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Microorganisms
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Fungal Biology and Interactions, 2nd Edition
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Fungal Biology and Interactions, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (30 April 2025) | Viewed by 9469

Special Issue Editors

Prof. Dr. Renato Graciano de Paula

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Guest Editor
1. Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitoria 29047-105, ES, Brazil
2. National Institute of Science and Technology in Human Pathogenic Fungi (INCT-FUNVIR), São Paulo, Brazil
Interests: functional genomics; cellular signaling; biotechnology; secondary metabolism; filamentous fungi
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Roberto Nascimento Silva

E-Mail Website
Guest Editor
Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto 14049-900, SP, Brazil
Interests: filamentous fungi; molecular biology; cell signaling
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue “Fungal Biology and Interactions”.

Interactions involving fungi are of fundamental importance to human life and in biotechnological processes. Thus, in this Special Issue on "Fungal Biology and Interactions", we aim to present new research and trends regarding fungi–fungi, fungi–plants, fungi–environment, and fungi–microbial community interactions. Articles to be submitted should address basic biology, molecular interactions, cell signaling, pathogen–host relationships, climate change, biofuels and biomaterials, and sustainable agriculture.

Reviews, original research, and communications are welcome.

Prof. Dr. Renato Graciano de Paula
Prof. Dr. Roberto Nascimento Silva
Guest Editors

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Published Papers (9 papers)

