Journal of Fungi

22 pages, 4780 KiB

Open AccessArticle

The Effects of Fungal Pathogen Infestation on Soil Microbial Communities for Morchella sextelata Cultivation on the Qinghai–Xizang Plateau

by Ming-Chen Guo, Bo-Chun Wu, Cai-Yun Luo, Wei Sa, Le Wang, Zhong-Hu Li and Qian-Han Shang

J. Fungi 2025, 11(4), 264; https://doi.org/10.3390/jof11040264 (registering DOI) - 28 Mar 2025

Abstract

Fungi infestation as a disease has serious impacts on the cultivation of Morchella species. To investigate the effects of fungi infestation on the microbial diversity and community structure of soil when cultivating Morchella sextelata, we sampled soil samples of Morchella cultivars in [...] Read more.

Fungi infestation as a disease has serious impacts on the cultivation of Morchella species. To investigate the effects of fungi infestation on the microbial diversity and community structure of soil when cultivating Morchella sextelata, we sampled soil samples of Morchella cultivars in the Qinghai–Xizang Platea and used metagenome sequencing technology to identify the disease fungi and analyze the differences in microbial diversity and structure between disease-infested and healthy soils. The disease fungi identified were Tricharina gilva and Peziza lohjaoensis, and the microbial diversity of T. gilva-infected soil was higher than that of healthy soil, while the diversity of P. lohjaoensis-infected soil was lower. Interestingly, whether infected with T. gilva or P. lohjaoensis, the soil microbial community was changed, and the dominant phyla and genera were different in different soil samples. When infected with P. lohjaoensis, the dominant phyla with relatively high abundances included Proteobacteria, Bacteroidetes, and Ascomycota, with average relative abundances of 44%, 18%, and 15%, respectively, and the dominant genera with high relative abundances encompassed Pseudomonadaceae, Terfezia, and Pedobacter, with average relative abundances of 8%, 9%, and 5%, respectively. Following infection with T. gilva, the dominant phyla with higher relative abundances were Proteobacteria, Acidobacteria, and Bacteroidetes, with average relative abundances of 46%, 15%, and 12%, respectively, and the dominant genera with high relative abundances included Hydrogenophaga, Sphingomonas, and Polaromonas, with average relative abundances of 9%, 3%, and 2%, respectively. Additionally, we found that lipid-metabolism-related genes were less abundant in the soil infected with P. lohjaoensis than in the other soil samples, and glycoside hydrolase diversity was lower in the soil infected with T. gilva than in other healthy soils. The results showed that the effects of different disease fungi on soil microbial communities and functional genes were different, which provided a theoretical basis for the sustainable cultivation of Morchella. Full article

24 pages, 1950 KiB

Open AccessReview

Fusarium Species Associated with Diseases of Citrus: A Comprehensive Review

by Mihlali Badiwe, Régis Oliveira Fialho, Charles Stevens, Paul-Henri Lombard and Jan van Niekerk

J. Fungi 2025, 11(4), 263; https://doi.org/10.3390/jof11040263 - 28 Mar 2025

Abstract

The citrus industry contributes to the cultivation of one of the most important fruit crops globally. However, citrus trees are susceptible to numerous Bisifusarium, Fusarium, and Neocosmospora-linked diseases, with dry root rot posing a serious threat to citrus orchards worldwide. [...] Read more.

The citrus industry contributes to the cultivation of one of the most important fruit crops globally. However, citrus trees are susceptible to numerous Bisifusarium, Fusarium, and Neocosmospora-linked diseases, with dry root rot posing a serious threat to citrus orchards worldwide. These infections are exacerbated by biotic and abiotic stresses, leading to increased disease incidence. Healthy trees unexpectedly wilt and fall, exhibiting symptoms such as chlorosis, dieback, necrotic roots, root rot, wood discolouration, and eventual decline. Research indicates that the disease is caused by a complex of species from the Nectriaceae family, with Neocosmospora solani being the most prominent. To improve treatment and management strategies, further studies are needed to definitively identify these phytopathogens and understand the conditions and factors associated with Bisifusarium, Fusarium, and Neocosmospora-related diseases in citrus. This review focuses on the epidemiology and symptomatology of Fusarium and Neocosmospora species, recent advances in molecular techniques for accurate phytopathogen identification, and the molecular mechanisms of pathogenicity and resistance underlying Fusarium and Neocosmospora–citrus interactions. Additionally, the review highlights novel alternative methods, including biological control agents, for disease control to promote environmentally friendly and sustainable agricultural practices. Full article

(This article belongs to the Special Issue Fusarium, Alternaria and Rhizoctonia: A Spotlight on Fungal Pathogens, 2nd Edition)

► Show Figures

Figure 1

15 pages, 6910 KiB

Open AccessArticle

Fungal Community Complexity and Stability in Clay Loam and Sandy Soils in Mangrove Ecosystems

by Shengyao Zhou, Xiaojie Deng, Rajapakshalage Thashikala Nethmini, Huaxian Zhao, Qing He, Gonglingxia Jiang, Qinghua Hou, Qingxiang Chen, Xiaolei Li, Ke Dong and Nan Li

J. Fungi 2025, 11(4), 262; https://doi.org/10.3390/jof11040262 - 28 Mar 2025

Abstract

Soil fungi in mangroves are diverse and crucial for organic matter decomposition and element cycling. However, the drivers influencing network complexity and the stability of fungal communities across different mangrove soil habitats remain unclear. This study investigated the main factors driving the composition, [...] Read more.

