First report on in-depth genome and comparative genome analysis of a metal-resistant bacterium Acinetobacter pittii S-30, isolated from environmental sample

Rajnish Prakash Singh; Ayushi Sinha; Sushanta Deb; Kiran Kumari

doi:10.3389/fmicb.2024.1351161

First report on in-depth genome and comparative genome analysis of a metal-resistant bacterium Acinetobacter pittii S-30, isolated from environmental sample

Front Microbiol. 2024 Apr 29:15:1351161. doi: 10.3389/fmicb.2024.1351161. eCollection 2024.

Authors

Rajnish Prakash Singh¹, Ayushi Sinha¹, Sushanta Deb², Kiran Kumari³

Affiliations

¹ Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
² Department of Veterinary Microbiology and Pathology, Washington State University (WSU), Pullman, WA, United States.
³ Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.

Abstract

A newly isolated bacterium Acinetobacter pittii S-30 was recovered from waste-contaminated soil in Ranchi, India. The isolated bacterium belongs to the ESKAPE organisms which represent the major nosocomial pathogens that exhibit high antibiotic resistance. Furthermore, average nucleotide identity (ANI) analysis also showed its closest match (>95%) to other A. pittii genomes. The isolate showed metal-resistant behavior and was able to survive up to 5 mM of ZnSO₄. Whole genome sequencing and annotations revealed the occurrence of various genes involved in stress protection, motility, and metabolism of aromatic compounds. Moreover, genome annotation identified the gene clusters involved in secondary metabolite production (biosynthetic gene clusters) such as arylpolyene, acinetobactin like NRP-metallophore, betalactone, and hserlactone-NRPS cluster. The metabolic potential of A. pittii S-30 based on cluster of orthologous, and Kyoto Encyclopedia of Genes and Genomes indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux systems etc., which is relatively rare in A. pittii strains. Additionally, the presence of various carbohydrate-active enzymes such as glycoside hydrolases (GHs), glycosyltransferases (GTs), and other genes associated with lignocellulose breakdown suggests that strain S-30 has strong biomass degradation potential. Furthermore, an analysis of genetic diversity and recombination in A. pittii strains was performed to understand the population expansion hypothesis of A. pittii strains. To our knowledge, this is the first report demonstrating the detailed genomic characterization of a heavy metal-resistant bacterium belonging to A. pittii. Therefore, the A. pittii S-30 could be a good candidate for the promotion of plant growth and other biotechnological applications.

Keywords: CAZymes; PCR; genomics; pangenome; virulence.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Ramalingaswami Re-entry Fellowship, provided by Department of Biotechnology, Government of India.