Journal of Fungi

34 pages, 50154 KiB

Open AccessArticle

Recticladiella inexpectata gen. et sp. nov. (Nectriaceae) Pathogenic to Native Cinnamomum camphora (Lauraceae) Trees in Southeastern China

by Fangying Han and Shuaifei Chen

J. Fungi 2024, 10(12), 894; https://doi.org/10.3390/jof10120894 - 23 Dec 2024

Viewed by 447

Abstract

The ascomycete family Nectriaceae includes soil-borne saprobes, plant pathogens and human pathogens, biodegraders, and biocontrol agents for industrial and commercial applications. Cinnamomum camphora is a native tree species that is widely planted in southern China for landscaping purposes. During a routine survey of [...] Read more.

The ascomycete family Nectriaceae includes soil-borne saprobes, plant pathogens and human pathogens, biodegraders, and biocontrol agents for industrial and commercial applications. Cinnamomum camphora is a native tree species that is widely planted in southern China for landscaping purposes. During a routine survey of Eucalyptus diseases in southern China, disease spots were frequently observed on the leaves of Ci. camphora trees planted close to Eucalyptus. The asexual fungal structures on the leaf spots presented morphological characteristics typical of the Nectriaceae. The aim of this study is to identify these fungi and determine their pathogenic effect on Ci. camphora. Of the isolates obtained from 13 sites in the Fujian and Guangdong Provinces, 54 isolates were identified based on the DNA phylogeny of the tef1, tub2, cmdA, and his3 regions and morphological features. Two isolates were identified as Calonectria crousiana, and fifty-two isolates were described as a new genus, including a single species. These fungi were named Recticladiella inexpectata gen. et sp. nov. The identification of the new genus was based on strong DNA base differences in each of the four sequenced gene regions. The conidiophores of this fungus had several avesiculate stipe extensions tapering toward a straight, occasionally slightly curved terminal cell, distinguishing it from other phylogenetically close Nectriaceae genera. The results indicate that R. inexpectata is distributed in wide geographic regions in southern China. Inoculation showed that R. inexpectata and Ca. crousiana caused lesions on the leaves of Ci. camphora seedlings within 6 days of inoculation, indicating that they are pathogenic to native Ci. camphora in China. Full article

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

► Show Figures

Figure 1

69 pages, 16833 KiB

Open AccessArticle

Contributions to the Inocybe umbratica–paludinella (Agaricales) Group in China: Taxonomy, Species Diversity, and Molecular Phylogeny

by Xin Chen, Wen-Jie Yu, Tolgor Bau, P. Brandon Matheny, Egon Horak, Yu Liu, Li-Wu Qin, Li-Ping Tang, Yu-Peng Ge, Tie-Zhi Liu and Yu-Guang Fan

J. Fungi 2024, 10(12), 893; https://doi.org/10.3390/jof10120893 - 23 Dec 2024

Viewed by 489

Abstract

Inocybe is the largest genus in the family Inocybaceae, with approximately 1000 species worldwide. Basic data on the species diversity, geographic distribution, and the infrageneric framework of Inocybe are still incomplete because of the intricate nature of this genus, which includes numerous [...] Read more.

Inocybe is the largest genus in the family Inocybaceae, with approximately 1000 species worldwide. Basic data on the species diversity, geographic distribution, and the infrageneric framework of Inocybe are still incomplete because of the intricate nature of this genus, which includes numerous unrecognized taxa that exist around the world. A multigene phylogeny of the I. umbratica–paludinella group, initially designated as the “I. angustifolia subgroup”, was conducted using the ITS-28S-rpb2 nucleotide datasets. The seven species, I. alabamensis, I. angustifolia, I. argenteolutea, I. olivaceonigra, I. paludinella, I. subangustifolia, and I. umbratica, were confirmed as members of this species group. At the genus level, the I. umbratica–paludinella group is a sister to the lineage of the unifying I. castanea and an undescribed species. Inocybe sect. Umbraticae sect. nov. was proposed to accommodate species in the I. umbratica–paludinella group and the I. castanea lineage. This section now comprises eight documented species and nine new species from China, as described in this paper. Additionally, new geographical distributions of I. angustifolia and I. castanea in China are reported. The nine new species and I. angustifolia, I. castanea, I. olivaceonigra, and I. umbratica are described in detail and illustrated herein with color plates based on Chinese materials. A global key to 17 species in the section Umbraticae is provided. The results of the current study provide a more detailed basis for the accurate identification of species in the I. umbratica-paludinella group and a better understanding of their phylogenetic placement. Full article

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

► Show Figures

Figure 1

10 pages, 2047 KiB

Open AccessReview

From Random Perturbation to Precise Targeting: A Comprehensive Review of Methods for Studying Gene Function in Monascus Species

by Yunxia Gong, Shengfa Li, Deqing Zhao, Xi Yuan, Yin Zhou, Fusheng Chen and Yanchun Shao

J. Fungi 2024, 10(12), 892; https://doi.org/10.3390/jof10120892 - 23 Dec 2024

Viewed by 479

Abstract

Monascus, a genus of fungi known for its fermentation capability and production of bioactive compounds, such as Monascus azaphilone pigments and Monacolin K, have received considerable attention because of their potential in biotechnological applications. Understanding the genetic basis of these metabolic pathways [...] Read more.

Monascus, a genus of fungi known for its fermentation capability and production of bioactive compounds, such as Monascus azaphilone pigments and Monacolin K, have received considerable attention because of their potential in biotechnological applications. Understanding the genetic basis of these metabolic pathways is crucial for optimizing the fermentation and enhancing the yield and quality of these products. However, Monascus spp. are not model fungi, and knowledge of their genetics is limited, which is a great challenge in understanding physiological and biochemical phenomena at the genetic level. Since the first application of particle bombardment to explore gene function, it has become feasible to link the phenotypic variation and genomic information on Monascus strains. In recent decades, accurate gene editing assisted by genomic information has provided a solution to analyze the functions of genes involved in the metabolism and development of Monascus spp. at the molecular level. This review summarizes most of the genetic manipulation tools used in Monascus spp. and emphasizes Agrobacterium tumefaciens-mediated transformation and nuclease-guided gene editing, providing comprehensive references for scholars to select suitable genetic manipulation tools to investigate the functions of genes of interest in Monascus spp. Full article

(This article belongs to the Special Issue Monascus spp. and Their Relative Products)

► Show Figures

Figure 1

18 pages, 11980 KiB

Open AccessArticle

Role of the Anaphase-Promoting Complex Activator Cdh1 in the Virulence of Cryptococcus neoformans

by Qiu-Hong Liao, Lian-Tao Han, Meng-Ru Guo, Cheng-Li Fan and Tong-Bao Liu

J. Fungi 2024, 10(12), 891; https://doi.org/10.3390/jof10120891 - 23 Dec 2024

Viewed by 475

Abstract

Cryptococcus neoformans is a globally distributed human fungal pathogen that can cause cryptococcal meningitis with high morbidity and mortality. In this study, we identified an anaphase-promoting complex (APC) activator, Cdh1, and examined its impact on the virulence of C. neoformans. Our subcellular [...] Read more.