Soil fungi in mangroves are diverse and crucial for organic matter decomposition and element cycling. However, the drivers influencing network complexity and the stability of fungal communities across different mangrove soil habitats remain unclear. This study investigated the main factors driving the composition, diversity, complexity, and stability of fungal communities in clay loam and sandy soils in mangrove ecosystems. Results showed that Dothideomycetes and Sordariomycetes dominated in clay loam and sandy soils, respectively. Sandy soils exhibited higher alpha diversity than clay loam. Beta diversity analysis revealed significant differences in the fungal community structure between the two soil types. Network analysis demonstrated higher complexity and stability of fungal communities in clay loam than in sandy soil. Spearman’s correlation analysis revealed that NH₄⁺-N and total nitrogen were the main factors affecting complexity and stability in clay loam, respectively. Partial least squares path modeling demonstrated that alpha diversity and soil properties were closely linked to the complexity and stability of fungal communities in clay loam, whereas beta diversity was the primary driver in sandy soil. Our study enhances the understanding of the mechanisms that maintain fungal diversity and community stability in mangrove ecosystems, with important implications for restoring vegetation in degraded areas. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

► Show Figures

Figure 1

18 pages, 4585 KiB

Open AccessArticle

Associations Between Indoor Fungal Community Structures and Environmental Factors: Insights from the Evidence-Driven Indoor Air-Quality Improvement Study

by Iva Šunić, Dubravka Havaš Auguštin, Jelena Šarac, Kristina Michl, Tomislav Cernava, Rasmus Riemer Jakobsen, Armin Mešić, Natalija Novokmet and Mario Lovrić

J. Fungi 2025, 11(4), 261; https://doi.org/10.3390/jof11040261 - 28 Mar 2025

Abstract

Indoor fungal communities, found in household dust, significantly influence indoor air quality and health. These communities are shaped by environmental, socioeconomic, and household factors. However, studies on indoor mycobiomes, particularly in Croatia, remain limited. This study investigates the relationship between environmental and household [...] Read more.

Indoor fungal communities, found in household dust, significantly influence indoor air quality and health. These communities are shaped by environmental, socioeconomic, and household factors. However, studies on indoor mycobiomes, particularly in Croatia, remain limited. This study investigates the relationship between environmental and household factors and indoor fungal communities, focusing on their diversity, composition, and potential health impacts in Croatian households. Dust samples from 66 Croatian households were analyzed using fungal ITS sequencing. Statistical analyses, including alpha diversity measures, were conducted to evaluate the influence of variables such as pet ownership, number of siblings, and cleaning habits on fungal diversity and abundance. Dominant genera included Malassezia, Cladosporium, and the family Didymosphaeriaceae. Pet ownership and sibling presence were linked to higher fungal diversity, with outdoor-associated genera such as Aureobasidium being more abundant in these households. Cleaning practices selectively altered fungal communities, with frequent cleaning reducing diversity, but not eliminating resilient taxa like Malassezia. This study highlights the interplay between environmental, household, and socioeconomic factors in shaping indoor fungal communities. The findings underscore the importance of addressing indoor fungal diversity to improve air quality and health, particularly in households with vulnerable populations. Full article

(This article belongs to the Special Issue Fungal Diversity in Europe, 3rd Edition)

► Show Figures

Figure 1

20 pages, 2121 KiB

Open AccessReview

The Role of Oral Yeasts in the Development and Progression of Oral Squamous Cell Carcinoma: A Scoping Review

by Satutya Wicaksono, Zilefac Brian Ngokwe, Michael McCullough and Tami Yap

J. Fungi 2025, 11(4), 260; https://doi.org/10.3390/jof11040260 - 27 Mar 2025

Abstract

The role of oral yeasts in oral squamous cell carcinoma (OSCC) has gained attention due to evidence linking fungal dysbiosis to carcinogenesis. While Candida albicans has been the primary focus, emerging studies highlight the importance of non-Candida species yeast genera. This scoping [...] Read more.

