Identification and genome analysis of the violacein- producing Duganella sp. isolated from Brassica juncea var. tumida rhizosphere

Abstract:

[Objective] Rhizosphere contains a phylogenetically diverse array of microorganisms affecting the growth and health of plants. This study aims to examine the diversity and structure of the microbial community in Brassica juncea var. tumida rhizosphere. The isolated microbial strains can be explored to unleash their chemical potential. [Methods] Roots of B. juncea var. tumida were collected from two villages in Fuling Disctrict of Chongqing. Microbial isolates were then obtained after cultivation on different media. One strain was selected for genome sequencing (Pacbio RS II and Illumina HiSeq) and subsequent bioinformatic analysis. The antiSMASH 6.0 was used for the detection and comparison of biosynthetic gene clusters (BGCs) encoding secondary metabolites. A multiplex amplification-and-ligation strategy was employed to clone the gene cluster responsible for violacein biosynthesis. The gene cluster was then transferred into Streptomyces lividans TK23 by intergeneric conjugation. [Results] A total of 256 microbial isolates were obtained, of which 120 were identified. Duganella sp. BjR8, which produced violacein, was detected. Sequencing of the genome of BjR8 revealed a single circular chromosome of 7 205 593 bp in length with 64.67% G+C content and 6 421 coding sequences. Bioinformatic analysis showed that the strain contained 9 putative secondary metabolite BGCs, of which 7 had low similarities to BGCs encoding known compounds. Heterologous expression of the violacein gene cluster in S. lividans TK23 resulted in the production of deoxyviolacein. [Conclusion] The diversity and structure of the microbial community was examined by phylogenetic analysis of microorganisms isolated from B. juncea var. tumida rhizosphere. Bioinformatic analysis revealed that BjR8 had great biosynthetic potential for novel compounds. The vio gene cluster was cloned from BjR8 and expressed successfully in the surrogate host S. lividans TK23.