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Research

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18 pages, 1352 KiB  
Article
Biological Characteristics and Fungicide Screening of Bipolaris oryzae Causing Leaf Spot on Banana in China
by Yanxiang Qi, Hong Zhao, Zhaojing Zhang, Yanfei Ouyang and Xin Zhang
Microorganisms 2025, 13(6), 1285; https://doi.org/10.3390/microorganisms13061285 - 30 May 2025
Viewed by 256
Abstract
Foliar diseases caused by various fungi severely affect the yield and quality of banana crops. This study was conducted to clarify the biological characteristics of Bipolaris oryzae (teleomorph: Cochliobolus miyabeanus), a pathogen reported in 2023 as a new etiological agent of leaf [...] Read more.
Foliar diseases caused by various fungi severely affect the yield and quality of banana crops. This study was conducted to clarify the biological characteristics of Bipolaris oryzae (teleomorph: Cochliobolus miyabeanus), a pathogen reported in 2023 as a new etiological agent of leaf spot in the banana variety ‘Pisang Mas’ (Musa acuminata, AA group) in Hainan Province, China, and to screen effective fungicides for its control. The results indicated that banana leaf extract agar (BLEA) and cornmeal agar (CMA) were the best media for the growth and sporulation of the pathogen, respectively. The pathogen grew best on a Czapek’s agar (CZA) medium with sucrose as a carbon source and yeast extract as a nitrogen source, while the optimal carbon and nitrogen sources for sporulation were lactose and beef extract, respectively. The pathogen could grow within a temperature range from 5 °C to 35 °C, and the optimal temperatures for growth and sporulation were 30 °C and 25 °C, respectively. Exposure to 50 °C for 10 min was lethal. Additionally, the pathogen could grow and sporulate within pH ranges of 4 to 10 and 4 to 9, respectively, and the optimal pH values for growth and sporulation were 5 and 8, respectively. The optimal photoperiods for growth and sporulation were 16 h light/8 h dark and 24 h light, respectively. Among the 12 tested fungicides, 500 g/L of iprodione SC showed the highest toxicity against B. oryzae, with an EC50 value of 0.08 μg/mL, followed by 30% difenoconazole-azoxystrobin SC and 125 g/L of epoxiconazole SC, with EC50 values of 0.13 μg·mL−1 and 0.20 μg/mL, respectively. A fungicide containing 40% chlorothalonil SC had the poorest fungicidal activity, with an EC50 value of 155.98 μg/mL. An artificial inoculation pot experiment showed that 125 g/L of epoxiconazole SC at 250 μg/mL, 500 g/L of iprodione SC at 1667 μg/mL, and 30% difenoconazole-azoxystrobin SC at 250 μg/mL provided a protective control efficacy of 100% against B. oryzae, while 125 g/L of epoxiconazole SC at 250 μg/mL and 500 g/L of iprodione SC at 1667 μg/mL provided a curative control efficacy of greater than 60%. This study clarified the optimal conditions for the mycelial growth and sporulation of B. oryzae isolated from banana and screened out fungicides with effective inhibitory activities. These results can provide guidance for field applications and the management of leaf spot caused by B. oryzae in banana. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)
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18 pages, 4742 KiB  
Article
Characterization and Genome Analysis of Fusarium oxysporum Provides Insights into the Pathogenic Mechanisms of the Pokkah Boeng Disease in China
by Wenfeng Lin, Chi Zhang, Sehrish Akbar, Suyan Wu, Yabing Yue, Gege Wang, Yu Zhou, Charles A. Powell, Wei Yao, Jianlong Xu, Baoshan Chen, Muqing Zhang and Yixue Bao
Microorganisms 2025, 13(3), 573; https://doi.org/10.3390/microorganisms13030573 - 3 Mar 2025
Viewed by 874
Abstract
Pokkah Boeng Disease (PBD) is a severe and devastating disease that causes significant damage and yield losses in China. The pathogenic fungus Fusarium oxysporum is responsible for the rapid onset of top rot symptoms in sugarcane. In this study, we selected a representative [...] Read more.
Pokkah Boeng Disease (PBD) is a severe and devastating disease that causes significant damage and yield losses in China. The pathogenic fungus Fusarium oxysporum is responsible for the rapid onset of top rot symptoms in sugarcane. In this study, we selected a representative strain, BS2-6, to perform morphological observations of colonies and determine pathogenicity. We examined the effects of BS2-6 infestation on the ultrastructure of sugarcane leaves. Moreover, we sequenced the whole genome of BS2-6 and examined the effects of various nitrogen sources and chemical reagents on its growth and pathogenicity. Our results indicate that sugarcane leaves inoculated with BS2-6 quickly succumb to heart leaf and growing rot. Ultrastructural analysis revealed that the surface tissues of the diseased leaves were destroyed with mycelium, and conidia blocked leaf stomata, which ultimately led to the degradation of leaf tissues. Ammoniacal nitrogen significantly promoted mycelial growth, pigment secretion, and the expression of genes related to secondary metabolite synthesis, thereby accelerating the development of PBD. In addition, we found that carbendazim effectively inhibited the growth of BS2-6 at various concentrations. These findings provide important insights for the effective prevention and control of PBD during sugarcane production. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)
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21 pages, 1895 KiB  
Article
Putting Laccase Gene Differences on Genomic Level into Context: An Analysis of Botrytis cinerea Strains from Grapes
by Louis Backmann, Kim Marie Umberath, Pascal Wegmann-Herr, Fabian Weber, Andreas Jürgens and Maren Scharfenberger-Schmeer
Microorganisms 2025, 13(3), 483; https://doi.org/10.3390/microorganisms13030483 - 21 Feb 2025
Viewed by 457
Abstract
One of the most important crop pathogens is Botrytis cinerea. It overcomes plant defenses using laccase, an enzyme which is frequently researched. Yet the differences between strains regarding their laccase activity is poorly understood. The aim of this study was to analyze [...] Read more.
