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

Abstract

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.