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Agronomy
Special Issues
Research Progress of Beneficial Microorganisms in Controlling Crop Pathogens
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Research Progress of Beneficial Microorganisms in Controlling Crop Pathogens

A Special Issue of Agronomy (ISSN 2073-4395) belonging to the section "Pest and Disease Management".

Deadline for manuscript submissions: 20 December 2026 | Viewed by 4690

Editors

Dr. Sofia Palacios

E-Mail Website
Guest Editor
Instituto de Investigación en Micología y Micotoxicología (IMICO), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET). Departamento de Microbiología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, Argentina
Interests: biocontrol; plant growth promotion; mycotoxins; Fusarium
Dr. Nicolás Pastor

E-Mail Website
Guest Editor
Instituto de Investigación en Micología y Micotoxicología (IMICO), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET). Departamento de Microbiología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, Argentina
Interests: biocontrol; plant growth promotion; microbial consortia; effect of inoculation on soil microbial communities
Dr. Adriana Torres

E-Mail Website
Guest Editor
Instituto de Investigación en Micología y Micotoxicología (IMICO), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET). Departamento de Microbiología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, Argentina
Interests: biocontrol; plant growth promotion; microbial consortia; effect of inoculation on soil microbial communities; mycotoxins

Special Issue Information

Dear Colleagues,

The sustainability of agriculture and food security are threatened by the rising incidence of crop diseases, which are made worse by global climate change. Biological control has long been acknowledged as a successful method for controlling diseases in crops of agronomic significance. The potential of using beneficial microorganisms, such as bacteria, fungi, and their mixtures, to control pathogens through a variety of mechanisms continues to be explored by ongoing research, which will improve and refine their use for crop protection. Furthermore, the incorporation of molecular tools has reinforced our comprehension of the interactions between microbes and plants, which has made it possible to create biocontrol agents (BCAs) that are more efficient. In addition, research is evaluating formulations and delivery systems to enhance the stability and effectiveness of BCAs in a variety of field settings. In this regard, it is essential to guarantee the ecological suitability and feasible scalability of BCAs. This calls for a thorough assessment of their performance in various agroecosystems as well as the creation of effective, approachable bioformulations to enable broad adoption. The purpose of this Special Issue is to promote knowledge sharing on all facets of crop pathogen biological control, therefore expanding our knowledge of current developments, aiming at the improvement of crop yield and resilience in a range of agricultural conditions.

Dr. Sofia Palacios
Dr. Nicolás Pastor
Dr. Adriana Torres
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 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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access semimonthly 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

  • biocontrol
  • climate change
  • sustainability
  • crop protection
  • yield
  • biostimulation
  • crop pathogens

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Published Papers (4 papers)