The role of oral yeasts in oral squamous cell carcinoma (OSCC) has gained attention due to evidence linking fungal dysbiosis to carcinogenesis. While Candida albicans has been the primary focus, emerging studies highlight the importance of non-Candida species yeast genera. This scoping review synthesises the evidence on the role of oral yeasts, including Candida spp. and non-Candida species, in the development and progression of OSCC. A PRISMA-ScR-guided search was conducted in Medline, Embase, EBM Reviews, and CINAHL. Observational and experimental studies involving humans with OSCC, oral potentially malignant disorders (OPMDs), or oral epithelial dysplasia (OED) were included. This review analysed 75 studies. Research on oral yeast in OSCC has progressed since the 1970s, with advancements in identification techniques—from conventional culture methods to metagenomic sequencing and multi-omics approaches—alongside improved animal and cellular models of OSCC. These methodological advancements have identified notable distinctions in the oral mycobiome between carcinomatous and healthy states. Clinical findings reinforce the hypothesis that oral yeasts, particularly Candida spp., actively contribute to the dysplasia–carcinoma sequence. Emerging evidence suggests that oral yeasts may significantly modulate events contributing to OSCC progression. However, further mechanistic studies and robust clinical evidence are essential to establish causality and clarify their role in OSCC. Full article

► Show Figures

Figure 1

25 pages, 2928 KiB

Open AccessReview

Nutritional and Therapeutic Potential of Stropharia rugosoannulata and Macrolepiota procera: From Composition to Health-Promoting Effect

by Qian Wang, Xiaoyan Yang and Jiangxiong Zhu

J. Fungi 2025, 11(4), 259; https://doi.org/10.3390/jof11040259 - 27 Mar 2025

Abstract

Stropharia rugosoannulata and Macrolepiota procera have garnered considerable attention due to their distinctive flavor profile, culinary versatility, and potential nutritional and therapeutic benefits. They are a rich source of high-quality protein, dietary fiber, vitamins, and minerals, contributing to daily nutritional requirements and promoting [...] Read more.

Stropharia rugosoannulata and Macrolepiota procera have garnered considerable attention due to their distinctive flavor profile, culinary versatility, and potential nutritional and therapeutic benefits. They are a rich source of high-quality protein, dietary fiber, vitamins, and minerals, contributing to daily nutritional requirements and promoting overall well-being. Furthermore, they contain a diverse array of bioactive compounds, including polyphenols, flavonoids, and triterpenoids, which have demonstrated antioxidant, anti-inflammatory, and antitumor properties in previous studies. However, comprehensive reviews focusing on these two species remain limited. Therefore, this review summarizes the types of nutrients and bioactive compounds found in Stropharia rugosoannulata and Macrolepiota procera, along with their respective extraction methods. Moreover, the bioactivities of these compounds were discussed, aiming to provide a theoretical framework for the development of novel functional foods and nutraceuticals derived from Stropharia rugosoannulata and Macrolepiota procera. Full article

(This article belongs to the Special Issue Utilizing Fungal Diversity for Sustainable Biotechnology)

► Show Figures

Figure 1

18 pages, 368 KiB

Open AccessReview

Invasive Candidiasis in the Intensive Care Unit: Where Are We Now?

by Jose A. Vazquez, Lissette Whitaker and Ana Zubovskaia

J. Fungi 2025, 11(4), 258; https://doi.org/10.3390/jof11040258 - 27 Mar 2025

Abstract

Invasive fungal infections in the intensive care unit (ICU) are not uncommon and most cases are caused by Candida species, specifically Candida albicans. However, recently, there has been an increase in non-albicans Candida spp. (C. glabrata; C. parapsilosis) causing [...] Read more.

Invasive fungal infections in the intensive care unit (ICU) are not uncommon and most cases are caused by Candida species, specifically Candida albicans. However, recently, there has been an increase in non-albicans Candida spp. (C. glabrata; C. parapsilosis) causing invasive fungal infections. This has led to an increasing awareness of this infection due to the increase in documented antifungal resistance in many of these Candida species. In addition, manifestations of invasive candidiasis are often non-specific, and the diagnosis remains extremely challenging. Unfortunately, delays in antifungal therapy continue to hamper the morbidity; length of stay; and the mortality of these infections. Although the echinocandins are the drugs of choice in these infections, antifungal resistance among the non-albicans species (C. glabrata; C. krusei; C. auris; C. parapsilosis) is being observed more frequently. This has led to an increase in morbidity and mortality, specifically in critically ill patients. Overall, the diagnosis and management of invasive candidiasis in the ICU remain challenging. It is imperative that the critical care physician keeps this infection at the forefront of their differential diagnosis in order to decrease the mortality rate of these individuals. In this review, we discuss the current epidemiologic trends, diagnosis, and management of invasive candidiasis in the intensive care unit setting. Full article

(This article belongs to the Special Issue Fungal Infections in Intensive Care Medicine)

16 pages, 5605 KiB

Open AccessArticle

Study on Pathogenesis of Cytospora pyri in Korla Fragrant Pear Trees (Pyrus sinkiangensis)

by Yiwen Zhang, Zhe Wang, Zhen Zhang, Lan Wang and Hongzu Feng

J. Fungi 2025, 11(4), 257; https://doi.org/10.3390/jof11040257 - 27 Mar 2025

Abstract

Pear Valsa cankers were found in various Korla fragrant pear orchards in Alaer, Xinjiang. Disease samples underwent tissue isolation, resulting in six isolates. Pathogenicity tests revealed that the XLFL-6 isolate was the most virulent, demonstrating typical Valsa canker symptoms. Research on its biological [...] Read more.

