Rice phyllosphere bacteria mediates beneficial responses to pesticide stress

Pesticides are essential for agricultural productivity; however, pose significant risks to ecosystems and human health due to their persistence and non-target effects. This study investigates the role of phyllosphere bacteria Stenotrophomonas sp., in mitigating pesticide stress and enhancing plant resilience. We explored the adaptive responses of the rice phyllosphere microbiome to pesticide exposure using thifluzamide (TF), a widely used fungicide. High-throughput sequencing revealed that TF significantly reducing microbial communities’ richness while enriching specific bacterial genera such as Stenotrophomonas, Pantoea, and Sphingomonas. Metabolomic analysis indicated that TF increasing amino acids like leucine, which facilitated the recruitment and growth of Stenotrophomonas St10. This strain demonstrated high resistance to TF and effectively degraded the fungicide in vitro and in plant, reducing residual TF levels in rice tissues. Additionally, Stenotrophomonas St10 alleviated TF-induced physiological stress in rice by enhancing chlorophyll content, reducing malondialdehyde levels, and increasing antioxidant enzyme activities. Transcriptomic analysis revealed that Stenotrophomonas St10 activated pesticide detoxification-related genes in rice, including cytochrome P450s, glutathione transferases, and UDP-glycosyltransferases. These findings highlight the dual role of Stenotrophomonas St10 in directly degrading TF and enhancing host plant detoxification mechanisms. This study provides novel insights into the interactions between phyllosphere microbes and host plants under pesticide stress.