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

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

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.

Keywords

Salt stress Rhizobacteria Plant growth promoting traits NhaA gene Allele mining 

Abbreviations

Nha

Na+/H+ antiporter

PGPR

Plant growth promoting rhizobacteria

EC

Electrical conductivity

rRNA

Ribosomal RNA

PCR

Polymerase chain reaction

IAA

Indole acetic acid

SOPMA

Self-Optimized Prediction Method with Alignment

Notes

Acknowledgements

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)

References

  1. Axelrood PE, Chow ML, Radomski CC, McDermott JM, Davies J (2002) Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance. Can J Microbiol 48(7):655–674CrossRefGoogle Scholar
  2. Bhise KK, Bhagwat PK, Dandge PB (2017) Plant growth promoting characteristics of salt tolerant Enterobacter cloacae strain KBPD and its efficacy in amelioration of salt stress in Vigna radiata L. J Plant Growth Regul 36:215–226.  https://doi.org/10.1007/s13205-017-0739-0 CrossRefGoogle Scholar
  3. Egamberdieva D, Kucharova Z (2009) Selection for root colonising bacteria stimulating wheat growth in saline soils. Biol Fertil Soils 45:563–571.  https://doi.org/10.1007/s00374-009-0366-y CrossRefGoogle Scholar
  4. Eisenberg H, Wachtel EJ (1987) Structural studies of halophilic proteins, ribosomes, and organelles of bacteria adapted to extreme salt concentrations. Annu Rev Biophys Biophys Chem 16:69–92.  https://doi.org/10.1146/annurev.bb.16.060187.000441 CrossRefGoogle Scholar
  5. Gerchman Y, Olami Y, Rimon A, Taglicht D, Schuldiner S, Padan E (1993) Histidine-226 is part of the pH sensor of NhaA, a Na+/H+antiporter in Escherichia coli. Proc Natl Acad Sci 90:1212–1216CrossRefGoogle Scholar
  6. Gopalakrishnan S, Upadhyaya HD, Vadlamudi S, Humayun P, Vidya MS, Alekhya G, Singh A, Vijayabharathi Bhimineni RK, Seema M, Rathore Rupela O (2012) Plant growth promoting traits of biocontrol potential bacteria isolated from rice rhizosphere. Springer Plus 1:71–76.  https://doi.org/10.1186/2193-1801-1-71 CrossRefGoogle Scholar
  7. Gordon SA, Weber RA (1951) Colorimetric estimation of indole acetic acid. Plant Physiol 26:192–195CrossRefGoogle Scholar
  8. Hardy RWF, Holsten RD, Jackson EK, Burns RC (1968) The acetylene ethylene assay for N2 fixation: laboratory and field evaluation. Plant Physiol 43:1185–1207.  https://doi.org/10.1104/pp.43.8.1185 CrossRefGoogle Scholar
  9. Inaba M, Sakamoto A, Murata N (2001) Functional expression in Escherichia coli of low-affinity and high-affinity Na+(Li+)/H+ antiporters of Synechocystis. J Bacteriol 183:1376–1384.  https://doi.org/10.1128/JB.183.4.1376-1384.2001 CrossRefGoogle Scholar
  10. Inoue H, Nuomi T, Tsuchiya T, Kanzawa H (1995) Essential aspartic acid residues, Asp-133, Asp-163 and Asp-164, in the trans membrane helices of a Na+/H+ antiporter (NhaA) from Escherichia coli. FEBS Lett 363:264–268CrossRefGoogle Scholar
  11. Islam F, Tahira Y, Ali S, Basharat A, Sohail A, Weijun Z, Muhammad A (2016) Plant growth promoting bacteria confer salt tolerance in Vigna radiata by up-regulating antioxidant defense and biological soil fertility. Plant Growth Regul 80:23–26.  https://doi.org/10.1007/s10725-015-0142-y CrossRefGoogle Scholar
  12. Jackson ML (1973) Soil chemical analysis. Prentice Hall, New DelhiGoogle Scholar
  13. Jha B, Gontia I, Hartmann A (2012) The roots of the halophyte Salicornia brachiata are a source of new halotolerant diazotrophic bacteria with plant growth-promoting potential. Plant Soil 356:265–277.  https://doi.org/10.1007/s11104-011-0877-9 CrossRefGoogle Scholar
