Genomic analysis of a novel species Halomonas shambharensis isolated from hypersaline lake in Northwest India

Abstract

Genome analysis of Halomonas shambharensis, a novel species, was performed to understand the osmoprotectant strategies used by the strain to overcome the salinity stress and to explore the prospective industrial uses. It will also help to better understand the ecological roles of Halomonas species in hypersaline habitats. Ultrastructure of the cell was determined by using transmission electron microscopy. Standard microbiological methods were used to find out growth parameters and heterotrophic mode of nutrition. For Genome analysis, complete bacterial genome sequencing was performed using the Oxford Nanopore MinION DNA Sequencer. Assembly, annotation and finishing of the obtained sequence were done by using a Prokaryotic Genome Annotation Pipeline (PGAP) (SPAdes v. 3.10.1). Predicted Coading sequences (CDSs) obtained through the PGAP were used for functional annotation using Clusters of Orthologous Groups and Kyoto Encyclopedia of Genes and Genomes (KEGG) platforms. The H. shambharensis was found to be a Gram-stain-negative, rod-shaped bacterium, motile with a peritrichous flagella. The H. shambharensis bacterium can grow in a wide range of temperature (from 25 to 65 °C), pH (pH 4 to pH 12.0) and salt concentration (5.0% NaCl to 30.0% NaCl). After annotation and assembly, the total genome size obtained was 1,533,947 bp, which revealed 146 subsystems, 3847 coding sequences, and 19RNAs with G+C content of 63.6%. Gene annotation identified the genes related to various metabolic pathways, including carbohydrate metabolism, fatty acid metabolism and stress tolerance. The genomic dataset of H. shambharensis will be useful for analysis of protein-coding gene families and how these coding genes are significant for the survival and metabolism among the different species of Halomonas. The complete genome sequence presented here will help to unravel the biotechnological potential of H. shambharensis for production of the high-value products such as betaine, or as a source of gene-mining for individual enzymes.

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Data availability

The genome sequence and associated data for Halomonas sp. SBS 10 was deposited under GenBank accession number RXHI00000000, BioProject accession number PRJNA479678, SRA accession number SRP224914, and BioSample accession number SAMN09601649.

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Correspondence to Kapilesh Jadhav or Deepak Parashar.

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Jadhav, K., Kushwaha, B., Jadhav, I. et al. Genomic analysis of a novel species Halomonas shambharensis isolated from hypersaline lake in Northwest India. Mol Biol Rep 48, 1045–1053 (2021). https://doi.org/10.1007/s11033-020-06131-w

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Keywords

  • Genome analysis
  • Genome annotation
  • Halomonas shambharensis
  • Oxford Nanopore Technology
  • Sambhar Salt Lake