cellular homeostasis and are involved in numerous biological processes, including cell polarity establishment, energy metabolism, proliferation, and differentiation. However, research on fungal sphingolipids remains limited. This review provides an overview of sphingolipid species, structural features, and their biosynthesis and degradation in fungi. It also summarizes their essential functions in maintaining cell membrane structure, influencing morphological development, pathogenicity, and homeostasis, and participating in apoptosis. Additionally, the potential of antifungal agents targeting the sphingolipid pathway and their application prospects are discussed. Finally, current challenges and future directions in fungal sphingolipid research are highlighted to support the investigation of their mechanisms and the development of antifungal therapies targeting sphingolipid metabolic pathways. Full article

(This article belongs to the Special Issue Fungal Biosynthesis)

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13 pages, 4626 KB

Open AccessArticle

Genome-Scale Phylogenetic Analyses Provide Insights into the Phylogenetic Placement of Fusarium commune

by Shunsuke Nozawa, Yosuke Seto and Kyoko Watanabe

J. Fungi 2026, 12(2), 112; https://doi.org/10.3390/jof12020112 - 5 Feb 2026

Recent advances in high-throughput sequencing technologies have significantly enhanced the accuracy of phylogenetic inference, enabling comprehensive genome-wide analyses. Fusarium fungi, which include numerous agriculturally and medically important species, are typically classified at the species complex (SC) level. Clarifying the evolutionary relationships and distinctiveness [...] Read more.

Recent advances in high-throughput sequencing technologies have significantly enhanced the accuracy of phylogenetic inference, enabling comprehensive genome-wide analyses. Fusarium fungi, which include numerous agriculturally and medically important species, are typically classified at the species complex (SC) level. Clarifying the evolutionary relationships and distinctiveness of these SCs is therefore essential for accurate identification and understanding of their biology. Recent large-scale phylogenetic studies based on genomic data have provided a more resolved understanding of the evolutionary relationships among Fusarium SCs, supporting the view that most represent evolutionarily coherent and stable lineages. However, the phylogenetic position of Fusarium commune has not been explicitly examined, despite incongruence between phylogenies inferred from nucleotide and amino acid sequence data. This study aimed to clarify the phylogenetic placement of F. commune at the SC level by re-examining its position using a genome dataset independent of those employed in previous studies. Our results are largely consistent with previously reported genome-scale phylogenetic analyses of the genus Fusarium and support the stability of most SCs. However, F. commune was not clearly included in any of the currently recognized SCs and instead formed an independent lineage. These findings provide insights into the evolutionary history of Fusarium SCs and contribute to a better understanding of the taxonomic position of F. commune. Full article

(This article belongs to the Special Issue Ascomycete Fungi: From Biosystematics and Biodiversity to Biotechnology)

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18 pages, 4170 KB

Open AccessArticle

Uvpks1, Involved in Ustilaginoidin Biosynthesis, Contributes to the Metabolic Profile, Development, Stress Responses, and Pathogenicity in Villosiclava virens

by Xuwen Hou, Jie Dong, Dan Xu, Hao Liu, Yu Li, Yujun Huang, Jiahang Sun, Muhammad Abubakar Jakada, Daowan Lai and Ligang Zhou

J. Fungi 2026, 12(2), 111; https://doi.org/10.3390/jof12020111 - 5 Feb 2026

Villosiclava virens (anamorph: Ustilaginoidea virens) is a fungal pathogen that causes rice false smut, one of the most devastating diseases of rice. The Uvpks1 gene encoding polyketide synthase is responsible for the biosynthesis of ustilaginoidins, a major group of mycotoxins in V. [...] Read more.

Villosiclava virens (anamorph: Ustilaginoidea virens) is a fungal pathogen that causes rice false smut, one of the most devastating diseases of rice. The Uvpks1 gene encoding polyketide synthase is responsible for the biosynthesis of ustilaginoidins, a major group of mycotoxins in V. virens. In this study, three strains, including the Uvpks1 deletion mutant ΔUvpks1, the complementation strain ΔUvpks1-C1, and the wild-type isogenic strain P1 of V. virens, were employed to investigate the role of Uvpks1 in shaping the metabolic profile and in the development, stress responses, and pathogenicity of V. virens. The deletion of Uvpks1 led to both the elimination of ustilaginoidin biosynthesis and the induction of many other secondary metabolite biosynthetic pathways. It decreased mycelial growth and sporulation, fungal tolerance to Congo red-induced cell wall damage stress, and susceptibility to the fungicides epoxiconazole and prochloraz. Meanwhile, it increased hyphal hydrophobicity, resistance to H₂O₂-induced oxidative stress and metal cation stress, and susceptibility to the fungicide azoxystrobin. Furthermore, the deletion of Uvpks1 resulted in reduced fungal pathogenicity toward rice plants. The findings reveal the functions of Uvpks1 in shaping the metabolic profile, development, stress responses, and pathogenicity of V. virens, which will be beneficial for developing new strategies to control rice false smut and ustilaginoidins. Full article

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

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15 pages, 963 KB

Open AccessArticle

Temporal Turnover of Aquatic Fungal Communities Driven by Water Quality Changes in FLOCponics Japanese Eel Aquaculture System

by Seung-Yoon Oh, Ju-Ae Hwang, Hae Seung Jeong and Yehyeon Cha

J. Fungi 2026, 12(2), 110; https://doi.org/10.3390/jof12020110 - 5 Feb 2026

FLOCponics systems combine biofloc-based aquaculture with nutrient recycling and are considered sustainable for intensive aquaculture. However, fungal community dynamics in these systems and their links to water quality remain poorly understood. In this study, we examined temporal changes in fungal communities in a [...] Read more.

FLOCponics systems combine biofloc-based aquaculture with nutrient recycling and are considered sustainable for intensive aquaculture. However, fungal community dynamics in these systems and their links to water quality remain poorly understood. In this study, we examined temporal changes in fungal communities in a FLOCponics system-based Japanese eel aquaculture by integrating metabarcoding with weekly water quality monitoring. Electrical conductivity (EC), nitrite, and pH displayed significant temporal variation, whereas other water quality parameters remained stable. Metabarcoding yielded 217 fungal operational taxonomic units across all samples. Alpha diversity indices exhibited no significant differences among weeks, indicating stable richness and evenness. In contrast, beta diversity analyses revealed consistent temporal shifts in fungal community composition with time exerting a significant effect after accounting for tank identity. Community changes were significantly EC-associated, with associations to nitrite and nitrate. Variation partitioning indicated that time and water quality primarily explained variation through their overlapping contribution rather than independent effects. Beta diversity decomposition revealed that temporal differences were driven primarily by species replacement rather than nestedness. Environmentally responsive taxa were mainly composed of Rozellomycota, with fewer Ascomycota, including Metapochonia. These results demonstrate structured short-term temporal fungal community reassembly in FLOCponics systems and highlight fungal turnover as a potential indicator of water quality-linked microbial dynamics in sustainable aquaculture. Full article

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

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21 pages, 2775 KB

Open AccessArticle

Comparative Genomics Reveals Host-Specific Adaptation of Pyricularia oryzae Strains Isolated from Rice and Barnyard Grass

by Wenda Sun, Xiaohan Zhang, Zhuan Zhang, Xiaofang Xie, Song Tang, Tian Song, Baoxu Lu, Jiafeng Wang, Zhibin Liang, Xiaofan Zhou and Yizhen Deng

J. Fungi 2026, 12(2), 109; https://doi.org/10.3390/jof12020109 - 5 Feb 2026

Barnyard grass, a widespread and persistent weed in rice paddies, belongs to the same family as rice and may act as a bridge host for the rice blast fungus. This study utilized comparative genomics to analyze six Pyricularia oryzae strains isolated from barnyard [...] Read more.

Barnyard grass, a widespread and persistent weed in rice paddies, belongs to the same family as rice and may act as a bridge host for the rice blast fungus. This study utilized comparative genomics to analyze six Pyricularia oryzae strains isolated from barnyard grass (Baicao series) and rice (GDYJ7 and ZJX18), integrating pathogenicity assays, whole-genome sequencing, and functional annotation. Pathogenicity tests demonstrated host specificity, as Baicao series strains caused typical lesion symptoms on barnyard grass but not on rice leaves, while GDYJ7 and ZJX18 caused lesions mainly on rice. Genomic analyses indicated that Baicao series strains possessed larger genomes (41.04 Mb to 41.16 Mb) with a higher content of repetitive sequences (6.68% to 7.09%) compared to rice strains GDYJ7 and ZJX18 (38.69 Mb and 39.05 Mb; 3.66% and 3.71% repeats). Phylogenetic analysis confirmed that Baicao series strains represent a grass-infecting pathotype of P. oryzae species, as they were grouped with the established grass-isolated P. oryzae strains, while GDYJ7 and ZJX18 were grouped with rice-isolated P. oryzae strains. However, Baicao series, GDYJ7 and ZJX18 are all relatively distant from P. grisea species. PCR amplification revealed that Baicao series strains harbored significantly fewer avirulence genes (Avr-Pib, Avr-Pizt, PWL3) than GDYJ7 and ZJX18 (Avr-Pib, Avr-Pizt, Avr-Pi9, Avr-Pik, PWL2), with Baicao9 retaining only Avr-Pib. In summary, our results suggested that the genomic sequences of the barnyard grass-isolated strains serve as a valuable resource for the study of P. oryzae strains with differential host preference and provide novel insights into the evolution of pathogen genomes during host adaptation. Full article