  14. Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Muraki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109–136CrossRefGoogle Scholar
  15. Kapoor R, Gupta MK, Kumar N, Kanwar SS (2017) Analysis of nhaA gene from salt tolerant and plant growth promoting Enterobacter ludwigii. Rhizosphere 4:62–69.  https://doi.org/10.1016/j.rhisph.2017.07.002 CrossRefGoogle Scholar
  16. Kreig NR, Holf JG (1984) Bergeys manual of systematic bacteriology. William and Wilkins, Baltimore, USAGoogle Scholar
  17. Kumar GP, Mir Hassan Ahmed SK, Desai S, Amalraj ELD, Rasul A (2014) In vitro screening for abiotic stress tolerance in potent biocontrol and plant growth promoting strains of Pseudomonas and Bacillus spp. Int J Bacteriol. Article ID 195946. http://dx.doi.org/10.1155/2014/195946
  18. Li HQ, Jiang XW (2017) Inoculation with plant growth-promoting bacteria (PGPB) improves salt tolerance of maize seedling. Russ J Plant Physiol 64:235–241CrossRefGoogle Scholar
  19. Majernik A, Gottschalk G, Daniel R (2001) Screening of environmental DNA libraries for the presence of genes conferring Na+(Li+)/H+ antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products. J Bacteriol 183:6645–6653.  https://doi.org/10.1128/JB.183.22.6645-6653.2001 CrossRefGoogle Scholar
  20. Morihara K (1964) Production of elastase and proteinase by Pseudomonas aeruginosa. J Bacteriol 88:745–757Google Scholar
  21. Nakbanpote W, Panitlurtumpai N, Sangdee A, Sakulpone N, Sirisom P, Pimthong A (2014) Salt-tolerant and plant growth-promoting bacteria isolated from Zn/Cd contaminated soil: identification and effect on rice under saline conditions. J Plant Interact 9:379–387.  https://doi.org/10.1080/17429145.2013.842000 CrossRefGoogle Scholar
  22. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304.  https://doi.org/10.1038/35012500 CrossRefGoogle Scholar
  23. Padan E (2008) The enlightening encounters between structure and function in the NhaA Na+/H+ antiporter. Trends Biochem Sci 33:435–444.  https://doi.org/10.1016/j.tibs.2008.06.007 CrossRefGoogle Scholar
  24. Padan E, Schuldiner S (1994) Molecular physiology of the Na+/H+ antiporter in Escherichia coli. J Exp Biol 196:443–456Google Scholar
  25. Padan E, Maisler N, Taglicht D, Karpel R, Schuldiner S (1989) Deletion of ant in Escherichia coli reveals its function in adaptation to high salinity and an alternative Na+/H+ antiporter system(s). J Biol Chem 264:20297–20302Google Scholar
  26. Pandey A, Sharma E, Palni LMS (1998) Influence of bacterial inoculation on maize in upland farming systems of the Sikkim Himalaya. Soil Biol Biochem 30:379–384CrossRefGoogle Scholar
  27. Park JI, Yoon CJ, Park JS, Kim HE, Cho JY, Shin SK (2003) Characterization of the proteolytic activity of bacteria isolated from a rotating biological contactor. J Microbiol 41:73–77Google Scholar
  28. Rahi P, Kapoor R, Young JPW, Gulati A (2012) A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas. Mol Ecol 21:145–159.  https://doi.org/10.1111/j.1365-294X.2011.05368.x CrossRefGoogle Scholar
  29. Ramadoss D, Lakkineni VK, Bose P, Ali S, Annapurna K (2013) Mitigation of salt stress in wheat seedlings by halotolerant bacteria isolated from saline habitats. SpringerPlus 2:6.  https://doi.org/10.1186/2193-1801-2-6 CrossRefGoogle Scholar
  30. Rimon A, Gerchman Y, Olami Y, Schuldiner S, Padan E (1995) Replacements of histidine 226 of NhaA-Na+/H+antiporter of Escherichia coli: Cysteine (H226C) or serine (H226S) retain both normal activity and pH sensitivity, aspartate (H226D) shifts the pH profile toward basic pH, and alanine (H226A) inactivates the carrier at all pH values. J Biol Chem 270:26813–26817.  https://doi.org/10.1074/jbc.270.45.26813 CrossRefGoogle Scholar
