Genetic variations in salt tolerant and plant growth promoting rhizobacteria of the Western Himalayas

  • Ritika Kapoor
  • S. S. KanwarEmail author
Original Article


The nhaA gene conferring Na+/H+ antiporter activity was used to discriminate salt tolerant plant growth promoting bacteria isolated from Western Himalayas. Fifty two isolates were obtained from rhizospheric soil of four different plants growing around the salt mines of Himachal Pradesh (India). Only six isolates were found to tolerate salt up to 1.7 M NaCl and identified by 16S rRNA typing techniques. A phylogenetic tree grouped these native strains into two clusters, first comprising Bacillus and second Enterobacter strains along with strains from different countries. The plant growth promoting traits of selected bacteria were studied under salt stress (0.86 M NaCl) to expose functional divergence. At genetic level, nhaA gene sequences of native strains were compared with other lineages available in literature. The phylogenetic tree obtained from mining of nhaA gene and distance matrix index values showed significant variations in gene sequences of salt tolerant native strains in comparison to exotic non salt tolerant strains. The deduced NhaA protein of these strains showed variations in their putative secondary structure. The sequence variation of nhaA gene revealed it to be an appropriate marker to differentiate among native salt tolerant and non salt tolerant strains.


Salt stress Rhizobacteria Plant growth promoting traits NhaA gene Allele mining 



Na+/H+ antiporter


Plant growth promoting rhizobacteria


Electrical conductivity


Ribosomal RNA


Polymerase chain reaction


Indole acetic acid


Self-Optimized Prediction Method with Alignment



The authors gratefully acknowledge the technical support provided by the Himachal Pradesh Agriculture University, Palampur (HP), India.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13562_2019_489_MOESM1_ESM.docx (120 kb)
Supplementary material 1 (DOCX 119 kb)


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Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  1. 1.CSK Himachal Pradesh Agricultural UniversityPalampurIndia

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