Genomic insights into novelBurkholderia sp. Bmkn7 from coastal saline-affected rice fields unveils potential antimicrobial metabolites and plant growth-promoting traits.

An efficient siderophore-producing bacterium, Burkholderia sp. Bmkn7, was isolated from the rhizosphere of an inland rice variety cultivated in the underexplored coastal saline-affected rice fields of Kerala, India. The complete genome of Bmkn7 possessed a single circular chromosome of 8,397,732 bp with an average GC content of 66.5%. Phylogenetic and comparative genome studies identified Bmkn7 as a member of the genus Burkholderia, closely related to the plant-associated Burkholderia cepacia complex genomovar I. The antiSMASH analysis identified a rich repertoire of 20 biosynthetic gene clusters (BGCs) involved in the production of diverse specialized secondary metabolites, including non-ribosomal peptide synthetases (NRPSs) encoding siderophores (pyochelin, ornibactin), a pyrrolnitrin-encoding cluster, and terpenes. Furthermore, the presence of several orphan BGCs suggests the potential genetic ability of Bmkn7 to produce novel bioactive compounds. In addition, Bmkn7 exhibited potential antimicrobial activity against various bacterial and fungal phytopathogens involving metabolites dependent and independent of siderophores, including unidentified bioactive molecules. Additionally, Bmkn7 harbors several plant-associated and plant growth-promoting genes, including those involved in phosphate solubilization, 1-aminocyclopropane-1-carboxylate (ACC) deaminase production, mitigation of plant-derived oxidative stress, and the utilization of various plant-derived substrates. Notably, the Bmkn7 genome lacks key genes associated with animal-host interactions and virulence, suggesting a plant-associated lifestyle. Combining genomic analyses and phenotypic assays, we provide evidence suggesting Bmkn7 as an ideal candidate for phytopathogen suppression and plant growth promotion, further expanding knowledge on plant-associated Burkholderia strains.