Cryptococcus neoformans is a globally distributed human fungal pathogen that can cause cryptococcal meningitis with high morbidity and mortality. In this study, we identified an anaphase-promoting complex (APC) activator, Cdh1, and examined its impact on the virulence of C. neoformans. Our subcellular localization analysis revealed that Cdh1 is situated in the nucleus of C. neoformans. Disrupting or overexpressing the CDH1 gene caused abnormal capsule formation in C. neoformans. The cdh1Δ mutant displayed slight sensitivity when grown at 37 °C, indicating that Cdh1 plays a role in maintaining the growth of C. neoformans at 37 °C. A fungal virulence assay showed that Cdh1 is closely associated with the virulence of C. neoformans, and both the cdh1Δ mutant and CDH1^OE overexpression strains significantly diminished the virulence of C. neoformans. The Cryptococcus–macrophage interaction assay revealed that both the cdh1∆ mutant and the CDH1^OE strains had significantly lower proliferation ability inside macrophages. Furthermore, the infection of the cdh1Δ mutant significantly activated neutrophil recruitment, as well as Th2 and Th17 immune responses, in lung tissue. In summary, our findings indicate that Cdh1 is crucial for producing virulence factors and fungal virulence in C. neoformans. The findings of this study can offer valuable insights and form the basis for further study of the regulatory mechanisms governing the pathogenicity of C. neoformans, potentially leading to the development of novel therapeutic strategies. Full article

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

► Show Figures

Figure 1

17 pages, 4567 KiB

Open AccessArticle

Enhancing Digestibility and Intestinal Peptide Release of Pleurotus eryngii Protein: An Enzymatic Approach

by Dandan Wang, Meng Zhang, Jianing Wan, Haiquan Liu, Ying Wang, Ruiheng Yang, Yingying Wu, Dapeng Bao, Hongyu Chen, Gen Zou and Yong Zhao

J. Fungi 2024, 10(12), 890; https://doi.org/10.3390/jof10120890 - 23 Dec 2024

Viewed by 491

Abstract

Pleurotus eryngii is a tasty and low-calorie mushroom containing abundant high-quality protein. This study aims to improve the digestibility of P. eryngii protein (PEP) and hence to facilitate its development as a healthy alternative protein. The extracted PEP was pretreated with 1000–5000 U [...] Read more.

Pleurotus eryngii is a tasty and low-calorie mushroom containing abundant high-quality protein. This study aims to improve the digestibility of P. eryngii protein (PEP) and hence to facilitate its development as a healthy alternative protein. The extracted PEP was pretreated with 1000–5000 U of papain, neutral protease and alkaline protease. The Chyme collected from in vitro simulated gastrointestinal digestion was analyzed by fluorescence microscopy and protein particle analyzer, and the endpoint profiles of peptides and amino acids were determined by UHPLC-MS/MS and NanoLC-MS/MS. The particle size curve and fluorescence microscopy images jointly supported that protease hydrolysis improved decomposition and dispersion of PEP during digestion, particularly in the gastric phase. The impact on Zeta potential was minimal. Proteases effectively increased the abundance of amino acids after digestion, particularly L-isomer Lys and Arg Maximum release was achieved when pretreated with 5000 U of alkaline protease, reaching 7.54 times that of control. Pretreatments by proteases also notably increased digestive yields of 16,736–19,870 peptides, with the maximum reaching 1.70 times that of the control, which mainly consisted of small peptides composed of 7–15 amino acids with molecular weight below 800 Da. The findings indicated that protease hydrolysis, especially pretreatment with 5000 U of alkaline protease, effectively enhanced the digestibility of PEP, which shed light on providing enzymatic approaches for improving bioavailability and developing healthy fungal proteins. Full article

(This article belongs to the Special Issue Innovative Applications and Biomanufacturing of Fungi)

► Show Figures

Figure 1

17 pages, 7903 KiB

Open AccessArticle

Characterization of Endofungal Bacteria and Their Role in the Ectomycorrhizal Fungus Helvella bachu

by Caihong Wei, Mengqian Liu, Guoliang Meng, Miao Wang, Xin Zhou, Jianping Xu, Jianwei Hu, Lili Zhang and Caihong Dong

J. Fungi 2024, 10(12), 889; https://doi.org/10.3390/jof10120889 - 23 Dec 2024

Viewed by 623

Abstract

Helvella bachu, an ectomycorrhizal fungus, forms a symbiotic relationship with Populus euphratica, a rare and endangered species crucial to desert riparian ecosystems. In this study, endofungal bacteria (EFBs) within the fruiting bodies of H. bachu were confirmed by a polyphasic approach, [...] Read more.

Helvella bachu, an ectomycorrhizal fungus, forms a symbiotic relationship with Populus euphratica, a rare and endangered species crucial to desert riparian ecosystems. In this study, endofungal bacteria (EFBs) within the fruiting bodies of H. bachu were confirmed by a polyphasic approach, including genomic sequencing, real-time quantitative PCR targeting the 16S rRNA gene, full-length and next-generation sequencing (NGS) of the 16S rRNA gene, and culture methods. The genera Stenotrophomonas, Variovorax, Acidovorax, and Pedobacter were abundant in the EFBs of fruiting bodies associated with three Populus hosts and were consistently present across different developmental stages. Notably, S. maltophilia and V. paradoxus were detected in high abundance, as revealed by full-length 16S rRNA sequencing, with S. maltophilia also isolated by culture methods. KO-pathway analysis indicated that pathways related to primary, secondary, and energy metabolism were predominantly enriched, suggesting these bacteria may promote H. bachu growth by producing essential compounds, including sugars, proteins, and vitamins, and secondary metabolites. This study confirmed the presence of EFBs in H. bachu and provided the first comprehensive overview of their structure, functional potential, and dynamic changes throughout fruiting body maturation, offering valuable insights for advancing the artificial domestication of this species. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

► Show Figures

Figure 1

17 pages, 11981 KiB

Open AccessArticle

Arthrobotrys mendozadegivensis sp. nov. (Fungi: Orbiliales) from Mexico: Predatory Activity and Nematocidal Activity of Its Liquid Culture Filtrates Against Haemonchus contortus (Nematoda: Trichostrongylidae)

by Enrique Gutiérrez-Medina, Pedro Mendoza-de Gives, Gustavo Pérez-Anzúrez, Antonio Colinas-Picazo, Génesis Andrea Bautista-García, Miguel Ángel Alonso-Díaz, Elke von Son-de Fernex and María Eugenia López-Arellano

J. Fungi 2024, 10(12), 888; https://doi.org/10.3390/jof10120888 - 22 Dec 2024

Viewed by 2352

Abstract

During the isolation, identification, and assessment of nematode-trapping fungi (NTF) against nematodes, we discovered an unusual fungus in decaying wood from Morelos State, Mexico. This isolate exhibited some characteristics similar to those of the Arthrobotrys genus; however, we found that it did not [...] Read more.

During the isolation, identification, and assessment of nematode-trapping fungi (NTF) against nematodes, we discovered an unusual fungus in decaying wood from Morelos State, Mexico. This isolate exhibited some characteristics similar to those of the Arthrobotrys genus; however, we found that it did not match any previously reported species within this genus after conducting morphological and phylogenetic analyses using the ITS, TEF, and RPB2 regions. This new species displays conidiophores with two or three stems emerging from the same initial site and conidiophores with only a single stem and aerial thickened hyphae from which single conidiophores emerge, forming 3D adhesive nets. The conidia, which have one or two septa, range from obovoid to ellipsoidal, crowned by four to six conidia. This report provides evidence that this species has not been described before, and we hereby introduce it as a new species, naming it Arthrobotrys mendozadegivensis. This species displayed a predatory activity of 76.92%, and its liquid culture filtrates in Sweet Potato Dextrose Broth and Czapek–Dox Broth were effective in killing 40.90% and 34.91% of Haemonchus contortus larvae, respectively. This study provides information about a previously unreported species of nematophagous fungus, which is important for systematics and has potential biotechnological applications against nematodes that affect the livestock industry. Full article

(This article belongs to the Special Issue Role of Nematophagous Fungi in Veterinary Parasitology)

► Show Figures

Figure 1

19 pages, 3951 KiB

Open AccessArticle

Geographical Distribution, Host Range and Genetic Diversity of Fusarium oxysporum f. sp. cubense Causing Fusarium Wilt of Banana in India

by Raman Thangavelu, Hadimani Amaresh, Muthukathan Gopi, Murugan Loganathan, Boopathy Nithya, Perumal Ganga Devi, Chelliah Anuradha, Anbazhagan Thirugnanavel, Kalyansing Baburao Patil, Guy Blomme and Ramasamy Selvarajan

J. Fungi 2024, 10(12), 887; https://doi.org/10.3390/jof10120887 - 21 Dec 2024

Viewed by 903

Abstract

Fusarium wilt of banana is a major production constraint in India, prompting banana growers to replace bananas with less remunerative crops. Effective disease management practices thus need to be developed and implemented to prevent further spread and damage caused by Fusarium oxysporum f. [...] Read more.

