Journal of Fungi

16 pages, 3720 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of Toll-like Receptors (TLRs) in Diaphorina citri and Their Expression Patterns Induced by the Endophyte Beauveria bassiana

by Luis Carlos Ramos Aguila, Hafiza Javaira Ashraf, Jessica Paola Sánchez Moreano, Komivi Senyo Akutse, Bamisope Steve Bamisile, Liuyang Lu, Xiaofang Li, Jingyi Lin, Qing Wu and Liande Wang

J. Fungi 2022, 8(8), 888; https://doi.org/10.3390/jof8080888 - 22 Aug 2022

Cited by 3 | Viewed by 1729

Abstract

Toll-like receptors (TLRs) are pathogen recognition receptors (PRRs), which play key roles in helping the host immune system fight pathogen invasions. Systematic information on TLRs at the genome-wide level and expression profiling in response to endophytic colonization is very important to understand their [...] Read more.

Toll-like receptors (TLRs) are pathogen recognition receptors (PRRs), which play key roles in helping the host immune system fight pathogen invasions. Systematic information on TLRs at the genome-wide level and expression profiling in response to endophytic colonization is very important to understand their functions but is currently lacking in this field. Here, a total of two TLR genes were identified and characterized in Diaphorina citri. The TLR genes of D. citri were clustered into five families according to the phylogenetic analysis of different species’ TLRs. The domain organization analyses suggested that the TLRs were constituted of three important parts: a leucine-rich repeat (LRR) domain, a transmembrane region (TR) and a Toll/interleukin-1 receptor (TIR) domain. The mRNA expression levels of the two TLR genes (DcTOLL and DcTLR7) were highly regulated in both nymphs and adults of D. citri. These results elucidated the potentiated TLR gene expression in response to endophytically colonized plants. Furthermore, the 3D structures of the TIR domain were highly conserved during evolution. Collectively, these findings elucidate the crucial roles of TLRs in the immune response of D. citri to entomopathogens systematically established as endophytes, and provide fundamental knowledge for further understanding of the innate immunity of D. citri. Full article

(This article belongs to the Special Issue Entomopathogenic Fungi in Biological Plant Protection: The Machinery of Multicomponent System Interactions)

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15 pages, 2059 KiB

Open AccessArticle

Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris

by Pattsarun Cheawchanlertfa, Suwalak Chitcharoen, Nachon Raethong, Qing Liu, Pramote Chumnanpuen, Panyawarin Soommat, Yuanda Song, Mattheos Koffas, Kobkul Laoteng and Wanwipa Vongsangnak

J. Fungi 2022, 8(8), 887; https://doi.org/10.3390/jof8080887 - 22 Aug 2022

Cited by 3 | Viewed by 1742

Abstract

Cordyceps militaris is an industrially important fungus, which is often used in Asia as traditional medicine. There has been a published genome-scale metabolic model (GSMM) of C. militaris useful for predicting its growth behaviors; however, lipid metabolism, which plays a vital role [...] Read more.

Cordyceps militaris is an industrially important fungus, which is often used in Asia as traditional medicine. There has been a published genome-scale metabolic model (GSMM) of C. militaris useful for predicting its growth behaviors; however, lipid metabolism, which plays a vital role in cellular functions, remains incomplete in the GSMM of C. militaris. A comprehensive study on C. militaris was thus performed by enhancing GSMM through integrative analysis of metabolic footprint and transcriptome data. Through the enhanced GSMM of C. militaris (called iPC1469), it contained 1469 genes, 1904 metabolic reactions and 1229 metabolites. After model evaluation, in silico growth simulation results agreed well with the experimental data of the fungal growths on different carbon sources. Beyond the model-driven integrative data analysis, interestingly, we found key metabolic responses in alteration of lipid metabolism in C. militaris upon different carbon sources. The sphingoid bases (e.g., sphinganine, sphingosine, and phytosphingosine) and ceramide were statistically significant accumulated in the xylose culture when compared with other cultures; this study suggests that the sphingolipid biosynthetic capability in C. militaris was dependent on the carbon source assimilated for cell growth; this finding provides a comprehensive basis for the sphingolipid biosynthesis in C. militaris that can help to further redesign its metabolic control for medicinal and functional food applications. Full article

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

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15 pages, 2880 KiB

Open AccessArticle

Pseudo-Chromosomal Genome Assembly in Combination with Comprehensive Transcriptome Analysis in Agaricus bisporus Strain KMCC00540 Reveals Mechanical Stimulus Responsive Genes Associated with Browning Effect

by Ick-Hyun Jo, Jaewook Kim, Hyejin An, Hwa-Yong Lee, Yoon-Sup So, Hojin Ryu, Gi-Ho Sung, Donghwan Shim and Jong-Wook Chung

J. Fungi 2022, 8(8), 886; https://doi.org/10.3390/jof8080886 - 22 Aug 2022

Cited by 2 | Viewed by 1568

Abstract

Agaricus bisporus is one of the world’s most popular edible mushrooms, including in South Korea. We performed de novo genome assembly with a South Korean white-colored cultivar of A. bisporus, KMCC00540. After generating a scaffold-level genomic sequence, we inferred chromosome-level assembly by [...] Read more.

Agaricus bisporus is one of the world’s most popular edible mushrooms, including in South Korea. We performed de novo genome assembly with a South Korean white-colored cultivar of A. bisporus, KMCC00540. After generating a scaffold-level genomic sequence, we inferred chromosome-level assembly by genomic synteny analysis with the representative A. bisporus strains H97 and H39. The KMCC00540 genome had 13 pseudochromosomes comprising 33,030,236 bp mostly covering both strains. A comparative genomic analysis with cultivar H97 indicated that most genomic regions and annotated proteins were shared (over 90%), ensuring that our cultivar could be used as a representative genome. However, A. bisporus suffers from browning even from only a slight mechanical stimulus during transportation, which significantly lowers its commercial value. To identify which genes respond to a mechanical stimulus that induces browning, we performed a time-course transcriptome analysis based on the de novo assembled genome. Mechanical stimulus induces up-regulation in long fatty acid ligase activity-related genes, as well as melanin biosynthesis genes, especially at early time points. In summary, we assembled the chromosome-level genomic information on a Korean strain of A. bisporus and identified which genes respond to a mechanical stimulus, which provided key hints for improving the post-harvest biological control of A. bisporus. Full article

(This article belongs to the Special Issue Edible Mushrooms 2.0)

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14 pages, 2534 KiB

Open AccessArticle

A Novel Major Facilitator Superfamily Transporter Gene Aokap4 near the Kojic Acid Gene Cluster Is Involved in Growth and Kojic Acid Production in Aspergillus oryzae

by Tianming Chen, Ziming Chen, Yuzhen Li, Bin Zeng and Zhe Zhang

J. Fungi 2022, 8(8), 885; https://doi.org/10.3390/jof8080885 - 22 Aug 2022

Cited by 6 | Viewed by 1610

Abstract

Kojic acid is an important secondary metabolite of industrial importance produced by Aspergillus oryzae. The kojic acid gene cluster plays an essential role in kojic acid production, and harbors kojA, kojR and kojT. The deletion of kojT, encoding a [...] Read more.

Kojic acid is an important secondary metabolite of industrial importance produced by Aspergillus oryzae. The kojic acid gene cluster plays an essential role in kojic acid production, and harbors kojA, kojR and kojT. The deletion of kojT, encoding a major facilitator superfamily (MFS) transporter, did not completely abolish kojic acid production, implying that other transporters are required for the transport of kojic acid. The aim of this study is to look for the transporters involved in kojic acid production. Here, Aokap4 encoding a novel MFS transporter was identified, which was adjacent to kojT in the kojic acid gene cluster. The deletion of Aokap4 contributed to the hyphal growth, conidial production and biomass of A. oryzae. Moreover, Aokap4 is required for heat- and cell-wall-stress tolerance but not oxidative and osmotic stress. The disruption of Aokap4 impaired kojic acid production with the reduced expression of kojA, kojR and kojT. Furthermore, when kojT was deleted in the Aokap4-disrupted strain, the yield of kojic acid declined to the same level as that of the kojT-deletion mutant, whereas the production of kojic acid was recovered when kojT was overexpressed in the Aokap4 knockout strain, suggesting that kojT acts downstream of Aokap4. AoKap4 was the second identified MSF transporter involved in kojic acid production after kojT was found a decade ago. This study contributes to a better understanding of the biological roles of the MFS transporter and lays a foundation for future studies on kojic acid synthesis in A. oryzae. Full article

(This article belongs to the Special Issue Metabolic Engineering of Aspergillus via CRISPR-Based Systems)

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32 pages, 4766 KiB

Open AccessArticle

De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea

by Yvonne O. Ogaji, Robert C. Lee, Tim I. Sawbridge, Benjamin G. Cocks, Hans D. Daetwyler and Sukhjiwan Kaur

J. Fungi 2022, 8(8), 884; https://doi.org/10.3390/jof8080884 - 22 Aug 2022

Viewed by 3375

Abstract

Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for [...] Read more.

Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for these pathogens have been generated, which has hampered the implementation of effective management strategies and breeding for resistant cultivars. Using Oxford Nanopore long-read sequencing, we report the first high-quality, fully annotated, near-chromosome-level nuclear and mitochondrial genome assemblies for 18 isolates from the Australian AB complex. Comparative genome analysis was performed to elucidate the differences and similarities between species and isolates using phylogenetic relationships and functional diversity. Our data indicated that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic. More homology and orthologous gene clusters are shared between P. pinodes and P. pinodella compared to P. koolunga. The analysis of the repetitive DNA content showed differences in the transposable repeat composition in the genomes and their expression in the transcriptomes. Significant repeat expansion in P. koolunga’s genome was seen, with strong repeat-induced point mutation (RIP) activity being evident. Phylogenetic analysis revealed that genetic diversity can be exploited for species marker development. This study provided the much-needed genetic resources and characterization of the AB species to further drive research in key areas such as disease epidemiology and host–pathogen interactions. Full article

(This article belongs to the Special Issue Plant Fungal Pathogenesis 2022)

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17 pages, 2401 KiB

Open AccessArticle

Mycoremediation of Flotation Tailings with Agaricus bisporus

by Sylwia Budzyńska, Marek Siwulski, Anna Budka, Pavel Kalač, Przemysław Niedzielski, Monika Gąsecka and Mirosław Mleczek

J. Fungi 2022, 8(8), 883; https://doi.org/10.3390/jof8080883 - 22 Aug 2022

Cited by 5 | Viewed by 1814

Abstract

Due to their enzymatic and bioaccumulation faculties the use of macromycetes for the decontamination of polluted matrices seems reasonable for bioremediation. For this reason, the aim of our study was to evaluate the mycoremediation ability of Agaricus bisporus cultivated on compost mixed with [...] Read more.

Due to their enzymatic and bioaccumulation faculties the use of macromycetes for the decontamination of polluted matrices seems reasonable for bioremediation. For this reason, the aim of our study was to evaluate the mycoremediation ability of Agaricus bisporus cultivated on compost mixed with flotation tailings in different quantities (1, 5, 10, 15, and 20% addition). The biomass of the fruit bodies and the content of 51 major and trace elements were determined. Cultivation of A. bisporus in compost moderately polluted with flotation tailings yielded significantly lower (the first flush) and higher (the second flush) biomass of fruit bodies, compared with the control treatment. The presence of toxic trace elements did not cause any visible adverse symptoms for A. bisporus. Increasing the addition of flotation tailings to the compost induced an elevated level of most determined elements. A significant increase in rare earth elements (both flushes) and platinum group elements (first flush only) was observed. The opposite situation was recorded for major essential elements, except for Na and Mg in A. bisporus from the second flush under the most enriched compost (20%). Nevertheless, calculated bioaccumulation factor values showed a selective accumulation capacity—limited for toxic elements (except for Ag, As, and Cd) and the effective accumulation of B, Cu, K, and Se. The obtained results confirmed that A. bisporus can be used for practical application in mycoremediation in the industry although this must be preceded by larger-scale tests. This application seems to be the most favorable for media contaminated with selected elements, whose absorption by fruiting bodies is the most efficient. Full article

(This article belongs to the Special Issue Heavy Metals in Mushrooms)

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15 pages, 3882 KiB

Open AccessArticle

Transcriptomics Integrated with Metabolomics: Assessing the Central Metabolism of Different Cells after Cell Differentiation in Aureobasidium pullulans NG

by Nan Zeng, Ning Zhang, Xin Ma, Yunjiao Wang, Yating Zhang, Dandan Wang, Fangxiong Pu and Bingxue Li

J. Fungi 2022, 8(8), 882; https://doi.org/10.3390/jof8080882 - 22 Aug 2022

Cited by 3 | Viewed by 1508

Abstract

When organisms are stimulated by external stresses, oxidative stress is induced, resulting in the production of large amounts of reactive oxygen species (ROS) that inhibit cell growth and accelerate cellular aging until death. Understanding the molecular mechanisms of abiotic stress is important to [...] Read more.

When organisms are stimulated by external stresses, oxidative stress is induced, resulting in the production of large amounts of reactive oxygen species (ROS) that inhibit cell growth and accelerate cellular aging until death. Understanding the molecular mechanisms of abiotic stress is important to enhance cellular resistance, and Aureobasidium pullulans, a highly resistant yeast-like fungus, can use cellular differentiation to resist environmental stress. Here, swollen cells (SCs) from two different differentiation periods in Aureobasidium pullulans NG showed significantly higher antioxidant capacity and stress defense capacity than yeast-like cells (YL). The transcriptome and the metabolome of both cells were analyzed, and the results showed that amino acid metabolism, carbohydrate metabolism, and lipid metabolism were significantly enriched in SCs. Glyoxylate metabolism was significantly upregulated in carbohydrate metabolism, replacing the metabolic hub of the citric acid (TCA) cycle, helping to coordinate multiple metabolic pathways and playing an important role in the resistance of Aureobasidium pullulans NG to environmental stress. Finally, we obtained 10 key genes and two key metabolites in SCs, which provide valuable clues for subsequent validation. In conclusion, these results provide valuable information for assessing central metabolism-mediating oxidative stress in Aureobasidium pullulans NG, and also provide new ideas for exploring the pathways of eukaryotic resistance to abiotic stress. Full article

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

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11 pages, 838 KiB

Open AccessArticle

Fungal Infections in the ICU during the COVID-19 Era: Descriptive and Comparative Analysis of 178 Patients

by Evangelia Koukaki, Nikoletta Rovina, Kimon Tzannis, Zoi Sotiropoulou, Konstantinos Loverdos, Antonia Koutsoukou and George Dimopoulos

J. Fungi 2022, 8(8), 881; https://doi.org/10.3390/jof8080881 - 21 Aug 2022

Cited by 12 | Viewed by 1695

Abstract

Background: COVID-19-associated fungal infections seem to be a concerning issue. The aim of this study was to assess the incidence of fungal infections, the possible risk factors, and their effect on outcomes of critically ill patients with COVID-19. Methods: A retrospective observational study [...] Read more.

