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Biological Control of Fungal Plant Pathogens
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Biological Control of Fungal Plant Pathogens

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

Deadline for manuscript submissions: 20 August 2025 | Viewed by 6380

Special Issue Editors

Dr. Marta Cristina Corsi De Filippi

E-Mail Website
Guest Editor
Researchers from Embrapa Rice and Beans, Agricultural Microbiology Laboratory, GO-462, km 12, Countryside, C.P. 179, Santo Antônio de Goiás 75375-000, GO, Brazil
Interests: biological control of crop plant disease; plant pathology and microbiology; plant pathogenic fungi
Dr. Premila Achar

E-Mail Website
Guest Editor
Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
Interests: host–pathogen interaction; molecular interaction and early detection; sequencing and molecular relatedness; biological control including agrobacterium-mediated transformation and plant-based antimicrobials
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Crop losses due to fungal disease are key issues plant pathologists and microbiologist scientists must face in the present and, in the near future, to offer sustainable solutions to the world’s demands. The world population is estimated to reach 10.5 billion by 2050, and the total global food demand is expected to increase by 35 to 56% between 2010 and 20250. One strategy to meet the need for new sustainable strategies in agriculture is the insertion of biological control agents in the crop management systems, using products composted by beneficial microorganisms, such as beneficial filamentous fungi and yeasts, and bacteria from rhizosphere, philosophers and endophytes, second metabolites, essential oils, plant extracts, etc. This Special Issue aims to collect manuscripts that present data on the biological control of plant diseases caused by pathogenic fungi. The manuscripts should be in research and review format. The accepted manuscript will address all mechanisms involved in the interaction of plant hosts, pathogenic fungi, beneficial microorganisms and derivates, physiological, biochemical, and molecular aspects, epidemiological studies, integrated management, beneficial microorganism breeding, gene edition, microorganism’s genomics, proteomics, and metabolomics. The manuscripts in this Special Issue will perfectly fit within Agenda 2030 and is in line with the One Health concept, optimizing the health of people, animals, and ecosystem sustainability.

Dr. Marta Cristina Corsi De Filippi
Dr. Premila Achar
Guest 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 special issue 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

  • sustainability
  • biological control
  • disease suppression
  • integrated pest management
  • effectors
  • resistance induction
  • plant defense
  • growth promotion

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Published Papers (7 papers)