Pear Valsa cankers were found in various Korla fragrant pear orchards in Alaer, Xinjiang. Disease samples underwent tissue isolation, resulting in six isolates. Pathogenicity tests revealed that the XLFL-6 isolate was the most virulent, demonstrating typical Valsa canker symptoms. Research on its biological characteristics indicated that the optimal growth conditions for XLFL-6 were a temperature of 28 °C and a pH of five. Under these conditions, the colonies of XLFL-6 exhibited the largest growth diameter, and adding glucose and peptone separately to the Czapek medium was most conducive to the growth of its mycelium. Based on morphological observations and multigene sequence analyses (ITS+TEF+TUB), the pathogenic fungus was identified as C. pyri. The infection process of C. pyri was elucidated through tissue observations using both light and electron microscopy. The conidia displayed a similar germination pattern on both wounded and intact twigs. However, the infection process was delayed in the case of intact bark. By 8 h post-inoculation, the conidia achieved a germination rate of 15%. Although germination had occurred, the infection process had not yet commenced. In contrast, for wounded bark tissue, it was observed that 24 h post-inoculation, the fungal hyphae from the conidia directly invaded the wounded tissue. These hyphae penetrate the cell walls, proliferate within the host tissue, and spread throughout the phloem and xylem. After 20 d, numerous pycnidia had breached the bark surface, and yellow waxy gums filled with conidia flowed abundantly from the pycnidia ostioles, with the host tissue being nearly totally disintegrated. Regarding enzyme activity, the polygalacturonase (PG) activity, the primary cell wall-degrading enzyme in the treatment group, was seven times greater than that of the control group. The carboxymethyl cellulose (Cx) activity within the treatment group continued to increase. Xylanase activity rose swiftly to its peak between days 1 and 4, then decreased from days 5 to 10, although it remained higher than that of the control group. Overall, this study is the first to provide a detailed report on the characteristics and proliferation of C. pyri and further elucidates its modes and pathways of invasion. Full article

► Show Figures

Figure 1

17 pages, 1317 KiB

Open AccessReview

Molecular Mechanisms of Pathogenic Fungal Virulence Regulation by Cell Membrane Phospholipids

by Yitong Li, Hongchen Wang, Hengxiu Wang, Tianming Wang, Daqiang Wu and Wenfan Wei

J. Fungi 2025, 11(4), 256; https://doi.org/10.3390/jof11040256 - 26 Mar 2025

Abstract

Pathogenic fungi represent a growing concern for human health, necessitating a deeper understanding of their molecular mechanisms of virulence to formulate effective antifungal strategies. Recent research has increasingly highlighted the role of phospholipid components in fungal cell membranes, which are not only vital [...] Read more.

Pathogenic fungi represent a growing concern for human health, necessitating a deeper understanding of their molecular mechanisms of virulence to formulate effective antifungal strategies. Recent research has increasingly highlighted the role of phospholipid components in fungal cell membranes, which are not only vital for maintaining cellular integrity but also significantly influence fungal pathogenicity. This review focuses on the impact of membrane phospholipid composition on fungal growth, morphogenesis, stress responses, and interactions with host cells. To be specific, membrane phospholipid composition critically influences fungal virulence by modulating growth dynamics and morphogenesis, such as the transition from yeast to hyphal forms, which enhances tissue invasion. Additionally, phospholipids mediate stress adaptation, enabling fungi to withstand host-derived oxidative and osmotic stresses, crucial for survival within hostile host environments. Phospholipid asymmetry also impacts interactions with host cells, including adhesion, phagocytosis evasion, and the secretion of virulence factors like hydrolytic enzymes. These adaptations collectively enhance fungal pathogenicity by promoting colonization, immune evasion, and damage to host tissues, directly linking membrane architecture to infection outcomes. By elucidating the molecular mechanisms involved, we aim to underscore the potential of targeting phospholipid metabolic pathways as a promising avenue for antifungal therapy. A comprehensive understanding of how membrane phospholipid composition regulates the virulence of pathogenic fungi can provide valuable insights for developing novel antifungal strategies. Full article

(This article belongs to the Special Issue Design and Mechanism of Action of Genomic-Based Antifungals)

► Show Figures

Figure 1

21 pages, 1529 KiB

Open AccessArticle

Characterization of Virulence Factors, Cellular Stress Response, and Antifungal Susceptibility Testing of Trichosporon spp. Isolated from Northeast Brazilian Patients

by Márcia Gabriele de Souza Jimenez, Matheus Firmino de Azevedo, Elaine Cristina Francisco, Ana Maria de Andrade Oliveira Boczar, Ana Carolina Barbosa Padovan, Eveline Pipolo Milan, Walicyranison Plinio da Silva Rocha and Guilherme Maranhão Chaves

J. Fungi 2025, 11(4), 255; https://doi.org/10.3390/jof11040255 - 26 Mar 2025

Abstract

Trichosporon spp. are emerging pathogens that may cause high mortality rates, specifically among immunocompromised individuals. The objectives of this study were to perform a phylogenetic analysis of Trichosporon spp. clinical isolates. We also evaluated the expression of different virulence factors in vitro. In [...] Read more.

