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Beyond Fungitoxicity: Recent Achievements in Targeted Fungicide Discovery
β-Glucans, Pneumocystis jirovecii and Atherogenic Inflammation: From Pulmonary Immunity to Cardiovascular Risk
Ten-Year Trends in Candidemia at a Tertiary-Care Hospital in Spain (2015–2024): Epidemiological Shifts, Diagnostic Acceleration, and Impact of Antifungal Stewardship in the COVID-19 and Post-Pandemic Era
Can Patients with Hematologic Disease and Prior Mucormycosis Undergo Stem Cell Transplantation?
Trichoderma asperellum and T. asperelloides: Comparative Genomic Study for Genes Implicated in Biocontrol and Biofertilizer Activities

Journal Description

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 18.2 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the first half of 2026).
Recognition of Reviewers: Reviewers whose reports are timely and of high quality receive an APC discount voucher for a future publication in an MDPI journal. Become a reviewer.
Journal Cluster of Microbiology: Acta Microbiologica Hellenica, Applied Microbiology, Bacteria, Journal of Fungi, Microorganisms, Microbiology Research, Pathogens, Viruses, Fermentation and Germs.

Impact Factor: 4.3 (2025); 5-Year Impact Factor: 4.8 (2025)

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

Latest Articles

14 pages, 995 KB

Open AccessArticle

Clinical Features and Immunological Markers Associated with Invasive Pulmonary Fungal Disease in Organizing Pneumonia: A Matched Case–Control Study

by Longzhen Lu, Yun Li, Zhiwei Long, Lejin Liang, Xidong Wang, Hongling Liu, Juan Cao, Shaoqiang Li, Yan Wang, Zhengtu Li and Feng Ye

J. Fungi 2026, 12(10), 716; https://doi.org/10.3390/jof12100716 - 23 Sep 2026

Background/Objectives: Invasive pulmonary fungal disease (IPFD) is a serious complication of organizing pneumonia (OP), but associated clinical and immunological features remain poorly defined. Methods: We conducted a retrospective 1:2 age- and sex-matched case–control study of 126 adults with OP, including 42 with concomitant [...] Read more.

Background/Objectives: Invasive pulmonary fungal disease (IPFD) is a serious complication of organizing pneumonia (OP), but associated clinical and immunological features remain poorly defined. Methods: We conducted a retrospective 1:2 age- and sex-matched case–control study of 126 adults with OP, including 42 with concomitant IPFD and 84 controls. Clinical, radiological, immunosuppressive exposure and admission lymphocyte-subset data were analyzed using a full-cohort clinical model and an immunological subgroup model (n = 39). Results: Pre-infection glucocorticoid and immunosuppressant exposure did not differ between groups. Invasive mechanical ventilation was more frequent with IPFD (59.5% vs. 21.4%, p < 0.001). Pleural effusion was associated with higher odds of IPFD (OR = 3.263, 95% CI: 1.237–8.607), whereas coexisting interstitial lung disease was associated with lower odds (OR = 0.168, 95% CI: 0.066–0.426). In the immunological subgroup, a lower CD4⁺ T-cell percentage was associated with IPFD (OR = 0.914, 95% CI: 0.849–0.983, p = 0.015), although statistical significance was lost after exclusion of possible IPFD cases. Conclusions: Pleural effusion and lower CD4⁺ T-cell percentage were associated with IPFD in OP; the potential clinical utility of lymphocyte-subset assessment should be evaluated prospectively. Full article

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

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19 pages, 499 KB

Open AccessArticle

Epidemiological Characteristics, Species Distribution, and Antifungal Resistance Profiles of Candidemia Cases

by Demet Timur, Emel Gürcüoğlu, Emre Özkarataş and Tuğba Bozdemir

J. Fungi 2026, 12(10), 715; https://doi.org/10.3390/jof12100715 - 23 Sep 2026

Local species distribution and antifungal susceptibility are important for empirical candidemia management. We retrospectively evaluated patients with Candida-positive blood cultures from August 2019 to May 2024. Episodes were defined using a 30-day window; species distribution and susceptibility were analysed at the episode–species [...] Read more.

Local species distribution and antifungal susceptibility are important for empirical candidemia management. We retrospectively evaluated patients with Candida-positive blood cultures from August 2019 to May 2024. Episodes were defined using a 30-day window; species distribution and susceptibility were analysed at the episode–species level and outcomes at the patient level. Among 566 patients, 605 episodes and 637 episode–species isolates were identified. Non-albicans Candida accounted for 59.7%; C. albicans (40.3%) and C. parapsilosis (34.2%) predominated. Of 217 C. parapsilosis isolates tested, 66 (30.4%) were fluconazole-susceptible, 58 (26.7%) were susceptible dose-dependent, and 93 (42.9%) were resistant. Recurrent candidemia occurred in 37 patients and documented microbiological persistence in 128 (22.6%); persistence was more frequent when the index culture included C. parapsilosis (27.6% vs. 20.1%; OR 1.52, 95% CI 1.01–2.28). Among 32 patients with a shared species in the initial and first recurrent episodes, newly detected resistance occurred in three, all involving fluconazole-resistant C. parapsilosis. Thirty-day all-cause mortality was 57.4%; older age, ICU care, mechanical ventilation, and solid malignancy were independently associated with higher mortality. These findings suggest that empirical reliance on fluconazole may be inappropriate in settings with similar resistance patterns and support species-level identification, repeat blood cultures, and episode-specific susceptibility testing. Full article

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

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13 pages, 4890 KB

Open AccessArticle

The First Complete Mitochondrial Genome of Lecanora argopholis and Its Phylogenetic Implications for Lichen-Forming Fungi

by Guldiyar Adil, Erfan Akberjan and Reyim Mamut

J. Fungi 2026, 12(10), 714; https://doi.org/10.3390/jof12100714 - 23 Sep 2026

We report the first complete mitochondrial genome of the crustose lichen-forming fungus Lecanora argopholis. The circular mitogenome is 48,790 bp in length, has an overall AT content of 70.4%, and contains 14 protein-coding genes (PCGs), two rRNA genes, and 29 tRNA genes. [...] Read more.

