Integrated analyses of miRNAome and transcriptome reveal growth promoting mechanism of Bacillus velezensis 9912 on rice seedlings

Bacillus velezensis, an excellent member of Plant Growth-Promoting Rhizobacteria (PGPR), exhibits effectively suppressing pathogens and promoting plant growth. Despite its well-recognized efficacy, the intricate molecular mechanisms underlying its growth-promoting attributes remain largely unexplored. In this study, rice seedlings were subjected to inoculation with Bacillus velezensis strain 9912, and subsequent construction of mRNA and small RNA libraries for high-throughput sequencing. Totally, 2,938 rice genes and 30 miRNAs responsive to B. velezensis 9912 inoculation were detected. Notably, differentially expressed genes (DEGs) encompassed key transcription factors like ERF, WRKY, and AP2. GO and KEGG enrichment analyses indicated that pathways associated with DNA replication, cell cycle, cell division, cytoskeleton organization were significantly enriched. In addition, secondary metabolites biosynthetic pathways, such as carotenoid, lipid, diterpenoid and brassinosteroid were also significantly enriched. Integrated analysis of the transcriptome and miRNAome identified several miRNA-mRNA regulatory networks like miR166-Os08g14940, miR396-Os07g9320, miR529-Os12g31540, and miR6249-Os05g07880, participated in the growth promotion process. In conclusion, our study provides deep insights into the dynamic responses of rice genes and miRNAs to B. velezensis 9912, unveiling potential miRNA-mRNA regulatory networks that play pivotal roles in growth promotion mechanism. Thereby establishing a foundation for in-depth molecular investigations.