Trichosporon spp. are emerging pathogens that may cause high mortality rates, specifically among immunocompromised individuals. The objectives of this study were to perform a phylogenetic analysis of Trichosporon spp. clinical isolates. We also evaluated the expression of different virulence factors in vitro. In addition, the isolates were grown in the presence of cell-wall and membrane stressors. The antifungal susceptibility profiling was determined. The most prevalent strains belonged to the recently described species T. austroamericanum, with 17 isolates. The other strains were identified as follows: T. asahii (n = 4), T. faecale (n = 2), and T. asteroides (n = 2). All the isolates of T. asahii, T. faecale, and T. asteroides were strong biofilm producers. Statistical analysis revealed that T. asahii strains produced more biofilm than T. austroamericanum. Higher cell surface hydrophobicity was also found for T. asahii isolates compared to T. austroamericanum counterparts. T. austroamericanum seems to be more susceptible to Congo Red, Calcofluor White, and SDS than T. asahii. It is possible to conclude that Trichosporon spp. may present peculiarities in terms of the expression of different virulence factors in vitro, besides displaying a variable susceptibility to different cellular stressors. T. faecale isolates may present high MICs to the azoles, while T. asahii against amphotericin B. Full article

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

► Show Figures

Figure 1

19 pages, 9560 KiB

Open AccessArticle

Pomegranate Woody Mycobiota Associated with Wood Decay

by Valentino Bergamaschi, Maria Teresa Valente and Rosario Muleo

J. Fungi 2025, 11(4), 254; https://doi.org/10.3390/jof11040254 - 26 Mar 2025

Abstract

The rapid expansion of pomegranate (Punica granatum L.) cultivation in central and southern Italy has revealed emerging phytosanitary challenges, including “pomegranate wood decay syndrome”, characterised by cortical cankers, wood browning, and progressive plant decline. This study investigates the fungal microbiota associated with [...] Read more.

The rapid expansion of pomegranate (Punica granatum L.) cultivation in central and southern Italy has revealed emerging phytosanitary challenges, including “pomegranate wood decay syndrome”, characterised by cortical cankers, wood browning, and progressive plant decline. This study investigates the fungal microbiota associated with symptomatic pomegranate wood using a combined approach of traditional fungal isolation and ITS2 metabarcoding analysis. Samples from two orchards in Lazio were examined, revealing a complex fungal community with a high prevalence of Neofusicoccum parvum (putative) and species belonging to the genus Diaporthe. Pathogenicity tests confirmed the role of N. parvum in causing significant wood browning, while other isolates showed variable virulence. Statistical analyses validated the pathogenicity of select isolates, with the putative Diaporthe eres (Nitschke) consistently demonstrating potential pathogenic activity across all trials. Metabarcoding identified 289 taxa, highlighting a richer fungal diversity in the symptomatic wood compared to the asymptomatic sections. Notably, Coniella granati, previously implicated in pomegranate decline, was absent in the studied orchards. The findings reveal that pomegranate wood decay is a complex syndrome driven by fungal pathogens and environmental stressors, such as low temperatures. This study highlights the value of integrative approaches for understanding and managing fungal-associated wood diseases in pomegranate orchards. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

► Show Figures

Figure 1

12 pages, 1929 KiB

Open AccessArticle

Trichoderma asperellum 22043: Inoculation Promotes Salt Tolerance of Tomato Seedlings Through Activating the Antioxidant System and Regulating Stress-Resistant Genes

by Guangyan Hu, Zhongjuan Zhao, Yanli Wei, Jindong Hu, Yi Zhou, Jishun Li and Hetong Yang

J. Fungi 2025, 11(4), 253; https://doi.org/10.3390/jof11040253 - 26 Mar 2025

Abstract

Salt stress poses a major threat to plant growth, and breeding for salt-tolerant varieties is not always successful to ameliorate this threat. In the present experiment, the effect of T. asperellum 22043 inoculation on the growth of salt-stressed tomatoes and the mechanisms by [...] Read more.

