Transcriptome profiling of rice roots in early response to Bacillus subtilis (RR4) colonization

Bacillus subtilis, a gram-positive soil bacterium, is widely used as a plant-growth-promoting agent. However, how Bacillus initially colonizes rice roots and evades the plant primary defense mechanisms, and how it influences root secretion of phytochemicals for further colonization remain obscure. To get an insight into how a plant perceives the bacterium upon initial root colonization, a microarray analysis was performed using rice roots treated with a rice rhizosphere isolate, B. subtilis RR4. About 891 transcripts (255 up-regulated and 636 downregulated) were differentially expressed, indicating that the bacteria reprogram the plant to colonize it. In our experiments, RR4 mainly caused the suppression of transcripts encoding defense response enzymes such as chitinase, cell-wall-modifying enzymes such as pectinesterase, and genes associated with transport/exudation of phytochemicals, signifying that the bacteria modulate the gene expression of the plant to facilitate its colonization. Genes that regulate secondary metabolite production were up-regulated. Although the defense response genes in rice roots were suppressed initially, they were induced gradually at 4 and 10 days post-treatment. This was accompanied by an increased level of salicylic acid in the colonized rice roots. Thus, our results show that B. subtilis alters the transcriptome of rice roots for initial colonization by initially lowering the plants' defenses, limiting root exudation and active cell growth, but boosting the plants' defenses at a later stage.