Taxonomic, metabolic traits and species description of aromatic compound degrading Indian soil bacterium Pseudomonas bharatica CSV86^T

Abstract

A soil bacterium, strain CSV86^T isolated from a petrol station in Bangalore, India displays a unique carbon source utilization hierarchy with preferential utilization of various genotoxic aromatic compounds over glucose. Cells were Gram-negative, motile rods, oxidase- and catalase-positive. Strain CSV86^T possess a 6.79 Mb genome with 62.72 G + C mol%. 16S rRNA gene phylogeny relates strain CSV86^T to the genus Pseudomonas, with highest similarity to Pseudomonas japonica WL^T (99.38%). Multi-locus sequence analyses of gyrB-rpoB-rpoD-recA and 33 ribosomal proteins (rps) displayed overall low similarities to its phylogenetic relatives with poor similarity score (6%). Average nucleotide identity (ANI) and in-silico DNA-DNA hybridization (DDH) showed poor (87.11% and 33.2%, respectively) genomic relatedness of strain CSV86^T to its closest relatives, indicating genomic distinctiveness. The major cellular fatty acids were 16:0, 17:0cyclo, summed-feature-3 (16:1ω7c/16:1ω6c) and −8 (18:1ω7c). Further, differential abundance of 12:0, 10:0 3-OH and 12:0 3-OH and phenotypic differences distinguished strain CSV86^T from closest relatives, hence designated as Pseudomonas bharatica. The unique aromatic degradation ability, resistance to heavy metals, efficient nitrogen-sulfur assimilation, beneficial eco-physiological traits (production of indole acetic acid, siderophore and fusaric acid efflux) and plasmid-free genome suggest strain CSV86^T to be a model organism for bioremediation and ideal host for metabolic engineering.

Keywords:

• Pseudomonas
• aromatic metabolism
• whole-genome sequencing
• phylogenomics
• chemotaxonomy
• eco-physiology
• species description

Acknowledgements

BM thanks Indian Institute of Technology, Bombay for providing Institute Post-Doctoral Fellowship and PSP thanks DST, DBT and BRNS for research funding.

Data availability statement

GenBank accession numbers: The full length 16S rRNA gene sequence (PCR amplified from the genome of CSV86^T) has been deposited with the accession number MN866057 and whole-genome shotgun sequencing project has been deposited as AMWJ02000000. The authors confirm that the data supporting the findings of this study are available with the article

Additional information

Funding

BM thanks Indian Institute of Technology, Bombay for providing Institute Post-Doctoral Fellowship and PSP thanks DST, DBT and BRNS for research funding.