Salt stress poses a major threat to plant growth, and breeding for salt-tolerant varieties is not always successful to ameliorate this threat. In the present experiment, the effect of T. asperellum 22043 inoculation on the growth of salt-stressed tomatoes and the mechanisms by which it improves salt tolerance were investigated. It was observed that tomato plants treated with T. asperellum 22043 spore suspension under salt tress (50 and 100 mM NaCl) consistently exhibited higher seeds germination, seedling survival rate, plant height, and chlorophyll content, but lower malondialdehyde and proline contents than the plants treated without the Trichoderma. T. asperellum 22043 effectively improved the stress resistance of tomato through regulating the transcriptional levels of reactive oxygen species (ROS) scavenging enzyme gene expression to modulate the activity of ROS scavenging enzymes and the expression of the genes related to transporter and aquaporin to maintain the balance of cell Na⁺. In conclusion, T. asperellum 22043 can enhance tomato seedlings’ salt tolerance by activating the antioxidant system and regulating the expression of stress-resistant genes. Full article

(This article belongs to the Special Issue The Potential of Trichoderma, SynCom and Their Metabolites for Enhancing Crop Yield and Resistance)

► Show Figures

Figure 1

24 pages, 2826 KiB

Open AccessReview

Aspergillus fumigatus in the Food Production Chain and Azole Resistance: A Growing Concern for Consumers

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

J. Fungi 2025, 11(4), 252; https://doi.org/10.3390/jof11040252 - 26 Mar 2025

Abstract

Aspergillosis is a fungal disease caused by the inhalation of Aspergillus spores, with Aspergillus fumigatus being the primary causative agent. This thermotolerant fungus affects both immunocompetent and immunocompromised individuals, posing a significant public health concern. In recent years, the detection of A. fumigatus [...] Read more.

Aspergillosis is a fungal disease caused by the inhalation of Aspergillus spores, with Aspergillus fumigatus being the primary causative agent. This thermotolerant fungus affects both immunocompetent and immunocompromised individuals, posing a significant public health concern. In recent years, the detection of A. fumigatus in food products and production environments has raised questions about its potential role as an additional route of exposure. Furthermore, the emergence of azole-resistant strains in agricultural settings highlights the need to better understand its transmission dynamics and implications for food safety. This review explores the occurrence of A. fumigatus in crops and food products, its possible routes of contamination, and the potential link between environmental exposure to azole fungicides and resistance development. Additionally, it identifies knowledge gaps and proposes future research directions to improve risk assessment and mitigation strategies within the food production chain. Full article

(This article belongs to the Special Issue Fungal Infections: New Challenges and Opportunities, 3rd Edition)

► Show Figures

Figure 1

16 pages, 1674 KiB

Open AccessArticle

Mating-Type Analysis in Diaporthe Isolates from Soybean in Central Europe

by Behnoush Hosseini, Lena Sophia Käfer and Tobias Immanuel Link

J. Fungi 2025, 11(4), 251; https://doi.org/10.3390/jof11040251 - 25 Mar 2025

Abstract

Species of the genus Diaporthe have a mating-type system with the two mating types MAT1-1 and MAT1-2, like other ascomycetes. They can either be heterothallic, which means that any isolate only possesses one of the two mating types and needs a mating partner [...] Read more.

Species of the genus Diaporthe have a mating-type system with the two mating types MAT1-1 and MAT1-2, like other ascomycetes. They can either be heterothallic, which means that any isolate only possesses one of the two mating types and needs a mating partner for sexual reproduction, or homothallic, which means that they possess both mating types and are self-fertile. For several Diaporthe species, no sexual reproduction has been observed so far. Using PCR with primers specific to the defining genes MAT1-1-1 and MAT1-2-1, we determined the mating types of 33 isolates of Diaporthe caulivora, D. eres, D. longicolla, and D. novem from central Europe. In addition, we partially sequenced the mating-type genes of 25 isolates. We found that different D. longicolla isolates either possess MAT1-1-1 or MAT1-2-1, making the species heterothallic, which is in contrast to previous studies and the general assumption that D. longicolla only reproduces asexually. D. eres and D. novem were also found to be heterothallic. Using genomic sequence information and re-sequencing of DNA and RNA, we identified the MAT1-1-1 gene in D. caulivora and present here the full sequence of the mating-type locus of this homothallic species. Finally, we used sequence information from MAT1-1-1 and MAT1-2-1, respectively, for improved phylogenetic resolution of our isolates. Full article

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

► Show Figures

Figure 1

26 pages, 4642 KiB

Open AccessArticle

Harnessing Xylanase Potential in Thermothelomyces fergusii: Insights from Computational and Functional Analysis

by Abdul Waheed, Yi Chen, Ying Su, Yuxin Yan and Gang Liu

J. Fungi 2025, 11(4), 250; https://doi.org/10.3390/jof11040250 - 25 Mar 2025

Abstract

Xylanases are crucial for the breakdown of hemicellulose, enabling the conversion of lignocellulosic biomass into fermentable sugars for biofuels and other industrial applications. For the first time, we investigated the biochemical and genetic characteristics of 22 xylanase genes from Thermothelomyces fergusii within glycoside hydrolase [...] Read more.