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Research

15 pages, 2083 KiB  
Article
Identifying Key Pathogens and Effective Control Agents for Astragalus membranaceus var. mongholicus Root Rot
by Bo Zhang, Bingyan Xia, Chunyan Wang, Ouli Xiao, Tielin Wang, Haoran Zhao, Xiaofeng Dai, Jieyin Chen, Yonggang Wang and Zhiqiang Kong
J. Fungi 2025, 11(7), 544; https://doi.org/10.3390/jof11070544 - 21 Jul 2025
Viewed by 383
Abstract
Root rot is one of the most serious diseases affecting Astragalus membranaceus, significantly reducing its yield and quality. This study focused on root rot in Astragalus membranaceus var. mongholicus. Pathogenic fungi were isolated and identified. The pathogenicity of seven strains of [...] Read more.
Root rot is one of the most serious diseases affecting Astragalus membranaceus, significantly reducing its yield and quality. This study focused on root rot in Astragalus membranaceus var. mongholicus. Pathogenic fungi were isolated and identified. The pathogenicity of seven strains of pathogenic fungi was verified according to Koch’s postulates. The inhibitory effects of eight classic fungicides and nine strains of biocontrol agents on the pathogenic fungi were determined using the mycelial growth rate method. Through morphological and ITS phylogenetic analyses, strains CDF5, CDF6, and CDF7 were identified as Fusarium oxysporum, while strains CDF1, CDF2, CDF3, and CDF4 were identified as Fusarium solani. Indoor virulence tests showed that, among the eight tested fungicides, carbendazim exhibited the strongest inhibitory effect on the mycelial growth of both F. oxysporum and F. solani, with a half-maximal effective concentration (EC50) value of (0.44 ± 0.24) mg/mL, making it a highly promising chemical agent for the control of A. membranaceus var. mongholicus root rot. Among the nine biocontrol agents, KRS006 showed the best inhibitory effect against the seven pathogenic strains, with an inhibition rate ranging from 42.57% to 55.51%, and it can be considered a candidate strain for biological control. This study identified the biocontrol strain KRS006 and the chemical fungicide carbendazim as promising core agents for the biological and chemical control of A. membranaceus var. mongholicus root rot, respectively, providing a theoretical foundation for establishing a dual biocontrol–chemical control strategy. Based on the excellent performance of the biocontrol bacteria and fungicides in the pathogen control tests, future research should focus on field trials to verify the synergistic effect of this integrated control strategy and clarify the interaction mechanism between the antibacterial metabolites produced by the biocontrol bacteria KRS006 and carbendazim. Additionally, continuous monitoring of the evolution of Fusarium spp. resistance to carbendazim is critical to ensure the long-term sustainability of the integrated control system. Full article
(This article belongs to the Special Issue Biological Control of Fungal Plant Pathogens)
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21 pages, 2903 KiB  
Article
Compost Tea Combined with Fungicides Modulates Grapevine Bacteriome and Metabolome to Suppress Downy Mildew
by Giuliano Bonanomi, Giuseppina Iacomino, Ayoub Idbella, Giandomenico Amoroso, Alessia Staropoli, Andrea De Sio, Franco Saccocci, Ahmed M. Abd-ElGawad, Mauro Moreno and Mohamed Idbella
J. Fungi 2025, 11(7), 527; https://doi.org/10.3390/jof11070527 - 16 Jul 2025
Viewed by 284
Abstract
Downy mildew, caused by Plasmopara viticola, is a major threat to grapevine (Vitis vinifera) cultivation in humid climates. Restrictions on synthetic pesticides and inconsistent efficacy of current biocontrol agents, especially under rainy conditions, complicate disease management. This study evaluated the [...] Read more.