One of the most important crop pathogens is Botrytis cinerea. It overcomes plant defenses using laccase, an enzyme which is frequently researched. Yet the differences between strains regarding their laccase activity is poorly understood. The aim of this study was to analyze laccase genes in the context of the regionality, vintage, and laccase activity of the strains. Eight strains were analyzed using whole genome sequencing, and the laccase activity was assessed. The strains were differentiated by SSR-PCR. We looked at all 14 known laccase genome regions as well as the promoter and terminator regions using variant metrics and phylogenetic trees. The laccase genes seem to be correlated with the regionality of the strains rather than the laccase activity, which provides new understanding to the study of pathogen adaption in specific environments. Some of the laccase gene regions showed little to no evolutionary change, while other regions showed a great variety of changes. This research highlights taking different laccase gene regions into context. We provide fundamental information for further research. Further studies, especially on gene expression, could provide insightful information regarding the potential of pathogen infection. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)
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16 pages, 1962 KiB  
Article
Screening and Optimization of Solid-State Fermentation for Esteya vermicola, an Entomopathogenic Fungus Against the Major Forest Pest Pine Wood Nematode
by Lanwen Zhang, Yongxia Li, Xiaojian Wen, Xuan Wang, Wei Zhang, Dongzhen Li, Yuqian Feng, Zhenkai Liu and Xingyao Zhang
Microorganisms 2025, 13(2), 434; https://doi.org/10.3390/microorganisms13020434 - 17 Feb 2025
Viewed by 637
Abstract
Pine wilt disease (PWD), caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus), is one of the most serious threats to pine forests worldwide. The fungus Esteya vermicola, with its lunate conidia capable of parasitizing the PWN, has shown promise as [...] Read more.
Pine wilt disease (PWD), caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus), is one of the most serious threats to pine forests worldwide. The fungus Esteya vermicola, with its lunate conidia capable of parasitizing the PWN, has shown promise as an efficient biological control agent against PWD. Solid-state fermentation (SSF) is preferred for large-scale applications in the field, as it facilitates microbial agent transport and ensures a long shelf life. However, research on enhancing the yield of lunate conidia from E. vermicola through SSF is limited. In this study, we initially achieved a yield of 3.04 × 108 conidia/g using a basic SSF medium composed of wheat bran, corn flour, and soybean flour. To improve this yield, we employed an orthogonal experimental design (OED) to identify the optimal medium composition, which required a wheat bran-to-corn flour-to soybean flour ratio of 7:2:1 (w/w/w), a substrate-to-water ratio of 1:0.7 (w/v), and the addition of 1.33% (w/w) glucose, 1.33% (w/w) yeast extract fermentation, and 1.33% (w/w) MgSO4. Using the response surface methodology (RSM), we calculated the optimal fermentation conditions, which were 24.9 °C, 78.0% relative humidity (RH), an inoculation volume of 16.3% (v/w), and a fermentation time of 7.1 days. Under these conditions, the yield of lunate conidia reached a maximum of 16.58 × 108 conidia/g, a 4.45-fold increase after optimization. This study improved the yield of E. vermicola lunate conidia and provides insights for developing biopesticides based on this strain. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)
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11 pages, 8238 KiB  
Article
Discovery of a New Starship Transposon Driving the Horizontal Transfer of the ToxA Virulence Gene in Alternaria ventricosa
by Fei Liu, Ratchadawan Cheewangkoon and Rui-Lin Zhao
Microorganisms 2025, 13(2), 376; https://doi.org/10.3390/microorganisms13020376 - 9 Feb 2025
Viewed by 852
Abstract
The virulence gene ToxA has been proposed to be horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ~14 kb ToxhAT transposon. Here, our analysis of 2137 fungal species-representative [...] Read more.
The virulence gene ToxA has been proposed to be horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ~14 kb ToxhAT transposon. Here, our analysis of 2137 fungal species-representative assemblies revealed that the ToxA gene is an isolate of Alternaria ventricosa and shows a remarkable 99.5% similarity to those found in B. sorokiniana and P. tritici-repentis. Analysis of the regions flanking ToxA within A. ventricosa revealed that it was embedded within a 14 kb genomic element nearly identical to the corresponding ToxhAT regions in B. sorokiniana, P. nodorum, and P. tritici-repentis. Comparative analysis further showed that ToxhAT in A. ventricosa resides within a larger mobile genetic element, which we identified as a member of the Starship transposon superfamily, named Frontier. Our analysis demonstrated that ToxhAT has been independently captured by three distinct Starships—Frontier, Sanctuary, and Horizon—which, despite having minimal sequence similarity outside of ToxhAT, facilitate its mobilization. These findings place Frontier, Sanctuary, and Horizon within a growing class of Starships implicated in the horizontal transfer of adaptive genes among fungal species. Moreover, we identified three distinct HGT events involving ToxA across these four fungal species, reinforcing the hypothesis of a single evolutionary origin for the ToxhAT transposon. These findings underscore the pivotal role of transposon-mediated HGT in the adaptive evolution of eukaryotic pathogens, offering new insights into how transposons facilitate genetic exchange and shape host–pathogen interactions in fungi. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)
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14 pages, 1414 KiB  
Article
High Spatial but Low Temporal Variability in Ectomycorrhizal Community Composition in Abies alba Forest Stands