Fusarium wilt of banana is a major production constraint in India, prompting banana growers to replace bananas with less remunerative crops. Effective disease management practices thus need to be developed and implemented to prevent further spread and damage caused by Fusarium oxysporum f. sp. cubense (Foc), the cause of Fusarium wilt. Currently, knowledge of disease incidence, affected varieties, and the geographical spread of Foc races in India are only scantily available. An extensive field survey was conducted in 53 districts of 16 major banana-growing states of and one union territory of India that covered both tropical and subtropical regions. Disease incidence ranged from 0 to 95% on farms, with Cavendish bananas (AAA) most affected. No Fusarium wilt symptoms due to Foc R1 were observed in Nendran (AAB) or Red Banana (AAA) in South India. During the survey, 293 Foc isolates were collected from Cavendish, Pisang Awak (ABB), Silk (AAB), Monthan (ABB), Neypoovan (AB), and Mysore (AAB) bananas. Isolate diversity was assessed through Vegetative Compatibility Group (VCG) analyses, sequencing of EF1α gene sequences, phylogenetic analyses, and characterisation by SIX gene composition. Thirteen VCGs were identified, of which VCGs 0124, 0125, 01220, and 01213/16 were dominant and infected Cavendish bananas. Phylogenetic analysis divided the Indian Foc isolates into race 1 (R1), subtropical race 4 (STR4), and tropical race 4 (TR4). Secreted in Xylem (SIX) gene analyses indicated that the effector genes SIX4 and SIX6 were present in the VCGs 0124, 0124/5, 0125, and 01220 of race 1, SIX7 was present only in Foc STR4, and SIX8 was found only in Foc R4 (TR4 and STR4) isolates. Insights into the geographical distribution of Foc races, and their interactions with banana varieties, can guide integrated disease management intervention strategies across India. Full article

► Show Figures

Figure 1

19 pages, 4807 KiB

Open AccessArticle

Optimization of Protoplast Preparation Conditions in Lyophyllum decastes and Transcriptomic Analysis Throughout the Process

by Xiaobin Li, Ying Qin, Yufei Kong, Samantha Chandranath Karunarathna, Yunjiang Liang and Jize Xu

J. Fungi 2024, 10(12), 886; https://doi.org/10.3390/jof10120886 - 21 Dec 2024

Viewed by 714

Abstract

Protoplasts are essential tools for genetic manipulation and functional genomics research in fungi. This study systematically optimized protoplast preparation conditions and examined transcriptional changes throughout the preparation and regeneration processes to elucidate the molecular mechanisms underlying the formation and regeneration of protoplasts in [...] Read more.

Protoplasts are essential tools for genetic manipulation and functional genomics research in fungi. This study systematically optimized protoplast preparation conditions and examined transcriptional changes throughout the preparation and regeneration processes to elucidate the molecular mechanisms underlying the formation and regeneration of protoplasts in Lyophyllum decastes. The results indicated an optimal protoplast yield of 5.475 × 10⁶ cells/mL under conditions of fungal age at 10 days, digestion time of 2.25 h, enzyme concentration of 2%, and digestion temperature of 28 °C. The Z5 medium supplemented with L. decastes mycelial extract achieved a high regeneration rate of 2.86. RNA-seq analysis revealed 2432 differentially expressed genes (DEGs) during protoplast formation and 5825 DEGs during regeneration. Casein kinase I, cytochrome P450 (CYP52), and redox-regulated input receptor (PEX5) were significantly upregulated during the protoplast stage, while β-1,3-glucan synthase (SKN1), chitin synthase (CHS2), hydrophobin-1, and hydrophobin-2 showed significant upregulation during the protoplast regeneration phase. These findings provide a reference for the efficient preparation and regeneration of protoplasts and offer new insights into the molecular mechanisms of protoplast formation and cell wall regeneration in fungi. Full article

(This article belongs to the Special Issue Current Trends in Mycological Research in Southeast Asia)

► Show Figures

Figure 1

14 pages, 1911 KiB

Open AccessArticle

Potential of Streptomyces rochei G-6 for Biocontrol of Cucumber Wilt Disease and Growth Enhancement

by Chengyu Zhu, Xin Li, Yan Gao, Xueying Yang, Yuliang Gao and Kuihua Li

J. Fungi 2024, 10(12), 885; https://doi.org/10.3390/jof10120885 - 20 Dec 2024

Viewed by 540

Abstract

Cucumber wilt disease, caused by Fusarium oxysporum f. sp. cucumerinum (FOC), is a major threat to cucumber production, especially in greenhouses. This study used a fermentation product derived from a new strain of Streptomyces rochei (G-6) to investigate the potential for biocontrol of [...] Read more.

Cucumber wilt disease, caused by Fusarium oxysporum f. sp. cucumerinum (FOC), is a major threat to cucumber production, especially in greenhouses. This study used a fermentation product derived from a new strain of Streptomyces rochei (G-6) to investigate the potential for biocontrol of cucumber wilt disease and the effect on promoting cucumber growth. In the first experiment, the inhibitory effect of S. rochei G-6 fermentation product (SGFP) on FOC growth was evaluated, then the effect of SGFP on wilt incidence and severity, as well as cucumber growth, antioxidant system, and soil nutrient conversion capacity were investigated. The results showed that SGFP inhibited FOC growth by 85.3% in the antimicrobial experiment. In the potting experiment, the incidence rate in the FOC group reached 88.7%, but it was only 56.0% in the SGFP1 group and 64.7% in the SGFP2 group, indicating the efficient inhibitory effect of SGFP on cucumber wilt, with the biocontrol effect of SGFP1 being higher than that of SGFP2. In addition, the disease index decreased significantly (p < 0.05) in both SGFP treatments, which was significantly (p < 0.05) lower in the SGFP1 group than in the SGFP2 group, indicating that pre-treatment was better than post-treatment in reducing the disease severity. In addition, SGFP promoted the growth of cucumber seedlings, as indicated by indicators related to the growth of aboveground and underground parts. Furthermore, the activities of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) in the cucumber seedlings increased after SGFP treatment and the malondialdehyde level was decreased, indicating a reduction in oxidative stress. SGFP also improved the soil nutrient conversion capacity by increasing the activities of urease, phosphatase, and sucrase, which may enhance nutrient uptake by cucumber seedling. The findings of this study suggest that SGFP is an effective biocontrol agent against cucumber wilt and also promotes cucumber growth by regulating the antioxidant system and soil environment, and its application is a promising solution to reduce wilt incidence in cucumber production. Full article

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

► Show Figures

Figure 1

11 pages, 416 KiB

Open AccessArticle

Epidemiology, Clinical, Radiological and Biological Characteristics, and Outcomes of Mucormycosis: A Retrospective Study at a French University Hospital

by Tom Cartau, Sylvain Chantepie, Angélique Thuillier-Lecouf, Bénédicte Langlois and Julie Bonhomme

J. Fungi 2024, 10(12), 884; https://doi.org/10.3390/jof10120884 - 19 Dec 2024

Viewed by 665

Abstract

Purpose: Mucormycosis is a rare but emerging and life-threatening infection caused by environmental mold, with a mortality rate of 30–70% despite progress in management. A better understanding could improve its management. Method: We conducted a single-center retrospective study of all cases of mucormycosis [...] Read more.