Downy mildew, caused by Plasmopara viticola, is a major threat to grapevine (Vitis vinifera) cultivation in humid climates. Restrictions on synthetic pesticides and inconsistent efficacy of current biocontrol agents, especially under rainy conditions, complicate disease management. This study evaluated the potential of compost tea to suppress downy mildew in a two-year field experiment (2023 and 2024), combined with reduced synthetic fungicide applications. The study design compared two phytosanitary management strategies on a commercial vineyard: a conventional fungicide against a compost tea strategy supplemented with two cymoxanil applications. The experiment set up had three replicated blocks, each consisting of 100 plants for a total of 600 plants. Mechanistic insights were provided through controlled laboratory experiments involving pre- and post-infection leaf assays, vineyard bacteriome profiling, via 16S rRNA gene sequencing for bacterial communities, across vineyard compartments, i.e., bulk soil, rhizosphere, and phyllosphere, and grapevine metabolomic analysis by GC-MS analysis. Field trials demonstrated that compost tea combined with two fungicide applications effectively reduced disease severity, notably outperforming the fungicide alone in the particularly rainy year of 2023. Bacteriome analysis revealed that compost tea treatment enriched beneficial bacterial genera, including Pseudomonas, Sphingomonas, Enterobacter, Massilia, and Bacillus, known for their growth-promoting and biocontrol activity in the rhizosphere and phyllosphere. Laboratory assays on detached leaves further showed that compost tea alone could suppress both infection and sporulation of P. viticola. Metabolomic analysis highlighted the accumulation of compounds such as tartaric and shikimic acids in compost tea treated leaves, suggesting a potential role in induced resistance. The findings indicate that applying compost tea with reduced fungicide treatments represents a promising and sustainable strategy for managing grapevine downy mildew, even in challenging climates. Full article
(This article belongs to the Special Issue Biological Control of Fungal Plant Pathogens)
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17 pages, 3260 KiB  
Article
Interaction of Trichoderma Species with Fusarium graminearum Growth and Its Trichothecene Biosynthesis as Further Contribution in Selection of Potential Biocontrol Agents
by Xianfeng Ren, Lixia Fan, Guidong Li, Ilya V. Lyagin, Bingchun Zhang, Mingxiao Ning, Mengmeng Yan, Jing Gao, Fei Wang, Changying Guo and Antonio F. Logrieco
J. Fungi 2025, 11(7), 521; https://doi.org/10.3390/jof11070521 - 14 Jul 2025
Viewed by 346
Abstract
The interactions of Fusarium graminearum PG-Fg1 and its main trichothecenes with the 28 Trichoderma isolates were studied in vitro. The antagonistic effect assessed by dual-culture tests showed that Trichoderma isolates arrested the growth of PG-Fg1 after contact, overgrew the PG-Fg1 colony and inhibited [...] Read more.
The interactions of Fusarium graminearum PG-Fg1 and its main trichothecenes with the 28 Trichoderma isolates were studied in vitro. The antagonistic effect assessed by dual-culture tests showed that Trichoderma isolates arrested the growth of PG-Fg1 after contact, overgrew the PG-Fg1 colony and inhibited the production of deoxynivalenol (DON), 3-acetyl-deoxynivalenol (3-ADON), and 15-acetyldeoxynivalenol (15-ADON) by up to 95.3%, 99.4%, and 99.6%, respectively. PG-Fg1 was hard to overgrow Trichoderma for further extension. Additionally, the inhibitory effects on PG-Fg1 by the Trichoderma metabolites, including volatiles and non-volatiles, were also investigated. Most of the Trichoderma isolates produced metabolites which inhibited PG-Fg1 growth and mycotoxins production. Specifically, Trichoderma non-volatiles and volatiles showed Fusarium growth inhibition rates ranging from 7% to 72% and 3% to 32%, respectively. Notably, non-volatile compounds from two isolates and volatiles from one isolate up-regulated the expression of DON biosynthesis genes (tri4 and tri5), leading to increased production of DON, 3-ADON, and 15-ADON. This study highlights the potential risk posed by certain Trichoderma strains as microbial agents, which can stimulate toxigenic fungi to produce higher levels of mycotoxins. Based on our results and previous reports, when selecting Trichoderma species as biocontrol agents against Fusarium graminearum, its effects on mycotoxins production should be carefully assessed, particularly given observed stimulatory impacts. Full article
(This article belongs to the Special Issue Biological Control of Fungal Plant Pathogens)
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19 pages, 2039 KiB  
Article
The Study of Metschnikowia pulcherrima E1 in the Induction of Improved Gray Spot Disease Resistance in Loquat Fruit
by Xiaoya Li, Kunkun Wu, Xin Li, Yuhao Zhao and Weihong Sun
J. Fungi 2025, 11(7), 497; https://doi.org/10.3390/jof11070497 - 30 Jun 2025
Viewed by 425
Abstract