by Tina Unuk Nahberger, Hojka Kraigher and Tine Grebenc
Microorganisms 2025, 13(2), 308; https://doi.org/10.3390/microorganisms13020308 - 30 Jan 2025
Viewed by 696
Abstract
The ectomycorrhizal symbionts of silver fir have rarely been analyzed and identified, so little is known about their diversity and distribution. The aim of this study was (1) to analyze the diversity of ectomycorrhizal fungal species in three geographically distinct forest stands of [...] Read more.
The ectomycorrhizal symbionts of silver fir have rarely been analyzed and identified, so little is known about their diversity and distribution. The aim of this study was (1) to analyze the diversity of ectomycorrhizal fungal species in three geographically distinct forest stands of Abies alba and (2) to demonstrate the high temporal variability of the ectomycorrhizal community over two consecutive growing seasons using repeated monthly sampling. Root samples were taken every month during two growing seasons in three silver fir-dominated forest stands. The ectomycorrhizal root tips were first assigned to a morphotype based on morphological characteristics and then identified by sequencing the internal transcribed spacer region. Alpha and beta diversity differed significantly between all three study sites, with the most diverse and even ectomycorrhizal community described in plot Jelovški boršt. The diversity indices over the growing season were different at two of the three study sites, supporting the idea of a fluctuation of ectomycorrhizal taxa during the growing seasons of the two consecutive years. While significant temporal variability was only confirmed for certain ectomycorrhizal taxa, there were no significant changes in the ectomycorrhizal community in general. Thus, we confirmed the high spatial but low temporal variability of the ectomycorrhizal community associated with silver fir. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)
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21 pages, 16886 KiB  
Article
Histological Dissection of Fusarium-Banana Interaction Using a GFP-Tagged Subtropical Race 4 Strain of Fusarium oxysporum f. sp. cubense on Banana Cultivars with Differing Levels of Resistance
by Andrew Chen, Ting-Yan Chou, Yi Chen, Sumayyah M. A. Fallatah, Jay Anderson, Jiaman Sun, Harry Cosgrove, Siyuan Gao, Brett J. Ferguson, Amelie Soper, Donald M. Gardiner and Elizabeth A. B. Aitken
Microorganisms 2024, 12(12), 2472; https://doi.org/10.3390/microorganisms12122472 - 1 Dec 2024
Viewed by 1440
Abstract
Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), poses a significant threat to global banana production. This study used a GFP-tagged subtropical race 4 strain of Foc (GFP-Foc-STR4) to trace the pathogen’s movement in different banana cultivars. [...] Read more.
Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), poses a significant threat to global banana production. This study used a GFP-tagged subtropical race 4 strain of Foc (GFP-Foc-STR4) to trace the pathogen’s movement in different banana cultivars. These include a race 4 resistant cultivar FHIA25 and the Cavendish somaclone ‘GCTCV119’, as well as susceptible cultivars including ‘Lady Finger’, ‘FHIA02’, and ‘Williams’ Cavendish. GFP localization revealed that GFP-Foc-STR4 was able to infect all tested cultivars, moving from the roots to the rhizome and aerial parts of the plant. Tyloses formation in root and rhizome vasculature, visualised with GFP autofluorescence and confirmed by scanning electron microscopy, was found to restrict Foc within the xylem vessels, slowing its spread but not fully preventing infection. This containment mechanism contributes to the host tolerance of ‘FHIA25’ and ‘GCTCV119’, though it does not confer complete immunity. The use of the fluorescently tagged Foc strain provides valuable insight into the infection process, and supports efforts in the integrated management of Fusarium wilt of banana. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)
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13 pages, 1133 KiB  
Article
Analysis of the Mycotoxin Levels and Expression Pattern of SWN Genes at Different Time Points in the Fungus Slafractonia leguminicola
by Sumanjari Das, Dale R. Gardner, Daniel Cook and Rebecca Creamer
Microorganisms 2024, 12(4), 670; https://doi.org/10.3390/microorganisms12040670 - 27 Mar 2024
Viewed by 1687
Abstract
The fungal plant pathogen Slafractonia leguminicola produces two mycotoxins that affect animals: slaframine, which causes slobbers, and swainsonine, which causes locoism. Slafractonia leguminicola contains the swainsonine-associated orthologous gene clusters, “SWN”, which include a multifunctional swnK gene (NRPS-PKS hybrid), swnH1 and swnH2 (nonheme iron [...] Read more.
The fungal plant pathogen Slafractonia leguminicola produces two mycotoxins that affect animals: slaframine, which causes slobbers, and swainsonine, which causes locoism. Slafractonia leguminicola contains the swainsonine-associated orthologous gene clusters, “SWN”, which include a multifunctional swnK gene (NRPS-PKS hybrid), swnH1 and swnH2 (nonheme iron dioxygenase genes), swnN and swnR (reductase genes), and swnT (transmembrane transporter). In addition to these genes, two paralogs of swnK, swnK1 (paralog1) and swnk2 (paralog2), are found in S. leguminicola. cDNAs from total mRNA were isolated from the S. leguminicola mycelia grown in the culture plates as well as from leaves inoculated with the fungal mycelia at different time points, and expression pattern of the SWN genes were analyzed using RT-qPCR. The concentrations of swainsonine and slaframine production from this fungus at different time points were also examined using liquid chromatography–mass spectrometry. The timing of gene expression was similar in cultured fungus and inoculated leaves and agreed with our proposed biosynthetic pathway. Substantially more swainsonine was produced than slaframine during time course studies. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)
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Review

