Rice phyllospheric Pantoea spp. suppress blast disease

Rice is a major food crop in China as well as Asian, yet its production is threatened by microbial diseases including blast disease caused by fungal pathogen (Magnaporthe oryzae) and bacterial blight caused by several bacterial pathogens. To screen for bacterial microbiota associated with rice blast occurrence, and/or contributing to resistance of rice to blast disease, we performed microbiota analysis with phyzospheric soil, root, stem, and leaf samples of blast susceptible (CO39) and resistant (Y33R) rice grown in a blast disease nursery garden. Our result showed no significant difference in microbiota of rhyzospheric soil, root, or leaf between the 2 rice cultivars, but stem microbiota were significantly different. Pantoea spp. was enriched in stem of blast susceptible rice, suggesting a role in mediating blast resistance. A total of 822 bacterial strains were isolated from the phyllospheric samples of Y33R and CO39 rice, among which 3 strains were identified as P. ananatis and 1 as P. dispersa based on 16S rDNA, gyrB, leuS and rpoB sequences. Average Nucleotide Identity (ANI) analysis confirmed that A25-H1 and B10-A1 strain was P. ananatis and P. dispersa respectively. The P. ananatis consortium (A25-F1, A25-G1 and A25-H1 combination) A25-11 and P. dispersa strain B10-A1 displayed suppressive effect on blast disease, when applied to the susceptible rice CO39. Although a P. ananatis strain SC7 has been reported to cause bacterial blight in rice, A25-11 or B10-A1 were non-pathogenic to rice. Furthermore, they could also suppress bacterial blight caused by SC7 or Xanthomonas oryzae pv.oryzae (Xoo) strain Pxo99. The bio-control effect of A25-11 or B10-A1 may lie in immunity priming rather than antagonistic effect to mycelial growth. We further showed that A25-11 and B10-A1 were capable of producing indole 3-acetic acid (IAA), a known plant auxin, thus promoting growth of rice shoot and root. Overall, our result established a comparative microbiome method for identifying the rice phyllospheric bacterial communitie