Halotolerant Microbes for Amelioration of Salt-Affected Soils for Sustainable Agriculture

  • Sanjay AroraEmail author
Part of the Environmental and Microbial Biotechnology book series (EMB)


Soil salinity is one of the major abiotic stresses that adversely affect the sustainable agricultural production globally. About 20% of the total land area is affected by salinity, and the area is increasing at an alarming rate. There is a damaging effect of salinity on soil microbial communities, and their activities have been reported in majority of the studies. Excess accumulation of salts in the root zone often deteriorates the soil properties, viz. physical, chemical and biological to such an extent that crop production is adversely affected. Also, salt-affected soils are poor in organic matter content and thus the biomass as well as microbial activity, thereby affecting the microbiologically mediated processes required for plant growth. The methods available for reclamation of salt-affected soils are not cost effective, and further the availability of good-quality waters required for leaching salts in saline soils and mineral gypsum or organic amendments for sodic soils is scarce. Halotolerant and halophilic microorganisms having plant growth-promoting (PGP) traits have the potential to assuage salt stress and enhance plant growth and production in salt-affected soils. These plant growth-promoting rhizobacteria (PGPR) tolerate wide range of salt stress and thus enable plants to withstand salinity by different mechanisms such as hydraulic conductance, osmotic accumulation, sequestering toxic Na+ ions, maintaining the higher osmotic conductance and photosynthetic activities. The halophilic microbes have the potential to influence direct growth promotion of plants by fixing atmospheric nitrogen, solubilizing insoluble nutrients and secreting hormones such as IAA, GAs and kinetins besides ACC deaminase production, which helps in regulation of ethylene. Some of the recent researchers have confirmed the possibility of using halophiles in recovery of salt-affected soils and sustain agricultural production in degraded lands. We also observed beneficial effects of using PGP halophilic bacteria isolated from the native salty soils for enhancing crop production under salt stress conditions. For easy application in agriculture, liquid bioformulations have been prepared for efficient strains, and their use has enhanced the yield of rice and wheat by 11–14% and also for other crops like mustard, vegetables and fodder crops under salt stress conditions. Therefore, the bioremediation approach being cheap and eco-friendly is being promoted to optimize crop yields under sodic and saline-sodic soils of the Indo-Gangetic plains of north India.


Soil salinity Plant growth-promoting rhizobacteria (PGPR) Halophiles 


  1. Abrol IP, Yadav JSP, Massoud FI (1988) Salt-affected soils and their management. Food and Agriculture Organization of the United Nations, Soils Bull. 39, Rome, ItalyGoogle Scholar
  2. Akbarimoghaddam H, Galavi M, Ghanbari A, Panjehkeh N (2011) Salinity effects on seed germination and seedling growth of bread wheat cultivars. Trakia J Sci 9(1):43–50Google Scholar
  3. Aliasgharzadeh N, Saleh Rastin N, Towfighi H, Alizadeh A (2001) Occurrence of arbuscular mycorrhizal fungi in saline soils of the Tabriz plain of Iran in relation to some physical and chemical properties of soil. Mycorrhiza 11:119–122CrossRefGoogle Scholar
