Bacillus pumilus strain TUAT1, a type of plant growth – promoting rhizobacteria (PGPR), is used as an ingredient in biofertilizer. Although we confirmed that B. pumilus TUAT1 promotes the growth of rice seedlings at 25°C, this effect has not been shown at lower temperatures. In this study, we confirmed that inoculation of rice seedlings with spores of B. pumilus TUAT1 promoted seedling emergence from soil and subsequent growth at 15°C. Except for the effect on root growth, these effects disappeared when seeds were treated with 2–4-carboxyphenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide, a nitric oxide (NO) scavenger, simultaneously with B. pumilus TUAT1 inoculation. Increased NO accumulation was detected in seed embryos 3 h after inoculation, suggesting that NO plays a role in the effects of B. pumilus TUAT1 inoculation. Transcriptome analysis using RNA-seq suggested the involvement of immune responses and cytochrome respiratory pathways in increasing NO levels in embryos after inoculation with B. pumilus TUAT1. Transcriptome analysis also indicated that transcription of genes involved in cold tolerance was accelerated in embryos following the increase in NO resulting from inoculation with B. pumilus TUAT1. These findings suggest that a novel NO signaling mechanism is involved in PGPR-induced growth promotion in plants. These results also indicate that inoculation with B. pumilus TUAT1 spores may help overcome the initial growth failure of seedlings in direct sowing culture of rice in cold regions.