Genome sequencing, annotation and application of a strain of Microbacterium paraoxydans – A bacterium with arsenic bioremediation and plant growth promoting potential

Abstract

A heavy metal hypertolerant plant growth-promoting bacterium was isolated from the arsenic-contaminated garden soil of Bhagobangola I block (Murshidabad district). Metagenomic classification identified the bacterial isolate as a member of the genus Microbacterium. Taxonomic assessment of the isolated strain revealed its maximum average nucleotide identity (89.99%) with the Microbacterium paraoxydans strain DSM 15019. Prokaryotic genome annotation was performed by Prokka, DFAST and RAST. The entire genome consisted of 3365911 bases with 69.90% GC content. Prokka detected 3216 coding sequences (1461 hypothetical sequences), 3283 genes, 10 miscellaneous RNAs, 3 rRNAs, 53 tRNAs and 1 tmRNA in the bacterial genome. DFAST detected 3257 coding sequences (1217 hypothetical sequences), 3 rRNA sequences and 53 tRNA sequences in the bacterial genome. RAST detected 3285 coding sequences and 49 RNAs in the genome. Only 25% of these coding sequences could be categorised in the RAST subsystems. In RAST, 789 and 32 coding sequences were considered as non-hypothetical and hypothetical, respectively. The genes and gene clusters responsible for arsenic resistance (arsR, arsB, arsC, acr1, acr2 and acr3), tolerance to other heavy metals (copper, manganese, zinc, etc.) and plant growth promotion (auxin biosynthesis, siderophore-mediated iron acquisition, phosphate and polyphosphate metabolism, trehalose biosynthesis, etc.) were also identified in the Microbacterium paraoxydans genome. The bioremediation potential and plant growth-promoting nature of the bacterium were confirmed by silver diethyl dithio carbamate (SDDC) method and pot experiments, respectively. The aforementioned traits point towards potential of the bacterium as a bioremediation tool and biofertilizer for reducing arsenic toxicity and promoting plant growth.