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Advances in Plant Pathogenic Fungi: Diagnosis, Biological Control, and Eco-Sustainable...
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Advances in Plant Pathogenic Fungi: Diagnosis, Biological Control, and Eco-Sustainable Formulations

A topical collection in Journal of Fungi (ISSN 2309-608X). This collection belongs to the section "Fungi in Agriculture and Biotechnology".

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Editors

Dr. Santa Olga Cacciola

E-Mail Website
Collection Editor
Department of Agriculture, Food and Environment (di3A), University of Catania, 95123 Catania, Italy
Interests: oomycetes and fungal diseases diagnosis; molecular diagnosis; emerging plant diseases; plant disease management strategies; diversity of plant pathogens; trachemycoses; bioremediation strategies
Special Issues, Collections and Topics in MDPI journals
Dr. Carlos Agustí-Brisach

E-Mail Website
Collection Editor
Agroforestal Pathology Research Group, Department of Agronomy, ETSIAM, University of Cordoba, 14071 Cordoba, Spain
Interests: biocontrol; etiology; epidemiology; fungi; integrated pest management; Mediterranean fruit crops; phytopathology; plant–pathogen–environment interactions; fungal trunk and vascular diseases
Special Issues, Collections and Topics in MDPI journals
Dr. Josep Armengol

E-Mail Website
Collection Editor
Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera S/N, 46022 Valencia, Spain
Interests: etiology; integrated pest management; Mediterranean fruit crops; Mediterranean vegetables; mycology; plant diseases; plant pathogenic fungi

Topical Collection Information

Dear Colleagues,

The widespread presence of plant pathogenic fungi poses a formidable challenge to agricultural and forest ecosystems, and requires concerted research efforts to effectively understand and counter the dynamic landscape of fungal infections. The advent of molecular techniques, such as DNA sequencing and genomics, has introduced a new era of rapid diagnosis for plant pathogenic fungi. In parallel, there has been a growing focus on cultivating sustainable and environmentally friendly strategies to mitigate the impact of these fungi, including advancements in new eco-friendly formulations. Innovative biological control approaches, such as bio-pesticides, beneficial microbes, secondary metabolites of microorganisms, plant extracts, and plant-mediated defences, are considered promising alternatives to conventional chemical interventions.

This Topical Collection is devoted to studying the efficacy of biocontrol agents and their metabolites against fungal pathogens, as well as applying molecular techniques for the identification of fungi associated with agricultural and forest plants. Additionally, it focuses on the development of new environmentally friendly and low-impact formulations, also aiming to address the challenges inherent in species identification—a key aspect of disease management.

Objectives:

To explore recent advances in molecular diagnostics, including genomics and diagnostic tools.

To present sustainable and ecological strategies for the management of plant pathogenic fungi through innovative biological control approaches or novel eco-formulates with low environmental impact.

To explore the integration of diagnostic tools with biological control measures to enhance overall disease management.

Dr. Santa Olga Cacciola
Dr. Carlos Agustí-Brisach
Dr. Josep Armengol
Collection Editors

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 collection website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Journal of Fungi 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 2600 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

  • plant pathogenic fungi 
  • endophytes
  • pathobiome
  • microbiome
  • diagnosis
  • next-generation sequencing
  • multi-locus sequence phylogeny
  • biological control
  • eco-sustainable agriculture

Published Papers (4 papers)

