Comparative genome analysis of arsenic reducing, hydrocarbon metabolizing groundwater bacterium Achromobacter sp. KAs 3-5T explains its competitive edge for survival in aquifer environment

Abstract

Whole genome sequence of arsenic (As) reducing, hydrocarbon metabolizing groundwater bacterium Achromobacter sp. KAs 3-5T was explored to understand the genomic basis of its As-ecophysiology and niche adaptation in aquifer environment. The genome (5.6 Mbp, 65.5 G + C mol %) encodes 4840 proteins, 1138 enzymes, 53 tRNAs, 11 rRNAs, 608 signal peptides, and 1.13% horizontally transferred genes. Presence of genes encoding cytosolic As5+-reduction (arsRCBH, ACR3), aromatics utilization (bph, naph, catABC, boxABCD, genACB), Fe-transformation (tonB, achromobactin, FUR, FeR), and denitrification (nar, nap) processes were observed and validated through proteomics. Phylogenomic analysis (< 90% ANI, < 50% DDH) confirmed strain KAs 3-5T to be a novel representative of the genus Achromobacter. An asymptotic open pan-genome (20,855 genes) and high correlation between genomic and ecological diversity suggested niche preference ability of this genus. Assemblage of species specific genes affiliated to transcription-regulation, membrane transport, and redox-transformation explained the strain's competitive survival strategies in As-rich oligotrophic groundwater.