Microbiome Responses to RYMV Infection: Insights from Rice Cultivation in Mali

Background: The Rice Yellow Mottle Virus (RYMV) is one of the most significant viral pathogens affecting rice production in Sub-Saharan Africa, leading to yield losses as high as 100% in severely affected areas. In Mali, particularly in the Office du Niger region, RYMV poses a constant threat to rice cultivation. This study aimed to explore the microbiome diversity associated with RYMV-infected and non-infected rice plants, using next-generation sequencing (NGS) and metagenomics approaches. The presence of RYMV was confirmed by RT-PCR, and microbial DNA was extracted for sequencing. Results: A total of 40 samples (leaves and roots) were collected from both infected and non-infected plants. The results revealed alterations in bacterial community composition between infected and non-infected plants. Alpha diversity indices, such as Shannon and Simpson indicated reduced microbial diversity in infected plants. Notably, certain bacterial genera, including Bacillus, Pseudomonas, and Kaistobacter, were statistically more abundant in non-infected plants, suggesting their potential role in conferring resistance to RYMV. Conclusions: This study provided new insights into the microbial dynamics associated with RYMV infection and highlights the potential for leveraging the rice microbiome in developing biocontrol strategies to manage viral diseases. Future research should focus on isolating and characterizing the functional roles of these beneficial microorganisms in enhancing rice resistance to RYMV. That will serve for sustainable agriculture strategies development.