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Microorganisms
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Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control
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Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 5755

Special Issue Editor

Dr. Micael F. M. Gonçalves

E-Mail Website
Guest Editor
1. Biology Department, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
2. Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
Interests: fungal diversity; global changes and plant pathogenic microorganisms; microorganisms as biocontrol agents; marine fungi and related bioactive compounds; systematics and evolutionary microbiology; environmental and clinical microbiology

Special Issue Information

Dear Colleagues,

This Special Issue will focus on recent advances in the study of fungal plant pathogens, encompassing their diagnosis, plant resistance mechanisms, and innovative control strategies. Fungal diseases pose a significant threat to global agriculture, leading to substantial economic losses and food security challenges. Understanding pathogen biology, host interactions, and resistance mechanisms is crucial for developing effective management strategies.

We welcome original research articles, reviews, and short communications addressing topics such as novel diagnostic tools, molecular and genetic approaches to plant resistance, and sustainable disease control methods, including biocontrol, chemical treatments, and integrated pest management. Studies exploring the impact of climate change on fungal pathogen dynamics and resistance evolution are also encouraged.

We look forward to providing a platform on which researchers can promote the latest findings in fungal plant pathology.

Dr. Micael F. M. Gonçalves
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fungal plant pathogens
  • disease diagnosis
  • plant resistance
  • biocontrol strategies
  • sustainable disease management

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Published Papers (7 papers)