Purpose: Mucormycosis is a rare but emerging and life-threatening infection caused by environmental mold, with a mortality rate of 30–70% despite progress in management. A better understanding could improve its management. Method: We conducted a single-center retrospective study of all cases of mucormycosis observed over a decade at the University Hospital of Caen. Results: Between 2014 and 2024, 18 cases of mucormycosis were identified, predominantly in males (n = 11, 65%). Most patients had hematological malignancies (n = 16, 89%). Seven cases were proven, and eleven were classified as probable. The main locations of infection were pulmonary (n = 12, 67%). Since 2021, we have observed an increase in the number of cases, rising from three between 2014 and 2021 to fifteen between 2021 and 2024. Among the 12 patients with pulmonary mucormycosis, all presented with fever except 1, and 67% required oxygen therapy. Chest computed tomography scans revealed an inverse halo sign in one-third of the patients. The first-line treatment consisted of amphotericin B in seventeen patients, posaconazole in one patient, and isavuconazole in one patient. Surgery was performed on seven patients. In cases of cutaneous mucormycosis, all patients underwent surgery, and none died within three months after the diagnosis. Overall, the three-month mortality rate was 39%. Surgical management was associated with a reduction in mortality (0% vs. 64%, p = 0.013). Conclusions: This study highlights the role of PCR for early diagnosis and the key role of surgery in improving clinical outcomes while underscoring the need for better-adapted therapeutic protocols for these rare infections. Full article

► Show Figures

Figure 1

17 pages, 3842 KiB

Open AccessArticle

Global Analysis of microRNA-like RNAs Reveals Differential Regulation of Pathogenicity and Development in Fusarium oxysporum HS2 Causing Apple Replant Disease

by Ruxin Zhao, Xiangmin Suo, Xianglong Meng, Yanan Wang, Pengbo Dai, Tongle Hu, Keqiang Cao, Shutong Wang and Bo Li

J. Fungi 2024, 10(12), 883; https://doi.org/10.3390/jof10120883 - 19 Dec 2024

Viewed by 694

Abstract

This study investigated the expression profiles of microRNA-like RNAs (milRNAs) in Fusarium oxysporum HS2 (FoHS2), a key pathogen causing Apple replant disease (ARD), across spore to mycelium formation stages. Using small RNA sequencing (sRNA-seq) and bioinformatics, we identified and analyzed milRNAs, [...] Read more.

This study investigated the expression profiles of microRNA-like RNAs (milRNAs) in Fusarium oxysporum HS2 (FoHS2), a key pathogen causing Apple replant disease (ARD), across spore to mycelium formation stages. Using small RNA sequencing (sRNA-seq) and bioinformatics, we identified and analyzed milRNAs, revealing their targeting of 2364 mRNAs involved in 20 functional categories, including metabolic and cellular processes, based on gene ontology (GO) analysis. An analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these mRNAs are related to carbohydrate and amino acid metabolism pathways. Notably, the highest number of differentially or specifically expressed milRNAs (DEmilRNAs/SEmilRNAs) was found during the spore stage, with FoHS2-milR19 targeting genes encoding histone acetyltransferases, methyltransferases, and cell wall-degrading enzymes (CWDEs), which are crucial for growth, development, and pathogenicity. We validated the reliability of our sRNA-seq data and the expression of target genes using stem-loop RT-PCR and qRT-PCR. Our results highlight the stage-specific expression of milRNAs in FoHS2, particularly in the spore stage, suggesting a key role in regulating host life activities and providing a theoretical basis for developing RNA-based pesticides to control ARD. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

► Show Figures

Figure 1

19 pages, 17567 KiB

Open AccessArticle

Whole-Genome Sequencing and Genome Annotation of Pathogenic Elsinoë batatas Causing Stem and Foliage Scab Disease in Sweet Potato

by Yuan Xu, Yuqing Liu, Yihan Wang, Yi Liu and Guopeng Zhu

J. Fungi 2024, 10(12), 882; https://doi.org/10.3390/jof10120882 - 18 Dec 2024

Viewed by 770

Abstract

A pathogen strain responsible for sweet potato stem and foliage scab disease was isolated from sweet potato stems. Through a phylogenetic analysis based on the rDNA internal transcribed spacer (ITS) region, combined with morphological methods, the isolated strain was identified as Elsinoë batatas. [...] Read more.

A pathogen strain responsible for sweet potato stem and foliage scab disease was isolated from sweet potato stems. Through a phylogenetic analysis based on the rDNA internal transcribed spacer (ITS) region, combined with morphological methods, the isolated strain was identified as Elsinoë batatas. To comprehensively analyze the pathogenicity of the isolated strain from a genetic perspective, the whole-genome sequencing of E. batatas HD-1 was performed using both the PacBio and Illumina platforms. The genome of E. batatas HD-1 is about 26.31 Mb long in 167 scaffolds, with a GC content of 50.81%, and 7898 protein-coding genes, 131 non-coding RNAs, and 1954 interspersed repetitive sequences were predicted. Functional annotation revealed that 408 genes encode virulence factors involved in plant disease (DFVF—Plant). Notably, twenty-eight of these virulence genes encode secretory carbohydrate-active enzymes (CAZymes), including two endo-1,4-β-xylanase genes and seven cutinase genes, which suggested that endo-1,4-β-xylanase and cutinase play a vital role in the pathogenicity of E. batatas HD-1 within sweet potato. In total, twelve effectors were identified, including five LysM effectors and two CDIP effectors, suggesting that LysM and CDIP effectors play significant roles in the interaction between E. batatas HD-1 and sweet potato. Additionally, our analysis of biosynthetic gene clusters (BGCs) showed that two gene clusters are involved in melanin and choline metabolism. This study enriches the genomic resources of E. batatas and provides a theoretical foundation for future investigations into the pathogenic mechanisms of its infection in sweet potatoes, as well as potential targets for disease control. Full article

► Show Figures

Figure 1

30 pages, 10648 KiB

Open AccessArticle

Diversity of Lignicolous Freshwater Fungi from Yuanjiang River in Yunnan (China), with the Description of Four New Species

by Liang Zhang, Dan-Feng Bao, Hong-Wei Shen and Zong-Long Luo

J. Fungi 2024, 10(12), 881; https://doi.org/10.3390/jof10120881 - 18 Dec 2024

Viewed by 646

Abstract

Yuanjiang River (Red River) is one of the six major water systems in Yunnan Province, which originates from western Yunnan Province. This river system features numerous tributaries, complex terrain, and abundant natural resources. During the investigation on the diversity of lignicolous freshwater fungi [...] Read more.

Yuanjiang River (Red River) is one of the six major water systems in Yunnan Province, which originates from western Yunnan Province. This river system features numerous tributaries, complex terrain, and abundant natural resources. During the investigation on the diversity of lignicolous freshwater fungi in the Yuanjiang River, nine species were collected and identified, five belonging to Dothideomycetes and four to Sordariomycetes. Based on morphology and multigene phylogenetic analyses, four species, namely, Aquadictyospora aquatica, Dictyosporium fluminicola, Myrmecridium submersum, and Neomyrmecridium fusiforme, are described as new species. Dictyocheirospora aquadulcis is reported as a new national record, and Myrmecridium hydei is reported as a new habitat record. Dictyocheirospora rotunda, Halobyssothecium aquifusiforme, and Pseudohalonectria lutea were known earlier from freshwater habitats, but we described them in detail in this paper. This study contributes significantly to the understanding of the diversity of lignicolous freshwater fungi in southwestern China. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 2nd Edition)

► Show Figures

Figure 1

4 pages, 212 KiB

Open AccessEditorial

New Strategies to Combat Human Fungal Infections

by André Luis Souza dos Santos and Marta Helena Branquinha

J. Fungi 2024, 10(12), 880; https://doi.org/10.3390/jof10120880 - 18 Dec 2024

Viewed by 640

Abstract

Over the past few decades, numerous reports have highlighted the significant rise in fungal infections worldwide, contributing to considerable morbidity, mortality, and escalating healthcare costs [...] Full article

(This article belongs to the Special Issue New Strategies to Combat Human Fungal Infections)

16 pages, 6782 KiB

Open AccessArticle

Functional Characterization of FgAsp, a Gene Coding an Aspartic Acid Protease in Fusarium graminearum

by Ping Li, Zhizhen Fu, Mengru Wang, Tian Yang, Yan Li and Dongfang Ma

J. Fungi 2024, 10(12), 879; https://doi.org/10.3390/jof10120879 - 17 Dec 2024

Viewed by 670

Abstract

Aspartic proteases (APs), hydrolases with aspartic acid residues as catalytic active sites, are closely associated with processes such as plant growth and development and fungal and bacterial pathogenesis. F. graminearum is the dominant pathogenic fungus that causes Fusarium head blight (FHB) in wheat. [...] Read more.