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2025

Jump to: 2024

40 pages, 2452 KiB  
Review
Groundbreaking Technologies and the Biocontrol of Fungal Vascular Plant Pathogens
by Carmen Gómez-Lama Cabanás and Jesús Mercado-Blanco
J. Fungi 2025, 11(1), 77; https://doi.org/10.3390/jof11010077 - 18 Jan 2025
Viewed by 701
Abstract
This review delves into innovative technologies to improve the control of vascular fungal plant pathogens. It also briefly summarizes traditional biocontrol approaches to manage them, addressing their limitations and emphasizing the need to develop more sustainable and precise solutions. Powerful tools such as [...] Read more.
This review delves into innovative technologies to improve the control of vascular fungal plant pathogens. It also briefly summarizes traditional biocontrol approaches to manage them, addressing their limitations and emphasizing the need to develop more sustainable and precise solutions. Powerful tools such as next-generation sequencing, meta-omics, and microbiome engineering allow for the targeted manipulation of microbial communities to enhance pathogen suppression. Microbiome-based approaches include the design of synthetic microbial consortia and the transplant of entire or customized soil/plant microbiomes, potentially offering more resilient and adaptable biocontrol strategies. Nanotechnology has also advanced significantly, providing methods for the targeted delivery of biological control agents (BCAs) or compounds derived from them through different nanoparticles (NPs), including bacteriogenic, mycogenic, phytogenic, phycogenic, and debris-derived ones acting as carriers. The use of biodegradable polymeric and non-polymeric eco-friendly NPs, which enable the controlled release of antifungal agents while minimizing environmental impact, is also explored. Furthermore, artificial intelligence and machine learning can revolutionize crop protection through early disease detection, the prediction of disease outbreaks, and precision in BCA treatments. Other technologies such as genome editing, RNA interference (RNAi), and functional peptides can enhance BCA efficacy against pathogenic fungi. Altogether, these technologies provide a comprehensive framework for sustainable and precise management of fungal vascular diseases, redefining pathogen biocontrol in modern agriculture. Full article
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2024