In this study, the dominant pathogenic fungus of gray spot disease in loquat, which was isolated from postharvest decaying loquat fruits in Zhenjiang, was identified as Pestalotiopsis vismiae (P. vismiae) by morphological characteristics and DNA sequencing. At the same time, a [...] Read more.
In this study, the dominant pathogenic fungus of gray spot disease in loquat, which was isolated from postharvest decaying loquat fruits in Zhenjiang, was identified as Pestalotiopsis vismiae (P. vismiae) by morphological characteristics and DNA sequencing. At the same time, a strain of yeast E1, which could effectively inhibit the pathogen, was isolated from the loquat leaves and soil and identified as Metschnikowia pulcherrima (M. pulcherrima) by morphological and molecular biological characteristics. It significantly reduced the natural decay of loquat fruits without affecting fruit quality. Metschnikowia pulcherrima E1 (M. pulcherrima E1) exhibited significant biocontrol efficacy against P. vismiae, the causal agent of gray spot in loquat, reducing disease incidence to 22.73% compared to 100% in the control group. Transcriptome analysis revealed 1444 differentially expressed genes (DEGs) (1111 upregulated, 333 downregulated), with key genes (CML19, XTH23, GSTU10) validated by RT-qPCR. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighted enrichment in plant–pathogen interactions, glutathione metabolism, and phenylpropanoid biosynthesis. These findings provided molecular insights into yeast-induced resistance, bridging biocontrol applications with mechanistic studies. Full article
(This article belongs to the Special Issue Biological Control of Fungal Plant Pathogens)
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21 pages, 2694 KiB  
Article
Isolation and Identification of Endophytic Bacterium B5 from Mentha haplocalyx Briq. and Its Biocontrol Mechanisms Against Alternaria alternata-Induced Tobacco Brown Spot
by Qunying Qin, Boyu Liu, Baige Ma, Xihong Wei, Yi Zhou and Zhengxiang Sun
J. Fungi 2025, 11(6), 446; https://doi.org/10.3390/jof11060446 - 12 Jun 2025
Viewed by 1248
Abstract
The fungus Alternaria alternata, which causes tobacco brown spot disease, poses a serious threat to the tobacco industry. Beneficial microorganisms and their secondary metabolites have emerged as a promising green strategy for disease management. This study recovered 16 endophytic bacterial strains from [...] Read more.
The fungus Alternaria alternata, which causes tobacco brown spot disease, poses a serious threat to the tobacco industry. Beneficial microorganisms and their secondary metabolites have emerged as a promising green strategy for disease management. This study recovered 16 endophytic bacterial strains from Mentha haplocalyx Briq., a therapeutic herb. The study revealed that strain B5, with an inhibition rate of 82.76%, exhibited the highest antifungal activity against A. alternata. This strain exhibited broad-spectrum antifungal activity, with inhibition rates ranging from 66.34% to 87.23%. Phylogenetic analysis of 16S rDNA and gyrA gene sequences identified it as Bacillus velezensis (GenBank: PV168970 and PV173738). Further characterization revealed that strain B5 can secrete cell wall-degrading enzymes, produce IAA, and synthesize siderophores. The growth of mycelium in A. alternata was greatly reduced by both the ethyl acetate extract and the filtered liquid from the sterile fermentation, resulting in marked morphological abnormalities. Multiple antifungal active substances were identified through liquid LC-MS analysis. Greenhouse experiments demonstrated that the B5 fermentation broth effectively suppressed the occurrence of tobacco brown spot disease, achieving a relative control efficacy of 60.66%, comparable to that of 10% difenoconazole water dispersible granule (WDG). Additionally, strain B5 enhances plant disease resistance by activating the activities of key defense enzymes. B. velezensis B5 serves as a safe alternative to chemical fungicides and is highly effective at controlling tobacco brown spot disease. Full article
(This article belongs to the Special Issue Biological Control of Fungal Plant Pathogens)
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18 pages, 20467 KiB  
Article
Isolation and Biological Control of Colletotrichum sp. Causing Anthracnosis in Theobroma cacao L. in Chiapas, Mexico
by Nadia Denisse Rodríguez-Velázquez, Irene Gómez-de la Cruz, Guillermo López-Guillen, Belén Chávez-Ramírez and Paulina Estrada-de los Santos
J. Fungi 2025, 11(4), 312; https://doi.org/10.3390/jof11040312 - 15 Apr 2025