Xylanases are crucial for the breakdown of hemicellulose, enabling the conversion of lignocellulosic biomass into fermentable sugars for biofuels and other industrial applications. For the first time, we investigated the biochemical and genetic characteristics of 22 xylanase genes from Thermothelomyces fergusii within glycoside hydrolase (GH) families GH10, GH11, and GH43. Xylanase genes structural diversity clustered the phylogenetic tree into GH10, GH11, GH43-I, and GH43-II groups. Structural analysis revealed that all TfGH10 and TfGH11 genes contained conserved GH domains, with CBM1 present in TfGH10-5 and TfGH11-4. Secondary domains, including CBM35, CBM42, and CBM91, were found in the GH43 gene family. The presence of key glutamic (Glu) and aspartic (Asp) residues in active sites is essential for substrate binding and catalysis. RT-qPCR analysis revealed substrate-dependent gene expression, with peak upregulation on day three in beechwood xylan (BWX) cultures and day two in corncob xylan (CCX) and rice straw (RS) cultures. Consistent with these findings, enzymatic assays demonstrated the highest xylanase activity in BWX-induced cultures, followed by RS and CCX, underscoring the differential regulation of these enzymes in response to distinct hemicellulosic substrates. These findings provide valuable insights into the structural, functional, and regulatory mechanisms of T. fergusii xylanases, facilitating their industrial application. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

► Show Figures

Figure 1

9 pages, 1247 KiB

Open AccessBrief Report

A Barcoded ITS Primer-Based Nanopore Sequencing Protocol for Detection of Alternaria Species and Other Fungal Pathogens in Diverse Plant Hosts

by Vladimer Baramidze, Luca Sella, Tamar Japaridze, Nino Dzotsenidze, Daviti Lamazoshvili, Nino Abashidze, Maka Basilidze and Giorgi Tomashvili

J. Fungi 2025, 11(4), 249; https://doi.org/10.3390/jof11040249 - 25 Mar 2025

Abstract

Alternaria is a genus that contains several important plant pathogens affecting nearly 400 plant species worldwide, including economically important crops such as grapes, citrus, and ornamental plants. Rapid, scalable, and efficient methods of pathogen detection are crucial for managing plant diseases and ensuring [...] Read more.

Alternaria is a genus that contains several important plant pathogens affecting nearly 400 plant species worldwide, including economically important crops such as grapes, citrus, and ornamental plants. Rapid, scalable, and efficient methods of pathogen detection are crucial for managing plant diseases and ensuring agricultural productivity. Current amplicon sequencing protocols for Alternaria detection often require the enzymatic barcoding of amplicons, increasing hands-on time, cost, and contamination risk. We present a proof-of-concept study using custom barcoded primers, combining universal primers targeting ITS1 and ITS2 regions (600 bp) coupled with Oxford Nanopore Technologies (ONT) barcode sequences. Sequencing was performed on infected grapevine, mandarin orange, thuja, and maple tree samples. In total, we analyzed 38 samples using qPCR; 8 tested positive for Alternaria, which were sequenced using a newly developed protocol. As a result, we could identify Alternaria in every positive sample, and besides the pathogen of interest, we could identify the associated mycobiome. This protocol reduces hands-on time and cost, making a significant advancement over current sequencing methods. Future work will focus on optimizing our approach for high-throughput sequencing of up to 96 samples and determining the method’s applicability for large-scale mycobiome analysis. Full article

(This article belongs to the Collection Advances in Plant Pathogenic Fungi: Diagnosis, Biological Control, and Eco-Sustainable Formulations)

► Show Figures

Figure 1

10 pages, 1513 KiB

Open AccessCase Report

First Report of Trichophyton indotineae Infection in Hungary

by Zoltán Tóth, Beatrix Ványai, Renátó Kovács, Ágnes Jakab, Andrea Szegedi, Bence Balázs and László Majoros

J. Fungi 2025, 11(4), 248; https://doi.org/10.3390/jof11040248 - 25 Mar 2025

Abstract

Trichophyton indotineae is associated with difficult-to-treat, often extensive dermatophytosis and resistance to the commonly used antifungal agents. Successful therapy often necessitates higher than usual doses of systemic therapy for prolonged periods. The spread of this species has gained much attention lately, as several [...] Read more.

Trichophyton indotineae is associated with difficult-to-treat, often extensive dermatophytosis and resistance to the commonly used antifungal agents. Successful therapy often necessitates higher than usual doses of systemic therapy for prolonged periods. The spread of this species has gained much attention lately, as several European and other Western hemisphere countries have recently reported their first respective cases or increasing numbers of them. Until recently, this species was not described in Hungary. Here, we report a case caused by this species in a patient with a travel history to an endemic region. The isolate was identified preliminarily by MALDI-TOF mass spectrometry and confirmed by DNA sequencing; furthermore, it was subject to phenotypic antifungal susceptibility testing by broth microdilution to fluconazole, voriconazole, posaconazole, itraconazole, and terbinafine. According to the susceptibility results, the isolate was wild type to all tested agents, including terbinafine which was in line with the sequencing data, and with the uncommon excellent therapeutic response to topical allylamine treatment. This case also further confirms the applicability of the MSI-2 database for the rapid identification of T. indotineae in routine clinical microbiology laboratories as a cost-effective and simple method. Full article