We report the first complete mitochondrial genome of the crustose lichen-forming fungus Lecanora argopholis. The circular mitogenome is 48,790 bp in length, has an overall AT content of 70.4%, and contains 14 protein-coding genes (PCGs), two rRNA genes, and 29 tRNA genes. Comparative analysis of four Lecanora species showed that mitochondrial tRNA features were generally conserved, although limited variation in tRNA length and predicted base-pairing patterns was observed among the sampled taxa. Relative synonymous codon usage analysis of 13 shared mitochondrial PCGs revealed a similar preference for A/U-ending codons across the four species, indicating that this pattern is not unique to L. argopholis. Expanded synteny analysis of eight lichen-forming fungal mitogenomes identified conserved homologous blocks together with variation in mitochondrial gene order; among the sampled taxa, L. argopholis and L. cinereofusca showed the highest gene-order conservation. Phylogenetic analysis based on 14 concatenated mitochondrial PCGs from 17 lichen-forming fungi recovered L. argopholis as sister to L. cinereofusca, providing additional mitochondrial evidence relevant to the placement of L. argopholis within the taxonomically complex Lecanora s. lat. These results expand the mitogenomic resources available for Lecanora and provide comparative information on mitochondrial genome organization and evolution in lichen-forming fungi. Full article

(This article belongs to the Special Issue Taxonomy, Phylogeny, Ecology, and Metabolites of Lichen)

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19 pages, 2079 KB

Open AccessArticle

Deciphering the Molecular Basis of Cadmium Stress Adaptation in Lentinula edodes: Genome-Wide Identification of MAPK Cascade Genes and Their Functional Characterization

by Dandan Zhai, Xiaoxia Song, Tengye Luan, Xiaodong Shang, Meina He, Guirong Tang, Jianyu Liu, Yang Fu, Yansha Wu, Yu Li and Hailong Yu

J. Fungi 2026, 12(10), 713; https://doi.org/10.3390/jof12100713 - 23 Sep 2026

Mitogen-activated protein kinase (MAPK) cascades play a central role in eukaryotic signal transduction, regulating diverse biological processes including development and stress responses. However, despite Lentinula edodes being the most widely cultivated edible mushroom worldwide, its MAPK cascade gene families remain uncharacterized, and their [...] Read more.

Mitogen-activated protein kinase (MAPK) cascades play a central role in eukaryotic signal transduction, regulating diverse biological processes including development and stress responses. However, despite Lentinula edodes being the most widely cultivated edible mushroom worldwide, its MAPK cascade gene families remain uncharacterized, and their involvement in cadmium (Cd) stress responses is completely unknown. In this study, we performed genome-wide identification of MAPK cascade genes in L. edodes, uncovering 16 members comprising three LeMAPKKK genes, four LeMAPKK genes, and nine LeMAPK genes. Phylogenetic and homology analyses classified these genes into three putative MAPK cascade pathways. qRT-PCR analysis demonstrated strain-specific, concentration-dependent, and temporally dynamic expression patterns under Cd stress. Notably, four genes (LeMAPK1, LeMAPK7, LeMAPKK2, and LeMAPKKK1) exhibited consistent upregulation across both strains and high Cd concentrations (1 and 10 mg/L) at the 7 h time point. Based on these findings, we propose a working model for Cd stress response in L. edodes centered on these core regulatory genes. These findings may inform breeding strategies for low-Cd-accumulating cultivars and the optimization of cultivation practices to reduce Cd content, with potential implications for the sustainable development of the L. edodes industry and human health. Full article

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

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17 pages, 6306 KB

Open AccessArticle

Coffee Anthracnose-Associated Fungi from Wanning, Hainan: Fungicide Sensitivity and Broad-Spectrum Antagonism by Mangrove-Derived Streptomyces sp. CD103

by Jiajun Li, Jiayi Li, Zhicheng Zheng, Wenxin Yuan, Rongsuo Hu, Xiaoxiong Xu and Huimin Feng

J. Fungi 2026, 12(10), 712; https://doi.org/10.3390/jof12100712 - 23 Sep 2026

Fungi associated with coffee leaf lesions provide a diverse target panel for evaluating fungicide sensitivity and microbial antagonism. This study evaluated the antagonistic spectrum of mangrove-derived Streptomyces sp. CD103 and fungicide sensitivity in selected lesion-associated fungi. Of 49 isolates recovered from symptomatic Coffea [...] Read more.

