Genome sequencing, annotation and application of a strain of Microbacterium paraoxydans – a heavy metal hypertolerant and plant growth promoting bacterium

Abstract

A heavy metal hypertolerant plant growth promoting bacterium was isolated from arsenic contaminated garden soil of Bhagobangola I block (Murshidabad district). Metagenomic classification identified the bacterial isolate as a member of genus Microbacterium. Taxonomic assessment showed maximum average nucleotide identity (89.99%) with 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 RNA, 3 rRNA, 53 tRNA and 1 tmRNA. DFAST detected 3257 coding sequences (1217 hypothetical sequences), 3 rRNA and 53 tRNA. Both Prokka and DFAST failed to detect any CRISPR sequence. RAST could detect 3285 coding sequences and 49 RNAs in the genome. Only 25% (821) of these sequences fell within the subsystem of RAST, which included 789 coding sequences as non-hypothetical and 32 sequences as hypothetical. Genes and Gene clusters responsible for arsenic resistance (arsR, arsB, arsC, acr1, acr2, acr3), other heavy metal (Copper, Manganese, Zinc, etc.) tolerance and plant growth promotion (Auxin biosynthesis, Siderophore mediated iron acquisition, Phosphate and polyphosphate metabolism, Trehalose biosynthesis, etc.) could also be identified in the Microbacterium paraoxydans genome. The heavy metal (arsenic) hypertolerance, bioremediation potential and plant growth promoting nature of the bacterium were confirmed by plate assay, SDDC assay and pot experiments, respectively. The aforementioned traits point towards the probable application of the bacterium as a bioremediation tool and biofertilizer, for reduction of arsenic toxicity and promotion of plant growth.