Aspartic proteases (APs), hydrolases with aspartic acid residues as catalytic active sites, are closely associated with processes such as plant growth and development and fungal and bacterial pathogenesis. F. graminearum is the dominant pathogenic fungus that causes Fusarium head blight (FHB) in wheat. However, the relationship of APs to the growth, development, and pathogenesis of F. graminearum is not clear. Therefore, we selected the FGSG_09558 gene, whose function annotation is aspartate protease, for further study. In this study, FGSG_09558 was found to contain a conserved structural domain and signal peptide sequence of aspartic acid protease and was therefore named FgAsp. The function of FgAsp in F. graminearum was investigated by constructing the knockout and complementation mutants of this gene. The results showed that with respect to the wild type (PH-1), the knockout mutant showed a significant reduction in mycelial growth, asexual spore production, and sexual spore formation, highlighting the key role of FgAsp in the growth and development of F. graminearum. In addition, the mutants showed a significant reduction in the virulence and accumulation level of deoxynivalenol (DON) content on maize whiskers, wheat germ sheaths, and wheat ears. DON, as a key factor of virulence, plays an important role in the F. graminearum infection of wheat ears, suggesting that FgAsp is involved in the regulation of F. graminearum pathogenicity by affecting the accumulation of the DON toxin. FgAsp had a significant effect on the ability of F. graminearum to utilize various sugars, especially arabinose. In response to the stress, hydrogen peroxide inhibited the growth of the mutant most significantly, indicating the important function of FgAsp in the strain’s response to environmental stress. Finally, FgAsp plays a key role in the regulation of F. graminearum growth and development, pathogenicity, and environmental stress response. Full article

(This article belongs to the Special Issue Growth and Virulence of Plant Pathogenic Fungi)

► Show Figures

Figure 1

13 pages, 1337 KiB

Open AccessArticle

Probiotic Potential of Yeasts Isolated from Fermented Beverages: Assessment of Antagonistic Strategies Against Salmonella enterica Serovar Enteritidis

by Silvia Cristina Vergara Alvarez, María Dolores Pendón, Ana Agustina Bengoa, María José Leiva Alaniz, Yolanda Paola Maturano and Graciela Liliana Garrote

J. Fungi 2024, 10(12), 878; https://doi.org/10.3390/jof10120878 - 17 Dec 2024

Viewed by 895

Abstract

Global concern about pathogenic resistance to antibiotics is prompting interest in probiotics as a strategy to prevent or inhibit infections. Fermented beverages are promising sources of probiotic yeasts. This study aimed to evaluate the antagonistic effects of Kluyveromyces marxianus, Wickerhamomyces anomalus, [...] Read more.

Global concern about pathogenic resistance to antibiotics is prompting interest in probiotics as a strategy to prevent or inhibit infections. Fermented beverages are promising sources of probiotic yeasts. This study aimed to evaluate the antagonistic effects of Kluyveromyces marxianus, Wickerhamomyces anomalus, and Pichia manshurica strains from kefir and wine against Salmonella enterica serovar Enteritidis in intestinal epithelial cells. The ability of these yeasts to adhere to Caco-2/TC-7 cells was evaluated, as well as their influence on the ability of Salmonella to associate and invade these cells. The behavior of the pathogen was analyzed by (a) incubation of enterocytes with yeast before adding Salmonella, (b) co-incubation of Salmonella with yeast before contact with the enterocytes, and (c) incubation of Salmonella with yeast metabolites before contact with enterocytes. All yeast strains demonstrated adherence to Caco-2/TC-7 cells (33–100%) and effectively inhibited Salmonella invasion. Among the treatments, co-culture showed the greatest effect, reducing Salmonella association and invasion by more than 50%. Additionally, these yeasts modulated the epithelial immune response, significantly decreasing CCL20-driven luminescence by 60–81% (p < 0.0001). These results highlight the potential of yeasts from fermented beverages as probiotics to counteract Salmonella infections, offering a promising alternative in the fight against antibiotic resistance. Full article

(This article belongs to the Special Issue Yeasts with Probiotic and Postbiotic Potential)

► Show Figures

Figure 1

13 pages, 3351 KiB

Open AccessArticle

Identification and Characterization of Endophytic Fungus DJE2023 Isolated from Banana (Musa sp. cv. Dajiao) with Potential for Biocontrol of Banana Fusarium Wilt

by Longqi Jin, Rong Huang, Jia Zhang, Zifeng Li, Ruicheng Li, Yunfeng Li, Guanghui Kong, Pinggen Xi, Zide Jiang and Minhui Li

J. Fungi 2024, 10(12), 877; https://doi.org/10.3390/jof10120877 - 17 Dec 2024

Viewed by 671

Abstract

This study characterized an endophytic fungus, DJE2023, isolated from healthy banana sucker of the cultivar (cv.) Dajiao. Its potential as a biocontrol agent against banana Fusarium wilt was assessed, aiming to provide a novel candidate strain for the biological control of the devastating [...] Read more.

This study characterized an endophytic fungus, DJE2023, isolated from healthy banana sucker of the cultivar (cv.) Dajiao. Its potential as a biocontrol agent against banana Fusarium wilt was assessed, aiming to provide a novel candidate strain for the biological control of the devastating disease. The fungus was isolated using standard plant tissue separation techniques and fungal culture methods, followed by identification through morphological comparisons, multi-gene phylogenetic analyses, and molecular detection targeting Fusarium oxysporum f. sp. cubense (Foc) race 1 and race 4. Furthermore, assessments of its characteristics and antagonistic effects were conducted through pathogenicity tests, biological trait investigations, and dual-culture experiments. The results confirmed isolate DJE2023 to be a member of the Fusarium oxysporum species complex but distinct from Foc race 1 or race 4, exhibiting no pathogenicity to banana plantlets of cv. Fenza No.1 or tomato seedlings cv. money maker. Only minute and brown necrotic spots were observed at the rhizomes of banana plantlets of ‘Dajiao’ and ‘Baxijiao’ upon inoculation, contrasting markedly with the extensive necrosis induced by Foc tropical race 4 strain XJZ2 at those of banana cv Baxijiao. Notably, co-inoculation with DJE2023 and XJZ2 revealed a significantly reduced disease severity compared to inoculation with XJZ2 alone. An in vitro plate confrontation assay showed no significant antagonistic effects against Foc, indicating a suppressive effect rather than direct antagonism of DJE2023. Research on the biological characteristics of DJE2023 indicated lactose as the optimal carbon source for its growth, while maltose favored sporulation. The optimal growth temperature for this strain is 28 °C, and its spores can germinate effectively within the range of 25–45 °C and pH 4–10, demonstrating a strong alkali tolerance. Collectively, our findings suggest that DJE2023 exhibits weak or non-pathogenic properties and lacks direct antagonism against Foc, yet imparts a degree of resistance against banana Fusarium wilt. The detailed information provides valuable insight into the potential role of DJE2023 in integrated banana disease control, presenting a promising candidate for biocontrol against banana Fusarium wilt. Full article

(This article belongs to the Special Issue Fusarium spp.: A Trans-Kingdom Fungus)

► Show Figures

Figure 1

10 pages, 3030 KiB

Open AccessArticle

Real-World Antifungal Therapy Patterns Across the Continuum of Care in United States Adults with Invasive Aspergillosis

by Barbara D. Alexander, Melissa Johnson, Mark Bresnik, Vamshi Ruthwik Anupindi, Lia Pizzicato, Mitchell DeKoven, Belinda Lovelace and Craig I. Coleman

J. Fungi 2024, 10(12), 876; https://doi.org/10.3390/jof10120876 - 17 Dec 2024

Viewed by 674

Abstract

Changes to antifungal therapy (AFT) in invasive aspergillosis (IA) may occur due to intolerance, side effects, drug interactions, or lack of response. We describe AFT change patterns in IA patients. This was a US claims data study. IA patients were identified during the [...] Read more.

