Whole Genome Analysis of Sugarcane Root-Associated Endophyte Pseudomonas aeruginosa B18—A Plant Growth-Promoting Bacterium With Antagonistic Potential Against Sporisorium scitamineum

Abstract

Sugarcane smut is a significant fungal disease that causes a major loss in sugar yield and quality. In this study, we isolated an endophytic strain B18 from a sugarcane root, which showed plant growth-promotion, hydrolytic enzyme production, antifungal activity against sugarcane pathogens (<i>Sporisorium scitamineum, Ceratocystis paradoxa, Fusarium verticillioides</i>), and the presence of <i>nifH</i>, <i>acdS</i>, and antibiotic genes (<i>hcn, prn</i>, and <i>phCA</i>) under <i>in vitro</i> conditions. BIOLOG^(R) phenotypic profiling of B18 established its ability to use various carbon and nitrogen sources and tolerate a range of pH and osmotic and temperature stresses. Whole-genome analysis of B18, identified as <i>Pseudomonas aeruginosa</i>, showed that it consists of a single circular chromosome of 6,490,014 bp with 66.33% GC content. Genome annotation has identified 5,919 protein-coding genes, and 65 tRNA, and 12 rRNA genes. The <i>P. aeruginosa</i> B18 genome encodes genes related to ethylene, nitrogen (<i>nifU</i>, <i>norBCDERQ</i>, <i>gltBDPS</i>, and <i>aatJMPQ</i>), and phosphate (<i>pstABCS</i> and <i>phoBDHRU</i>) metabolism and produce indole-3-acetic acid and siderophores. This also includes genes encoding hydrolases and oxidoreductases, those associated with biocontrol mechanisms (<i>hcnABC</i>, <i>phzA_B</i>, <i>phzDEFGMS</i>, and <i>pchA</i>), colonization (<i>minCDE</i> and <i>lysC</i>), and biofilm formation (<i>efp</i>, <i>hfq</i>, <i>flgBCDEFGHI</i>, and <i>motAB</i>), and those associated with metabolism of secondary metabolites. Collectively, these results suggest a role for <i>P. aeruginosa</i> B18 in plant growth enhancement and biocontrol mechanisms. The <i>P. aeruginosa</i> B18 strain was found to be an efficient colonizer in sugarcane; it can improve growth through modulation of plant hormone production and enhanced host-plant resistance to smut pathogen <i>S. scitamineum</i> in a smut-susceptible sugarcane variety (Yacheng71-374). These biocontrol and plant growth promotion properties of <i>P. aeruginosa</i> B18 area are discussed in this report.