Delving into the lifestyle of Sundarban Wetland resident, biofilm producing, halotolerant Salinicoccus roseus: a comparative genomics-based intervention

    Dutta, B and Halder, U and Chitikineni, A and Varshney, R K and Bandopadhyay, R (2023) Delving into the lifestyle of Sundarban Wetland resident, biofilm producing, halotolerant Salinicoccus roseus: a comparative genomics-based intervention. BMC Genomics (TSI), 24. pp. 1-15. ISSN 1471-2164

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    Abstract

    Background Microbial community played an essential role in ecosystem processes, be it mangrove wetland or other intertidal ecologies. Several enzymatic activities like hydrolases are effective ecological indicators of soil microbial function. So far, little is known on halophilic bacterial contribution and function on a genomic viewpoint of Indian Sundarban Wetland. Considering the above mentioned issues, the aims of this study was to understand the life style, metabolic functionalities and genomic features of the isolated bacterium, Salinicoccus roseus strain RF1H. A comparative genome-based study of S. roseus has not been reported yet. Henceforth, we have considered the inclusion of the intra-species genome comparison of S. roseus to gain insight into the high degree of variation in the genome of strain RF1H among others. Results Salinicoccus roseus strain RF1H is a pink-red pigmented, Gram-positive and non-motile cocci. The bacterium exhibited high salt tolerance (up to 15% NaCl), antibiotic resistance, biofilm formation and secretion of extracellular hydrolytic enzymes. The circular genome was approximately 2.62978 Mb in size, encoding 574 predicted genes with GC content 49.5%. Presence of genomic elements (prophages, transposable elements, CRISPR-Cas system) represented bacterial virulence and multidrug-resistance. Furthermore, genes associated with salt tolerance, temperature adaptation and DNA repair system were distributed in 17 genomic islands. Genes related to hydrocarbon degradation manifested metabolic capability of the bacterium for potential biotechnological applications. A comparative pangenome analysis revealed two-component response regulator, modified C4-dicarboxylate transport system and osmotic stress regulated ATP-binding proteins. Presence of genes encoding arginine decarboxylase (ADC) enzyme being involved in biofilm formation was reported from the genome. In silico study revealed the protein is thermostable and made up with ~ 415 amino acids, and hydrophilic in nature. Three motifs appeared to be evolutionary conserved in all Salinicoccus sequences. Conclusion The first report of whole genome analysis of Salinicoccus roseus strain RF1H provided information of metabolic functionalities, biofilm formation, resistance mechanism and adaptation strategies to thrive in climate-change induced vulnerable spot like Sundarban. Comparative genome analysis highlighted the unique genome content that contributed the strain’s adaptability. The biomolecules produced during metabolism are important sources of compounds with potential beneficial applications in pharmaceuticals.

    Item Type: Article
    Divisions: Center of Excellence in Genomics and Systems Biology
    CRP: UNSPECIFIED
    Uncontrolled Keywords: Salinicoccus roseus, Environmental adaptation, Biofilm, Genome sequencing, Comparative genomics
    Subjects: Others > Genetics and Genomics
    Depositing User: Mr Nagaraju T
    Date Deposited: 15 Feb 2024 04:23
    Last Modified: 15 Feb 2024 04:23
    URI: http://oar.icrisat.org/id/eprint/12476
    Official URL: https://link.springer.com/article/10.1186/s12864-0...
    Projects: UNSPECIFIED
    Funders: UNSPECIFIED
    Acknowledgement: BD is grateful for Senior Research Fellowship provided by the Department of Science and Technology (DST), New Delhi, India, under PURSE Phase II project. We are thankful to the UGC-Centre for Advanced Study (CAS) and DST FIST II, Department of Botany, The University of Burdwan. We convey thanks to the University Science Instrumentation Centre (USIC), The University of Burdwan for Fluorescence, SEM, and TEM study.
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