Changes to antifungal therapy (AFT) in invasive aspergillosis (IA) may occur due to intolerance, side effects, drug interactions, or lack of response. We describe AFT change patterns in IA patients. This was a US claims data study. IA patients were identified during the index hospitalization from October 2015 to November 2022. Patients were stratified by whether they ‘changed’ or ‘did not change’ AFT during or after the index hospitalization. AFT patterns were assessed for four lines of therapy or until loss of follow-up. First-line AFT began during the index hospitalization. Discontinuation with restart, modification, or switch in AFT ended the current line and initiated a subsequent line. Inverse probability-of-treatment weighting was utilized. Among 1192 adults with IA, 59.3% changed their AFT (60.0% modified AFT, 22.1% stopped first-line AFT and later initiated a new AFT for second line, and 18% immediately switched to a different AFT). Among those who changed AFT, triazole use predominated, with voriconazole (37.3–49.3%) and isavuconazole (19.3–26.7%) the most used across all AFT lines. Echinocandin use varied between 25.3 and 33.6% over all lines, and amphotericin B use increased over lines 1–4 (13.4–20.7%). Among the 40.7% of patients that completed AFT without changes, most received triazole monotherapy (62.8% voriconazole; 15.2% isavuconazole). Most patients required changes to their AFT. Full article

► Show Figures

Figure 1

15 pages, 1781 KiB

Open AccessArticle

Influence of Fungal Colonization on Exacerbations in Patients with Cystic Fibrosis

by Claudia Janeth Madrid-Carbajal, Teresa Peláez-García de la Rasilla, Marta Iscar-Urrutia, Marta Solís-García, Ramón Fernández-Álvarez, Liliana Pérez-Martínez, María Soledad Zapico-González and Marta Garcia-Clemente

J. Fungi 2024, 10(12), 875; https://doi.org/10.3390/jof10120875 - 17 Dec 2024

Viewed by 644

Abstract

The importance of fungal pathogens in cystic fibrosis (CF) patients and their diagnosis remains a challenge, so our aim was to analyze the influence of the detection of fungi in sputum by using conventional culture and molecular techniques, polymerase chain reaction (PCR), lateral [...] Read more.

The importance of fungal pathogens in cystic fibrosis (CF) patients and their diagnosis remains a challenge, so our aim was to analyze the influence of the detection of fungi in sputum by using conventional culture and molecular techniques, polymerase chain reaction (PCR), lateral flow devices (LFDs), and galactomannan (GM) on exacerbations in patients with cystic fibrosis. A prospective study was conducted in patients via follow-up in the CF Unit of the Central University Hospital of Asturias from January 2021 to April 2022. Adult patients with at least one documented exacerbation were included. A complete fungal analysis of sputum samples was performed both in a period of clinical stability and in the exacerbation period. The microbiological study included conventional cultures for fungi, qPCR (polymerase chain reaction), LFDs (lateral flow devices), and galactomannan (GM) in sputum. We found that there were changes in their detection according to whether the patient is in a period of clinical stability or exacerbation; the positivity of the molecular tests and biomarkers in the period of exacerbation increased by 14%, 25%, and 21% for the analysis by qPCR, GM, and LFDs for Aspergillus and by 15% for the sputum culture for Aspergillus, which may mean that fungal isolates may play a role in the exacerbations of these patients. Full article

(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)

► Show Figures

Figure 1

17 pages, 9737 KiB

Open AccessArticle

Nanopore Data-Driven T2T Genome Assemblies of Colletotrichum lini Strains

by Elizaveta A. Sigova, Ekaterina M. Dvorianinova, Alexander A. Arkhipov, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Antoniy M. Kaplun, Yakov V. Bodrov, Valeria A. Pavlova, Elena V. Borkhert, Daiana A. Zhernova, Elena N. Pushkova, Nataliya V. Melnikova and Alexey A. Dmitriev

J. Fungi 2024, 10(12), 874; https://doi.org/10.3390/jof10120874 - 16 Dec 2024

Viewed by 747

Abstract

Colletotrichum lini is a pathogenic fungus that infects flax and causes significant yield losses. In this study, we assembled the genomes of four highly virulent C. lini strains using the Oxford Nanopore Technologies (ONT, R10.4.1 flow cells) and Illumina platforms. The performance of [...] Read more.

Colletotrichum lini is a pathogenic fungus that infects flax and causes significant yield losses. In this study, we assembled the genomes of four highly virulent C. lini strains using the Oxford Nanopore Technologies (ONT, R10.4.1 flow cells) and Illumina platforms. The performance of two tools developed for telomere-to-telomere (T2T) genome assembly was compared: Verkko and Hifiasm. Prior to the assembly, ONT reads were corrected using the HERRO algorithm. Verkko generated genome assemblies of high completeness but low contiguity, while Hifiasm allowed the generation of T2T assemblies. Despite significantly different genome coverage with ONT data (25–100×), four assemblies of equal contiguity were obtained: 53.6–54.7 Mb, ten core chromosomes, and two or three accessory chromosomes. A comparative analysis of different polishing tools showed that at a certain genome coverage with the corrected ONT data (≥35×), the additional polishing of the assembly did not improve its accuracy, even with the Illumina data. An analysis of the genome structures of the four C. lini strains revealed a high similarity between the core chromosomes. Thus, our approach enabled assembling T2T Colletotrichum genomes only from the ONT data obtained using R10.4.1 flow cells and may be promising for other fungal genera. These assemblies will allow the accurate identification of strain-specific differences at the chromosome level and will aid in the development of effective strategies to protect flax from anthracnose. Full article

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

► Show Figures

Figure 1

19 pages, 4171 KiB

Open AccessArticle

Characterisation of Itersonilia spp. from Parsnip and Other Hosts

by Lauren H. K. Chappell, Guy C. Barker and John P. Clarkson

J. Fungi 2024, 10(12), 873; https://doi.org/10.3390/jof10120873 - 16 Dec 2024

Viewed by 629

Abstract

Parsnips (Pastinaca sativa) are a speciality UK crop with an economic value of at least 31M GBP annually. Currently, the major constraints to production are losses associated with root canker disease due to a range of fungal pathogens, among which Itersonilia [...] Read more.

Parsnips (Pastinaca sativa) are a speciality UK crop with an economic value of at least 31M GBP annually. Currently, the major constraints to production are losses associated with root canker disease due to a range of fungal pathogens, among which Itersonilia pastinacae is of most concern to growers. With limited research conducted on this species, this work aimed to provide a much-needed characterisation of isolates from across the UK, continental Europe, and New Zealand. Previously, up to four separate Itersonilia species have been proposed based on the formation of chlamydospores and host specificity: I. pastinacae, I. perplexans, I. pyriformans, and I. pannonica. However, Itersonilia spp. isolates principally from parsnip, but also from a range of other hosts, which were found to infect both parsnip roots and leaves in pathogenicity tests. In growth rate assays, isolates were found to grow at temperatures of 0–25 °C and produce both chlamydospores and ballistospores across the same range of temperatures, although chlamydospore production was found to decrease as temperature increased. Following whole genome sequencing, specific primers were designed for the molecular characterisation of the isolates using six housekeeping genes and three highly variable functional genes. Phylogenetic analysis separated isolates into two and six clades, respectively, but the grouping was not associated with hosts or locations. Based on the results of this research, there was no evidence to support more than a single species of Itersonilia among the isolates studied. Full article

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

► Show Figures

Figure 1

25 pages, 15769 KiB

Open AccessArticle

Additions to Dictyosporiaceae: Neoxylochrysis typhicola comb. et gen. nov., Two New Species and Four New Host Records from Medicinal Plants in Southwestern China

by Na Wu, Hong-Zhi Du, Kandawatte Wedaralalage Thilini Chethana, Kitiphong Khongphinitbunjong, Sajeewa S. N. Maharachchikumbura, Kevin D. Hyde and Jian-Kui Liu

J. Fungi 2024, 10(12), 872; https://doi.org/10.3390/jof10120872 - 16 Dec 2024

Viewed by 649

Abstract

Medicinal plants serve as vital resources for preventing and treating diseases, with their flowers, fruits, leaves, roots, or entire plants being utilized in the pharmaceutical industry or as direct therapeutic agents. During our investigation of microfungi associated with medicinal plants in Guizhou and [...] Read more.