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Research

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13 pages, 954 KB  
Article
Pathogenicity Analysis and Molecular Characterization of Three Avr Genes in Magnaporthe oryzae Population from Central Jilin Province
by Yimeng Wang, Nuozhou Zhang, Rui Han, Aozheng Lu, Nan Nan, Dayong Li and Wenxian Sun
Microorganisms 2026, 14(5), 1017; https://doi.org/10.3390/microorganisms14051017 - 30 Apr 2026
Viewed by 392
Abstract
Rice fungal blast, one of the most devastating diseases caused by Magnaporthe oryzae, poses a severe threat to global rice production. For the breeding and deployment of rice varieties with blast resistance, it is critical to elucidate the frequencies and genetic variations [...] Read more.
Rice fungal blast, one of the most devastating diseases caused by Magnaporthe oryzae, poses a severe threat to global rice production. For the breeding and deployment of rice varieties with blast resistance, it is critical to elucidate the frequencies and genetic variations in avirulence genes among M. oryzae populations. In this study, a total of 294 M. oryzae isolates were collected in 2022 from central Jilin Province, China. Pathogenicity assays on 24 monogenic rice lines revealed extensive virulence variations among the 294 isolates, with highly pathogenic strains being dominant and clear geographic differences in pathogenicity profiles. Resistance frequencies differed markedly among 24 monogenic lines, with Pi3, Pit, Pi7, Pikh, Pik, and Pia showing resistance rates over 50% and Pish exhibiting the lowest efficacy. Moreover, resistance profiles varied significantly across four sampling regions in central Jilin Province, with Pit being the most effective in Changchun and Jilin, Pi3 in Tonghua, and Pikm in Liaoyuan. In addition, the Avr genotypes of the isolates were postulated based on phenotypic data from the monogenic rice lines. Among the postulated Avr genotypes, the frequencies of Avr-Pi11 and Avr-Pish were the lowest at 29.25%. Furthermore, molecular characterization of three Avr genes (Avr-Pi9, Avr-Pita2, and Avr-Pizt) was performed by sequencing a subsample of 50 randomly selected isolates. Natural mutation sites were identified in Avr-Pita2 and Avr-Pizt, which were located within the coding sequence regions, leading to non-synonymous mutations and nonsense mutations that cause premature termination. Notably, no mutation was detected within the coding sequences of Avr-Pi9. Collectively, the findings provide a theoretical basis for breeding blast-resistant rice varieties that can be deployed in central Jilin Province, China. Full article
(This article belongs to the Special Issue Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control)
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22 pages, 4238 KB  
Article
Bacillus velezensis LW-66: A Broad-Spectrum Biocontrol Agent Against Apple Tree Canker and Other Plant Fungal Diseases
by Dandan Liu, Wei Xiao, Wenwen Li, Shengli Li, Juanli Cheng and Jinshui Lin
Microorganisms 2026, 14(4), 889; https://doi.org/10.3390/microorganisms14040889 - 16 Apr 2026
Viewed by 643
Abstract
Plant fungal diseases, such as apple tree canker caused by Valsa mali, have caused severe losses in agricultural production. Traditional chemical fungicides induce drug resistance in pathogens and cause environmental pollution. Therefore, it is of substantial importance to screen efficient and environmentally [...] Read more.
Plant fungal diseases, such as apple tree canker caused by Valsa mali, have caused severe losses in agricultural production. Traditional chemical fungicides induce drug resistance in pathogens and cause environmental pollution. Therefore, it is of substantial importance to screen efficient and environmentally friendly bacterial strains as potential biocontrol agents. The tea rhizosphere harbors abundant microbial resources, and previous research has identified microorganisms with antifungal activity existing in this environment. Therefore, in this study, we isolated antagonistic bacteria with broad-spectrum biocontrol potential from tea rhizosphere soil. In this study, a strain with strong antagonistic activity against V. mali was isolated from tea rhizosphere soil. Based on morphological characteristics, 16S rRNA gene sequencing, and whole-genome analysis, the isolated strain was identified as Bacillus velezensis and designated as LW-66. This strain demonstrated broad-spectrum antifungal activity against various plant pathogenic fungi, including Valsa mali, Fusarium graminearum, Bipolaris sorokinianum, Alternaria solani, and Exserohilum turcicum. The active extract of B. velezensis maintained strong stability across a wide range of temperatures (25–90 °C) and pH values (2–8), with stability decreasing only when the temperature reached 100 °C or pH ≥ 10. In a preventive assay using detached apple branches inoculated with V. mali, the control efficacy of LW-66 against apple tree canker reached more than 90%. Additionally, in a therapeutic assay using V. mali-infected potted apple seedlings, the LW-66 bone-glue bacterial agent achieved a survival rate of up to 90%. Whole-genome analysis revealed that the genome of LW-66 contains 13 predicted secondary metabolite biosynthetic gene clusters, seven of which showed high homology (≥92% similarity) with known antimicrobial gene clusters, including surfactin, bacillaene, macrolactin H, fengycin, difficidin, bacillibactin, and bacilysin. These gene clusters may be connected to the broad-spectrum antifungal activity of B. velezensis, as well as its ability to disrupt hyphal morphology. The volatile organic compounds produced by LW-66 inhibited V. mali growth by 91.70%. Collectively, these findings demonstrate that B. velezensis LW-66 has a wide antimicrobial range and strong antagonistic effects against multiple plant pathogenic fungi. Therefore, B. velezensis shows promise as a biocontrol agent for managing fungal diseases in plants, providing a basis for developing LW-66-derived biocontrol products aimed at controlling diseases such as apple tree canker. Full article
(This article belongs to the Special Issue Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control)
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17 pages, 6558 KB  
Article
Secretome-Wide Lysine Acetylation Profiling of Fusarium oxysporum Reveals Potential Virulence Factors in Sugarcane Pokkah Boeng Disease
by Gege Wang, Jie Zheng, Chi Zhang, Sehrish Akbar, Yibin Wei, Yu Zhou, Muqing Zhang and Yixue Bao
Microorganisms 2026, 14(2), 462; https://doi.org/10.3390/microorganisms14020462 - 13 Feb 2026
Viewed by 580
Abstract
Fusarium oxysporum is the causal agent of Pokkah Boeng disease (PBD) in sugarcane. Lysine acetylation (Kac) is a dynamic and reversible post-translational modification that plays a critical role in regulating diverse cellular processes. Although Kac is known to significantly influence protein function, its [...] Read more.
Fusarium oxysporum is the causal agent of Pokkah Boeng disease (PBD) in sugarcane. Lysine acetylation (Kac) is a dynamic and reversible post-translational modification that plays a critical role in regulating diverse cellular processes. Although Kac is known to significantly influence protein function, its specific role within the F. oxysporum secretome during PBD pathogenesis remains poorly understood. In this study, we conducted a comprehensive analysis of the lysine acetylome across the F. oxysporum secretome. Utilizing highly sensitive immunoaffinity purification coupled with high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified 291 acetylation sites within 85 potentially secreted proteins. Bioinformatics analysis revealed that these acetylated proteins are involved in a wide array of biological functions and exhibit diverse subcellular localizations. Notably, these secreted proteins represent a valuable resource for identifying novel effectors; specifically, eight upregulated genes encoding Kac proteins were identified as potential players during the initial asymptomatic stages of infection. Collectively, these findings provide a global overview of the F. oxysporum secretome acetylome and offer a foundational resource for elucidating the functional significance of lysine acetylation in sugarcane PBD pathogenesis. Full article
(This article belongs to the Special Issue Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control)