Background: COVID-19-associated fungal infections seem to be a concerning issue. The aim of this study was to assess the incidence of fungal infections, the possible risk factors, and their effect on outcomes of critically ill patients with COVID-19. Methods: A retrospective observational study was conducted in the COVID-19 ICU of the First Respiratory Department of National and Kapodistrian University of Athens in Sotiria Chest Diseases Hospital between 27 August 2020 and 10 November 2021. Results: Here, 178 patients were included in the study. Nineteen patients (10.7%) developed fungal infection, of which five had COVID-19 associated candidemia, thirteen had COVID-19 associated pulmonary aspergillosis, and one had both. Patients with fungal infection were younger, had a lower Charlson Comorbidity Index, and had a lower PaO₂/FiO₂ ratio upon admission. Regarding health-care factors, patients with fungal infections were treated more frequently with Tocilizumab, a high regimen of dexamethasone, continuous renal replacement treatment, and were supported more with ECMO. They also had more complications, especially infections, and subsequently developed septic shock more frequently. Finally, patients with fungal infections had a longer length of ICU stay, as well as length of mechanical ventilation, although no statistically significant difference was reported on 28-day and 90-day mortality. Conclusions: Fungal infections seem to have a high incidence in COVID-19 critically ill patients and specific risk factors are identified. However, fungal infections do not seem to burden on mortality. Full article

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19 pages, 3628 KiB

Open AccessArticle

Small GTPase FoSec4-Mediated Protein Secretion Is Important for Polarized Growth, Reproduction and Pathogenicity in the Banana Fusarium Wilt Fungus Fusarium odoratissimum

by Yuru Zheng, Pingting Guo, Huobing Deng, Yaqi Lin, Guilan Huang, Jie Wu, Songmao Lu, Shuai Yang, Jie Zhou, Wenhui Zheng, Zonghua Wang and Yingzi Yun

J. Fungi 2022, 8(8), 880; https://doi.org/10.3390/jof8080880 - 20 Aug 2022

Cited by 2 | Viewed by 1663

Abstract

Apical secretion at hyphal tips is important for the growth and development of filamentous fungi. In this study, we analyzed the role of the Rab GTPases FoSec4 involved in the secretion of the banana wilt fungal pathogen Fusarium odoratissimum. We found that [...] Read more.

Apical secretion at hyphal tips is important for the growth and development of filamentous fungi. In this study, we analyzed the role of the Rab GTPases FoSec4 involved in the secretion of the banana wilt fungal pathogen Fusarium odoratissimum. We found that the deletion of FoSEC4 affects the activity of extracellular hydrolases and protein secretion, indicating that FoSec4 plays an important role in the regulation of protein secretion in F. odoratissimum. As a typical Rab GTPase, Sec4 participates in the Rab cycle through the conversion between the active GTP-bound state and the inactive GDP-bound state, which is regulated by guanine nucleate exchange factors (GEFs) and GTPase-activating proteins (GAPs). We further found that FoSec2 can interact with dominant-negative FoSec4 (GDP-bound and nucleotide-free form, FoSec4DN), and that FoGyp5 can interact with dominant active FoSec4 (GTP-bound and constitutively active form, FoSec4CA). We evaluated the biofunctions of FoSec4, FoSec2 and FoGyp5, and found that FoSec4 is involved in the regulation of vegetative growth, reproduction, pathogenicity and the environmental stress response of F. odoratissimum, and that FocSec2 and FoGyp5 perform biofunctions consistent with FoSec4, indicating that FoSec2 and FoGyp5 may work as the GEF and the GAP, respectively, of FoSec4 in F. odoratissimum. We further found that the amino-terminal region and Sec2 domain are essential for the biological functions of FoSec2, while the carboxyl-terminal region and Tre-2/Bub2/Cdc16 (TBC) domain are essential for the biological functions of FoGyp5. In addition, FoSec4 mainly accumulated at the hyphal tips and partially colocalized with Spitzenkörper; however, FoGyp5 accumulated at the periphery of Spitzenkörper, suggesting that FoGyp5 may recognize and inactivate FoSec4 at a specific location in hyphal tips. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens)

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14 pages, 1631 KiB

Open AccessCase Report

Breakthrough Acute Necrotizing Invasive Fungal Rhinosinusitis by Alternariaalternata in a Patient with Acute Lymphoblastic Leukemia on Anidulafungin Therapy and Case-Based Literature Review

by Giorgos Tyrellis, Maria Siopi, Danai Leventakou, Alexander Delides, Pavlos Maragkoudakis, George Korres, Christina Apostolopoulou, Alina-Roxani Gouloumi, Vasiliki Pappa, Spyros Pournaras, Ioannis Panayiotides and Joseph Meletiadis

J. Fungi 2022, 8(8), 879; https://doi.org/10.3390/jof8080879 - 20 Aug 2022

Viewed by 1580

Abstract

Alternaria spp. have emerged as opportunistic pathogens particularly in immunosuppressed patients. A case of a breakthrough acute invasive fungal rhinosinusitis (AIFRS), caused by Alternaria alternata, is reported in a patient with acute lymphoblastic leukemia (ALL) on anidulafungin therapy, who was successfully treated [...] Read more.

Alternaria spp. have emerged as opportunistic pathogens particularly in immunosuppressed patients. A case of a breakthrough acute invasive fungal rhinosinusitis (AIFRS), caused by Alternaria alternata, is reported in a patient with acute lymphoblastic leukemia (ALL) on anidulafungin therapy, who was successfully treated with liposomal amphotericin B and surgical intervention. To date, 20 cases of AIFRS due to Alternaria spp. have been described, 19 in the USA and 1 in Chile, making this case report the first case of AIFRS due to Alternaria in Europe. The patients had median (range) age 25 (2–56) years (65% female), almost all of them (19/20) with hematological diseases and severe neutropenia (8–41 days pre-infection). Amphotericin B was the most frequently used antifungal agent, either alone or in combination. In all of the cases, systemic antifungal therapy was combined with surgery. Despite stabilization or improvement of the AIFRS, mortality was 38% (5 days to 8 months post-surgical debridement) due to their underlying disease or other infections without sign of AIFRS at autopsy. Full article

(This article belongs to the Special Issue Invasive Fungal Disease in the Immunocompromised Host)

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12 pages, 1753 KiB

Open AccessArticle

Alternative Splicing in Trichophyton rubrum Occurs in Efflux Pump Transcripts in Response to Antifungal Drugs

by Marcos E. R. Lopes, Tamires A. Bitencourt, Pablo R. Sanches, Maíra P. Martins, Vanderci M. Oliveira, Antonio Rossi and Nilce M. Martinez-Rossi

J. Fungi 2022, 8(8), 878; https://doi.org/10.3390/jof8080878 - 20 Aug 2022

Cited by 1 | Viewed by 1718

Abstract

Dermatophytes are challenging to treat because they have developed many strategies to neutralize the stress triggered by antifungals. Drug tolerance is achieved by mechanisms such as drug efflux and biofilm formation, and cellular efflux is a consequence of the synergistic and compensatory regulation [...] Read more.

Dermatophytes are challenging to treat because they have developed many strategies to neutralize the stress triggered by antifungals. Drug tolerance is achieved by mechanisms such as drug efflux and biofilm formation, and cellular efflux is a consequence of the synergistic and compensatory regulation of efflux pumps. Alternative splicing (AS) has also been considered as a mechanism that enhances fungal adaptive responses. We used RNA-seq data from the dermatophyte Trichophyton rubrum exposed to undecanoic acid (UDA) to search for and validate AS in genes encoding efflux pumps. The magnitude of this phenomenon was evaluated using UDA and other antifungals (caspofungin, itraconazole, and terbinafine) in planktonic and biofilm cultures. In addition to the conventional isoforms, the efflux pump encoded by TERG_04309 presented two intron-retained isoforms. Biofilms trigger the simultaneous production of at least two isoforms. The intron-retained isoforms showed short lengths and topologically different organization. Furthermore, we identified the putative interaction of efflux pumps (TERG_04309 and TERG_04224). Co-expression of these genes suggests a synergistic action in antifungal resistance. Our data provide new insights into drug tolerance related to differential isoform usage and the co-expression of stress-responsive genes, which may lead to higher antifungal resistance, mainly in biofilms. Full article

(This article belongs to the Special Issue Dermatophytes and Dermatophytoses)

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34 pages, 12799 KiB

Open AccessArticle

Polyphasic Systematics of the Fungicolous Genus Cladobotryum Based on Morphological, Molecular and Metabolomics Data

by Nikola Milic, Anastasia C. Christinaki, Dimitra Benaki, Aimilia A. Stavrou, Nikolaos Tsafantakis, Nikolas Fokialakis, Vassili N. Kouvelis and Zacharoula Gonou-Zagou

J. Fungi 2022, 8(8), 877; https://doi.org/10.3390/jof8080877 - 20 Aug 2022

Cited by 2 | Viewed by 2339

Abstract

(1) Background: Species of the anamorphic genus Cladobotryum, are known for their fungicolous lifestyle, making them important mycopathogens in fungiculture. Many morphological, ecological, and molecular phylogenetic studies of the genus have been done to date, but taxonomic uncertainties and challenges still remain. [...] Read more.

