Transcriptomic and physiological responses of Rhizobium sp. IRBG74 to Sesbania cannabina and rice (Oryza sativa L) rhizosphere

Abstract

Abstract Purpose Rhizobium sp. IRBG74 (IRBG74), is a symbiont of Sesbania cannabina and a growth promoting endophyte of rice. Here, we compare the transcriptomic and physiological responses of IRBG74 in the rhizosphere of S. cannabina and rice. Methods We used RNA sequencing to determine transcriptomic changes at 12 and 72 hours post inoculation (hpi) in rhizosphere. Upregulation of key pathways was confirmed using β-glucuronidase (GUS) reporter strains and by histochemical and quantitative GUS activity. Results Significant changes in transcriptome with S. cannabina were detected at 12hpi but most gene expression changes with rice were observed at 72hpi. Many pathways including Nod factor synthesis, two component systems, ABC transporters, and synthesis of indole acetic acid (IAA) were upregulated whereas translation, RNA degradation, protein export and sulfur metabolism were downregulated with both plants. In contrast, motility and chemotaxis genes were induced specifically with S. cannabina. The upregulation of nod and IAA genes was confirmed using reporter strains. Nod factor synthesis provides competitive advantage for colonization of rice and chemotaxis is required for colonization of S. cannabina but not of rice. Conclusion IRBG74 responded to S. cannabina and rice using specific as well as common transcriptional changes. A mutant defective in Nod factor synthesis was outcompeted for rice colonization. Chemotaxis was required for colonization of S. cannabina but not for rice. IAA synthesis by IRBG74 could be a major mechanism of rice growth promotion. These results provide a foundation for further improvement of rhizobial interactions with rice and other cereals.