  4. Alvarez MI, Sueldo RJ, Barassi CA (1996) Effect of Azospirillum on coleoptiles growth in wheat seedlings under water stress. Cereal Res Commun 24:101–107Google Scholar
  5. Antoun H, Prevost D (2005) Ecology of plant growth promoting rhizobacteria. In: Siddiqui ZA (ed) PGPR: biocontrol and biofertilization. Springer, The Netherlands, pp 1–39Google Scholar
  6. Arahal DR, Ventosa A (2002) Moderately halophilic and halotolerant species of Bacillus and related genera. In: Berkeley R, Heyndrickx M, Logan N, De Vos P (eds) Applications and systematics of Bacillus and relatives. Blackwell, Oxford, pp 83–99CrossRefGoogle Scholar
  7. Arora S, Vanza M (2017) Microbial approach for bioremediation of saline and sodic soils. In: Arora SS, Singh AK, Singh YP (eds) Bioremediation of salt affected soils: an Indian perspective. Springer International Publishing, Switzerland, pp 87–100CrossRefGoogle Scholar
  8. Arora NK, Tewari S, Singh S, Lal N, Maheshwari DK (2012) PGPR for protection of plant health under saline conditions. In: Maheshwari DK (ed) Bacteria in agrobiology: stress management. Springer, Berlin. Scholar
  9. Arora S, Patel P, Vanza M, Rao GG (2014a) Isolation and characterization of endophytic bacteria colonizing halophyte and other salt tolerant plant species from coastal Gujarat. Afr J Microbiol Res 8(17):1779–1788CrossRefGoogle Scholar
  10. Arora S, Vanza M, Mehta R, Bhuva C, Patel P (2014b) Halophilic microbes for bio-remediation of salt affected soils. Afr J Microbiol Res 8(33):3070–3078CrossRefGoogle Scholar
  11. Arora S, Singh AK, Sahni D (2017) Bioremediation of salt-affected soils: challenges and opportunities. In: Arora S, Singh AK, Singh YP (eds) Bioremediation of salt affected soils: an Indian perspective. Springer International Publishing, Switzerland, pp 275–302CrossRefGoogle Scholar
  12. Arshad M, Saleem M, Hussain S (2007) Perspectives of bacterial ACC-deaminase in phyto-remediation. Trends Biotechnol 25:356–362CrossRefGoogle Scholar
  13. Barea JM (2015) Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions. J Soil Sci Plant Nutr 15(2):261–282Google Scholar
  14. Barea JM, Pozo MJ, López-Ráez JA, Aroca R, Ruíz-Lozano JM, Ferrol N, Azcón R, Azcón-Aguilar C (2013) Arbuscular mycorrhizas and their significance in promoting soil-plant systems sustainability against environmental stresses. In: Rodelas B, González-López J (eds) Beneficial plant-microbial interactions: ecology and applications. CRC Press, Boca Raton, FL, pp 353–387CrossRefGoogle Scholar
  15. Chinnusamy V, Zhu J, Zhu J-K (2006) Gene regulation during cold acclimation in plants. Physiol Plant 126(1):52–61CrossRefGoogle Scholar
  16. Creus CM, Sueldo RJ, Barassi CA (1997) Shoot growth and water status in Azospirillum-inoculated wheat seedlings grown under osmotic and salt stresses. Plant Physiol Biochem 35:939–944Google Scholar
  17. Creus CM, Sueldo RJ, Barassi CA (1998) Water relations in Azospirillum inoculated wheat seedlings under osmotic stress. Can J Bot 76:238–244Google Scholar
  18. Dimkpa C, Weinand T, Asch F (2009) Plant rhizobacteria interactions alleviate abiotic stress conditions. Plant Cell Environ 32:1682–1694CrossRefGoogle Scholar
  19. Dodd IC, Perez-Alfocea F (2012) Microbial alleviation of crop salinity. J Exp Bot 63:3415–3428CrossRefPubMedPubMedCentralGoogle Scholar
  20. Duan J, Muller KM, Charles TC, Vesely S, Glick BR (2009) 1-Aminocyclopropane-1-carboxylate (ACC) deaminase genes in rhizobia from southern Saskatchewan. Microb Ecol 57:423–436CrossRefPubMedPubMedCentralGoogle Scholar