(1) Background: Species of the anamorphic genus Cladobotryum, are known for their fungicolous lifestyle, making them important mycopathogens in fungiculture. Many morphological, ecological, and molecular phylogenetic studies of the genus have been done to date, but taxonomic uncertainties and challenges still remain. Fungal secondary metabolites, being vastly diverse, are utilised as an extra tool in fungal systematics. Despite being studied for their potentially bioactive compounds, Cladobotryum species are insufficiently investigated regarding metabolomics. (2) Methods: The aim of this study is the identification of Greek strains of Cladobotryum by integrating morphological data, ITS-based phylogeny, and ¹H NMR-based metabolomics into a polyphasic approach. (3) Results: Twenty-three strains, isolated from sporophores of macromycetes inhabiting diverse Greek ecosystems, were morphologically identified as Cladobotryum apiculatum, C. fungicola, C. mycophilum, C. varium, C. verticillatum, and Hypomyces rosellus (anamorph C. dendroides), whereas seven strains, which produced red-pigmented metabolites, presented an ambiguous taxonomic position at the species level. Molecular phylogenetics and metabolomics corroborated the morphological findings. (4) Conclusions: Thorough morphological study, ITS region-based phylogeny, and NMR-based metabolomics contribute complementarily to resolving the genus Cladobotryum systematics. Full article

(This article belongs to the Special Issue Fungal Diversity in Europe)

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14 pages, 2054 KiB

Open AccessArticle

Characterization of the Fungal Community in Fritillariae Cirrhosae Bulbus through DNA Metabarcoding

by Jingsheng Yu, Wenjuan Zhang, Yujie Dao, Meihua Yang and Xiaohui Pang

J. Fungi 2022, 8(8), 876; https://doi.org/10.3390/jof8080876 - 19 Aug 2022

Cited by 2 | Viewed by 1323

Abstract

Fritillariae Cirrhosae Bulbus (FCB) is a well-known and precious traditional Chinese medicine with a medicinal history spanning thousands of years. In recent years, it has been reported that fungal and mycotoxin contamination influenced the safety and quality of FCB. It is essential to [...] Read more.

Fritillariae Cirrhosae Bulbus (FCB) is a well-known and precious traditional Chinese medicine with a medicinal history spanning thousands of years. In recent years, it has been reported that fungal and mycotoxin contamination influenced the safety and quality of FCB. It is essential to systematically study the fungal community for the early warning of fungal and mycotoxin contamination in this herb. A total of 15 FCB samples were collected from five provinces in China, and the fungal communities in the FCB samples were analyzed via amplifying the internal transcribed spacer 2 region through the Illumina Miseq PE300 platform. Furthermore, we compared the differences in fungal community in five groups based on collection areas. Results showed that Ascomycota (41.58–99.66%) and Mucoromycota (0–57.42%) were dominant at the phylum level. Eurotiomycetes (8.49–63.93%), Eurotiales (8.49–63.53%), and Aspergillaceae (8.49–63.51%) were the most abundant at the class, order, and family levels. Aspergillus (8.49–63.41%), Rhizopus (0–57.42%), Fusarium (0–22.81%), Cladosporium (0.16–9.14%), and Alternaria (0.06–17.95%) were the main genera in FCB samples. A total of 34 fungal taxa were identified at the species level, including five potentially toxigenic fungi namely Penicillium brevicompactum, P. citrinum, P. oxalicum, Trichothecium roseum, and Aspergillus restrictus. The differences in fungal community between the five groups were observed. Our findings provide references for the safe utilization and quality improvement of FCB. Full article

(This article belongs to the Special Issue Molecular Markers for Fungal Detection and Identification)

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16 pages, 13492 KiB

Open AccessReview

Epigenetic Regulation of Antifungal Drug Resistance

by Sandip Patra, Mayur Raney, Aditi Pareek and Rupinder Kaur

J. Fungi 2022, 8(8), 875; https://doi.org/10.3390/jof8080875 - 19 Aug 2022

Cited by 3 | Viewed by 3154

Abstract

In medical mycology, epigenetic mechanisms are emerging as key regulators of multiple aspects of fungal biology ranging from development, phenotypic and morphological plasticity to antifungal drug resistance. Emerging resistance to the limited therapeutic options for the treatment of invasive fungal infections is a [...] Read more.

In medical mycology, epigenetic mechanisms are emerging as key regulators of multiple aspects of fungal biology ranging from development, phenotypic and morphological plasticity to antifungal drug resistance. Emerging resistance to the limited therapeutic options for the treatment of invasive fungal infections is a growing concern. Human fungal pathogens develop drug resistance via multiple mechanisms, with recent studies highlighting the role of epigenetic changes involving the acetylation and methylation of histones, remodeling of chromatin and heterochromatin-based gene silencing, in the acquisition of antifungal resistance. A comprehensive understanding of how pathogens acquire drug resistance will aid the development of new antifungal therapies as well as increase the efficacy of current antifungals by blocking common drug-resistance mechanisms. In this article, we describe the epigenetic mechanisms that affect resistance towards widely used systemic antifungal drugs: azoles, echinocandins and polyenes. Additionally, we review the literature on the possible links between DNA mismatch repair, gene silencing and drug-resistance mechanisms. Full article

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

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13 pages, 309 KiB

Open AccessArticle

Interactive Effects of Water Deficiency and Endophytic Beauveria bassiana on Plant Growth, Nutrient Uptake, Secondary Metabolite Contents, and Antioxidant Activity of Allium cepa L.

by Lizeka Pretty Gana, Ninon G. E. R. Etsassala and Felix Nchu

J. Fungi 2022, 8(8), 874; https://doi.org/10.3390/jof8080874 - 19 Aug 2022

Cited by 5 | Viewed by 1567

Abstract

The main aim of this research study was to assess the interactive effects of water deficiency and the inoculation of a growth medium with Beauveria bassiana on plant growth, nutrient uptake, secondary metabolite contents, and antioxidant capacity of Allium cepa. A. cepa [...] Read more.

The main aim of this research study was to assess the interactive effects of water deficiency and the inoculation of a growth medium with Beauveria bassiana on plant growth, nutrient uptake, secondary metabolite contents, and antioxidant capacity of Allium cepa. A. cepa seedlings were simultaneously exposed to one of three watering regime treatments (3-day, 5-day, and 7-day watering intervals) and B. bassiana or no-fungus treatment. While the longest watering interval induced reduced plant growth, plants inoculated with B. bassiana had better results than those in the no-fungus treatment. Significant interactive effects (DF = 2.0; p < 0.05) between fungus and the watering regime on P, K, and Fe contents were observed. Remarkably, at the 7-day watering interval, the polyphenol content (64.0 mg GAE/L) was significantly higher in the plants treated with B. bassiana than in the no-fungus-treated plants. The watering interval significantly affected (DF = 2, 6; F = 7.4; p < 0.05) total flavonol contents among the fungus-treated plants. The interaction of the watering interval and B. bassiana inoculation (DF = 2.0; F = 3.8; p < 0.05) significantly influenced the flavonol content in the onion bulbs and the antioxidant activities of onion bulbs in the FRAP assay (DF = 2.0; F = 4.1; p < 0.05). Full article

(This article belongs to the Special Issue Entomopathogenic Fungi in Biological Plant Protection: The Machinery of Multicomponent System Interactions)

12 pages, 1331 KiB

Open AccessArticle

Exploring Biocontrol of Unwanted Fungi by Autochthonous Debaryomyces hansenii Strains Isolated from Dry Meat Products

by Helena Chacón-Navarrete, Francisco Ruiz-Pérez, Francisco J. Ruiz-Castilla and José Ramos

J. Fungi 2022, 8(8), 873; https://doi.org/10.3390/jof8080873 - 19 Aug 2022

Cited by 3 | Viewed by 1991

Abstract

The exploration of alternatives to the use of chemical preservatives in food is a topic that has attracted great attention. The implementation of regulations associated with the reduction of these elements directly affects the production of cured meat products, with the premise of [...] Read more.