Medicinal plants serve as vital resources for preventing and treating diseases, with their flowers, fruits, leaves, roots, or entire plants being utilized in the pharmaceutical industry or as direct therapeutic agents. During our investigation of microfungi associated with medicinal plants in Guizhou and Sichuan Provinces, China, several asexual and sexual fungal morphs were collected. Multi-locus phylogenetic analysis based on combined ITS, LSU, SSU and TEF1-α datasets revealed that these taxa are related to the family Dictyosporiaceae. Morphological characteristics, along with multi-locus phylogenetic analysis, supported the establishment of Dictyocheirospora alangii sp. nov. and Pseudocoleophoma rosae sp. nov., as well as the introduction of a novel genus Neoxylochrysis, which accommodates Neoxylochrysis typhicola comb. nov. (≡Pseudocoleophoma typhicola). In addition, four new host records are introduced for Aquadictyospora lignicola from Periploca forrestii, Dendryphiella eucalyptorum from Leonurus japonicus, Ophiopogon japonicus and Sambucus javanica, D. vinosa from Phytolacca americana, and Dictyocheirospora rotunda from Euonymus japonicus and Prinsepia utilis. Detailed descriptions, micrographs of the new taxa and a phylogenetic tree are provided. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 2nd Edition)

► Show Figures

Figure 1

25 pages, 2086 KiB

Open AccessReview

New Ground in Antifungal Discovery and Therapy for Invasive Fungal Infections: Innovations, Challenges, and Future Directions

by Gustavo A. Niño-Vega, Leonardo Padró-Villegas and Everardo López-Romero

J. Fungi 2024, 10(12), 871; https://doi.org/10.3390/jof10120871 - 15 Dec 2024

Viewed by 1158

Abstract

This review explores current advancements and challenges in antifungal therapies amid rising fungal infections, particularly in immunocompromised patients. We detail the limitations of existing antifungal classes—azoles, echinocandins, polyenes, and flucytosine—in managing systemic infections and the urgent need for alternative solutions. With the increasing [...] Read more.

This review explores current advancements and challenges in antifungal therapies amid rising fungal infections, particularly in immunocompromised patients. We detail the limitations of existing antifungal classes—azoles, echinocandins, polyenes, and flucytosine—in managing systemic infections and the urgent need for alternative solutions. With the increasing incidence of resistance pathogens, such as Candida auris and Aspergillus fumigatus, we assess emerging antifungal agents, including Ibrexafungerp, T-2307, and N′-Phenylhydrazides, which target diverse fungal cell mechanisms. Innovations, such as nanoparticles, drug repurposing, and natural products, are also evaluated for their potential to improve efficacy and reduce resistance. We emphasize the importance of novel approaches to address the growing threat posed by fungal infections, particularly for patients with limited treatment options. Finally, we briefly examine the potential use of artificial intelligence (AI) in the development of new antifungal treatments, diagnoses, and resistance prediction, which provides powerful tools in the fight against fungal pathogens. Overall, we highlight the pressing need for continued research to advance antifungal treatments and improve outcomes for high-risk populations. Full article

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

► Show Figures

Figure 1

14 pages, 1610 KiB

Open AccessArticle

Puccinia striiformis f. sp. tritici Exhibited a Significant Change in Virulence and Race Frequency in Xinjiang, China

by Hong Yang, Muhammad Awais, Feifei Deng, Li Li, Jinbiao Ma, Guangkuo Li, Kemei Li and Haifeng Gao

J. Fungi 2024, 10(12), 870; https://doi.org/10.3390/jof10120870 - 14 Dec 2024

Viewed by 1017

Abstract

Xinjiang is an important region due to its unique epidemic characteristics of wheat stripe rust disease caused by Puccinia striiformis f. sp. tritici. Some previous studies on race identification were conducted in this region, but it is still unclear how temporal changes [...] Read more.

Xinjiang is an important region due to its unique epidemic characteristics of wheat stripe rust disease caused by Puccinia striiformis f. sp. tritici. Some previous studies on race identification were conducted in this region, but it is still unclear how temporal changes affect the dynamics, diversity, and virulence characteristics of Pst races in Xinjiang. To gain a better understanding, we compared the race data from spring and winter wheat crops of 2022 with that of 2021. Our results showed a significant change in virulence frequency in 2022. Vr10, Vr13, and Vr19 exhibited an increasing trend, with a frequency of ≥18%, while the maximum decline was observed in Vr1, Vr3, and Vr9, with a frequency of ≤−25%. It was found that Yr5 and Yr15 remained effective against Xinjiang Pst races. The race diversity increased from 0.92 (70 races out of 345 isolates) to 0.94 (90 races out of 354 isolates) in 2022, with G22G being the dominant race group. Race CYR34 became prevalent in the region in 2022, while the LvG grouped was wiped out in 2022, from both summer and winter crop seasons. HyG and SuG groups showed an overall declining trend. Overall prevalent races showed over-summering and over-wintering behaviors in Xinjiang. The number of new races occurrence frequency increased by 34% in 2022, indicating a potential change in the population structure of Pst. It is crucial to introduce newly resistant gene cultivars in this region and to establish rust-monitoring protocols to prepare for any future epidemics. Full article

(This article belongs to the Special Issue Growth and Virulence of Plant Pathogenic Fungi)

► Show Figures

Figure 1

23 pages, 3057 KiB

Open AccessArticle

Comparative Genomics of Different Lifestyle Fungi in Helotiales (Leotiomycetes) Reveals Temperature and Ecosystem Adaptations

by Daniel Vasconcelos Rissi, Maham Ijaz and Christiane Baschien

J. Fungi 2024, 10(12), 869; https://doi.org/10.3390/jof10120869 - 14 Dec 2024

Viewed by 861

Abstract

Helotiales, a diverse fungal order within Leotiomycetes (Ascomycota), comprises over 6000 species occupying varied ecological niches, from plant pathogens to saprobes and symbionts. Despite their importance, their genetic adaptations to temperature and environmental conditions are understudied. This study investigates temperature adaptations in infection [...] Read more.

Helotiales, a diverse fungal order within Leotiomycetes (Ascomycota), comprises over 6000 species occupying varied ecological niches, from plant pathogens to saprobes and symbionts. Despite their importance, their genetic adaptations to temperature and environmental conditions are understudied. This study investigates temperature adaptations in infection genes and substrate degradation genes through a comparative genomics analysis of 129 Helotiales species, using the newly sequenced genomes of Gyoerffyella rotula and Anguillospora crassa. Key gene families such as cytochrome P450 enzymes, virulence factors, effector proteins, and carbohydrate-active enzymes (CAZymes) were analyzed to understand their roles in temperature and lifestyle adaptations, uncovering possible alternative lifestyle mechanisms. Our findings reveal that Helotiales fungi possess genes associated with nutrient acquisition, pathogenicity, and symbiotic relationships strongly adapted to cold environments that might be impacted by global warming. On the other hand, some species demonstrate potential for adaptation to warmer climates, suggesting increased activity in response to global warming. This study reveals the adaptive mechanisms enabling Helotiales fungi to thrive in both cold and warm environments. These findings provide valuable insights into their ecological success and evolutionary resilience, which may facilitate their ability to transition between pathogenic, symbiotic, and saprobic phases in response to changing environmental conditions. Full article

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

► Show Figures

Figure 1

18 pages, 2894 KiB

Open AccessArticle

Comparative Genomics and Pathogenicity Analysis of Three Fungal Isolates Causing Barnyard Grass Blast

by Na Zhang, Xinyang Li, Liangping Ming, Wenda Sun, Xiaofang Xie, Cailing Zhi, Xiaofan Zhou, Yanhua Wen, Zhibin Liang and Yizhen Deng

J. Fungi 2024, 10(12), 868; https://doi.org/10.3390/jof10120868 - 13 Dec 2024

Viewed by 901

Abstract

Barnyard grass is one of the most serious rice weeds, often growing near paddy fields and therefore potentially serving as a bridging host for the rice blast fungus. In this study, we isolated three fungal strains from diseased barnyard grass leaves in a [...] Read more.

