Elucidating the Growth‐Promoting Mechanism of Bacillus safensis in Nipponbare Rice Through Integrated Phenotypic and Transcriptome Analysis

A growing global demand for rice necessitates improvements in grain productivity to support sustainable agricultural developments. Bacillus safensis, a halophilic soil bacterium, has been shown to enhance crop growth, but its effects on rice (Oryza sativa L.) remain unclear. In this study, we tested how B. safensis affects rice yields and agronomic traits. We applied B. safensis to roots and panicles of rice and measured plant height, tiller number, panicle length, panicle weight, grain number per panicle, 1000-grain weight, grain setting rate and theoretical yield. The results showed that root treatment and root-panicle co-treatment increased theoretical yield by 4.33% and 2.78%, respectively, accompanied by significant improvements in plant height, tiller number, panicle length, and grain number per panicle. RNA-seq analysis revealed shifts in gene expression and alternative splicing associated with these agronomic improvements. KEGG pathway analysis showed B. safensis treatment regulated genes involved in stress tolerance, metabolic regulation, and secondary metabolite production. Field experiments further demonstrated that B. safensis application significantly increased tiller number, grain number per panicle, 1000-grain weight and grain setting rate, leading to an 8.98% increase in theoretical yield. Overall, this study suggests B. safensis is a promising biostimulant for sustainable rice farming and provides a reference for the application of B. safensis in rice production.