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16 pages, 3081 KB  
Article
Identification of Fungal Pathogens of Chinese Chestnut Fruit Rot and Analysis of Resistance Differences Among Major Cultivars
by Haijiao Xu, Wenshi Zhao, Yan Guo, Jianchao Cui, Gang Niu, Shuhang Zhang, Ying Li, Litao Li, Rui Jiao, Xumin Wang, Guangpeng Wang and Limin He
Microorganisms 2026, 14(1), 113; https://doi.org/10.3390/microorganisms14010113 - 5 Jan 2026
Cited by 2 | Viewed by 674
Abstract
This study aimed to identify fungal species causing fruit rot of chestnut (Castanea mollissima Blume) in Hebei Province, China and analyze the resistance differences among major cultivars. A total of 220 fungal isolates were obtained from healthy and diseased kernels, which were [...] Read more.
This study aimed to identify fungal species causing fruit rot of chestnut (Castanea mollissima Blume) in Hebei Province, China and analyze the resistance differences among major cultivars. A total of 220 fungal isolates were obtained from healthy and diseased kernels, which were classified into six distinct genera: Diaporthe (48.6%), Talaromyces (22.3%), Alternaria (10.5%), Mucor (9.5%), Fusarium (5.5%), and Rhizopus (3.6%). Based on both morphological and molecular analyses, six representative isolates of the six genera were identified as Diaporthe eres Nitschke, Talaromyces rugulosus Samson, N. Yilmaz, Frisvad & Seifert, Alternaria alternata (Fr.) Keissl., Mucor circinelloides Tiegh., Fusarium proliferatum (Matsush.) Nirenberg, and Rhizopus stolonifer (Ehrenb.) Vuill. Among these, D. eres was first reported to cause fruit rot on C. mollissima in China. Moreover, disease resistance evaluation of major cultivars showed significant differences: YG, YSSF, and DBH exhibited strong resistance under both natural conditions (with 1.67% to 5.27% DI after 180 days storage) and artificial inoculation (with 32.96 ± 0.64 to 52.61 ± 0.55 DI); while YJ was highly susceptible (with 47.71% decay incidence and 70.50 ± 7.22 DI). Correlation analysis revealed that the disease index was negatively correlated with sucrose and sorbitol contents, but positively correlated with stachyose and fructose contents. This study advances the understanding of postharvest chestnut fruit rot and provides a theoretical basis for breeding resistant cultivars and developing control strategies to mitigate losses and ensure food safety. Full article
(This article belongs to the Special Issue Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control)
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23 pages, 2891 KB  
Article
Effect of Xylopia frutescens Essential Oil on the Activation of Defense Mechanisms Against Phytopathogenic Fungi
by Dalmarcia de Souza C. Mourão, Bruna L. Dias, Mateus S. Dalcin, Luis O. Viteri, Manuel A. Gonzales, Paulo R. S. Fernandes, Vitória B. Silva, Mariana A. Costa, Maria J. González, Ana G. Amaral, Ildon R. do Nascimento, Cristiano B. de Moraes, Vânia Thais S. Gomes, Marcos P. Câmara, Marcos G. da Silva, Adalberto C. Café-Filho, Wellington S. Moura and Gil R. dos Santos
Microorganisms 2025, 13(11), 2571; https://doi.org/10.3390/microorganisms13112571 - 11 Nov 2025
Cited by 1 | Viewed by 950
Abstract
The induction of resistance in plants involves prior activation of physiological and biochemical systems in the face of external stimuli, promoting greater tolerance to biotic stresses. Faced with the growing challenge of emerging diseases in agricultural plants and the search for more sustainable [...] Read more.
The induction of resistance in plants involves prior activation of physiological and biochemical systems in the face of external stimuli, promoting greater tolerance to biotic stresses. Faced with the growing challenge of emerging diseases in agricultural plants and the search for more sustainable phytosanitary practices, natural substances are promising alternatives. Xylopia frutescens, known as “pindaiba-da-folha-pequena”, native to the Brazilian Cerrado and traditionally used as an antimicrobial treatment, is still little-explored in the literature and presents potentially effective compounds for the control of plant diseases. This study characterized the chemical composition and thermal stability of the X. frutescens essential oil (XEO), while evaluating its physiological and phytotoxic effects and the potential for disease control in maize and cowpea plants. The main constituents found in X. frutescens essential oil were nopinone (13.75%), spatulenol (12.94%), myrtenal (12.47%), and β-pinene (11.02%). Thermogravimetric analysis indicated that X. frutescens is highly volatile, with a large mass loss at 94.74 °C. In bioassays, the oil preserved chlorophyll levels at adequate amounts and activated several antioxidant mechanisms, but also showed a dose-dependent phytotoxic effect. In vitro assays further confirmed its antifungal activity against key phytopathogens, supporting its potential use in disease control. A general increase in the activities of the enzymes superoxide dismutase (SOD), ascorbate peroxidase (APx) and—partially—chitinase (CHIT) was observed. Catalase (CAT) decreased in both maize and cowpea plants treated with this essential oil but was higher in untreated infected plants. Such enzymatic changes suggest that the oil acts as a natural elicitor of resistance, strengthening biochemical and physiological defenses. Finally, disease severities, as measured by AUDPCs, demonstrated significant reductions in the progress of maize “Curvularia leaf spot” (Curvularia lunata) and cowpea “Web blight” (Rhizoctonia solani). The results highlight the potential of X. frutescens essential oil as an active compound stimulating defense mechanisms for applications in sustainable agricultural systems. Full article
(This article belongs to the Special Issue Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control)
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20 pages, 4396 KB  
Article
Unveiling Species Diversity of Plectosphaerellaceae (Sordariomycetes) Fungi Involved in Rhizome and Root Rots of Ginger in Shandong Province, China
by Qian Zhao, Ao Jia, Hongjuan Yang, Jinming Hu, Xuli Gao, Weiqin Zhao, Lifeng Zhou, Miao Zhang, Zhaoxia Li and Weihua Zhang
Microorganisms 2025, 13(9), 2180; https://doi.org/10.3390/microorganisms13092180 - 18 Sep 2025
Viewed by 1525
Abstract
Ginger holds significant economic importance in both China and worldwide agriculture. Fungi from the family Plectosphaerellaceae are globally recognized as aggressive plant pathogens. However, the effects of Plectosphaerellaceae species on ginger have been poorly understood. In this research, we identified two novel Musidium [...] Read more.
Ginger holds significant economic importance in both China and worldwide agriculture. Fungi from the family Plectosphaerellaceae are globally recognized as aggressive plant pathogens. However, the effects of Plectosphaerellaceae species on ginger have been poorly understood. In this research, we identified two novel Musidium species (M. shandongensis sp. nov. and M. zingiberis sp. nov.), one newly recorded species (Gibellulopsis serrae) and one new host record (Plectosphaerella cucumerina) from the rotten rhizomes and roots of ginger in Shandong Province, China, utilizing morphological observations combined with multilocus phylogenetic analysis of the 28S large subunit (LSU), internal transcribed spacer (ITS) region, and translation elongation factor 1-alpha (TEF1-α) gene, along with pathogenicity analyses. Key diagnostic features include M. shandongensis exhibiting abundant mycelium ropes and coils, M. zingiberis showing dark olivaceous colonies, G. serrae producing brown chlamydospores, and P. cucumerina displaying conspicuous guttulae conidia. Comparative analyses with closely related taxa were based on detailed morphological descriptions, illustrations, and phylogenetic analyses. Artificial inoculation of healthy ginger in vitro and in vivo assays caused characteristic symptoms, such as wilt, leaf yellowing, and rhizome necrosis, identical to those observed on naturally infected plants. Our findings broaden current knowledge on the diversity of Plectosphaerellaceae associated with ginger, revealing them as serious threats to ginger cultivation in China. Full article
(This article belongs to the Special Issue Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control)
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Review

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39 pages, 1977 KB  
Review
Soil Reservoirs of Antifungal-Resistant Fungi: Implications for Plant Disease Management with a Focus on Fusarium
by Ana B. Neves, Tiago M. Gonçalves, Artur Alves and Micael F. M. Gonçalves
Microorganisms 2026, 14(5), 1018; https://doi.org/10.3390/microorganisms14051018 - 30 Apr 2026
Viewed by 388
Abstract
Crop losses driven by fungal pathogens remain a major constraint to global food production, reinforcing agriculture’s dependence on fungicide-based disease control. Soil acts as a long-term reservoir and key hotspot for the evolution and persistence of antifungal-resistant Fusarium. The intensive, prolonged use [...] Read more.
Crop losses driven by fungal pathogens remain a major constraint to global food production, reinforcing agriculture’s dependence on fungicide-based disease control. Soil acts as a long-term reservoir and key hotspot for the evolution and persistence of antifungal-resistant Fusarium. The intensive, prolonged use of overlapping single-site fungicides in agriculture strongly selects for both intrinsic and acquired resistance in soilborne Fusarium populations, contributing to major crop losses, food insecurity, and One Health concerns. This review synthesizes current knowledge on (i) target-site (CYP51, β-tubulin, cytochrome b, SDH, myosin-5) and non-target-site (ABC/MFS efflux, multidrug resistance, epigenetic regulation) resistance mechanisms across the genus Fusarium; (ii) the influence of management practices and fungicide characteristics and behaviour in soil in reshaping microbial communities and selecting for resistant Fusarium; (iii) the consequences for plant disease management and the limitations of practices like cultural and biological control; and (iv) innovative strategies for plant disease management, as well as the monitoring and detection of antifungal resistance in soils. These aspects show that soil reservoirs of antifungal-resistant Fusarium are compromising fungicide-based control and increasing risks across sectors, highlighting the urgent need for sustainable, multi-layered, integrated pest management strategies combined with robust, molecularly informed resistance monitoring. Full article
(This article belongs to the Special Issue Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control)
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