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Research

16 pages, 7336 KB  
Article
Bacillus cereus AR156 Induces Defense Responses in Rice Against Sheath Blight Caused by Rhizoctonia solani
by Mingzhou Yu, Xibao Xu, Bin Lei, Wenhui Li, Huicheng Shi, Yiyang Yu and Yonghong Hu
Agronomy 2026, 16(16), 1610; https://doi.org/10.3390/agronomy16161610 - 20 Aug 2026
Viewed by 332
Abstract
Rice sheath blight, caused by Rhizoctonia solani, is a major constraint on rice production, and its management still relies mainly on chemical fungicides. We evaluated the biocontrol agent Bacillus cereus AR156 against the disease and examined the transcriptional and biochemical changes in [...] Read more.
Rice sheath blight, caused by Rhizoctonia solani, is a major constraint on rice production, and its management still relies mainly on chemical fungicides. We evaluated the biocontrol agent Bacillus cereus AR156 against the disease and examined the transcriptional and biochemical changes in rice that accompany protection. AR156 achieved a biocontrol efficacy of 71.81% at 6 days after inoculation. RNA sequencing compared AR156-treated and control plants with and without pathogen challenge, and we identified 4554 and 2740 differentially expressed genes at 24 and 48 h after inoculation, respectively. AR156-responsive genes were enriched in secondary metabolism, plant-pathogen interaction, hormone signaling, phosphoinositide signaling, and membrane transport. Of the defense-associated DEGs, 97 TF/TRs and 86 predicted PRGs were shared between 24 and 48 h, most of which reversed their direction of change over time. Prominent TF/TR families included SNF2, bHLH, MYB, MYB-related, FAR1, PHD and WRKY, with KIN and RLK prominent among the predicted PRG classes. Quantitative RT-PCR and enzyme assays showed higher expression of several pathogenesis-related and hormone-associated markers, together with increased superoxide dismutase, peroxidase, and catalase activity after challenge. Together, these results indicate that AR156 suppresses rice sheath blight by temporally reshaping coordinated transcriptional and biochemical defenses rather than a single pathway. Full article
(This article belongs to the Special Issue Research Progress of Beneficial Microorganisms in Controlling Crop Pathogens)
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22 pages, 2157 KB  
Article
Suppression of Fusarium graminearum and Mycotoxin Mitigation in Durum Wheat by Trichoderma harzianum ITEM 3636
by Jessica Erazo, Paula Vanella, Juan Palazzini, Silvana Plem, Adriana M. Torres and Sofía A. Palacios
Agronomy 2026, 16(15), 1492; https://doi.org/10.3390/agronomy16151492 - 3 Aug 2026
Viewed by 1298
Abstract
Durum wheat is highly susceptible to Fusarium head blight (FHB), a severe fungal disease caused primarily by Fusarium graminearum. FHB affects durum wheat production by causing significant yield losses and grain contamination with mycotoxins such as deoxynivalenol (DON) and zearalenone (ZEA). Given [...] Read more.
Durum wheat is highly susceptible to Fusarium head blight (FHB), a severe fungal disease caused primarily by Fusarium graminearum. FHB affects durum wheat production by causing significant yield losses and grain contamination with mycotoxins such as deoxynivalenol (DON) and zearalenone (ZEA). Given the limitations of chemical fungicides, finding sustainable biological control agents is essential. This study evaluated the antagonistic and biocontrol capabilities of Trichoderma harzianum ITEM 3636 against F. graminearum through in vitro and greenhouse experiments. In vitro dual and sandwich culture assays demonstrated that T. harzianum significantly inhibits pathogen mycelial growth through direct interaction and the emission of volatile compounds. In a competition test on rice kernels, co-inoculation with ITEM 3636 significantly reduced pathogen biomass, leading to maximum reductions of 96.5% for DON and 98% for ZEA. Furthermore, greenhouse trials on a commercial durum wheat cultivar revealed that T. harzianum ITEM 3636 significantly decreased FHB severity by 40% and reduced DON contamination by up to 32% only when a combined seed-coating and spike-spraying application was performed. Additionally, ITEM 3636 exhibited biostimulant-like effects on yield parameters, causing an increase in kernel weight of 33% in the greenhouse assay. These findings highlight T. harzianum ITEM 3636 as a promising and ecological alternative to synthetic fungicides for managing FHB, safeguarding crop production, and ensuring food safety. Full article
(This article belongs to the Special Issue Research Progress of Beneficial Microorganisms in Controlling Crop Pathogens)
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15 pages, 2355 KB  
Article
Distinct Seed Endophytic Bacterial Communities Are Associated with Blast Resistance in Yongyou Hybrid Rice Varieties