  21. Dundas I (1998) Was the environment for primordial life hypersaline? Extremophiles 2:375–377CrossRefPubMedPubMedCentralGoogle Scholar
  22. Dutta S, Podile AR (2010) Plant growth promoting rhizobacteria (PGPR): the bugs to debug the root zone. Crit Rev Microbiol 36:232–244CrossRefPubMedPubMedCentralGoogle Scholar
  23. Etesami H, Beattie GA (2017) Plant-microbe interactions in adaptation of agricultural crops to abiotic stress conditions. In: Kumar V et al (eds) Probiotics and plant health. Springer Nature Singapore Pte Ltd., Singapore, pp 163–200CrossRefGoogle Scholar
  24. Garabito MJ, Marquez MC, Ventosa A (1998) Halotolerant Bacillus diversity in hypersaline environments. Can J Microbiol 44:95–102CrossRefGoogle Scholar
  25. Ghosh S, Penterman JN, Little RD, Chavez R, Glick BR (2003) Three newly isolated plant growth-promoting bacilli facilitate the seedling growth of canola, Brassica campestris. Plant Physiol Biochem 41:277–281CrossRefGoogle Scholar
  26. Glick BR (1995) The enhancement of plant growth by free-living bacteria. Can J Microbiol 41:109–117CrossRefGoogle Scholar
  27. Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169:30–39CrossRefPubMedPubMedCentralGoogle Scholar
  28. Glick BR, Cheng Z, Czarny J, Duan J (2007) Promotion of plant growth by ACC deaminase-producing soil bacteria. Eur J Plant Pathol 119(3):329–339CrossRefGoogle Scholar
  29. Govindasamy V, Senthilkumar M, Gaikwad K, Annapurna K (2008) Isolation and characterization of ACC deaminase gene from two plant growth-promoting rhizobacteria. Curr Microbiol 57(4):312–317CrossRefPubMedPubMedCentralGoogle Scholar
  30. Grichko VP, Glick BR (2001) Amelioration of flooding stress by ACC deaminase-containing plant growth-promoting bacteria. Plant Physiol Biochem 39:11–17CrossRefGoogle Scholar
  31. Hirch AM, Fang Y (1994) Plant hormones and nodulation: what’s the connection? Plant Mol Biol 26:5–9CrossRefGoogle Scholar
  32. Hu Y, Schmidhalter U (2002) Limitation of salt stress to plant growth. In: Hock B, Elstner CF (eds) Plant toxicology. Marcel Dekker Inc., New York, pp 91–224Google Scholar
  33. Ilyas N, Bano A, Iqbal S, Raja NI (2012) Physiological, biochemical and molecular characterization of Azospirillum spp. isolated from maize under water stress. Pak J Bot 44:71–80Google Scholar
  34. Jamil A, Riaz S, Ashraf M, Foolad MR (2011) Gene expression profiling of plants under salt stress. Crit Rev Plant Sci 30(5):435–458CrossRefGoogle Scholar
  35. Juniper S, Abbott L (1993) Vesicular and arbuscular mycorrhizae and soil salinity. Mycorrhizae 4:45–57CrossRefGoogle Scholar
  36. Kamekura M, Seno Y (1990) A halophilic extracellular protease from a halophilic archaebacterium strain 172 P1. Biochem Cell Biol 68(1):352–359CrossRefPubMedPubMedCentralGoogle Scholar
  37. Kausar R, Shahzad SM (2006) Effect of ACC-deaminase containing rhizobacteria on growth promotion of maize under salinity stress. J Agri Soc Sci 2:216–218Google Scholar
  38. Ladeiro B (2012) Saline agriculture in the 21 st century : using salt contaminated resources to cope food requirement. J Bot 2012:1. Scholar
  39. Ligero F, Caba JM, Lluch C, Oliverase J (1991) Nitrate inhibition of nodulation can be overcome by ethylene inhibitor amino ethoxy vinyl glycine. Plant Physiol 97(3):1221–1225CrossRefPubMedPubMedCentralGoogle Scholar