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

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5 pages, 192 KB

Open AccessEditorial

Diversity of Microscopic Fungi

by Miloš Stupar

J. Fungi 2026, 12(2), 108; https://doi.org/10.3390/jof12020108 - 4 Feb 2026

Microscopic fungi constitute one of the most varied and ecologically significant groups of organisms on Earth; nonetheless, a substantial portion of their richness remains uncharted and little studied [...] Full article

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

13 pages, 5075 KB

Open AccessArticle

Amino Acid-Optimized Medium Improves Long-Term Growth, Conidiation, Stress Tolerance, and Biocontrol Performance of Esteya vermicola Against Pinewood Nematode

by Xuan Peng, Yilan Wang, Zhongwu Cheng, Tengqing Ye, Lihui Han, Ping Lin, Jun Li and Chengjian Xie

J. Fungi 2026, 12(2), 107; https://doi.org/10.3390/jof12020107 - 3 Feb 2026

Esteya vermicola is a nematophagous fungus with strong parasitic ability against the pinewood nematode (Bursaphelenchus xylophilus) and shows great potential for the biological control of pine wilt disease. However, this fungus is highly sensitive to environmental stress factors and often exhibits [...] Read more.

Esteya vermicola is a nematophagous fungus with strong parasitic ability against the pinewood nematode (Bursaphelenchus xylophilus) and shows great potential for the biological control of pine wilt disease. However, this fungus is highly sensitive to environmental stress factors and often exhibits early necrosis when cultured on conventional nutrient-rich media, limiting its large-scale application. In this study, we optimized the long-term cultivation and conidiation conditions of E. vermicola CBS115803 by supplementing minimal medium (MM) with amino acids, and evaluated its stress tolerance and infectivity against the pinewood nematode. Among 20 tested amino acids, histidine significantly increased total conidia production, while arginine, glutamine, and proline markedly promoted the formation of lunate conidia. The combination of arginine, histidine, glutamine, and proline (AHGP) produced the highest overall conidia yield and lunate conidia proportion. The MM + AHGP medium maintained long-term colony viability, whereas colonies on PDA and CM media showed obvious degeneration. This formulation also improved mycelial growth, total conidiation, and the proportion of lunate conidia. Moreover, conidia produced on MM + AHGP exhibited the highest germination rates and infectivity under various stress conditions, including cold, heat, oxidative, osmotic, and UV stresses. Conidia germination was significantly enhanced following treatment at 0 °C, suggesting that low temperatures may activate dormancy-breaking pathways. This amino acid-optimized medium offers an effective technical foundation for stable large-scale production and storage of E. vermicola conidia, providing a new avenue for the biocontrol of pine wilt disease. Full article

(This article belongs to the Special Issue Fungal Development and Interactions Under Hostile Environments)

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14 pages, 711 KB

Open AccessArticle

Fluconazole-Resistant and Virulence-Associated Yeasts from the Vulva: Evidence of a Potential Reservoir

by Maria Margarida Silva, Mariana Zagalo Fernandes, Sofia Moura, Ana Sofia Esteves, Ana Sofia Oliveira, Carlos Gaspar, José Martinez-de-Oliveira, Ana Palmeira-de-Oliveira and Joana Rolo

J. Fungi 2026, 12(2), 106; https://doi.org/10.3390/jof12020106 - 3 Feb 2026

Vulvovaginal candidosis is an affliction caused by yeasts. Symptoms in the vulva are generally associated with the spreading of infected vaginal fluid. To better understand the role of the vulva in these dynamics, in this study we aim to fully identify and characterize [...] Read more.

Vulvovaginal candidosis is an affliction caused by yeasts. Symptoms in the vulva are generally associated with the spreading of infected vaginal fluid. To better understand the role of the vulva in these dynamics, in this study we aim to fully identify and characterize non-Candida albicans vulvar yeast isolates. Fifty-four vulvar swabs were obtained from 31 women attending a gynecological consultation. After species identification, fluconazole susceptibility was assessed by the microdilution broth method. Biofilm biomass was quantified using crystal violet staining, and phospholipase and hemolysin production were assessed by plating a calibrated suspension in suitable culture media. Finally, adherence to cervical cells was assessed by infecting a monolayer of HeLa cells. Among the 54 vulvar isolates obtained, 12 different species were identified. About 54% (29/54) of vulvar isolates were resistant to fluconazole. All isolates were able to produce a high amount of biofilm biomass. Pichia kudriavzevii and Rhodotorula mucilaginosa were the only species that produced phospholipase; hemolysin production was detected in isolates belonging to almost all species. Almost all species had the ability to adhere to HeLa cells. These results indicate that the vulva act as a reservoir for fluconazole-resistant yeasts, which are also potentially virulent. Full article

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

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24 pages, 6844 KB

Open AccessArticle

Arbuscular Mycorrhizal Fungi-Mediated Reconfiguration of Poplar Leaf C-N-P Metabolic Networks: Environment-Dependent Synergies and Nutrient Interactions

by Xiaan Tang, Mengmeng Chen, Panpan Meng and Junyu Song

J. Fungi 2026, 12(2), 105; https://doi.org/10.3390/jof12020105 - 2 Feb 2026

The regulatory mechanisms by which AMF modulate the integrated carbon (C)-nitrogen (N)-phosphorus (P) metabolic network in woody plant leaves remain unclear. We investigated how varying nitrate (NO₃⁻) and phosphate (Pi) supply, with or without AMF inoculation, reshapes the leaf metabolic [...] Read more.

The regulatory mechanisms by which AMF modulate the integrated carbon (C)-nitrogen (N)-phosphorus (P) metabolic network in woody plant leaves remain unclear. We investigated how varying nitrate (NO₃⁻) and phosphate (Pi) supply, with or without AMF inoculation, reshapes the leaf metabolic network in poplar seedlings. Key findings reveal that AMF acts as a central metabolic hub, optimizing C-N-P coordination in an environment-dependent manner. Under low Pi, NO₃⁻ supply enhanced P remobilization and photosynthetic efficiency, boosting growth. AMF further optimized low-Pi adaptation by promoting P storage and buffering, significantly improving photosynthesis and biomass. Under high Pi, NO₃⁻ supply shifted focus towards enhancing Rubisco-mediated carbon assimilation. AMF synergistically improved carbon assimilation efficiency and suppressed non-essential P recycling. N metabolism effects of Pi were contingent on NO₃⁻ availability, and AMF reprogrammed N assimilation pathways accordingly, balancing uptake and utilization under different N regimes. Critically, AMF orchestrated environment-specific metabolic adjustments, reinforcing P buffering and photosynthetic gain under Pi limitation, and enhancing C assimilation efficiency while minimizing P waste under Pi sufficiency. This study demonstrates that poplar leaf C-N-P networks are reconfigured through N-P synergisms modulated by AMF, positioning AMF as a pivotal integrator of nutrient acquisition and allocation. These insights provide a physiological foundation for developing efficient forestry nutrient management and mycorrhizal application strategies. Full article

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

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22 pages, 949 KB

Open AccessReview

Biomarkers in Invasive Pulmonary Fungal Infections: Where Do We Stand?

by Isabel Montesinos and Hector Rodriguez-Villalobos

J. Fungi 2026, 12(2), 104; https://doi.org/10.3390/jof12020104 - 1 Feb 2026

Invasive pulmonary fungal infections remain a major cause of morbidity and mortality among immunocompromised and critically ill patients. Rapid and accurate diagnosis is crucial for improving outcomes, yet conventional methods such as culture and histopathology suffer from limited sensitivity and slow turnaround times. [...] Read more.

Invasive pulmonary fungal infections remain a major cause of morbidity and mortality among immunocompromised and critically ill patients. Rapid and accurate diagnosis is crucial for improving outcomes, yet conventional methods such as culture and histopathology suffer from limited sensitivity and slow turnaround times. Recently, significant progress has been made in the development and standardization of serological and molecular biomarkers that enhance the early detection of the key pulmonary fungal diseases, particularly invasive pulmonary aspergillosis and pneumocystosis. Diagnostic tools for mucormycosis, however, remain scarce. PCR tools have strong potential to significantly improve early detection, but they are not yet widely implemented, and standardized commercial assays remain limited. Accessible antigen-based tests with robust performance are highly anticipated and expected to become available soon. This review summarizes the current evidence regarding the optimal use of galactomannan, β-D-glucan and PCR-based assays, emphasizing how their performance varies according to the pathogen, the type of specimen and the host population. Specific challenges, such as differentiating colonization from infection in non-HIV Pneumocystis pneumonia or interpreting galactomannan and PCR in patients receiving mold-active prophylaxis, are highlighted. We also discuss how combining biomarkers can enhance diagnostic accuracy and support timely therapeutic decisions. A clear understanding of the strengths, limitations and appropriate interpretation of these diagnostic tools is crucial in an era of increasing host complexity, shifting fungal epidemiology, and expanding antifungal options. Full article

(This article belongs to the Special Issue Advances and Innovations in Fungal Infections)

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11 pages, 2357 KB

Open AccessArticle

Co-Infection of Three Novel Deltaflexiviruses in an Isolate of the Edible Fungus Pleurotus ostreatus Reduces Fruiting Body Yield by Inhibiting Cellulase Activity

by Yifei Zhang, Wenhui Xie, Wenlian Zhong, Meijia Zeng, Huaping Li and Pengfei Li

J. Fungi 2026, 12(2), 103; https://doi.org/10.3390/jof12020103 - 31 Jan 2026

Pleurotus ostreatus, a globally cultivated oyster mushroom, is susceptible to viral infections that threaten yield and quality. This study reports the identification and characterization of three novel viruses from a symptomatic P. ostreatus strain K3: Pleurotus ostreatus deltaflexivirus 2, 3, and 4 [...] Read more.

Pleurotus ostreatus, a globally cultivated oyster mushroom, is susceptible to viral infections that threaten yield and quality. This study reports the identification and characterization of three novel viruses from a symptomatic P. ostreatus strain K3: Pleurotus ostreatus deltaflexivirus 2, 3, and 4 (PoDFV2, PoDFV3, PoDFV4). Complete genome sequencing revealed that they are single-stranded, positive-sense RNA viruses with lengths of 7809 nt, 7771 nt, and 7786 nt, encoding 5, 2, and 4 open reading frames (ORFs), respectively. The largest open reading frame (ORF1) encodes a putative replication-associated polyprotein (RP) containing three conserved domains—viral RNA methyltransferase (Mtr), viral RNA helicase (Hel), and RNA-dependent RNA polymerase (RdRp). Based on genomic sequence analysis, multiple sequence alignments, and phylogenetic analysis, PoDFV2–4 were identified as novel viruses of the genus Deltaflexivirus within the family Deltaflexiviridae. PoDFV2–4 had no significant effects on mycelial growth rate, plate mycelial biomass, or laccase activity. However, they significantly inhibited mycelial cellulase activity and resulted in malformed fruiting bodies, as well as a substantial reduction in yield. Full article

(This article belongs to the Special Issue Mycoviruses: Emerging Investigations on Virus-Fungal Host Interaction, 2nd Edition)

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35 pages, 5754 KB

Open AccessArticle

Novel Freshwater Ascomycetes from Submerged Plant Debris in the Zújar River (Extremadura Community, Spain)

by María Barnés-Guirado, Alberto Miguel Stchigel and José Francisco Cano-Lira

J. Fungi 2026, 12(2), 102; https://doi.org/10.3390/jof12020102 - 31 Jan 2026

Freshwater fungi remain insufficiently documented in the Mediterranean river systems despite their key roles in organic-matter turnover. Here, we surveyed filamentous fungi associated with submerged decaying plant debris in the Zújar River (Extremadura, southwestern Spain) using a culture-based approach combined with phenotypic characterization [...] Read more.

Freshwater fungi remain insufficiently documented in the Mediterranean river systems despite their key roles in organic-matter turnover. Here, we surveyed filamentous fungi associated with submerged decaying plant debris in the Zújar River (Extremadura, southwestern Spain) using a culture-based approach combined with phenotypic characterization and multilocus phylogenetic analyses (ITS, LSU, rpb1, rpb2 and tef-1α). A total of 49 strains were isolated and identified, revealing a diverse assemblage of Ascomycota. Five taxa are described as new to science: Arachnopeziza torrehermosensis, Conioscypha clavatispora, Neoanungitea torrehermosensis, Ophioceras diversisporum and Polyscytalum submersum. Notably, Polyscytalum submersum represents the first record of the genus for the Iberian Peninsula, while Arachnopeziza torrehermosensis, Neoanungitea torrehermosensis and Ophioceras diversisporum constitute the first records of their respective genera for Spain (and Neoanungitea torrehermosensis also for Europe). In addition, phylogenetic evidence supports taxonomic refinements within the orders Magnaporthales and Conioscyphales, including the establishment of Protophioceras to accommodate Ophioceras sichuanense and the establishment of Protoconioscypha for two previously misclassified Conioscypha species. Overall, this first mycological report of submerged plant debris in the Zújar River substantially expands knowledge of freshwater fungal diversity in the region and provides a refined framework for the taxonomy of several lineages of aquatic-associated ascomycetes. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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13 pages, 2132 KB

Open AccessSystematic Review

The Rise of China in Fungal Taxonomic Studies and Biodiversity Cataloging in the Past Decade

by Ke Wang, Ming-Jun Zhao and Lei Cai

J. Fungi 2026, 12(2), 101; https://doi.org/10.3390/jof12020101 - 31 Jan 2026

Mycological studies in China have achieved substantial and encouraging progress in recent decades. In this paper, the discoveries of novel fungal taxa published by Chinese mycologists and the documented records of fungi distributed in China are statistically summarized based on the data retrieved [...] Read more.

Mycological studies in China have achieved substantial and encouraging progress in recent decades. In this paper, the discoveries of novel fungal taxa published by Chinese mycologists and the documented records of fungi distributed in China are statistically summarized based on the data retrieved from Fungal Names and the Checklist of Fungi in the China database, respectively. Our analysis reveals that a total of 2875 Chinese scholars have published 20,826 new fungal taxa to date, 65% of which were published within the past decade. During the same period, Chinese mycologists placed great importance on archiving fungal diversity data and have completed the compilation of the national checklist of fungi. Based on 382,503 records derived from over 18,200 research articles and 300 books, a total of 31,180 fungal species, spanning 17 phyla, 65 classes, 240 orders, 840 families, and 4531 genera, have been documented in China. The southwestern region, especially Yunnan Province, exhibits the highest richness of documented species. These results provide a comprehensive overview of the current status of fungal biodiversity and taxonomic studies in China, providing a valuable foundation for future investigations. Full article

(This article belongs to the Special Issue Current and Future Development of Mycology: The 10th Anniversary of Journal of Fungi)

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16 pages, 2349 KB

Open AccessArticle

Fungal Community Composition and Diversity Across Soil Depths Under Different Cover Crop Treatments

by Ephantus J. Muturi, Christopher A. Dunlap, Jose L. Ramirez, William L. Perry, Nicholas Heller and Robert L. Rhykerd

J. Fungi 2026, 12(2), 100; https://doi.org/10.3390/jof12020100 - 31 Jan 2026

Fungi are a critical component of microbial biomass in agricultural soils, but their distribution across soil depths under different cover crops remains poorly understood. We used high-throughput sequencing of fungal ITS1 amplicons to characterize fungal communities across four soils depths (0–2, 2–4, 4–10, [...] Read more.

Fungi are a critical component of microbial biomass in agricultural soils, but their distribution across soil depths under different cover crops remains poorly understood. We used high-throughput sequencing of fungal ITS1 amplicons to characterize fungal communities across four soils depths (0–2, 2–4, 4–10, and 10–20 cm) in experimental field plots under four cover crop treatments: winter fallow reference (REF), cereal rye (CRYE), wild pennycress (WPEN), and a mixture of pea, crimson clover, radish, and oat (PCRO). There was no significant interaction between soil depth and cover crop treatment on both alpha diversity and beta diversity. CRYE and PCRO cover crops had low abundance of Fusarium, a genus including many important plant pathogens, and different fungal community composition relative to REF. Fungal diversity was significantly higher at 4–10 cm compared to 0–2 cm depth, but fungal richness was not affected by soil depth. Fungal community composition differed significantly between 0–4 and 10–20 cm soil depths. The relative abundance of Mortierella and unclassified Basidiomycota increased with increasing soil depth while that of Calvatia, Cryptococcus, Fusarium, and Idriella decreased with increasing soil depth. Most fungal taxa were assigned to more than one guild, but the few taxa that were classified as strict saprophytes decreased with increasing soil depth while those classified as strict symbionts increased with increasing soil depth. These differences were associated with low pH and high content of OM, K, S, P, and Zn in the topsoil layer compared to the deeper soil layer. The findings may inform the development of targeted soil management practices to promote beneficial fungi, but additional studies covering multiple study sites and sampling dates are needed for clarity. Full article