Viewed by 1185
Abstract
Anthracnose is a phytosanitary issue caused by various species of Colletotrichum. This study aims to revise the presence of Colletotrichum in the south of Mexico (the Soconusco area in Chiapas) and assess the inhibitory capacity of Paenibacillus sp. NMA1017 against Colletotrichum in [...] Read more.
Anthracnose is a phytosanitary issue caused by various species of Colletotrichum. This study aims to revise the presence of Colletotrichum in the south of Mexico (the Soconusco area in Chiapas) and assess the inhibitory capacity of Paenibacillus sp. NMA1017 against Colletotrichum in in vitro and field experiments. The study involved sampling pods with anthracnose from 17 sites in the Soconusco area, Chiapas, Mexico. The incidence of the disease ranged from 0.6 to 11.63%. A total of 142 isolates exhibiting the morphological characteristics of the Colletotrichum genus were obtained. Fifty selected isolates were identified using the ITS region and were classified as Colletotrichum gloeosporioides with 99% similarity. The concatenation of morphological and physiological characteristics resulted in nine main clusters. The in vitro test showed that Paenibacillus sp. NMA1017 inhibited the fungal growth of selected strains by 30–50%. The field experiments included three commercial biocontrol agents, Paenibacillus sp. NMA1017, and a water control. The incidence of anthracnose (control with water) ranged from 32 to 65%, while the commercial biocontrol agents and Paenibacillus showed an incidence range of 12 to 20%. These findings support the use of Paenibacillus sp. NMA1017 as a biocontrol agent for cacao anthracnose. Full article
(This article belongs to the Special Issue Biological Control of Fungal Plant Pathogens)
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17 pages, 13117 KiB  
Article
Aflatoxin B1 Contamination Association with the Seed Coat Biochemical Marker Polyphenol in Peanuts Under Intermittent Drought
by Maman Moutari Aminou, Hamidou Falalou, Harou Abdou and Venugopal Mendu
J. Fungi 2024, 10(12), 850; https://doi.org/10.3390/jof10120850 - 10 Dec 2024
Cited by 2 | Viewed by 1743
Abstract
Aflatoxin B1 (AFB1) contamination (AC) increases as the severity of drought stress increases in peanuts. Identifying drought-tolerant (DT) genotypes with resistance to Aspergillus flavus colonization and/or infection may aid in developing peanuts resistant to aflatoxin contamination in the semi-arid tropics. The goal of [...] Read more.
Aflatoxin B1 (AFB1) contamination (AC) increases as the severity of drought stress increases in peanuts. Identifying drought-tolerant (DT) genotypes with resistance to Aspergillus flavus colonization and/or infection may aid in developing peanuts resistant to aflatoxin contamination in the semi-arid tropics. The goal of this study is to identify DT genotypes with seed coat biochemical resistance to A. flavus infestation and aflatoxin contamination. Experiments were carried out at ICRISAT Sahelian Center; fifty-five genotypes were assessed under adjacent intermittent water-stressed (WS) conditions imposed from the 60th day after sowing to the maturity date and well-watered (WW) conditions in an alpha lattice design with two factors. The yield and its components, the incidence of A. flavus colonization, aflatoxin contamination, and seed coat total polyphenol (SCTPP) were investigated. Our findings show that the water deficit reduced the pod yield, seed yield, and haulm yield by up to 19.49%, 27.24%, and 22.07%, respectively, while it increased the number of immature pods per plant (IMPN) and the aflatoxin contamination by up to 67.16% and 54.95%, respectively. The drought tolerant genotypes ICG 2106, ICG 311, ICG 4684, ICG 4543, and ICG 1415 maintained a high yield, small number of IMPN under WS and low aflatoxin content variation between WW and WS. Our findings revealed that in the drought-tolerant genotypes ICG 1415, ICG 2106, ICG 311, ICG 4684, and ICG 4543, there was a significant relationship between the aflatoxin resistance and the seed coat total polyphenol under the two water treatments (r2 = 0.80; r2 = 0.82). This suggests that these drought-tolerant genotypes kept their seed coat intact and minimized the aflatoxin contamination under an intermittent water deficit. Full article
(This article belongs to the Special Issue Biological Control of Fungal Plant Pathogens)
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