The exploration of alternatives to the use of chemical preservatives in food is a topic that has attracted great attention. The implementation of regulations associated with the reduction of these elements directly affects the production of cured meat products, with the premise of looking for more “natural” alternatives. From a previously identified collection of 24 strains of Debaryomyces hansenii, isolated from dry meat products of the “Valle de los Pedroches” (Córdoba), a screening was carried out to determine which strains had inhibitory potential against a battery of fungi belonging to the genera Aspergillus, Penicillium, and Candida. After a series of general trials, four strains showing the greatest potential were selected by a streak inhibition assay performed at several concentrations of NaCl. The inhibitory activity of the selected D. hansenii strains was later evaluated by measuring their fungal antagonistic diffusible and volatile compound production following radial inhibition and mouth-to-mouth approaches, respectively. Growth aspects, sporulation, and morphology changes were also considered during these assays. The results support ideas already raised in previous studies, such as the presence of D. hanseniii could imply a reduction of pathogenic fungi in food. Autochthonous yeast strains inhibited not only the mycelial growth, but also sporulation, which strengthens the biocontrol activity of this yeast. Our results show that, under certain conditions, all tested D. hansenii strains were able to alter the growth/development of fungi, being especially evident in the cases of Penicillium expansum and Aspergillus niger. Finally, our research can facilitate the future comparison of results in this area, since we contributed to standardize the methodology described to date, we quantified the number of yeast cells and spores used during the experiments, we homogenized growth conditions for both, yeasts, and molds, and applied an image analyzer software to quantify the growth of the studied microorganisms in solid media. Full article

(This article belongs to the Special Issue Recent Advances in Fundamental Research and Biotechnological Applications in Debaryomyces hansenii)

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10 pages, 2699 KiB

Open AccessArticle

In Vitro Activity of Novel Lipopeptides against Triazole-Resistant Aspergillus fumigatus

by Simona Fioriti, Oscar Cirioni, Oriana Simonetti, Lucia Franca, Bianca Candelaresi, Francesco Pallotta, Damian Neubauer, Elzbieta Kamysz, Wojciech Kamysz, Benedetta Canovari, Lucia Brescini, Gianluca Morroni and Francesco Barchiesi

J. Fungi 2022, 8(8), 872; https://doi.org/10.3390/jof8080872 - 18 Aug 2022

Cited by 3 | Viewed by 2306

Abstract

Aspergillosis, which is mainly sustained by Aspergillus fumigatus, includes a broad spectrum of diseases. They are usually severe in patients with co-morbidities. The first-line therapy includes triazoles, for which an increasing incidence of drug resistance has been lately described. As a consequence [...] Read more.

Aspergillosis, which is mainly sustained by Aspergillus fumigatus, includes a broad spectrum of diseases. They are usually severe in patients with co-morbidities. The first-line therapy includes triazoles, for which an increasing incidence of drug resistance has been lately described. As a consequence of this, the need for new and alternative antifungal molecules is absolutely necessary. As peptides represent promising antimicrobial molecules, two lipopeptides (C14-NleRR-NH₂, C14-WRR-NH₂) were tested to assess the antifungal activity against azole-resistant A. fumigatus. Antifungal activity was evaluated by determination of minimum inhibitory concentrations (MICs), time–kill curves, XTT assay, optical microscopy, and checkerboard combination with isavuconazole. Both lipopeptides showed antifungal activity, with MICs ranging from 8 mg/L to 16 mg/L, and a dose-dependent effect was confirmed by both time–kill curves and XTT assays. Microscopy showed that hyphae growth was hampered at concentrations equal to or higher than MICs. The rising antifungal resistance highlights the usefulness of novel compounds to treat severe fungal infections. Although further studies assessing the activity of lipopeptides are necessary, these molecules could be effective antifungal alternatives that overcome the current resistances. Full article

(This article belongs to the Special Issue Pharmacodynamics of Antifungal Drugs)

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50 pages, 8346 KiB

Open AccessArticle

Ecological Factors Influencing the Occurrence of Macrofungi from Eastern Mountainous Areas to the Central Plains of Jilin Province, China

by Jia-Jun Hu, Gui-Ping Zhao, Yong-Lan Tuo, Zheng-Xiang Qi, Lei Yue, Bo Zhang and Yu Li

J. Fungi 2022, 8(8), 871; https://doi.org/10.3390/jof8080871 - 18 Aug 2022

Cited by 7 | Viewed by 2345

Abstract

Macrofungi are essential in forest ecological functioning. Their distribution and diversity are primarily impacted by vegetation, topography, and environmental factors, such as precipitation and temperature. However, the composition and topographical changes of the macrofungi between the eastern mountainous area and central plains of [...] Read more.

Macrofungi are essential in forest ecological functioning. Their distribution and diversity are primarily impacted by vegetation, topography, and environmental factors, such as precipitation and temperature. However, the composition and topographical changes of the macrofungi between the eastern mountainous area and central plains of Jilin Province are currently unknown. For this study, we selected six investigational sites representing three different topographical research sites in Jilin Province to assess macrofungal diversity, and applied a quadrat sampling method. Macro- and micro-morphological characteristics combined with the molecular method were used to identify the collected macrofungi. Meanwhile, selected meteorological data were obtained for statistical analysis. As a result, 691 species were identified, of which Agarics were the most common, accounting for 60.23%, while the Cantharelloid fungi were the least common (0.91%). Furthermore, most of the shared genera (species) were saprophytic. The α diversity showed that the species diversity and richness in Longwan National Forest Park (B2) were the highest at the genus level. The mycorrhizal macrofungi proportion revealed that Quanshuidong Forest Farm (A1) was the healthiest. Finally, species composition similarity decreased with the transition from mountainous to hilly plains. We concluded that the occurrence of macrofungi was most influenced by vegetation. The air humidity, precipitation, and wind velocity were also found to significantly impact the occurrence of macrofungi. Finally, the mycorrhizal:saprophytic ratios and species similarity decreased with the transition from the mountainous area to the plains. The results presented here help elucidate the macrofungi composition and their relationship with environmental factors and topography in Jilin Province, which is crucial for sustainable utilization and future conservation. Full article

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17 pages, 3299 KiB

Open AccessArticle

Cystathionine Gamma-Lyase Regulate Psilocybin Biosynthesis in Gymnopilus dilepis Mushroom via Amino Acid Metabolism Pathways

by Sen Yao, Chuanzheng Wei, Hui Lin, Peng Zhang, Yuanyuan Liu, Youjin Deng, Qianhui Huang and Baogui Xie

J. Fungi 2022, 8(8), 870; https://doi.org/10.3390/jof8080870 - 18 Aug 2022

Viewed by 2446

Abstract

As a potential medicine for the treatment of depression, psilocybin has gradually attracted attention. To elucidate the molecular mechanism regulating psilocybin synthesis in Gymnopilus dilepis, ultra-performance liquid chromatography (UPLC) was used to detect the changes in psilocybin content after S-adenosyl-l-homocysteine (SAH) treatment [...] Read more.

As a potential medicine for the treatment of depression, psilocybin has gradually attracted attention. To elucidate the molecular mechanism regulating psilocybin synthesis in Gymnopilus dilepis, ultra-performance liquid chromatography (UPLC) was used to detect the changes in psilocybin content after S-adenosyl-l-homocysteine (SAH) treatment and the changes of psilocybin content in different parts (stipe and pileus), and RNA-Seq was used to explore the mechanism of psilocybin content changes. In this study, the psilocybin content in G. dilepis mycelia treated with SAH was significantly lower than that in the control group, and the content of psilocybin in the stipe was significantly higher than that in the pileus. Transcriptome analysis revealed that differential expression genes (DEGs) were associated with cysteine and methionine metabolism. In particular, the transcription levels of genes encoding Cystathionine gamma-lyase (CTH) in different treatments and different parts were positively correlated with psilocybin content. In addition, we found that the exogenous addition of CTH activity inhibitor (DL-propargylglycine, PAG) could reduce the content of psilocybin and L-serine, and the content of psilocybin and L-serine returned to normal levels after L-cysteine supplementation, suggesting that psilocybin synthesis may be positively correlated with L-cysteine or CTH, and L-cysteine regulates the synthesis of psilocybin by affecting L-serine and 4-hydroxy-L-tryptophan. In conclusion, this study revealed a new molecular mechanism that affects psilocybin biosynthesis, which can provide a theoretical basis for improving psilocybin synthesis and the possibility for the development of biomedicine. Full article

(This article belongs to the Special Issue Fungal Applications in Bioenergy, Bioremediation, Biomedicine, Biocontrol, and Biomaterials)

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25 pages, 6817 KiB

Open AccessArticle

Virulence-Associated Genes of Calonectria ilicola, Responsible for Cylindrocladium Black Rot

by Xinyu Chen, Mei Luo, Wei Wu, Zhangyong Dong and Huasong Zou

J. Fungi 2022, 8(8), 869; https://doi.org/10.3390/jof8080869 - 18 Aug 2022

Cited by 4 | Viewed by 1635

Abstract

The Cylindrocladium black rot caused by Calonectria ilicicola is a destructive disease affecting a broad range of crops. Herein, we study virulence-associated genes of C. ilicicolaCi14017 isolated from diseased peanut roots (Arachis hypogaea L.). Ci14017 was identified via phylogenetic [...] Read more.

