Whole Genome Sequencing and Comparative Genomic Analysis of Pseudomonas aeruginosa SF416, a Potential Broad-Spectrum Biocontrol Agent Against Xanthomonas oryzae pv. oryzae

Rice is one of the most important staple crops worldwide. However, the bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) poses a major threat to the production of rice. In this study, we isolated and identified the strain Pseudomonas aeruginosa SF416, which exhibited significant antagonistic activity against Xoo, from a soil sample collected in a winter wheat field in Shannanzhalang County, Tibet, China. The bacterial solution (BS) and cell-free supernatant (CFS) of SF416 had significant prevention effects for the bacterial blight of rice, with an efficacy of 45.1% and 34.18%, respectively, while they exhibited a slightly lower therapeutic efficiency of 31.64% and 25.09%. The genomic analysis showed that P. aeruginosa SF416 contains genes involved in cell motility, colonization, cold and hot shock proteins, antibiotic resistance, and plant growth promotion. SF416 also harbors two sets of phenazine-1-carboxylic acid (PCA) synthesis gene clusters, phz1 (phzA1-G1) and phz2 (phzA2-G2), and other phenozine product-synthesis--related genes phzS, phzM, and phzH, as well as genes in the SF416 genome that share high similarity with the ones in the genomes of P. aeruginosa M18, suggesting that the two sets of PCA synthesis gene clusters are responsible for the antagonistic effect of SF416 against Xoo. A comparative antiSMASH analysis revealed that P. aeruginosa SF416 contains 17 gene clusters related to secondary metabolite synthesis, 7 of which, encoding for pyochelin, azetidomonamide A/B, L-2-amino-4-methoxy-trans-3-butenoic acid, hydrogen cyanide, pyocyanine, pseudopaline, and bicyclomycin, are conserved in strains of P. aeruginosa. Moreover, SF416 can produce protease and siderophores and display a broad-spectrum antagonistic activity against various major plant pathogenic bacteria and fungi. The results suggest that P. aeruginosa SF416 could be a potential candidate agent for the bacterial blight of rice.