  40. Mandal AK, Sharma RC, Singh G (2009) Assessment of salt affected soils in India using GIS. Geocarto Int 24(6):437–456CrossRefGoogle Scholar
  41. Mayak S, Tirosh T, Glick BR (1999) Effect of wild-type and mutant plant growth promoting rhizobacteria on the rooting of mung bean cuttings. J Plant Growth Regul 18:49–53CrossRefGoogle Scholar
  42. Mayak S, Tirosh T, Glick BR (2004) Plant growth promoting bacteria confer resistance in tomato plants to salt stress. Plant Physiol Biochem 42:565–572CrossRefGoogle Scholar
  43. Moral AD, Prado B, Quesda E, Gacria T, Ferrer R, Ramos-Comenzana A (1988) Numerical taxonomy of moderately halophilic Gram-negative rods from an inland saltern. J Gen Microbiol 134:733–741Google Scholar
  44. Munns R (2002) Comparative physiology of salt and water stress. Plant Cell Environ 25:239–250CrossRefGoogle Scholar
  45. Nadeem SM, Zahir ZA, Naveed M, Arshad M (2007) Preliminary investigation on inducing salt tolerance in maize through inoculation with rhizobacteria containing ACC-deaminase activity. Can J Microbiol 53:1141–1149CrossRefPubMedPubMedCentralGoogle Scholar
  46. Ondrasek G, Rengel Z, Romic D, Savic R (2010) Environmental salinization processes in agro-ecosystem of neretva river estuary. Novenytermeles 59:223–226Google Scholar
  47. Oren A (1999) Bioenergetic aspects of halophilism. Microbiol Mol Biol Rev 63:334–348CrossRefPubMedPubMedCentralGoogle Scholar
  48. Porras-Soriano A, Soriano-Martin ML, Porras-Piedra A, Azcon R (2009) Arbuscular mycorrhizal fungi increased growth, nutrient uptake and tolerance to salinity in olive trees under nursery conditions. J Plant Physiol 166:1350. Scholar
  49. Pozo M, López-Ráez J, Azcón-Aguilar C, García-Garrido J (2015) Phytohormones as integrators of environmental signals in the regulation of mycorrhizal symbioses. New Phytol 205:1431–1436CrossRefPubMedPubMedCentralGoogle Scholar
  50. Reinhold B, Hurek T, Fendrik I, Pot B, Gillis M, Kersters K, Thielemans S, De L (1987) Azospirillum halopraeferens sp. nov., a nitrogen fixing organism associated with roots of Kallar grass (Leptochloa fusca (L.) Kunth.). Int J Syst Bacteriol 37:43–51CrossRefGoogle Scholar
  51. Rengasamy P (2006) World salinization with emphasis on Australia. J Exp Bot 57:1017–1023CrossRefPubMedPubMedCentralGoogle Scholar
  52. Rodriguez-Valera F (1988) Characteristics and microbial ecology of hypersaline environments. In: Rodriguez-Valera F (ed) Halophilic bacteria, vol 1. CRC Press, Boca Raton, FL, pp 3–30Google Scholar
  53. Rodriguez-Valera F, Ventosa A, Juez G, Imhoff LF (1985) Variation of environmental features and microbial populations with the salt concentrations in a multi-pond saltern. Microb Ecol 11:107–111CrossRefGoogle Scholar
  54. Roohi A, Ahmed I, Iqbal M, Jamil M (2012) Preliminary isolation and characterization of halotolerant and halophilic bacteria from salt mines of Karak, Pakistan. Pak J Bot 44:365–370Google Scholar
  55. Savka MA, Dessaux Y, McSpadden Gardener BB, Mondy S, Kohler PRA, de Bruijn FJ, Rossbach S (2013) The “biased rhizosphere” concept and advances in the omics era to study bacterial competitiveness and persistence in the phytosphere. In: de Bruijn FJ (ed) Molecular microbial ecology of the rhizosphere, vol 2. Wiley Blackwell, Hoboken, NJ, pp 1147–1161Google Scholar
  56. Shivanand P, Mugeraya G (2011) Halophilic bacteria and their compatible solutes – osmoregulation and potential applications. Curr Sci 100(10):1516–1521Google Scholar