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

► Show Figures

Figure 1

14 pages, 1487 KiB

Open AccessArticle

Can Metarhizium anisopliae Reduce the Feeding of the Neotropical Brown Stink Bug, Euschistus heros (Fabricius, 1798), and Its Damage to Soybean Seeds?

by André Cirilo de Sousa Almeida, Mayara Alves Rodrigues, Heloiza Alves Boaventura, Angélica Siqueira Vieira, José Francisco Arruda e Silva, Flávio Gonçalves de Jesus and Eliane Dias Quintela

J. Fungi 2025, 11(4), 247; https://doi.org/10.3390/jof11040247 - 25 Mar 2025

Abstract

The fungus Metarhizium anisopliae is under development as a bioinsecticide for Euschistus heros. To further elucidate the effect of this fungus on E. heros behavior, we monitored the feeding activities of adults treated with the fungus at 1 × 10⁸ conidia [...] Read more.

The fungus Metarhizium anisopliae is under development as a bioinsecticide for Euschistus heros. To further elucidate the effect of this fungus on E. heros behavior, we monitored the feeding activities of adults treated with the fungus at 1 × 10⁸ conidia mL⁻¹ on soybean in the pod-filling stage (R5) through electropenetrography (EPG) AC-DC. We also determined the virulence of M. anisopliae to adults and its damage to soybean seeds. M. anisopliae displayed high levels of virulence to adults even at low concentrations of 5 × 10⁶ conidia mL⁻¹ (98% mortality). E. heros females were more susceptible to M. anisopliae than males, exhibiting a lower LT₅₀ for mycosed adults (7.1 and 9.7 days, respectively). The EPG experiment showed that fungus-treated adults spent significantly less time on probing activities (reduced by 86% at day four and ceased at day five) than untreated insects, and the number of waveform events per insect significantly decreased. This information is valuable for managing stink bugs at the field level, as it shows that even though the insect is alive, its feeding is compromised, consequently minimizing the damage inflicted to the crop. This study paves the way for further research employing entomopathogenic fungi in pest control. Full article

(This article belongs to the Special Issue Fungi and Insect Interactions: Pathogenicity, Immune Defenses and Biocontrol)

► Show Figures

Figure 1

39 pages, 8285 KiB

Open AccessArticle

The Three-Dimensional Structure of the Genome of the Dark Septate Endophyte Exophiala tremulae and Its Symbiosis Effect on Alpine Meadow Plant Growth

by Chu Wu, Junjie Fan, Die Hu, Honggang Sun, Guangxin Lu, Yun Wang and Yujie Yang

J. Fungi 2025, 11(4), 246; https://doi.org/10.3390/jof11040246 - 24 Mar 2025

Abstract

The establishment of artificial grassland is a good pathway for resolving serious social and economic problems in the Qinghai–Tibet Plateau. Some beneficial indigenous microbes may be used to improve productivity in artificial grassland. The genome of the indigenous dark septate fungus, Exophiala tremulae [...] Read more.

The establishment of artificial grassland is a good pathway for resolving serious social and economic problems in the Qinghai–Tibet Plateau. Some beneficial indigenous microbes may be used to improve productivity in artificial grassland. The genome of the indigenous dark septate fungus, Exophiala tremulae CICC2537, was sequenced and assembled at the chromosome level using the PacBio sequencing platform, with the assistance of the Hi-C technique for scaffolding, and its 3D genome structures were investigated. The genome size of E. tremulae is 51.903848 Mb, and it contains eight chromosomes. A total of 12,277 protein-coding genes were predicted, and 11,932 genes (97.19%) were annotated. As for the distribution of exon and intron number and the distribution of gene GC and CDS GC, E. tremulae showed similar distribution patterns to the other investigated members of the genus Exophiala. The analysis of carbohydrate-active enzymes showed that E. tremulae possesses the greatest number of enzymes with auxiliary activities and the lowest number of enzymes with carbohydrate-binding modules among the investigated fungi. The total number of candidate effector proteins was 3337, out of which cytoplasmic and apoplastic effector proteins made up 3100 and 163, respectively. The whole genome of E. tremulae contained 40 compartment As and 76 compartment Bs, and there was no significant difference in GC content in its compartment As and Bs. The whole genome of E. tremulae was predicted to contain 155 topologically associating domains (TADs), and their average length was 250,000 bp, but there were no significant differences in the numbers of genes and the GC content per bin localized within the boundaries and interiors of TADs. Comparative genome analysis showed that E. tremulae diverged from Exophiala mesophila about 34.1 (30.0–39.1) Myr ago, and from Exophiala calicioides about 85.6 (76.1–90.6) Myr ago. Compared with all the investigated fungi, the numbers of contraction and expansion gene families in the E. tremulae genome were 13 and 89, respectively, and the numbers of contraction and expansion genes were 14 and 670, respectively. Our work provides a basis for the use of the dark septate fungus in alpine artificial grassland and further research into its symbiosis mechanisms, which may improve the growth of plant species used in the Qinghai–Tibet Plateau. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

► Show Figures

Figure 1

Journal Description

Journal of Fungi

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI