Rhizosphere Engineering and Agricultural Productivity

  • Javid Ahmad Parray
  • Mohammad Yaseen Mir
  • Nowsheen Shameem


Animal and plant microbiomes encompass diverse microbial communities that colonize every accessible host tissue. These microbiomes enhance host functions, contributing to host health and fitness. A novel approach to improve animal and plant fitness is to artificially select upon microbiomes, thus engineering evolved microbiomes with specific effects on host fitness. We call this engineering approach host-mediated microbiome selection, because this method selects upon microbial communities indirectly through the host and leverages host traits that evolved to influence microbiomes. In essence, host phenotypes are used as probes to gauge and manipulate those microbiome functions that impact host fitness. To facilitate research on host-mediated microbiome engineering, we explain and compare the principal methods to impose artificial selection on microbiomes; discuss advantages and potential challenges of each method; offer a skeptical appraisal of each method in light of these potential challenges; and outline experimental strategies to optimize microbiome engineering. Finally, we develop a predictive framework for microbiome engineering that organizes research around principles of artificial selection, quantitative genetics, and microbial community-ecology.


Microbiome PGPR Biocontrol Stress Tolerance Plant architect 


  1. Abed, R. M. M., Dobretsov, S., & Sudesh, K. (2009). Applications of cyanobacteria in biotechnology. Journal of Applied Microbiology, 106, 1–12.PubMedCrossRefPubMedCentralGoogle Scholar
  2. Adl, S. (2016). Rhizosphere, food security, and climate change: A critical role for plant-soil research. Rhizosphere, 1, 1–3.CrossRefGoogle Scholar
  3. Ahemad, M., & Khan, M. S. (2011). Toxicological assessment of selective pesticides towards plant growth promoting activities of phosphate solubilizing Pseudomonas aeruginosa. Acta Microbiologica et Immunologica Hungarica, 58, 169–187.PubMedCrossRefPubMedCentralGoogle Scholar
  4. Ahemad, M., & Khan, M. S. (2012). Effect of fungicides on plant growth promoting activities of phosphate solubilizing Pseudomonas putida isolated from mustard (Brassica compestris) rhizosphere. Chemosphere, 86, 945–950.PubMedCrossRefPubMedCentralGoogle Scholar
  5. Ahmad, F., Ahmad, I., & Khan, M. S. (2008). Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiological Research, 163, 173–181.PubMedCrossRefPubMedCentralGoogle Scholar
  6. Alabouvette, C., Lemanceau, P., & Steinberg, C. (1996). Biological control of fusarium wilts: Opportunitiesfor developing a commercial product. In R. Hall (Ed.), Principles and practice of managing soilborne plant pathogens (pp. 192–212). St. Paul: APS Press.Google Scholar
  7. Alami, Y., Achouak, W., Marol, C., & Heulin, T. (2000). Rhizosphere soil aggregation and plant growth promotion of sunflowers by an exopolysaccharide-producing Rhizobium sp. strain isolated from sunflower roots. Applied and Environmental Microbiology, 66, 3393–3398.PubMedCrossRefPubMedCentralGoogle Scholar
  8. Albert, R. A., Waas, N. E., Pavlons, S. C., Pearson, J. L., Ketelboeter, L., et al. (2013). Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water. International Journal of Systematic and Evolutionary Microbiology, 63(3), 952–958.PubMedCrossRefPubMedCentralGoogle Scholar
  9. Amrita, A., Usha, C., & Bishwanath, C. (2013). Improvement of health status of Listea monopetala using plant growth promoting rhizobacteria. International Journal of Bio-Resource and Stress Management, 4(2), 187–191.Google Scholar
  10. Anagnostidis, K., & Komárek, J. A. (1990). Modern approach to the classification systems of cyanophytes. 5-stigonematales. Algological Studies, 59, 1–73.Google Scholar
  11. Ansary, M. H., Rahmani, H. A., Ardakani, M. R., Paknejad, F., Habibi, D., & Mafakheri, S. (2012). Effect of Pseudomonas fluorescens on proline and phytohormonal status of maize (Zea mays L.) under water deficit stress. Annals of Biological Research, 3, 1054–1062.Google Scholar
  12. Antoun, H., Beauchamp, C. J., Goussard, N., Chabot, R., & Lalande, R. (1998). Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on non-legumes: Effects on radishes (Raphanus sativus L.). Plant and Soil, 204, 57–67.CrossRefGoogle Scholar
  13. Archetti, M., et al. (2011). Let the right one in: A microeconomic approach to partner choice in mutualisms. The American Naturalist, 177, 75–85.PubMedCrossRefPubMedCentralGoogle Scholar
  14. Arkhipova, T. N., Veselov, S. U., Melentiev, A. I., Martynenko, E. V., & Kudoyarova, G. R. (2005). Ability of bacterium Bacillus subtilis to produce cytokinins and to influence the growth and endogenous hormone content of lettuce plants. Plant and Soil, 272, 201–209.CrossRefGoogle Scholar
  15. Arkhipova, T. N., Prinsen, E., Veselov, S. U., Martinenko, E. V., Melentiev, A. I., & Kudoyarova, G. R. (2007). Cytokinin producing bacteria enhance plant growth in drying soil. Plant and Soil, 292, 305–315. Scholar
  16. Armada, E., Roldan, A., & Azcon, R. (2014a). Differential activity of autochthonous bacteria in controlling drought stress in native Lavandula and Salvia plants species under drought conditions in natural arid soil. Microbial Ecology, 67, 410–420.PubMedCrossRefPubMedCentralGoogle Scholar
  17. Armada, E., Roldan, A., & Azcon, R. (2014b). Differential activity of autochthonous bacteria in controlling drought stress in native Lavandula and Salvia plants species under drought conditions in natural arid soil. Microbial Ecology, 67, 410–420.PubMedCrossRefPubMedCentralGoogle Scholar
  18. Arnold, A. E., Mamit, L. J., Gehring, C. A., Bidartondo, M. I., & Callahan, H. (2010). Interwoven branches of the plant and fungal trees of life. New Phytologist, 185, 874–878.PubMedCrossRefPubMedCentralGoogle Scholar
  19. Arseneault, T., Goyer, C., & Filion, M. (2013). Phenazine production by Pseudomonas sp. LBUM223 contributes to the biological control of potato common scab. Phytopathology, 103, 995–1000.PubMedCrossRefPubMedCentralGoogle Scholar
  20. Arshad, M., Sharoona, B., & Mahmood, T. (2008). Inoculation with Pseudomonas spp. containing ACC deaminase partially eliminate the effects of drought stress on growth, yield and ripening of pea (Pisum sativum L.). Pedosphere, 18, 611–620.CrossRefGoogle Scholar
  21. Arzanesh, M. H., Alikhani, H. A., Khavazi, K., Rahimian, H. A., & Miransari, M. (2011). Wheat (Triticum aestivum L.) growth enhancement by Azospirillum sp. under drought stress. World Journal of Microbiology and Biotechnology, 27, 197–205.CrossRefGoogle Scholar
  22. Ashelford, K. E., Day, M. J., & Fry, J. C. (2003). Elevated abundance of bacteriophage infecting bacteria in soil. Applied and Environmental Microbiology, 69(1), 285–289.PubMedCrossRefPubMedCentralGoogle Scholar
  23. Auman, A. J., Breezee, J. L., Gosink, J. J., Kämpfer, P., & Staley, J. T. (2006). Psychromonas ingrahamii sp. nov., a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice. International Journal of Systematic and Evolutionary Microbiology, 56(5), 1001–1007.PubMedCrossRefPubMedCentralGoogle Scholar