  57. Singh KN, Chatrath R (2001) Salinity tolerance. In: Reynolds MP, Monasterio JIO, McNab A (eds) Application of physiology in wheat breeding. CIMMYT, Mexico, DF, pp 101–110Google Scholar
  58. Singh RP, Jha PN (2015) Plant growth potential of ACC deaminase rhizospheric bacteria isolated from Aerva javanica: a plant adapted to saline environments. Int J Curr Microbiol Appl Sci 4(7):142–152Google Scholar
  59. Skladany GJ, Metting FB (1993) Bioremediation of contaminated soil. In: Metting FB (ed) Soil microbial ecology: applications in agricultural and environmental management. Marcel Dekker, New York, pp 483–513Google Scholar
  60. Stahl PO, Williams SE (1986) Oil shale process water affects activity of vesicular-arbuscular fungi and Rhizobium four years after application to soil. Soil Biol Biochem 18:451–455CrossRefGoogle Scholar
  61. Trivedi R, Arora S (2013) Characterization of acid and salt tolerant Rhizobium sp. isolated from saline soils of Gujarat. Int Res J Chem 3(3):8–13Google Scholar
  62. Upadhyay SK, Singh DP, Saikia R (2009) Genetic diversity of plant growth promoting rhizobacteria isolated from rhizosphere soil of wheat under saline condition. Curr Microbiol 59:489–496CrossRefGoogle Scholar
  63. Ventosa A, Nieto JJ, Oren A (1998) Biology of moderately halophilic aerobic bacteria. Microbiol Mol Biol Rev 62(2):504–544CrossRefPubMedPubMedCentralGoogle Scholar
  64. Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizer. Plant Soil 255:571–586CrossRefGoogle Scholar
  65. Vivekanandan M, Karthik R, Leela A (2015) Improvement of crop productivity in saline soils through application of saline-tolerant rhizosphere bacteria - current perspective. Int J Adv Res 3(7):1273–1283Google Scholar
  66. Yadav RS, Mahatma MK, Thirumalaisamy PP, Meena HN, Bhaduri D, Arora S, Panwar J (2017) Arbuscular mycorrhizal fungi (AMF) for sustainable soil and plant health in salt-affected soils. In: Arora S, Singh AK, Singh YP (eds) Bioremediation of salt affected soils: an Indian perspective. Springer International Publishing, Switzerland, pp 133–156CrossRefGoogle Scholar
  67. Yancey PH, Clark ME, Hand SC, Bowlus RD, Somero GN (1982) Living with water stress: evolution of osmolyte systems. Science 217:1214–1216CrossRefGoogle Scholar
  68. Yoon JH, Kim IG, Kang KH, Oh TK, Park YH (2003) Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the yellow sea in Korea. Int J Syst Evol Microbiol 53:1297–1303CrossRefGoogle Scholar
  69. Yuhashi KI, Chikawa N, Ezuura H, Akao S, Minakawa Y, NuKui N, Yasuta T, Minamisawa K (2000) Rhizobitoxine production by Bradyrhizobium elkanii enhances nodulation and competitiveness of Macroptilium atropurpureum. Appl Environ Microbiol 66:2658–2663CrossRefPubMedPubMedCentralGoogle Scholar
  70. Zahir ZA, Munir A, Asghar HN, Shahroona B, Arshad M (2007) Effectiveness of Rhizobacterium containing ACC-deaminase for growth promotion of pea (Pisum sativum) under drought conditions. J Microbiol Biotechnol 18:958–963Google Scholar
  71. Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273CrossRefPubMedPubMedCentralGoogle Scholar
  72. Zolla G, Bakker MG, Badri DV, Chaparro JM, Sheflin AM, Manter DK, Vivanco J (2013) Understanding root-microbiome interactions. In: de Bruijn FJ (ed) Molecular microbial ecology of the rhizosphere, vol 2. Wiley Blackwell, Hoboken, NJ, pp 745–754Google Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  1. 1.ICAR-Central Soil Salinity Research InstituteLucknowIndia

Personalised recommendations