Diffusible signals from Azospirillum brasilense promote rice growth and induce distinct gene expression changes in plant roots

Abstract

Plants form associations with diverse beneficial microbes, including arbuscular mycorrhizal (AM) fungi, rhizobia, and plant growth-promoting bacteria (PGPB). Research on legume-rhizobia symbiosis (LRS) and AM symbiosis has demonstrated that molecular communication between symbiotic partners is essential for initiating these interactions. Genetic and biochemical studies have further identified both plant and microbial signals, as well as host genetic pathways, that regulate these interactions. However, most studies on plant-PGPB interactions have focused on direct application of PGPB to plant roots, leaving the early signaling mechanisms underlying these interactions poorly understood. In this study, we report that diffusible signals from A. brasilense can promote rice growth without direct contact between bacteria and plant roots, 7 days post-treatment (dpt). Using RNA sequencing, we identified 2,516 differentially expressed genes (DEGs) in rice roots in response to diffusible signals from A. brasilense at 1 dpt. We identified differential expression of genes involved in flavonoid synthesis, defense responses, receptor activity, transcription factors, and hormone pathways. Comparative transcriptomic analysis of rice roots with or without contact with A. brasilense revealed both shared and unique gene expression patterns. We observed upregulation of certain defense-response genes ( PAL , chitinase, thionin), transcription factors (AP2/ERFs, MYBs, WRKYs, and GRAS), and hormone-related (auxin and ethylene) genes without bacterial contact, but downregulation or no differential expression of these genes upon bacterial contact. This pattern suggests that initial induction followed by subsequent suppression of these genes may be crucial for establishing the interaction with A. brasilense. Our transcriptomic analysis also suggests that flavonoids may be required throughout the interaction, whereas nitrate transporters appear to be involved at later stages and likely require contact between plant roots and bacteria. Collectively, our findings reveal that diffusible signals from A. brasilense can promote rice growth and induce distinct gene expression changes in plant roots. These results provide novel insights into the early phase of rice- A. brasilense interaction and highlight the potential for leveraging plant-PGPB signaling mechanisms to enhance crop growth under adverse environmental conditions.