Jump to: 2025

12 pages, 3468 KiB  
Article
Development of an RPA-CRISPR/Cas12a Assay for Rapid and Sensitive Diagnosis of Plant Quarantine Fungus Setophoma terrestris
by Peng Zhao, Zhipeng Feng, Lei Cai, Dorji Phurbu, Weijun Duan, Fuhong Xie, Xuelian Li and Fang Liu
J. Fungi 2024, 10(10), 716; https://doi.org/10.3390/jof10100716 - 15 Oct 2024
Cited by 1 | Viewed by 1225
Abstract
Setophoma terrestris is an important phytopathogenic fungus listed by China as a harmful fungus subject to phytosanitary import control. This pathogen is a threat to a wide range of plants, particularly as the causal agent of onion pink root rot, one of the [...] Read more.
Setophoma terrestris is an important phytopathogenic fungus listed by China as a harmful fungus subject to phytosanitary import control. This pathogen is a threat to a wide range of plants, particularly as the causal agent of onion pink root rot, one of the most severe diseases of onions. In order to provide rapid identification and early warning of S. terrestris and prevent its spread, we have developed a rapid, accurate, and visually intuitive diagnostic assay for this pathogen, by utilizing recombinase polymerase amplification (RPA), coupled with CRISPR/Cas12a cleavage and fluorescence-based detection systems or paper-based lateral flow strips. The developed RPA-CRISPR/Cas12a assay exhibited remarkable specificity for the detection of S. terrestris. Moreover, this protocol can detect the pathogen at a sensitivity level of 0.01 pg/μL, which significantly outperforms the 1 pg/μL sensitivity achieved by the existing qPCR-based detection method. The entire diagnostic procedure, including DNA extraction, the RPA reaction, the Cas12a cleavage, and the result interpretation, can be accomplished in 40 min. Furthermore, the successful application of the assay in infected plant samples highlighted its potential for rapid and accurate pathogen detection in agricultural settings. In summary, this RPA-CRISPR/Cas12a diagnostic method offers a potentially valuable technological solution for quarantine and disease management. Full article
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18 pages, 4820 KiB  
Article
Pythium banihashemianum sp. nov. and Globisporangium izadpanahii sp. nov.: Two New Oomycete Species from Rice Paddies in Iran
by Fatemeh Salmaninezhad, Reza Mostowfizadeh-Ghalamfarsa and Santa Olga Cacciola
J. Fungi 2024, 10(6), 405; https://doi.org/10.3390/jof10060405 - 5 Jun 2024
Cited by 1 | Viewed by 1235
Abstract
An investigation into oomycete diversity in rice paddies of Fars Province in Iran led to the identification of two new Pythium sensu lato (s.l.) species as Globisporangium izadpanahii sp. nov. and Pythium banihashemianum sp. nov. The identification was based on morphological and [...] Read more.
An investigation into oomycete diversity in rice paddies of Fars Province in Iran led to the identification of two new Pythium sensu lato (s.l.) species as Globisporangium izadpanahii sp. nov. and Pythium banihashemianum sp. nov. The identification was based on morphological and physiological features as well as on the phylogenetic analysis of nuclear (ITS and βtub) and mitochondrial (cox1 and cox2) loci using Bayesian inference and Maximum Likelihood. The present paper formally describes these two new species and defines their phylogenetic relationships with other congeneric species. According to multiple gene genealogy analysis, G. izadpanahii sp. nov. was grouped with other species of Globisporangium (formerly, clade G of Pythium s.l.) and was closely related to both G. nagaii and the recently described G. coniferarum. The second species, designated P. banihashemianum sp. nov., was grouped with other species of Pythium sensu stricto (formerly, clade B of Pythium s.l.) and, according to the phylogenetic analysis, shared an ancestor with P. plurisporium. The production of globose hyphal swellings was a major characteristic of G. izadpanahii sp. nov., which did not produce vesicles and zoospores. In pathogenicity tests on rice seedlings, P. banihashemianum sp. nov. isolates were highly pathogenic and caused severe root and crown rot, while G. izadpanahii sp. nov. isolates were not pathogenic. Full article
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12 pages, 2421 KiB  
Article
A Lateral Flow-Recombinase Polymerase Amplification Method for Colletotrichum gloeosporioides Detection
by Wei-Teng Xu, Xin-Yu Lu, Yue Wang, Ming-Han Li, Ke Hu, Zi-Jie Shen, Xiao-Qin Sun and Yan-Mei Zhang
J. Fungi 2024, 10(5), 315; https://doi.org/10.3390/jof10050315 - 26 Apr 2024
Viewed by 1501
Abstract
The greater yam (Dioscorea alata), a widely cultivated and nutritious food crop, suffers from widespread yield reduction due to anthracnose caused by Colletotrichum gloeosporioides. Latent infection often occurs before anthracnose phenotypes can be detected, making early prevention difficult and causing [...] Read more.
The greater yam (Dioscorea alata), a widely cultivated and nutritious food crop, suffers from widespread yield reduction due to anthracnose caused by Colletotrichum gloeosporioides. Latent infection often occurs before anthracnose phenotypes can be detected, making early prevention difficult and causing significant harm to agricultural production. Through comparative genomic analysis of 60 genomes of 38 species from the Colletotrichum genus, this study identified 17 orthologous gene groups (orthogroups) that were shared by all investigated C. gloeosporioides strains but absent from all other Colletotrichum species. Four of the 17 C. gloeosporioides-specific orthogroups were used as molecular markers for PCR primer designation and C. gloeosporioides detection. All of them can specifically detect C. gloeosporioides out of microbes within and beyond the Colletotrichum genus with different sensitivities. To establish a rapid, portable, and operable anthracnose diagnostic method suitable for field use, specific recombinase polymerase amplification (RPA) primer probe combinations were designed, and a lateral flow (LF)-RPA detection kit for C. gloeosporioides was developed, with the sensitivity reaching the picogram (pg) level. In conclusion, this study identified C. gloeosporioides-specific molecular markers and developed an efficient method for C. gloeosporioides detection, which can be applied to the prevention and control of yam anthracnose as well as anthracnose caused by C. gloeosporioides in other crops. The strategy adopted by this study also serves as a reference for the identification of molecular markers and diagnosis of other plant pathogens. Full article
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