  31. Rojas-Tapias D, Moreno-Galván A, Pardo-Díaz S, Obando M, Rivera Dand Bonilla R (2014) Effect of inoculation with plant growth-promoting bacteria (PGPB) on amelioration of saline stress in maize (Zea mays). Appl Soil Ecol 61:264–271CrossRefGoogle Scholar
  32. Sanders ER (2012) Aseptic laboratory techniques: plating methods. J Vis Exp 63:3064.  https://doi.org/10.3791/3064 Google Scholar
  33. Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56CrossRefGoogle Scholar
  34. Sharma S, Kulkarni J, Jha B (2016) Halotolerant rhizobacteria promote growth and enhance salinity tolerance in peanut. Front Microbiol 7:1600Google Scholar
  35. Shoebitz M, Claudia MR, Martin AP, Maria LC, Luigi C, Jose AC (2009) Plant growth promoting properties of a strain of Enterobacter ludwigii isolated from Lolium perenne rhizosphere. Soil Biol Biochem 41:1768–1774CrossRefGoogle Scholar
  36. Siddikee MA, Chauhan PS, Anandham R, Han G-H, Sa T (2010) Isolation, characterization, and use for plant growth promotion under salt stress, of ACC deaminase-producing halotolerant bacteria derived from coastal soil. J Microbiol Biotechnol 20:1577–1584.  https://doi.org/10.4014/jmb.1007.07011 CrossRefGoogle Scholar
  37. Sleator RD, Hill C (2002) Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiol 26:49–71.  https://doi.org/10.1111/j.1574-6976.2002.tb00598.x CrossRefGoogle Scholar
  38. Smit E, Leeflang P, Gommans S, Broek VDJ, Mil VS, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67(5):2284–2291.  https://doi.org/10.1128/AEM.67.5.2284-2291.2001 CrossRefGoogle Scholar
  39. Suganthi C, Mageshwari A, Karthikeyan S, Anbalagan M, Sivakumar A, Gothandam KM (2013) Screening and optimization of protease production from a halotolerant Bacillus licheniformis isolated from saltern sediments. J Genet Eng Biotechnol 11:47–52.  https://doi.org/10.1016/j.jgeb.2013.02.002 CrossRefGoogle Scholar
  40. Vimal S, Jaya G, Jay SS (2018) Effect of salt tolerant Bacillus sp. and Pseudomonas sp. on wheat (Triticum aestivum L.) growth under soil salinity: a comparative study. Microbiol Res.  https://doi.org/10.4081/mr.2018.7462 Google Scholar
  41. Vincet JM (1947) Distortion of fungal hyphae in the presence of certain inhibitors. Nature 159:850.  https://doi.org/10.1038/159850b0 CrossRefGoogle Scholar
  42. Wang Y, Song N, Yang L, Abdel-Motaal H, Zhang R, Zhang Z, Meng F, Jiang J (2017) A novel NhaD-type Na+/H+ antiporter from the moderate halophile and alkaliphile Halomonas alkaliphila. Can J Microbiol 63:596–607.  https://doi.org/10.1139/cjm-2017-0104 CrossRefGoogle Scholar
  43. Weinisch L, Kuhner S, Roth R, Grimm M, Roth T, Netz DJA, Pierik AJ, Filker S (2018) Identification of osmoadaptive strategies in the halophile, heterotrophic ciliate Schmidingerothrix salinarum. PLoS Biol 16(1):e2003892.  https://doi.org/10.1371/journal.pbio.2003892 CrossRefGoogle Scholar
  44. Zhou J, Xia B, Huang H, Palumbo AV, Tiedje JM (2004) Microbial diversity and heterogeneity in sandy subsurface soils. Appl Environ Microbiol 70(3):1723–1734.  https://doi.org/10.1128/AEM.70.3.1723-1734.2004 CrossRefGoogle Scholar
  45. Zia-ur-Rehman M, Murtaza G, Qayyum M, Saqib M, Akhtar J (2017) Salt-affected soils: sources, genesis and management. In: Sabir M, Akhtar J, Hakeem KR (eds) Soil science concept and applications. University of Agriculture Faisalabad, pp 191–216Google Scholar

Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  1. 1.CSK Himachal Pradesh Agricultural UniversityPalampurIndia

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