Identifying and characterizing antimicrobial producing Burkholderia from medicinal plant rhizospheres and soil in the Western Ghats, India.

Abstract

The Burkholderia genus is a diverse group of Gram-negative bacteria found in soil, water, man-made products, plants, animals and as opportunistic pathogens in multiple hosts. The Burkholderia cepacia complex (Bcc) is a notorious group of Burkholderia species which can cause devastating infections in individuals with cystic fibrosis (CF). The biosynthetic capacity of Burkholderia species is substantial and has made the genus an interesting source for the discovery of specialized metabolites. This research sought to expand the understanding of Burkholderia diversity in the natural environment and the capability of this group to produce antimicrobial specialized metabolites. Bacteria were isolated from the rhizosphere of medicinal plants in the Western Ghats, India, and purified into a collection of 73 environmental isolates. Sequencing of recA and 16S rRNA genes identified 35 Burkholderia strains, which all grouped in the Burkholderia cepacia complex (Bcc). Seven B. cenocepacia strains were from the recA IIIA lineage, a group of virulent strains for which no clear environmental source has been defined. Draft genome sequences were obtained for 34 Burkholderia strains and used to carry out multiple phylogenomic analyses. Four known Bcc species groups and 5 putative novel Bcc taxa were found within the collection. Comparative genomic analysis of the 7 environmental B. cenocepacia IIIA strains against 32 well characterized reference genomes revealed they were closely related to a globally spread and virulent B. cenocepacia sequence type, ST-32. Antimicrobial activity screening revealed that 26 of the 35 Burkholderia strains were antagonistic towards other human and plant pathogenic microbes. Genome mining and chemical analysis of bioactive strains led to the discovery of the first collimonin producing Burkholderia, and the first enacyloxin-producing B. ubonensis strains, providing further novel insights into the biosynthetic potential of the Burkholderia genus