by Yanbo Chen, Caiyu Lu, Zhenyu Liu, Zhixin Chen, Jianfeng Chen, Xiaomeng Zhang, Xianting Wang, Bin Ma, Houjin Lv, Huiyun Dong and Yanling Liu
Agronomy 2026, 16(3), 280; https://doi.org/10.3390/agronomy16030280 - 23 Jan 2026
Viewed by 1096
Abstract
Rice blast, caused by the fungal pathogen Pyricularia oryzae, remains one of the most destructive diseases threatening global rice production. Although the deployment of resistant cultivars is widely regarded as the most effective and sustainable control strategy, resistance based solely on host [...] Read more.
Rice blast, caused by the fungal pathogen Pyricularia oryzae, remains one of the most destructive diseases threatening global rice production. Although the deployment of resistant cultivars is widely regarded as the most effective and sustainable control strategy, resistance based solely on host genetics often has limited durability due to the rapid adaptation of the pathogen. Increasing evidence suggests that plant-associated microbial communities contribute to host health and disease resistance, yet the role of seed-associated microbiota in shaping rice blast resistance remains insufficiently understood. In this study, we investigated seed endophytic bacterial communities across multiple indica–japonica hybrid rice varieties from the Yongyou series that exhibit contrasting levels of resistance to rice blast. By integrating amplicon sequencing, we identified distinct seed bacterial assemblages associated with blast-resistant and blast-susceptible varieties were identified. Notably, the microbial communities in blast-resistant varieties exhibited significantly higher Shannon index, with a median value of 3.478 compared to 2.654 in susceptible varieties (p < 0.001), indicating a greater diversity and more balanced community structure compared to those in susceptible varieties. Several bacterial taxa consistently enriched in resistant varieties showed negative ecological associations with P. oryzae, both at the local scale and across publicly available global metagenomic datasets. These findings indicate that seed endophytic bacterial communities are non-randomly structured in relation to host resistance phenotypes and may contribute to rice blast resistance through persistent ecological interactions with the pathogen. This work highlights the potential importance of seed-associated microbiota as intrinsic components of varietal resistance and provides a microbial perspective for improving durable disease resistance in rice breeding programs. Full article
(This article belongs to the Special Issue Research Progress of Beneficial Microorganisms in Controlling Crop Pathogens)
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18 pages, 1717 KB  
Article
Native Phosphate Solubilizing Bacteria Mitigate the Effect of the Phytopathogen Sclerotium rolfsii on Peanut (Arachis hypogaea L.) Plants in a P-Deficient Environment
by Ana Laura Gentile, Maria Soledad Figueredo, Maria Soledad Anzuay, Maria Laura Tonelli, Adriana Fabra, Tania Taurian and Liliana Ludueña
Agronomy 2025, 15(10), 2278; https://doi.org/10.3390/agronomy15102278 - 26 Sep 2025
Cited by 1 | Viewed by 1254
Abstract
Phosphorus (P) deficiency and soil-borne fungal diseases are major constraints to peanut (Arachis hypogaea L.) production. Phosphate-solubilizing bacteria (PSB) can improve P availability in the soil, thereby promoting plant growth. However, their potential to improve plant resistance against pathogens under P-limited conditions [...] Read more.
Phosphorus (P) deficiency and soil-borne fungal diseases are major constraints to peanut (Arachis hypogaea L.) production. Phosphate-solubilizing bacteria (PSB) can improve P availability in the soil, thereby promoting plant growth. However, their potential to improve plant resistance against pathogens under P-limited conditions remains poorly understood. In this study, we first evaluated the ability of two PSB strains, Enterobacter sp. J49 and Serratia sp. S119, to induce systemic resistance (ISR) in peanut plants against the fungal pathogen Sclerotium rolfsii. Results showed that strain S119 reduced disease severity by 40%, whereas strain J49 reduced both incidence (30%) and severity (40%). The protective effect produced by strain J49 was mediated by ISR, as evidenced by the early increase in phenolic compounds accumulation (48 h) and total peroxidase activity (72 h) in inoculated plants. Under P-deficient conditions, the J49 strain was also able to protect peanut plants against S. rolfsii, as demonstrated by a significant reduction in disease severity (55%). These findings highlight the potential of multifunctional bacterium Enterobacter sp. J49 to enhance sustainable peanut production by simultaneously improving P acquisition and strengthening plant defense mechanisms. Full article
(This article belongs to the Special Issue Research Progress of Beneficial Microorganisms in Controlling Crop Pathogens)
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