Barnyard grass is one of the most serious rice weeds, often growing near paddy fields and therefore potentially serving as a bridging host for the rice blast fungus. In this study, we isolated three fungal strains from diseased barnyard grass leaves in a rice field. Using a pathogenicity assay, we confirmed that they were capable of causing blast symptoms on barnyard grass and rice leaves to various extents. Based on morphology characterization and genome sequence analyses, we confirmed that these three strains were Epicoccum sorghinum (SCAU-1), Pyricularia grisea (SCAU-2), and Exserohilum rostratum (SCAU-6). The established Avirulence (Avr) genes Avr-Pia, Avr-Pita2, and ACE1 were detected by PCR amplification in SCAU-2, but not in SCAU-1 or SCAU-6. Furthermore, the whole-genome sequence analysis helped to reveal the genetic variations and potential virulence factors relating to the host specificity of these three fungal pathogens. Based on the evolutionary analysis of single-copy orthologous proteins, we found that the genes encoding glycoside hydrolases, carbohydrate esterases, oxidoreductase, and multidrug transporters in SCAU-1 and SCAU-6 were expanded, while expansion in SCAU-2 was mainly related to carbohydrate esterases. In summary, our study provides clues to understand the pathogenic mechanisms of fungal isolates from barnyard grass with the potential to cause rice blast. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

► Show Figures

Figure 1

20 pages, 2909 KiB

Open AccessArticle

Diversity and Distribution of Fungi in the Marine Sediments of Zhanjiang Bay, China

by Menghan Gao, Bihong Liu, Jianming Li, Yunyan Deng, Yulei Zhang, Ning Zhang, Feng Li, Changling Li, Xianghu Huang and Zhangxi Hu

J. Fungi 2024, 10(12), 867; https://doi.org/10.3390/jof10120867 - 13 Dec 2024

Viewed by 981

Abstract

Fungi are one of the major components of the eukaryotic microbial community in marine ecosystems, playing a significant role in organic matter cycling and food web dynamics. However, the diversity and roles of fungi in marine sediments remain poorly documented. To elucidate the [...] Read more.

Fungi are one of the major components of the eukaryotic microbial community in marine ecosystems, playing a significant role in organic matter cycling and food web dynamics. However, the diversity and roles of fungi in marine sediments remain poorly documented. To elucidate the diversity and spatial distribution of fungal communities in the marine sediments of an estuary–coast continuum across three distinct salinity regions in Zhanjiang Bay, China, the variations in fungal diversity, abundance, community structure, and distribution in the sediments were investigated through the application of high-throughput amplicon sequencing using the internal transcribed spacer (ITS) primers. Additionally, the FUNGuild database was employed to assess the potential functional traits of fungi. A total of 1242 ASV sequences, affiliated to 144 genera and five phyla, were identified. Ascomycota (68.97%) and Basidiomycota (6.41%) were the dominant fungal groups, together accounting for 75.38% of the total relative abundance of the fungal community. Significant differences were observed in the α-diversity indices (Shannon index and richness) and β-diversity of fungal communities across the three distinct salinity regions. The fungal molecular network exhibited primarily positive species interactions, with notable structural differences across salinity gradients. The low-salinity group had a large network with high modularity; the medium-salinity group a small, simple network with high centralization, and the high-salinity group a compact, moderately complex network. Symbiotrophs, saprotrophs, and pathotrophs, being the three trophic types with the highest proportions, were estimated based on ITS. A redundancy analysis (RDA) indicated that salinity was the primary factor influencing the distribution of Ascomycota communities, while the distributions of Basidiomycota, Chytridiomycota, Mucoromycota, and Rozellomycota were more strongly affected by environmental factors such as chlorophyll a, chemical oxygen demand (COD), pH, and temperature. Our work provides new scientific data on the diversity, composition, and distribution of fungal communities in Zhanjiang Bay, which helps to understand the biodiversity of fungi in the estuary–coast ecosystems. Full article

(This article belongs to the Special Issue Diversity of Marine Fungi, 2nd Edition)

► Show Figures

Figure 1

13 pages, 2150 KiB

Open AccessArticle

Effect of a Mating Type Gene Editing in Lentinula edodes Using RNP/Nanoparticle Complex

by Minseek Kim, Minji Oh, Ji-Hoon Im, Eun-Ji Lee, Hojin Ryu, Hyeon-Su Ro and Youn-Lee Oh

J. Fungi 2024, 10(12), 866; https://doi.org/10.3390/jof10120866 - 13 Dec 2024

Viewed by 764

Abstract

Gene editing using CRISPR/Cas9 is an innovative tool for developing new mushroom strains, offering a promising alternative to traditional breeding methods that are time-consuming and labor-intensive. However, plasmid-based gene editing presents several challenges, including the need for selecting appropriate promoters for Cas9 expression, [...] Read more.

Gene editing using CRISPR/Cas9 is an innovative tool for developing new mushroom strains, offering a promising alternative to traditional breeding methods that are time-consuming and labor-intensive. However, plasmid-based gene editing presents several challenges, including the need for selecting appropriate promoters for Cas9 expression, optimizing codons for the Cas9 gene, the unintended insertion of fragmented plasmid DNA into genomic DNA (gDNA), and regulatory concerns related to genetically modified organisms (GMOs). To address these issues, we utilized a Ribonucleoprotein (RNP) complex consisting of Cas9 and gRNA for gene editing to modify the A mating-type gene of Lentinula edodes. To overcome the challenges posed by the large size of the Cas9 protein, which limits its penetration through the protoplast membrane, and the susceptibility of sgRNA to degradation, we developed a nanoparticle complex using calcium phosphate and polyacrylic acid. This approach significantly improved gene editing efficiency. Consequently, we successfully edited the mating-controlling genes hd1 and hd2 in L. edodes and examined the effects of their disruption on mating. Disruption of the hd1 gene, which is known to influence mycelial growth, did not significantly affect growth or mating. In contrast, editing the hd2 gene disrupted mating with compatible partners, highlighting its critical role in the mating process. The RNP-based transformation technology presented here offers significant advancement over traditional plasmid-based methods, enhancing the efficiency of targeted gene modification while avoiding the insertion of foreign genetic material, thereby mitigating GMO-related regulatory concerns. Full article

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

► Show Figures

Figure 1

18 pages, 4899 KiB

Open AccessReview

Endophytic Entomopathogenic Fungi: Their Role in Enhancing Plant Resistance, Managing Insect Pests, and Synergy with Management Routines

by Krishnamoorthy Aravinthraju, Mookiah Shanthi, Marimuthu Murugan, Ramasamy Srinivasan, Lourena Arone Maxwell, Narayanan Manikanda Boopathi and Rangasamy Anandham

J. Fungi 2024, 10(12), 865; https://doi.org/10.3390/jof10120865 - 13 Dec 2024

Viewed by 1238

Abstract

The interaction between plants and microorganisms plays a major role in plant growth promotion and disease management. While most microorganisms directly influence plant health, some indirectly support growth through pest and disease suppression. Endophytic entomopathogenic fungi are diverse, easily localized, and have long-lasting [...] Read more.

The interaction between plants and microorganisms plays a major role in plant growth promotion and disease management. While most microorganisms directly influence plant health, some indirectly support growth through pest and disease suppression. Endophytic entomopathogenic fungi are diverse, easily localized, and have long-lasting effects on insect pests. When inhabiting plants, these fungi alter secondary metabolites, volatile organic compounds, and microbiomes, enhancing plant resistance to pests and diseases and sometimes improving growth. However, their persistence in plant systems may be challenged by the plant’s defense mechanisms or by human interventions such as insecticides, fungicides, herbicides, and phyto-insecticides, which are common in agriculture. As effective biocontrol agents, endophytic entomopathogenic fungi can also be integrated with other pest management strategies like predators, parasitoids, and chemicals. This review will explore the impact of endophytic entomopathogens on plant systems and their compatibility with other management practices. Full article

(This article belongs to the Special Issue Pathogenic Mechanisms and Biological Control in Entomopathogenic Fungi)

► Show Figures

Figure 1

Journal Menu

Journal Browser

J. Fungi, Volume 10, Issue 12 (December 2024) – 89 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI