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Revealing the potential of Klebsiella pneumoniae PVN-1 for plant beneficial attributes by genome sequencing and analysis

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Abstract

Genome sequencing of Klebsiella pneumoniae PVN-1, isolated from effluent treatment plant (ETP), generates a 5.064 Mb draft genome with 57.6% GC content. The draft genome assembled into 19 contigs comprises 4783 proteins, 3 rRNA, 44 tRNA, 8 other RNA, 4911 genes, and 73 pseudogenes. Genome information revealed the presence of phosphate metabolism/solubilizing, potassium solubilizing, auxin production, and other plant benefiting attributes like enterobactin and pyrroloquinoline quinone biosynthesis genes. Presence of gcd and pqq genes in K. pneumoniae PVN-1 genome validates the inorganic phosphate solubilizing potential (528.5 mg/L). Pangenome analysis identified a unique 5ʹ-Nucleotidase that further assists in enhanced phosphate acquisition. Additionally, the genetic potential for complete benzoate, catechol, and phenylacetate degradation with stress response and heavy metal (Cu, Zn, Ni, Co) resistance was identified in K. pneumoniae PVN-1. Functioning of annotated plant benefiting genes validates by the metabolic activity of auxin production (7.40 µg/mL), nitrogen fixation, catalase activity, potassium solubilization (solubilization index—3.47), and protease activity (proteolytic index—2.27). In conclusion, the K. pneumoniae PVN-1 genome has numerous beneficial qualities that can be employed to enhance plant growth as well as for phytoremediation.

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Acknowledgements

Varsha Jha is grateful to the University Grant Commission (UGC) for the award of Senior Research Fellow (SRF). The authors highly acknowledge the Director, CSIR-NEERI, for providing facilities for this work. The manuscript has been checked for plagiarism by Knowledge Resource Centre, CSIR-NEERI, Nagpur, India, and assigned KRC number [KRC No.: CSIR-NEERI/KRC/2021/APRIL/EBGD/3].

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Authors and Affiliations

  1. Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India

    Varsha Jha, Hemant Purohit & Nishant A. Dafale

  2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Varsha Jha & Nishant A. Dafale

Authors
  1. Varsha Jha
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  2. Hemant Purohit
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  3. Nishant A. Dafale
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Contributions

VJ performed lab experiments, bioinformatics analysis and manuscript writing. NAD conceptualized the study and improved the manuscript. HJP conceptualized study, review and editing.

Corresponding author

Correspondence to Nishant A. Dafale.

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The authors declare that they have no conflict of interest.

Additional information

Accession numbers: The 16S rRNA sequence and the whole genome shotgun (WGS) sequence of K. pneumoniae PVN-1 were submitted in the GenBank database with accession number MW440693.1 and NCBI-WGS database under accession number JACORD000000000, respectively.

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Jha, V., Purohit, H. & Dafale, N.A. Revealing the potential of Klebsiella pneumoniae PVN-1 for plant beneficial attributes by genome sequencing and analysis. 3 Biotech 11, 473 (2021). https://doi.org/10.1007/s13205-021-03020-2

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