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Fungal pathogens pose escalating challenges to global food security, as resistance has emerged against nearly all major fungicides used in agriculture. RNA-based antifungals offer a sustainable and environmentally friendly alternative for disease control, but their deployment is hindered by RNA instability under environmental conditions, especially in soil. In this study, we engineered two plant-beneficial soil bacteria-Bacillus subtilis (Gram-positive) and Pseudomonas putida (Gram-negative)-to produce double-stranded RNAs (dsRNAs) targeting fungal genes in the foliar and postharvest pathogen Botrytis cinerea and the soilborne pathogen Verticillium dahliae. We found that both bacterial species secrete RNA through extracellular vesicles (EVs) and that these RNAs are transported into fungal cells, demonstrating cross-kingdom RNA trafficking from bacteria to fungi. Application of dsRNA-containing bacterial EVs to plant leaves suppressed B. cinerea infection. In addition, direct treatment with dsRNA-producing bacteria protected both Arabidopsis thaliana and tomato plants from infections by B. cinerea and V. dahliae. Our findings establish beneficial bacteria as a scalable platform for continuous production and delivery of antifungal RNAs, enabling a cost-effective strategy for sustainable crop protection.
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This content will become publicly available on October 27, 2026
The biocontrol potential of endophyte Bacillus velezensis to reduce post-harvest tomato infection caused by Rhizopus microsporus
ABSTRACT Rhizopus microsporusis a necrotrophic post-harvest pathogen that causes significant economic losses in the agricultural sector. To explore alternatives to conventional management strategies for the mitigation of post-harvest infections, we investigated the potential of two previously identified endophyticBacillus velezensisstrains as biological control agents. Throughin vitroandin vivoexperiments, we examined the mechanisms of biocontrol displayed by twoB. velezensisstrains (KV10 and KV15) against threeR. microsporusstrains (W2-50, W2-51, and W2-58).In vitroassays assessed co-cultivability and the inhibitory effects ofB. velezensisagainstR. microsporus. The results demonstrated strain-specific antifungal activity with a reduction in fungal growth across treatments. Further analysis revealed that volatile organic compounds produced byB. velezensiscontributed to its antifungal properties. To evaluate the biocontrol efficacyin vivo, tomato fruits were inoculated withR. microsporusand subsequently treated withB. velezensis. The results support the strain-specific reduction in tomato spoilage, yielding various spoilage rates observed across treatments. Our findings highlight the potential ofB. velezensisas a promising biocontrol agent for the management ofR. microsporuspost-harvest infections in tomatoes. Further research is warranted to optimize the applicationof B. velezensisas a sustainable and environmentally friendly approach for controlling post-harvest diseases in tomatoes.IMPORTANCEOur study shows the significance of improving sustainable agriculture by offering an alternative to the use of chemical fungicides in post-harvest applications. Opportunistic fungal pathogens likeRhizopus microsporuscan have detrimental effects on post-harvest commodities like tomatoes. Post-harvest fungal infections are mainly controlled by chemical fungicides that pose health risks to humans and the environment. Utilizing biocontrol agents provides an environmentally safe alternative. Understanding the mechanisms of biocontrol employed by beneficial bacteria likeBacillus velezensison fungal pathogens gives insight into safer, more environmentally friendly alternatives to protect food crops. Our results suggest that targeted microbial solutions can mitigate post-harvest losses.
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- Award ID(s):
- 2030338
- PAR ID:
- 10644773
- Editor(s):
- Hockett, Kevin Loren
- Publisher / Repository:
- American Society for Microbiology
- Date Published:
- Journal Name:
- Microbiology Spectrum
- ISSN:
- 2165-0497
- Subject(s) / Keyword(s):
- biocontrol, post-harvest, endophyte, Bacillus velezensis, secondary metabolites, Rhizopus microsporus
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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