Fungi associated with coffee leaf lesions provide a diverse target panel for evaluating fungicide sensitivity and microbial antagonism. This study evaluated the antagonistic spectrum of mangrove-derived Streptomyces sp. CD103 and fungicide sensitivity in selected lesion-associated fungi. Of 49 isolates recovered from symptomatic Coffea arabica leaves in Wanning, Hainan, 39 induced necrosis following wound inoculation. These isolates were assigned to eight genera based on internal transcribed spacer (ITS) sequence comparisons and phylogenetic placement; Colletotrichum accounted for 64.1% of the necrosis-inducing isolates. Six fungicides were tested against seven isolates spanning four genera. Sensitivity varied among isolates and compounds; concentrations causing 50% inhibition of mycelial growth (EC₅₀) for thiophanate-methyl ranged from 0.57 to 22.53 µg mL⁻¹. Among 45 mangrove-derived actinomycetes screened against Colletotrichum gloeosporioides CCG3, CD103 showed the highest mean inhibition (99.21 ± 0.40%). In subsequent dual-culture assays, CD103 completely inhibited 19 of the 21 selected lesion-associated isolates spanning eight genera and all six reference plant pathogens. The two exceptions, a Fusarium isolate and an Alternaria isolate, showed 85.04% and 97.10% inhibition, respectively. These findings identify CD103 as a broad-spectrum in vitro antagonist against the tested fungi and warrant further evaluation of its disease-suppressive potential on coffee plants. Full article

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

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28 pages, 4007 KB

Open AccessArticle

Machine Learning Reveals Distinct Phenotypic Virulence Clusters in Candida Isolates Recovered from the Nasopharynx of COVID-19 Convalescents

by Yekaterina Koloskova, Bakhyt Ramazanova, Kamilya Mustafina, Tolkyn Begadilova, Rustam Yussupov, Zamzagul Khandilla, Darya Bunyayeva, Azat Kalmyrzayev, Mohamed Ahmed Mabrouk and Akmaral Bissekenova

J. Fungi 2026, 12(10), 711; https://doi.org/10.3390/jof12100711 (registering DOI) - 22 Sep 2026

Background: Candida spp. are opportunistic fungi whose pathogenic potential arises from interactions among multiple phenotypic traits that may not be captured by conventional single-factor analyses. This study aimed to identify multidimensional phenotypic virulence profiles among clinical Candida isolates using unsupervised machine learning. [...] Read more.

Background: Candida spp. are opportunistic fungi whose pathogenic potential arises from interactions among multiple phenotypic traits that may not be captured by conventional single-factor analyses. This study aimed to identify multidimensional phenotypic virulence profiles among clinical Candida isolates using unsupervised machine learning. Methods: A total of 107 nasopharyngeal isolates recovered from COVID-19 convalescent patients in Almaty, Kazakhstan, during 2021–2022 were evaluated for biofilm formation, phospholipase, proteinase, hemolytic activities and susceptibility to fluconazole, voriconazole, itraconazole, and amphotericin B. Phenotypic data were analyzed using principal component analysis, Uniform Manifold Approximation and Projection, hierarchical clustering, permutational multivariate analysis of variance (PERMANOVA), Random Forest, and SHAP analysis. Results: Candida albicans predominated among the isolates (69.2%), and non-albicans Candida species accounted for 30.8%. Interspecies differences were observed in biofilm formation (p = 0.048) and itraconazole minimum inhibitory concentrations (p < 0.001). Three phenotypic clusters independent of species were identified (PERMANOVA: pseudo-F = 6.72, p = 0.0002). Across 20 repeated 5-fold cross-validation runs, the Random Forest model achieved an aggregated accuracy of 0.785, a mean balanced accuracy of 0.518 (95% CI: 0.461–0.577), and a macro-F1 score of 0.504 (95% CI: 0.444–0.559). SHAP identified itraconazole susceptibility, biofilm formation, and phospholipase activity as the strongest predictors. Conclusions: These findings demonstrate that integrating microbiological phenotyping with machine learning can reveal multidimensional virulence profiles beyond conventional species-based classification. Full article

(This article belongs to the Special Issue Candidiasis: Changes and Challenges in Its Epidemiology, Pathogenesis, Diagnosis, Treatment and Prevention, 2nd Edition)

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29 pages, 986 KB

Open AccessReview

Healthcare-Associated Invasive Mould Diseases: From Rapid Diagnostics to Safe and Effective Management

by Sebastien Imbert, Annalise Unsworth, Priya Garg, Justin Beardsley, Catriona L. Halliday and Sharon C.-A. Chen

J. Fungi 2026, 12(10), 710; https://doi.org/10.3390/jof12100710 - 22 Sep 2026

Invasive mould diseases (IMDs) are an important component of healthcare-associated infections (HAIs). However, they can be difficult to identify, as the standard definition of HAIs do not always apply and usually have a longer and more variable onset after exposure. Identifying the source [...] Read more.

Invasive mould diseases (IMDs) are an important component of healthcare-associated infections (HAIs). However, they can be difficult to identify, as the standard definition of HAIs do not always apply and usually have a longer and more variable onset after exposure. Identifying the source of infection is also challenging, as moulds can colonise a wide range of indoor healthcare environments, and multiple sources of exposure are possible. Thus, healthcare-associated IMDs may reflect a broader failure of infection control measures rather than a single isolated event. In addition, IMDs may evolve into outbreaks that are hard to detect and investigate, as they can develop over extended periods before raising concern. Here, we review mould ecology in healthcare settings and describe the patient groups at risk for healthcare-associated IMDs. We also overview the investigative approaches used to identify case clusters—including case finding, environmental sampling and isolate genotyping—summarise major IMD outbreaks and highlight best management practices. Taken together, this knowledge will help identify high-risk situations and guide the implementation of targeted preventive measures and diagnostic strategies that enable the timely diagnosis and effective management of healthcare-associated IMDs. Full article

(This article belongs to the Special Issue Invasive Fungal Disease: Advances and Challenges in Diagnosis and Management from a Global Perspective, 2nd Edition)

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13 pages, 5779 KB

Open AccessArticle

Optimized Protoplasts Preparation of Fungus Magnaporthe oryzae by Novel Myxolase F Lyase

by Jun Liu, Mingze Gao, Erya Tang, Fanghui Ding, Zhoukun Li and Zhongli Cui

J. Fungi 2026, 12(10), 709; https://doi.org/10.3390/jof12100709 - 22 Sep 2026

Rice blast disease is one of most devastating fungal diseases caused by Magnaporthe oryzae. The preparation and transformation of protoplasm are of vital importance for understanding the pathogenic mechanism of M. oryzae and achieving the control of rice blast disease. In this [...] Read more.