The Cylindrocladium black rot caused by Calonectria ilicicola is a destructive disease affecting a broad range of crops. Herein, we study virulence-associated genes of C. ilicicolaCi14017 isolated from diseased peanut roots (Arachis hypogaea L.). Ci14017 was identified via phylogenetic analysis of the internal transcribed spacer region and standard Koch’s postulate testing. Virulence-associated genes were based on genome analyses and comparative analysis of transcriptome and proteome profiles of sensitive and resistant peanut cultivars. Ci14017 identified as C. ilicicola has a 66 Mb chromosome with 18,366 predicted protein-coding genes. Overall, 46 virulence-associated genes with enhanced expression levels in the sensitive cultivars were identified. Sequence analysis indicated that the 46 gene products included two merops proteins, eight carbohydrate-active enzymes, seven cytochrome P450 enzymes, eight lipases, and 20 proteins with multi-conserved enzyme domains. The results indicate a complex infection mechanism employed by Ci14017 for causing Cylindrocladium black rot in peanuts. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens)

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23 pages, 3500 KiB

Open AccessArticle

Two Novel Genera, Neostemphylium and Scleromyces (Pleosporaceae) from Freshwater Sediments and Their Global Biogeography

by Daniel Torres-Garcia, Dania García, José F. Cano-Lira and Josepa Gené

J. Fungi 2022, 8(8), 868; https://doi.org/10.3390/jof8080868 - 17 Aug 2022

Cited by 6 | Viewed by 2425

Abstract

Although the Pleosporaceae is one of the species-richest families in the Pleosporales, research into less-explored substrates can contribute to widening the knowledge of its diversity. In our ongoing survey on culturable Ascomycota from freshwater sediments in Spain, several pleosporacean specimens of taxonomic [...] Read more.

Although the Pleosporaceae is one of the species-richest families in the Pleosporales, research into less-explored substrates can contribute to widening the knowledge of its diversity. In our ongoing survey on culturable Ascomycota from freshwater sediments in Spain, several pleosporacean specimens of taxonomic interest were isolated. Phylogenetic analyses based on five gene markers (ITS, LSU, gapdh, rbp2, and tef1) revealed that these fungi represent so far undescribed lineages, which are proposed as two novel genera in the family, i.e., Neostemphylium typified by Neostemphylium polymorphum sp. nov., and Scleromyces to accommodate Scleromyces submersus sp. nov. Neostemphylium is characterized by the production of phaeodictyospores from apically swollen and darkened conidiogenous cells, the presence of a synanamorph that consists of cylindrical and brown phragmoconidia growing terminally or laterally on hyphae, and by the ability to produce secondary conidia by a microconidiation cycle. Scleromyces is placed phylogenetically distant to any genera in the family and only produces sclerotium-like structures in vitro. The geographic distribution and ecology of N. polymorphum and Sc. submersus were inferred from metabarcoding data using the GlobalFungi database. The results suggest that N. polymorphum is a globally distributed fungus represented by environmental sequences originating primarily from soil samples collected in Australia, Europe, and the USA, whereas Sc. submersus is a less common species that has only been found associated with one environmental sequence from an Australian soil sample. The phylogenetic analyses of the environmental ITS1 and ITS2 sequences revealed at least four dark taxa that might be related to Neostemphylium and Scleromyces. The phylogeny presented here allows us to resolve the taxonomy of the genus Asteromyces as a member of the Pleosporaceae. Full article

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

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17 pages, 4879 KiB

Open AccessArticle

The Characterization and the Biological Activity of Phytotoxin Produced by Paraphoma radicina

by Shu-Zhong Dang and Yan-Zhong Li

J. Fungi 2022, 8(8), 867; https://doi.org/10.3390/jof8080867 - 17 Aug 2022

Cited by 2 | Viewed by 1289

Abstract

Paraphoma radicina is a new pathogen that causes alfalfa paraphoma root rot (APRR), leading to alfalfa production losses. The resistance levels of 30 alfalfa cultivars to APRR have already been characterized. However, the pathogenic mechanism of P. radicina is still unclear. This study [...] Read more.

Paraphoma radicina is a new pathogen that causes alfalfa paraphoma root rot (APRR), leading to alfalfa production losses. The resistance levels of 30 alfalfa cultivars to APRR have already been characterized. However, the pathogenic mechanism of P. radicina is still unclear. This study aimed to assess the effects of a crude toxin extracted from P. radicina cell-free culture filtrate (CFCF) on susceptible and resistant cultivars of alfalfa. Meanwhile, the crude toxin components were detected using gas chromatography-mass spectrometry (GC-MS) analysis. CFCF cultured in MEB medium for 14 days and crude toxin extracted by ethyl acetate induced significant phytotoxicity caused the average lesion areas of 5.8 and 3.9 mm², respectively, on alfalfa leaves. The crude toxin exhibited resistance to high temperature, as shown by a lesion area of 3.6 mm² when treated at 120 °C for 30 min. Different concentrations of the crude toxin in water and MS medium had different effects on susceptible and resistant cultivars. Moreover, the crude toxin affected the plasma membrane, mitochondria, and nuclear membranes of alfalfa root cortical cells. Further, it induced significant phytotoxicity on Sonchus oleraceus L., Capsella bursa-pastoris (Linn.) Medic, and Chenopodium album L. Agropyron cristatum L. (average lesion areas; 11.6, 15.8, 21.4, and 6.2 mm², respectively), indicating that the crude toxin of P. radicina is a non-host-selective toxin. GC-MS analysis detected four possible active substances in the toxin (3-hydroxypyridine, 5-methylresorcinol, 3-Hydroxypropionic acid, and 4-Hydroxyphenylethanol). Therefore, this study may provide insight into the pathogenic mechanism of P. radicina to alfalfa. Full article

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

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13 pages, 1258 KiB

Open AccessArticle

Arbuscular Mycorrhizal Fungi Reduce Cadmium Leaching from Sand Columns by Reducing Availability and Enhancing Uptake by Maize Roots

by Zihao Yu, Xiaoling Zhao, Xinran Liang, Zuran Li, Lei Wang, Yongmei He and Fangdong Zhan

J. Fungi 2022, 8(8), 866; https://doi.org/10.3390/jof8080866 - 17 Aug 2022

Cited by 8 | Viewed by 1568

Abstract

To explore the effect of arbuscular mycorrhizal fungi (AMF) on the environmental migration of cadmium (Cd), a sand column-maize system containing 20 mg·L⁻¹ Cd solution was used to investigate the AMF effect on maize growth, Cd uptake by maize, Cd adsorption by [...] Read more.