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21 pages, 642 KiB  
Review
Halophilic Fungi—Features and Potential Applications
by Lyudmila Yovchevska, Yana Gocheva, Galina Stoyancheva, Jeny Miteva-Staleva, Vladislava Dishliyska, Radoslav Abrashev, Tsvetomira Stamenova, Maria Angelova and Ekaterina Krumova
Microorganisms 2025, 13(1), 175; https://doi.org/10.3390/microorganisms13010175 - 15 Jan 2025
Cited by 4 | Viewed by 1565
Abstract
Extremophiles are of significant scientific interest due to their unique adaptation to harsh environmental conditions and their potential for diverse biotechnological applications. Among these extremophiles, filamentous fungi adapted to high-salt environments represent a new and valuable source of enzymes, biomolecules, and biomaterials. While [...] Read more.
Extremophiles are of significant scientific interest due to their unique adaptation to harsh environmental conditions and their potential for diverse biotechnological applications. Among these extremophiles, filamentous fungi adapted to high-salt environments represent a new and valuable source of enzymes, biomolecules, and biomaterials. While most studies on halophiles have focused on bacteria, reports on filamentous fungi remain limited. This review compiles information about salt-adapted fungi and details their distribution, adaptation mechanisms, and potential applications in various societal areas. Understanding the adaptive mechanisms of halophilic fungi not only sheds light on the biology of extremophilic fungi but also leads to promising biotechnological applications, including the development of salt-tolerant enzymes and strategies for bioremediation of saline habitats. To fully realize this potential, a comprehensive understanding of their ecology, diversity and physiology is crucial. In addition, understanding their survival mechanisms in saline environments is important for the development of astrobiology. The significant potential of applications of halophilic fungi is highlighted. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)
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