Rice blast disease is one of most devastating fungal diseases caused by Magnaporthe oryzae. The preparation and transformation of protoplasm are of vital importance for understanding the pathogenic mechanism of M. oryzae and achieving the control of rice blast disease. In this study, we aim to optimize conditions for preparing and regenerating the protoplasts of M. oryzae using a novel commercial fungal cell wall-decomposing enzyme, Myxolase F lyase. By optimizing the enzyme concentration, lysis time and pH, osmatic stabilizer and agar percentage in regeneration medium, an applicable protoplast preparation system for M. oryzae was established. Following lysis of M. oryzae mycelium with 5 mg/mL Myxolase F lyase for 3 h, a 49.7% regeneration rate was achieved using a regenerative medium consisting of 0.8 M sucrose and 1% agar at pH 7.0 (50 mM Tris-HCl buffer) under optimum conditions. Moreover, the prepared M. oryzae protoplasts were available for subsequent genetic transformation, with a regeneration rate of 54.28% using Myxolase F compared with 26.86% using the commercial enzyme. The simplified operations, robust reproducibility and improved efficiency give Myxolase F lyase an advantage over other available products, thus providing powerful tools for the efficient genetic transformation of M. oryzae. Full article

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

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18 pages, 3837 KB

Open AccessArticle

Physio-Morphological Assessment and Multi-Omics Analysis of Flammulina filiformis Mycelial Ageing

by Keming Zhu, Zenan Huang, Waner Lv, Yingjie Liu, Zhiying Lin, Zhiyuan Wang, Haoran Xu, Chengzhen Gu and Shujing Sun

J. Fungi 2026, 12(9), 708; https://doi.org/10.3390/jof12090708 - 21 Sep 2026

Flammulina filiformis is one of the most important commercially cultivated species, and the assessment of strain quality is of paramount importance. The analysis measured physiological-biochemical indicators, morphological indicators, combined non-targeted metabolomics, and microbiomics in F. filiformis strains of different ages. The results indicate [...] Read more.

Flammulina filiformis is one of the most important commercially cultivated species, and the assessment of strain quality is of paramount importance. The analysis measured physiological-biochemical indicators, morphological indicators, combined non-targeted metabolomics, and microbiomics in F. filiformis strains of different ages. The results indicate that, as the culture age increased, ergosterol content and catalase (CAT) activity declined continuously. The morphology of the mycelia gradually deteriorated, and yield continued to decrease. The relative content of lipids and lipid-like molecules decreased overall, while the proportion of organic acids and their derivatives increased; the oxidative phosphorylation pathway continued to be significantly enriched. The richness and diversity of the mycelium-associated bacterial community in the mycelia decreased significantly, and the microbial community structure changed. The community was dominated by the genus Acinetobacter from 15 to 60 days, whereas the genus Serratia was predominant in 90 days group. Correlation analysis revealed that the core differential signature metabolites MG 14:1_0:0_0:0, aspartic acid-threonine-aspartamide, and nicotinamide adenine dinucleotide (NAD⁺) were significantly correlated with multiple physiological-biochemical indicators. N-arachidonyl glycine showed significant correlations with 21 core bacterial genera; the dominant genera Acinetobacter and Serratia exhibited strong correlations with membrane homeostasis, core indicators of oxidative damage, and signature metabolites. These results indicate that the mycelial vitality of F. filiformis remains good within the first 15 days of cultivation, with significant ageing occurring after 60 days. These findings provide a theoretical basis for optimizing fungal strain preservation techniques and regulating mycelial ageing. Full article

(This article belongs to the Special Issue Research Progress on Edible Fungi, 2nd Edition)

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16 pages, 5059 KB

Open AccessCase Report

Diagnostic Challenges of Non-Sporulating Fungal Isolates Recovered from Traumatic Wounds Following Motor Vehicle Collisions: Subramaniula asteroides and Aspergillus quadrilineatus in the United Arab Emirates

by Hari Pankaj Vanam, Deema Abdulrahim Alamoodi, Akela Ghazawi, Connie Cañete-Gibas, Nathan P. Wiederhold and Fatima Al Dhaheri

J. Fungi 2026, 12(9), 707; https://doi.org/10.3390/jof12090707 - 21 Sep 2026

Environmental fungi may be recovered from traumatic wounds following motor vehicle collisions (MVCs), but distinguishing transient environmental inoculation, colonization, or contamination from true fungal infection can be challenging. Diagnostic challenges arise when fungal isolates recovered from clinical specimens remain non-sporulating (i.e., sterile), limiting [...] Read more.

Environmental fungi may be recovered from traumatic wounds following motor vehicle collisions (MVCs), but distinguishing transient environmental inoculation, colonization, or contamination from true fungal infection can be challenging. Diagnostic challenges arise when fungal isolates recovered from clinical specimens remain non-sporulating (i.e., sterile), limiting conventional morphological identification and potentially remaining unidentified by routine laboratory platforms such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We describe two cases involving the recovery and diagnostic characterization of Subramaniula asteroides and Aspergillus quadrilineatus from traumatic wounds following MVC-related polytrauma in the United Arab Emirates. In Case 1, a 55-year-old man with a severe crush–degloving hand injury underwent infectious disease evaluation for a suspected complicated skin and soft tissue infection (SSTI), prompting wound culture and antibacterial therapy. The recovered non-sporulating mold was identified as S. asteroides by ITS and D1/D2 sequencing and phylogenetic analysis; histopathologic assessment for fungal tissue invasion was not performed, no antifungal therapy was documented, and the wound improved following surgical and antibacterial management. In Case 2, a 40-year-old man with extensive upper-limb trauma underwent debridement and skin grafting, with wound culture yielding an initially non-sporulating mold subsequently identified as A. quadrilineatus by multilocus analysis of ITS, β-tubulin, and calmodulin. Voriconazole was initiated following communication of the species-level identification and discontinued after 15 days when the isolate was considered more likely to represent colonization or contamination than true wound infection. Although invasive fungal disease was not established in either case, these reports highlight the diagnostic challenges posed by non-sporulating molds, particularly in distinguishing fungal recovery from true infection in traumatic wounds. They also demonstrate the value of reference mycology laboratories integrating phenotypic and molecular approaches in accurately identifying uncommon environmental fungi and informing the interpretation of their clinical significance. Full article

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

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18 pages, 10591 KB

Open AccessArticle

SgtrCypB Formulated with Freund’s Adjuvant Confers Protective Immunity Against S. globosa and Partial Cross-Protection Against S. schenckii Infections in Mice

by Ling Hu, Baicheng Deng, Yuyan Hong, Meizhen Zhong, Xiaoyu Zhi, Xuchu Hu and Huaiqiu Huang

J. Fungi 2026, 12(9), 706; https://doi.org/10.3390/jof12090706 - 21 Sep 2026

Sporothrix globosa is the predominant cause of sporotrichosis in China, highlighting the need for effective vaccine strategies. Cyclophilins from pathogenic microorganisms have emerged as potential vaccine antigens. We previously generated a high-yield, high-purity recombinant truncated S. globosa cyclophilin B protein (SgtrCypB) [...] Read more.

Sporothrix globosa is the predominant cause of sporotrichosis in China, highlighting the need for effective vaccine strategies. Cyclophilins from pathogenic microorganisms have emerged as potential vaccine antigens. We previously generated a high-yield, high-purity recombinant truncated S. globosa cyclophilin B protein (SgtrCypB) retaining its functional domain. Here, BALB/c mice were immunized subcutaneously with SgtrCypB alone or formulated with Freund’s adjuvant to evaluate immunogenicity. Only the adjuvant-formulated vaccine induced a high antibody titer (1:51,200). Then, the infection-challenge experiments compared the SgtrCypB formulated with Freund’s adjuvant and PBS formulated with Freund’s adjuvant groups. Following challenge, SgtrCypB plus adjuvant reduced cutaneous lesion size (0.6 vs. 1.0 cm at week 1) without significantly affecting ulcer incidence. In systemic S. globosa infection, vaccination increased survival to 90% versus 40% in controls and reduced organ fungal burdens. Partial cross-protection was observed against S. schenckii, with 60% versus 20% survival and lower fungal burdens in the kidneys and lungs. Protection against C. albicans was minimal. These findings identify SgtrCypB as a promising protective antigen against S. globosa and S. schenckii and support further evaluation with clinically applicable adjuvants. Full article

(This article belongs to the Special Issue Sporothrix and Sporotrichosis, 4th Edition)

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15 pages, 6314 KB

Open AccessArticle

Systematic Profiling of ssODN Determinants Establishes Optimized LbCas12a-Mediated HDR for Precise Genome Editing in Flammulina filiformis

by Dinghong Jia, Xun Liu, Di Wang, Xiaolan He, Xinmin Liang and Weihong Peng

J. Fungi 2026, 12(9), 705; https://doi.org/10.3390/jof12090705 - 21 Sep 2026

Although gene editing technologies have advanced considerably, research on gene editing in Flammulina filiformis remains in its infancy, and a systematic evaluation of how ssODN donor properties affect HDR efficiency in this species is still lacking. To enable precise genome editing in the [...] Read more.

Although gene editing technologies have advanced considerably, research on gene editing in Flammulina filiformis remains in its infancy, and a systematic evaluation of how ssODN donor properties affect HDR efficiency in this species is still lacking. To enable precise genome editing in the edible mushroom F. filiformis, we established an LbCas12a ribonucleoprotein (RNP)-mediated homology-directed repair (HDR) platform in protoplasts and systematically evaluated key ssODN donor design parameters: PAM-site mutation, homology arm distance, RAD51-preferred sequences (RPSs), truncated Cas target sequences (tCTSs), the RS-1 enhancer, and thermodynamic stability (ΔG). A PAM-disrupting mutation greatly increased HDR efficiency, up to 58.5%. Extending the left homology arm 174 bp upstream of the break still yielded 20.2% HDR, expanding the tolerable distance. RPSs showed context-dependent effects: enhancing HDR up to 287.8% in some designs but reducing it by 61.9% in another. Both tCTS and RS-1 consistently suppressed HDR. No strong linear correlation between ΔG and HDR efficiency was observed. Collectively, from experiments conducted at a single genomic locus, our results not only establish a versatile precision-editing platform for F. filiformis through optimized ssODN design, but also offer tentative and transferable insights into the HDR-mediated genome editing of other heterokaryotic basidiomycetes facing similar genetic operation challenges. Full article

(This article belongs to the Special Issue Edible Mushrooms: Advances and Perspectives)

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38 pages, 41616 KB

Open AccessReview

Phenotypic Analysis of Edible Mushroom Fruiting Bodies in Monocular RGB Images: A Problem-Oriented Critical Review

by Wei Zhao, Xin Tian, Lu Yuan, Yinglong Wang, Quan Wei, Hua Yin and Ziwei Song

J. Fungi 2026, 12(9), 704; https://doi.org/10.3390/jof12090704 - 21 Sep 2026

Monocular RGB imaging offers a low-cost, flexible approach to morphological measurement, quality assessment, growth monitoring, and production automation for edible mushroom fruiting bodies. However, the relationships among visible phenotypes, visual methods, measurement reliability, and production requirements remain insufficiently integrated. This problem-oriented review synthesizes [...] Read more.

Monocular RGB imaging offers a low-cost, flexible approach to morphological measurement, quality assessment, growth monitoring, and production automation for edible mushroom fruiting bodies. However, the relationships among visible phenotypes, visual methods, measurement reliability, and production requirements remain insufficiently integrated. This problem-oriented review synthesizes 76 core studies published between 2016 and the final search date in 2026 through a framework linking visible phenotypes, visual tasks, key bottlenecks, and production applications. It covers individual localization and separation, structural measurement, spatial estimation, quality and species recognition, temporal analysis, and production deployment. The reviewed studies reveal a transition from static two-dimensional detection and counting toward instance-level morphological measurement, three-dimensional parameter estimation, and spatiotemporal growth modeling, extending phenotyping from visible appearance description to spatial trait estimation and growth prediction. Quantitative results also highlight the importance of evaluation conditions: for example, MSH-YOLOv8 achieved an

{AP}_{50}

of 98.49% on the Fungi dataset, whereas

{AP}_{50 : 95}

and small-object AP were 75.29% and 39.73%, respectively, indicating that high

{AP}_{50}

alone does not adequately characterize detection performance under stricter localization criteria or for small targets. These study-specific results cannot be directly extrapolated to commercial production environments. Severe occlusion, projection errors, inconsistent phenotype definitions, and temporal instability continue to constrain measurement reliability. Moreover, reliable performance without extensive retraining following changes in strains, substrates, or lighting systems remains insufficiently demonstrated. Future research should prioritize standardized multi-task and temporal datasets, unified phenotype definitions, uncertainty evaluation, occlusion-robust spatial and temporal modeling, and closed-loop production validation. Commercial scaling of low-cost monocular RGB imaging in protected mushroom cultivation depends on translating its affordability into reliable performance under severe occlusion and across production conditions, thereby enabling accessible automation for small and medium-scale producers. Full article

(This article belongs to the Special Issue Edible Mushrooms: Advances and Perspectives)

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24 pages, 13327 KB

Open AccessArticle

Reference Database Selection Influences Both Taxonomic Annotation and Ecological Inference in Arbuscular Mycorrhizal Fungal Communities

by Yajie Liu, Na Li, Xiaoshuang Ma, Kaiyuan Zhang, Nianci Li and Chunxue Yang

J. Fungi 2026, 12(9), 703; https://doi.org/10.3390/jof12090703 - 20 Sep 2026

Arbuscular mycorrhizal (AM) fungi are keystone microorganisms in soil ecosystems, and their community composition plays a crucial role in regulating ecosystem functions. Although high-throughput sequencing is widely used to characterize their communities, the selection of reference databases for sequence annotation remains inconsistent. To [...] Read more.

Arbuscular mycorrhizal (AM) fungi are keystone microorganisms in soil ecosystems, and their community composition plays a crucial role in regulating ecosystem functions. Although high-throughput sequencing is widely used to characterize their communities, the selection of reference databases for sequence annotation remains inconsistent. To assess database performance at the species level, rhizosphere soil and root samples from four plant species with contrasting communities were subjected to amplicon sequencing. Taxonomic annotations generated using the MaarjAM, SILVA, and NCBI databases were compared. NCBI provided the highest taxonomic resolution, identifying 18 genera and 108 species, including Rhizophagus intraradices and Funneliformis mosseae, with assignments supported by spore isolation and nomenclatural verification. In contrast, MaarjAM recovered the most ASVs but contained numerous virtual taxa, whereas SILVA showed limited annotation depth and fewest assignments. Comparative analyses showed that NCBI was more sensitive in distinguishing samples based on alpha diversity and community structure and produced species distributions more consistent with ecological expectations. Although core metabolic profiles were conserved across databases, suggesting functional redundancy that may contribute to ecosystem stability, database selection influenced relationship interpretation between environmental variables and communities. Overall, NCBI is recommended for species-level annotation and community analysis, whereas inappropriate database selection may bias biodiversity assessment and ecological inference. Full article

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

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18 pages, 5246 KB

Open AccessArticle

Early Detection of Postharvest Potato Tuber Dry Rot Based on Hyperspectral Imaging and a Dual-Branch ResNet12-SE Spatial–Spectral Fusion Network

by Hanwen Cao, Jiahui Liu, Tao Liu, Mingmin Zhao, Huali Xue and Min Hao

J. Fungi 2026, 12(9), 702; https://doi.org/10.3390/jof12090702 - 20 Sep 2026

Potato tuber dry rot is a major postharvest decay caused predominantly by Fusarium spp. During early infection, external symptoms may be absent even when faint internal browning, localized dehydration, and tissue structure changes have begun. Manual inspection, destructive cutting, and culture- or molecular-based [...] Read more.