To explore the effect of arbuscular mycorrhizal fungi (AMF) on the environmental migration of cadmium (Cd), a sand column-maize system containing 20 mg·L⁻¹ Cd solution was used to investigate the AMF effect on maize growth, Cd uptake by maize, Cd adsorption by sand and Cd leaching loss. The results showed that AMF significantly increased the content of EE-GRSP and T-GRSP by 34.9% and 37.2%, respectively; the secretion of malonic acid, oxalic acid and succinic acid increased by 154.2%, 54.0% and 11.0%, respectively; the secretion of acetic acid and citric acid increased by 95.5% and 59.9%, respectively; and the length, surface area, volume, tip number and cross number of maize roots decreased by 10%, 15%, 17%, 20% and 36.4%, respectively. AMF significantly increased Cd adsorption by sand by 6.2%, Cd uptake by maize by 68.1%, and Cd leaching loss by 84.6%. In the sand column-maize system, 92.3% of the total Cd was adsorbed by sand, 5.9% was taken up by maize and 1.8% was lost due to leaching. Moreover, Cd adsorption by sand was significantly positively correlated with the GRSP content and oxalic acid secretion, and Cd uptake by roots was significantly negatively correlated with Cd leaching loss. Overall, AMF reduced the loss of Cd in the leaching solution by promoting the release of oxalic acid and GRSP, increasing the adsorption of Cd in the sand and fixing the Cd in the plant to the roots. Full article

(This article belongs to the Special Issue Plant and Fungal Interactions, 2nd Edition)

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16 pages, 8845 KiB

Open AccessArticle

Kinase Hog1 and Adr1 Opposingly Regulate Haploid Cell Morphology by Controlling Vacuole Size in Sporisorium scitamineum

by Enping Cai, Meixin Yan, Xian Sun, Rong Zeng, Wenqiang Zheng, Yizhen Deng, Zide Jiang and Changqing Chang

J. Fungi 2022, 8(8), 865; https://doi.org/10.3390/jof8080865 - 17 Aug 2022

Cited by 2 | Viewed by 1290

Abstract

Morphogenesis is a strictly regulated efficient system in eukaryotes for adapting to environmental changes. However, the morphogenesis regulatory mechanism in smut fungi is not clear. This study reports a relationship between MAP kinase Hog1 and cAMP-dependent protein kinase A catalytic subunit (Adr1) for [...] Read more.

Morphogenesis is a strictly regulated efficient system in eukaryotes for adapting to environmental changes. However, the morphogenesis regulatory mechanism in smut fungi is not clear. This study reports a relationship between MAP kinase Hog1 and cAMP-dependent protein kinase A catalytic subunit (Adr1) for the morphological regulation in the sugarcane pathogen Sporisorium scitamineum. The results demonstrated that MAP kinase Hog1 and cAMP/PKA signaling pathways are essential for the morphological development of S. scitamineum. Interestingly, MAP kinase Hog1 and cAMP/PKA signaling pathways’ defective mutants exhibit an opposite morphological phenotype. The morphology of cAMP/PKA defective mutants is recovered by deleting the SsHOG1 gene. However, MAP kinase Hog1 and cAMP-dependent protein kinase catalytic subunit Adr1 do not interfere with each other. Further investigations showed that kinase Hog1 and Adr1 antagonistically regulates the vacuolar size, which contributes to the cell size and determines the cellular elongation rates. Kinase Hog1 and Adr1 also antagonistically balanced the cell wall integrity and permeability. Taken together, kinase Hog1- and Adr1-based opposing morphogenesis regulation of S. scitamineum by controlling the vacuolar size and cell wall permeability is established during the study. Full article

(This article belongs to the Special Issue Smut Fungi 2.0)

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15 pages, 2655 KiB

Open AccessArticle

Effect of Vitamin-D-Enriched Edible Mushrooms on Vitamin D Status, Bone Health and Expression of CYP2R1, CYP27B1 and VDR Gene in Wistar Rats

by Muneeb Ahmad Malik, Yasmeena Jan, Lamya Ahmed Al-Keridis, Afrozul Haq, Javed Ahmad, Mohd Adnan, Nawaf Alshammari, Syed Amir Ashraf and Bibhu Prasad Panda

J. Fungi 2022, 8(8), 864; https://doi.org/10.3390/jof8080864 - 17 Aug 2022

Cited by 3 | Viewed by 2785

Abstract

Vitamin D deficiency is highly prevalent in India and worldwide. Mushrooms are important nutritional foods, and in this context shiitake (Lentinula edodes), button (Agaricus bisporus) and oyster (Pleurotus ostreatus) mushrooms are known for their bioactive properties. The [...] Read more.

Vitamin D deficiency is highly prevalent in India and worldwide. Mushrooms are important nutritional foods, and in this context shiitake (Lentinula edodes), button (Agaricus bisporus) and oyster (Pleurotus ostreatus) mushrooms are known for their bioactive properties. The application of ultraviolet (UV) irradiation for the production of substantial amounts of vitamin D₂ is well established. Levels of serum 25-hydroxy vitamin D (25-OHD), parathyroid hormone (PTH), calcium, phosphorus and alkaline phosphatase (ALP) were significantly (p < 0.05) improved in vitamin-D-deficient rats after feeding with UVB irradiated mushrooms for 4 weeks. Further, microscopic observations indicate an improvement in the osteoid area and the reduction in trabecular separation of the femur bone. In addition, the level of expression of the vitamin D receptor (VDR) gene and genes metabolizing vitamin D were explored. It was observed that in mushroom-fed and vitamin-D-supplemented groups, there was upregulation of CYP2R1 and VDR, while there was downregulation of CYP27B1 in the liver. Further, CYP2R1 was downregulated, while CYP27B1 and VDR were upregulated in kidney tissue. Full article

(This article belongs to the Special Issue Mushrooms—Mycotherapy and Mycochemistry 2.0)

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10 pages, 602 KiB

Open AccessArticle

Targeted NGS-Based Analysis of Pneumocystis jirovecii Reveals Novel Genotypes

by Dora Pungan, Taylor Eddens, Kejing Song, Meredith A. Lakey, Nicolle S. Crovetto, Simran K. Arora, Shahid Husain and Jay K. Kolls

J. Fungi 2022, 8(8), 863; https://doi.org/10.3390/jof8080863 - 17 Aug 2022

Cited by 1 | Viewed by 1911

Abstract

Pneumocystis jirovecii is an important etiological agent of pneumonia that is underdiagnosed due to the inability to culture the organism. The 2019 PERCH study identified Pneumocystis as the top fungal cause of pneumonia in HIV-negative children using a PCR cutoff of 10⁴ [...] Read more.

Pneumocystis jirovecii is an important etiological agent of pneumonia that is underdiagnosed due to the inability to culture the organism. The 2019 PERCH study identified Pneumocystis as the top fungal cause of pneumonia in HIV-negative children using a PCR cutoff of 10⁴ copies of Pneumocystis per mL of sample in nasopharyngeal/oropharyngeal (NP/OP) specimens. Given that Pneumocystis consists of an environmental ascus form and a trophic from (the latter is the form that attaches to the lung epithelium), it is possible that life-form-specific molecular assays may be useful for diagnosis. However, to accomplish this goal, these assays require genotypic information, as the current fungal genomic data are largely from the US and Europe. To genotype Pneumocystis across the globe, we developed an NGS-based genotyping assay focused on genes expressed in asci as well as trophs using PERCH throat swabs from Africa, Bangladesh, and Thailand, as well as North American samples. The NGS panel reliably detected 21 fungal targets in these samples and revealed unique genotypes in genes expressed in trophs, including Meu10, an ascospore assembly gene; two in mitochondrial gene ATP8, and the intergenic region between COX1 and ATP8. This assay can be used for enhanced Pneumocystis epidemiology to study outbreaks but also permits more accurate RT-CPR- or CRISPR-based assays to be performed to improve the non-bronchoscopic diagnosis of this under-reported fungal pathogen. Full article

(This article belongs to the Special Issue Antifungal Immune Responses against Invasive Mycoses)

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17 pages, 1928 KiB

Open AccessArticle

Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602

by Thomas Schafhauser, Daniel Wibberg, Antonia Binder, Christian Rückert, Tobias Busche, Wolfgang Wohlleben and Jörn Kalinowski

J. Fungi 2022, 8(8), 862; https://doi.org/10.3390/jof8080862 - 16 Aug 2022

Cited by 1 | Viewed by 1567

Abstract

The gilled mushroom Clitopilus passeckerianus (Entolomataceae, Agaricales, Basidiomycota) is well known to produce the terpenoid pleuromutilin, which is the biotechnological basis for medically important antibiotics such as lefamulin and retapamulin. Their unique mode of action and good tolerance entails an increasing demand of [...] Read more.

