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In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium

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Abstract

The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.

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Acknowledgements

J.K., H.V., J.K., G.G.D., and P.L. thank Gargi College, Ramjas College, Maitreyi College, Kirori Mal College, and Department of Zoology, University of Delhi for providing infrastructural support. R.L. thanks the Indian National Science Academy for financial support under the INSA-Senior Scientist Scheme.

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The authors declare that no funds, grants, or other support were received during the preparation of this manuscript.

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Author notes

  1. Helianthous Verma and Jaspreet Kaur have been contributed equally to this manuscript.

Authors and Affiliations

  1. Department of Zoology, Gargi College, Siri Fort Road, New Delhi, 110049, India

    Jasvinder Kaur

  2. Department of Zoology, Ramjas College, University of Delhi, New Delhi, 110007, India

    Helianthous Verma

  3. Department of Zoology, Maitreyi College, University of Delhi, New Delhi, 110021, India

    Jaspreet Kaur

  4. Department of Zoology, University of Delhi, New Delhi, 110007, India

    Pushp Lata

  5. Department of Zoology, Kirori Mal College, University of Delhi, New Delhi, 110007, India

    Gauri Garg Dhingra

  6. Acharya Narendra Dev College, University of Delhi, New Delhi, 110019, India

    Rup Lal

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Conceptualization: Jasvinder Kaur; Methodology: Jasvinder Kaur and Helianthous; Formal analysis and investigation: Jasvinder Kaur, Helianthous, and Jaspreet Kaur; Writing—original draft preparation: Jasvinder Kaur; Writing—review and editing: All authors; Resources: Rup Lal; Supervision: Rup Lal.

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Kaur, J., Verma, H., Kaur, J. et al. In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium. Curr Microbiol 81, 233 (2024). https://doi.org/10.1007/s00284-024-03762-1

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