In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1

Kiran Kumari; Vaishnavi Rawat; Afreen Shadan; Parva Kumar Sharma; Sushanta Deb; Rajnish Prakash Singh

doi:10.3389/fmicb.2023.1140249

In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1

Front Microbiol. 2023 Jun 20:14:1140249. doi: 10.3389/fmicb.2023.1140249. eCollection 2023.

Authors

Kiran Kumari¹, Vaishnavi Rawat¹, Afreen Shadan², Parva Kumar Sharma³, Sushanta Deb⁴, Rajnish Prakash Singh¹

Affiliations

¹ Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India.
² Department of Microbiology, Dr. Shyama Prasad Mukerjee University, Ranchi, India.
³ Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States.
⁴ Department of Veterinary Microbiology and Pathology, Washington State University (WSU), Pullman, WA, United States.

Abstract

A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO₄ (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.

Keywords: Pseudomonas parafulva; carbohydrate active enzymes; genome; pan-genome; virulence.