The gilled mushroom Clitopilus passeckerianus (Entolomataceae, Agaricales, Basidiomycota) is well known to produce the terpenoid pleuromutilin, which is the biotechnological basis for medically important antibiotics such as lefamulin and retapamulin. Their unique mode of action and good tolerance entails an increasing demand of pleuromutilin-derived antibiotics in veterinary and human health care. Surprisingly, despite their pharmaceutical importance, no genome sequence is available of any pleuromutilin-producing fungus. Here, we present the high-quality draft genome sequence of the pleuromutilin-producer C. passeckerianus DSM1602 including functional genome annotation. More precisely, we employed a hybrid assembly strategy combining Illumina sequencing and Nanopore sequencing to assemble the mitochondrial genome as well as the nuclear genome. In accordance with the dikaryotic state of the fungus, the nuclear genome has a diploid character. Interestingly, the mitochondrial genome appears duplicated. Bioinformatic analysis revealed a versatile secondary metabolism with an emphasis on terpenoid biosynthetic enzymes in C. passeckerianus and also in related strains. Two alleles of biosynthetic gene clusters for pleuromutilin were found in the genome of C. passeckerianus. The pleuromutilin genes were reassembled with yeast-specific elements for heterologous expression in Saccharomyces cerevisiae. Our work lays the foundation for metabolic strain engineering towards higher yields of the valuable compound pleuromutilin. Full article

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

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11 pages, 2213 KiB

Open AccessArticle

Evaluation of the Potential Entomopathogenic Fungi Purpureocillium lilacinum and Fusarium verticillioides for Biological Control of Forcipomyia taiwana (Shiraki)

by Nian-Tong Ni, Sing-Shan Wu, Kuei-Min Liao, Wu-Chun Tu, Chuen-Fu Lin and Yu-Shin Nai

J. Fungi 2022, 8(8), 861; https://doi.org/10.3390/jof8080861 - 16 Aug 2022

Cited by 1 | Viewed by 2164

Abstract

Forcipomyia taiwana (Diptera: Ceratopogonidae) is a nuisance blood-sucking pest to humans in Taiwan. An F. taiwana bite causes itching and redness and usually causes serious harassment to human outdoor activity. In terms of F. taiwana control, chemical pesticides are ineffective. Therefore, other efforts [...] Read more.

Forcipomyia taiwana (Diptera: Ceratopogonidae) is a nuisance blood-sucking pest to humans in Taiwan. An F. taiwana bite causes itching and redness and usually causes serious harassment to human outdoor activity. In terms of F. taiwana control, chemical pesticides are ineffective. Therefore, other efforts are needed. Fungal mycosis in the larvae, pupae, and emerging F. taiwana adults was found during the rearing of F. taiwana. In this study, six fungal isolates were isolated from infected cadavers and subjected to molecular identification. In addition, their biocontrol potential was evaluated against different life stages of F. taiwana. Based on the pathogenicity screening, two fungal isolates, NCHU-NPUST-175 and -178, which caused higher mortality on the fourth instar larvae of F. taiwana, were selected for virulence tests against different life stages of F. taiwana larvae. The results of the phylogenetic analysis indicated that the NCHU-NPUST-175 and -178 belonged to Purpureocillium lilacinum and Fusarium verticillioides, respectively. Bioassay against different life stages of F. taiwana with different spore concentrations (5 × 10⁵ to 5 × 10⁷ conidia/mL) revealed a dose-dependent effect on larvae for both fungal isolates, while only 38% and 50% mortality was found in highest concentration (5 × 10⁷ conidia/mL) at fourth instar larvae by Pl-NCHU-NPUST-175 and Fv-NCHU-NPUST-178, respectively. Moreover, reductions in egg-hatching rate and adult emergence rate were found, when the last stage of F. taiwana was inoculated with both fungal isolates, indicating the ovicidal potential and the impact of entomopathogenic fungi on the development of F. taiwana. In conclusion, Pl-NCHU-NPUST-175 and Fv-NCHU-NPUST-178 showed larvicidal activity, ovicidal activity, and impact on adult emergence on F. taiwana. Full article

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25 pages, 16080 KiB

Open AccessEditor’s ChoiceArticle

Occurrence, Diversity and Anti-Fungal Resistance of Fungi in Sand of an Urban Beach in Slovenia—Environmental Monitoring with Possible Health Risk Implications

by Monika Novak Babič, Nina Gunde-Cimerman, Martin Breskvar, Sašo Džeroski and João Brandão

J. Fungi 2022, 8(8), 860; https://doi.org/10.3390/jof8080860 - 16 Aug 2022

Cited by 9 | Viewed by 2746

Abstract

Beach safety regulation is based on faecal indicators in water, leaving out sand and fungi, whose presence in both matrices has often been reported. To study the abundance, diversity and possible fluctuations of mycobiota, fungi from sand and seawater were isolated from the [...] Read more.

Beach safety regulation is based on faecal indicators in water, leaving out sand and fungi, whose presence in both matrices has often been reported. To study the abundance, diversity and possible fluctuations of mycobiota, fungi from sand and seawater were isolated from the Portorož beach (Slovenia) during a 1-year period. Sand analyses yielded 64 species of 43 genera, whereas seawater samples yielded 29 species of 18 genera. Environmental and taxonomical data of fungal communities were analysed using machine learning approaches. Changes in the air and water temperature, sunshine hours, humidity and precipitation, air pressure and wind speed appeared to affect mycobiota. The core genera Aphanoascus, Aspergillus, Fusarium, Bisifusarium, Penicillium, Talaromyces, and Rhizopus were found to compose a stable community within sand, although their presence and abundance fluctuated along with weather changes. Aspergillus spp. were the most abundant and thus tested against nine antimycotics using Sensititre Yeast One kit. Aspergillus niger and A. welwitschiae isolates were found to be resistant to amphotericin B. Additionally, four possible human pollution indicators were isolated during the bathing season, including Meyerozyma, which can be used in beach microbial regulation. Our findings provide the foundations for additional research on sand and seawater mycobiota and show the potential effect of global warming and extreme weather events on fungi in sand and sea. Full article

(This article belongs to the Special Issue Fungal Diversity in Europe)

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36 pages, 6409 KiB

Open AccessReview

Coccidioides Species: A Review of Basic Research: 2022

by Theo N. Kirkland, David A. Stevens, Chiung-Yu Hung, Sinem Beyhan, John W. Taylor, Lisa F. Shubitz, Sascha H. Duttke, Arash Heidari, Royce H. Johnson, Stanley C. Deresinski, Antje Lauer and Joshua Fierer

J. Fungi 2022, 8(8), 859; https://doi.org/10.3390/jof8080859 - 16 Aug 2022

Cited by 5 | Viewed by 5186

Abstract

Coccidioides immitis and posadasii are closely related fungal species that cause coccidioidomycosis. These dimorphic organisms cause disease in immunocompetent as well as immunocompromised individuals and as much as 40% of the population is infected in the endemic area. Although most infections resolve spontaneously, [...] Read more.

Coccidioides immitis and posadasii are closely related fungal species that cause coccidioidomycosis. These dimorphic organisms cause disease in immunocompetent as well as immunocompromised individuals and as much as 40% of the population is infected in the endemic area. Although most infections resolve spontaneously, the infection can be prolonged and, in some instances, fatal. Coccidioides has been studied for more than 100 years and many aspects of the organism and the disease it causes have been investigated. There are over 500 manuscripts concerning Coccidioides (excluding clinical articles) referenced in PubMed over the past 50 years, so there is a large body of evidence to review. We reviewed the most accurate and informative basic research studies of these fungi including some seminal older studies as well as an extensive review of current research. This is an attempt to gather the most important basic research studies about this fungus into one publication. To focus this review, we will discuss the mycology of the organism exclusively rather than the studies of the host response or clinical studies. We hope that this review will be a useful resource to those interested in Coccidioides and coccidioidomycosis. Full article

(This article belongs to the Special Issue Biology, Immunology, Epidemiology, and Therapy of Fungal Infections: A Themed Issue Dedicated to Professor David A. Stevens)

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J. Fungi, Volume 8, Issue 8 (August 2022) – 131 articles

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