Potato tuber dry rot is a major postharvest decay caused predominantly by Fusarium spp. During early infection, external symptoms may be absent even when faint internal browning, localized dehydration, and tissue structure changes have begun. Manual inspection, destructive cutting, and culture- or molecular-based assays are therefore poorly suited to rapid, nondestructive, high-throughput screening. We developed a near-infrared hyperspectral imaging method that combines spatial and spectral representations in a dual-branch ResNet12-SE network. The working dataset contained 1725 labeled records (862 healthy and 863 early-infected records); records were assigned to subsets by tuber identifier, and an infected volume ratio below 5% was used as an operational early infection threshold. The calibrated model input was a 224-band, 224 × 224 hyperspectral cube. The spatial branch used a ResNet-12 backbone with spatial squeeze-and-excitation (SE), whereas the spectral branch used spectral SE followed by bidirectional long short-term memory (BiLSTM). The two feature vectors were concatenated for binary classification. In the single-split test, the proposed model achieved 98.22% accuracy, compared with 90.67% for the ResNet-12 baseline and 97.43% for Vision Transformer. Preprocessing, principal component image, local binary pattern, and gray-level co-occurrence matrix analyses provide complementary interpretation of the spectral and spatial responses. The results support the feasibility of hyperspectral screening under the controlled laboratory protocol and define the validation work required before broader deployment. Full article

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

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18 pages, 8362 KB

Open AccessArticle

Solid Fermentation Products of Trichoderma viride Improve Soil Aggregation, Soil Nutrient Status and Plant Growth

by Xiaowei Wei, Yuqi Pan, Mingyue Sun, Guangyuan Yao, Shihan Feng, Yidi Gai, Yize Zhao and Xuechen Yang

J. Fungi 2026, 12(9), 701; https://doi.org/10.3390/jof12090701 - 19 Sep 2026

Soil degradation caused by intensive agricultural management has become a major constraint on sustainable crop production, highlighting the need for multifunctional soil amendments capable of simultaneously improving soil structural quality and crop performance. In this greenhouse pot experiment, the effects of Trichoderma viride [...] Read more.

Soil degradation caused by intensive agricultural management has become a major constraint on sustainable crop production, highlighting the need for multifunctional soil amendments capable of simultaneously improving soil structural quality and crop performance. In this greenhouse pot experiment, the effects of Trichoderma viride-fermented xylose residue on soil physical and chemical properties, aggregate stability, soil nutrient status, root development, photosynthetic characteristics, and cucumber (Cucumis sativus L.) growth were evaluated. The fermented amendment was incorporated into soil at application rates of 0 (CK), 0.5 (T1), 0.75 (T2), 1.0 (T3), 1.25 (T4), and 1.5% (T5) (w/w). Amendment application significantly affected soil structural characteristics and plant growth responses. Compared with the control, T3 and T4 increased the proportion of macroaggregates by 3.12% and 6.09%, respectively, whereas mean weight diameter increased by 26.81–29.76% under T3–T5. The T2 treatment produced the highest soil porosity, aeration porosity, capillary porosity, chlorophyll content, and net photosynthetic rate. Soil total nitrogen, total phosphorus, total carbon, and total organic carbon concentrations also differed significantly among treatments, while plant nitrogen and phosphorus contents were markedly enhanced under T2 and T3. Aboveground biomass increased by up to 59.80% relative to the control. Mantel analysis revealed significant associations among soil physical and chemical properties, aggregate characteristics, root morphology, plant nutrient contents, and biomass accumulation. Collectively, these findings demonstrate that T. viride-fermented corncob xylose residue can improve soil structural properties and promote cucumber growth under greenhouse pot conditions. Among the application rates evaluated, 0.75% provided the most balanced overall response across soil physical properties and plant performance. The present study provides a basis for the utilization of fermented lignocellulosic residues as integrated bio-organic amendments for sustainable soil management. Full article

(This article belongs to the Special Issue Trichoderma in Sustainable Agriculture: From Fundamental Research to Practical Applications)

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14 pages, 2333 KB

Open AccessArticle

Management of Twig Canker and Shoot Blight of Almond Caused by Diaporthe amygdali: Efficacy of Chemical Fungicides and Biological Control Agents

by Carolina Francia, Josep Armengol, Antonio Ramón and Mónica Berbegal

J. Fungi 2026, 12(9), 700; https://doi.org/10.3390/jof12090700 - 18 Sep 2026

This study evaluated the in vitro and in planta efficacy of six chemical fungicides (boscalid, captan, copper oxychloride, difenoconazole, pyraclostrobin, and potassium hydrogen carbonate) and two biological control agents (Bacillus amyloliquefaciens subsp. plantarum D747 and Trichoderma atroviride strain SC1) against Diaporthe amygdali [...] Read more.

This study evaluated the in vitro and in planta efficacy of six chemical fungicides (boscalid, captan, copper oxychloride, difenoconazole, pyraclostrobin, and potassium hydrogen carbonate) and two biological control agents (Bacillus amyloliquefaciens subsp. plantarum D747 and Trichoderma atroviride strain SC1) against Diaporthe amygdali, the causal agent of twig canker and shoot blight disease of almond. In vitro assays demonstrated that D. amygdali is highly sensitive to captan, difenoconazole, and pyraclostrobin. Regarding biological products, dual antagonism assays showed high efficacy for T. atroviride. Subsequently, the pre- and post-infection activity of all products was assessed on one-year-old almond plants. Efficacy varied significantly depending on the timing of application. Trichoderma atroviride was effective at all application times, achieving mean percent disease control (MPDC) values of 100% when applied preventively. Pre-infection applications of difenoconazole and pyraclostrobin resulted in 100% MPDC. However, their efficacy progressively decreased when applied post-infection. Bacillus amyloliquefaciens and captan showed variable results, reaching a maximum of 73% and 87% MPDC, respectively, when applied before inoculation. In contrast, boscalid, copper oxychloride, and potassium hydrogen carbonate exhibited very low MPDC values, regardless of application timing. These findings provide valuable information for improving management strategies against D. amygdali in almond orchards. Full article

(This article belongs to the Special Issue Fungal Diseases of Fruit and Woody Plants)

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13 pages, 492 KB

Open AccessArticle

Ten-Year Voriconazole Susceptibility Trends Among 1482 Clinical Aspergillus fumigatus Isolates: A Compositionally Controlled Multicenter Analysis of the VIVLI/SENTRY Platform (2010–2020)

by Jose W. Lopez, Alicia A. Segura-Grados, Emily Olascoaga-Mori and Harold J. Rodríguez-Madueño

J. Fungi 2026, 12(9), 699; https://doi.org/10.3390/jof12090699 - 18 Sep 2026

Azole resistance in Aspergillus fumigatus is an emerging threat to invasive and chronic aspergillosis management, yet multicenter trend analyses rarely verify whether the composition of surveillance data remained stable over time. We performed a longitudinal, secondary-data analysis of 2111 Aspergillus isolates registered in [...] Read more.

Azole resistance in Aspergillus fumigatus is an emerging threat to invasive and chronic aspergillosis management, yet multicenter trend analyses rarely verify whether the composition of surveillance data remained stable over time. We performed a longitudinal, secondary-data analysis of 2111 Aspergillus isolates registered in the VIVLI AMR platform (ATLAS Antifungals, SENTRY Program) between 2010 and 2020. Because Clinical and Laboratory Standards Institute (CLSI) voriconazole breakpoints are established only for A. fumigatus in this dataset, the susceptibility-trend analysis was restricted to A. fumigatus isolates with a valid interpretation (n = 1482/1483). A. fumigatus accounted for 70.3% of all Aspergillus isolates; most originated from Europe (43.9%) and North America (35.2%). Region and clinical specialty differed significantly across the three study periods (both p < 0.0001), while species, age, sex and specimen-source distributions remained stable (p > 0.10). Voriconazole susceptibility in A. fumigatus declined from 97.9% (2010) to 90.4% (2020), with a significant linear downward trend (Cochran–Armitage Z = −3.03, p = 0.002). This decline was statistically robust, but the concurrent shift in participating regions and specialties indicates that compositional changes in surveillance sampling should be considered alongside biological resistance emergence when interpreting multicenter antifungal surveillance trends. Full article

(This article belongs to the Special Issue Antifungal Resistance in Clinical Fungi)

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14 pages, 4105 KB

Open AccessArticle

Multimodal Analysis and Heterologous Expression Strategies Reveal the Crucial Role of the Lac2 Gene from Lentinus sajor-caju in Lignin Degradation

by Changlong Gou, Lilong Luo, Liang Zhang, Liming Chen, Yangci Liao and Yuqiong Wang

J. Fungi 2026, 12(9), 698; https://doi.org/10.3390/jof12090698 - 17 Sep 2026

The complex chemical structure of plant lignin limits roughage utilization. Biological modification is commonly used to enhance lignin properties. Lentinus sajor-caju (L. sajor-caju) is a potent white-rot fungus for lignocellulose pretreatment in animal roughage. However, the key lignin-degrading enzyme genes remain [...] Read more.

The complex chemical structure of plant lignin limits roughage utilization. Biological modification is commonly used to enhance lignin properties. Lentinus sajor-caju (L. sajor-caju) is a potent white-rot fungus for lignocellulose pretreatment in animal roughage. However, the key lignin-degrading enzyme genes remain unclear. This study evaluated the key enzyme genes involved in lignin degradation and their efficiency in decomposing alkaline lignin. Transcriptome and proteome comparative analyses of L. sajor-caju cultured in media with glucose and alkaline lignin as carbon sources revealed that the AA1 laccase aids lignin decomposition in L. sajor-caju. Additionally, a laccase heterologously expressing strain in Pichia pastoris X-33 was constructed. Compared with the wild-type L. sajor-caju strain W-2, Lac2 laccase activity increased by 67.35%. Electron microscopy showed that Lac2 degraded alkaline lignin, forming irregular pores and surface fusion. These findings indicate that Lac2 laccase has potential application value. In the future, it may be applied in agriculture, the chemical industry, and the energy sector to efficiently convert lignin into feed additives or energy products. Full article

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

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17 pages, 2791 KB

Open AccessArticle

Pan-Genome-Scale Metabolic Reconstruction Reveals Conserved Metabolic Functions in Candida albicans

by Ya Meng, Yiming Zhang and Lei Zhang

J. Fungi 2026, 12(9), 697; https://doi.org/10.3390/jof12090697 - 17 Sep 2026

Candida albicans is a major cause of human mucosal and invasive fungal infections, but the relationship between its intraspecific genomic diversity and metabolic variation remains poorly understood. Here, we integrated 80 public C. albicans genome assemblies, published fungal genome-scale metabolic models (GEMs), public [...] Read more.

Candida albicans is a major cause of human mucosal and invasive fungal infections, but the relationship between its intraspecific genomic diversity and metabolic variation remains poorly understood. Here, we integrated 80 public C. albicans genome assemblies, published fungal genome-scale metabolic models (GEMs), public reaction databases, and orthogroup-linked gene–protein–reaction (GPR) evidence to construct a species-level C. albicans pan-GEM and derived 80 strain-specific GEMs (ssGEMs) through genome projection. The pan-genome comprised 10,308 orthogroups, including 4215 core, 5947 accessory, and 146 singleton orthogroups. The final pan-GEM contained 1986 reactions, 1777 metabolites, and 865 genes. After feasibility rescue, all 80 ssGEMs met the feasibility criterion for predicted growth and passed the closed-uptake energy-generating-cycle test. Among experimentally essential genes with resolvable GPR associations, 23 were consistently predicted as model-essential across all final ssGEMs. As an application of the ssGEM collection, nutrient-boundary simulations showed that increasing D-glucose uptake markedly increased predicted growth across 79 feasible ssGEMs. This framework provides a reusable resource for comparing conserved metabolic functions and genome-projected reaction differences across C. albicans strains. Full article

(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi, 2nd Edition)

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