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

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12 pages, 1424 KB

Open AccessArticle

Effect of Arbuscular Mycorrhizal Fungi on the Growth and Cadmium Uptake of Paspalum notatum and Lolium perenne

by Chao Wang, Peiyin Li, Ao Yuan, Zhiwei Bian, Huiping Song and Zhengjun Feng

J. Fungi 2026, 12(2), 99; https://doi.org/10.3390/jof12020099 - 30 Jan 2026

To investigate the regulatory mechanisms of arbuscular mycorrhizal fungi (AMF) on the growth, cadmium (Cd) uptake and translocation of plants with distinct mycorrhizal dependency (MD), a pot experiment was conducted using Paspalum notatum (high MD) and Lolium perenne (low MD) under two Cd [...] Read more.

To investigate the regulatory mechanisms of arbuscular mycorrhizal fungi (AMF) on the growth, cadmium (Cd) uptake and translocation of plants with distinct mycorrhizal dependency (MD), a pot experiment was conducted using Paspalum notatum (high MD) and Lolium perenne (low MD) under two Cd gradients (5 mg·kg⁻¹, 50 mg·kg⁻¹) with AMF-inoculated/non-inoculated treatments, with 0 mg·kg⁻¹ set as the control group. AMF significantly enhanced the dry weight and colonization rate of both plant species, and the MD of Paspalum notatum remained consistently higher. The growth-promoting effect of AMF (quantified by MD) exceeded the toxicity induced by Cd stress, thereby mitigating growth inhibition by promoting hyphal growth in the rhizosphere. AMF improved the root bioconcentration factor (BCF) and total Cd extraction capacity of the plants, which was correlated with the plants’ inherent Cd absorption capacity but not with MD. AMF exerted species-specific regulatory effects on the translocation factor (TF): the TF of Paspalum notatum increased after inoculation, while that of Lolium perenne decreased. Full article

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

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18 pages, 8131 KB

Open AccessArticle

Unveiling Species Diversity Within Early-Diverging Fungi from China XII: Six New Species of Mucor (Mucoromycota)

by Wen-Xiu Liu, Fei Li, Zi-Ying Ding, Xin-Yu Ji, Shu-Ting Geng, Hong-Yu Zou, Heng Zhao, Shi Wang and Xiao-Yong Liu

J. Fungi 2026, 12(2), 98; https://doi.org/10.3390/jof12020098 - 30 Jan 2026

Cited by 1

Mucor is widely distributed in nature and extensively applied in industries, food, and other fields. Based on analyses of the internal transcribed spacer (ITS) and the large subunit (LSU) of the ribosomal RNA gene, RNA polymerase II largest subunit gene (RPB1), [...] Read more.

Mucor is widely distributed in nature and extensively applied in industries, food, and other fields. Based on analyses of the internal transcribed spacer (ITS) and the large subunit (LSU) of the ribosomal RNA gene, RNA polymerase II largest subunit gene (RPB1), and their morphological characteristics, six new species of Mucor were identified. Mucor catenatus sp. nov. forms chlamydospores in chains. Mucor jujubinus sp. nov. is characterized by jujube-shaped columellae. Mucor macrosporangium sp. nov. produces larger sporangia. Mucor multiramosus sp. nov. features extensively branched sporangiophores. Mucor oligorhizus sp. nov. shows a rare rhizoid formation. Mucor tumidus sp. nov. usually develops swellings in sporangiophores. This study represents the twelfth contribution in a series exploring early-diverging fungal diversity in China and raises the number of accepted Mucor species to 60. Full article

(This article belongs to the Special Issue Advances in Fungal Taxonomy: Novel Approaches to Species Identification and Diversity Assessment)

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