  24. Bailly, A., & Weisskopf, L. (2012). The modulating effect of bacterial volatiles on plant growth: Current knowledge and future challenges. Plant Signaling & Behavior, 7, 79–85. Scholar
  25. Bais, H. P., Loyola-Vargas, V. M., Flores, H. E., & Vivanco, J. M. (2001). Invited review: Rootspecific metabolism: The biology and biochemistry of underground organs. In Vitro Cellular & Developmental Biology-Plant, 37, 730–741.CrossRefGoogle Scholar
  26. Bakker, M. G., et al. (2014). Diffuse symbioses: Roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome. Molecular Ecology, 23, 1571–1583.PubMedCrossRefPubMedCentralGoogle Scholar
  27. Balogh, B., Jones, J. B., Momol, M. T., Olson, S. M., Obradovic, A., King, P., & Jackson, L. E. (2003a). Improved efficacy of newly formulated bacteriophages for management of bacterial spot on tomato. Plant Disease, 87, 949–954.PubMedCrossRefPubMedCentralGoogle Scholar
  28. Balogh, B., Jones, J. B., Momol, M. T., Olson, S. M., Obradovic, A., & Jackson, L. E. (2003b). Improved efficacy of newly formulated bacteriophages for management of bacterial spot on tomato. Plant Disease, 87, 949–954.PubMedCrossRefPubMedCentralGoogle Scholar
  29. Balogh, L., Polyak, A., Mathe, D., Kiraly, R., Thuroczy, J., Terez, M., Janoki, G., Ting, Y., Bucci, L. R., & Schauss, A. G. (2008). Absorption, uptake and tissue affinity of high- molecular-weight Hyaluronan after Oral Administration in Rats and Dogs. Journal of Agricultural and Food Chemistry, 56(22), 10582–10593.Google Scholar
  30. Balsanelli, E., de Baura, V. A., Pedrosa, F. D., de Souza, E. M., & Monteiro, R. A. (2014). Exopolysaccharide biosynthesis enables mature biofilm formation on abiotic surfaces by Herbaspirillum seropedicae. PLoS One, 9, e110392. Scholar
  31. Bano, Q., Ilyas, N., Bano, A., Zafar, N., Akram, A., & Ul Hassan, F. (2013). Effect of Azospirillum inoculation on maize (zea mays l.) under drought stress. Pakistan Journal of Botany, 45, 13–20.Google Scholar
  32. Barbhaiya, H. B., & Rao, K. K. (1985). Production of pyoverdine, the fluorescent pigment of Pseudomonas aeruginosa PAO1. FEMS Microbiology Letters, 27, 233–235.CrossRefGoogle Scholar
  33. Bargabus, R. L., Zidack, N. K., Sherwood, J. W., & Jacobsen, B. J. (2002). Characterization of systemic resistance in sugar beet elicited by a non-pathogenic, phyllosphere colonizing Bacillus mycoides, biological control agent. Physiological and Molecular Plant Pathology, 61, 289–298.CrossRefGoogle Scholar
  34. Bashan, Y., de-Bashan, L. E., Prabhu, S. R., & Hernandez, J.-P. (2014). Advances in plant growthpromoting bacterial inoculant technology: Formulations and practical perspectives. Plant and Soil, 378, 1–33.CrossRefGoogle Scholar
  35. Bauer, W. D., & Mathesius, U. (2004). Plant responses to bacterial quorum sensing signals. Current Opinion in Plant Biology, 7, 429–433.PubMedCrossRefPubMedCentralGoogle Scholar
  36. Belimov, A. A., Dodd, I. C., Hontzeas, N., Theobald, J. C., Safronova, V. I., & Davies, W. J. (2009). Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signaling. The New Phytologist, 181, 413–423.PubMedCrossRefPubMedCentralGoogle Scholar
  37. Benhamou, N., Kloepper, J. W., Quadt-Hallmann, A., & Tuzun, S. (1996). Induction of defense-related ultrastructural modifications in pea root tissues inoculated with endophytic bacteria. Plant Physiology, 112, 919–929.PubMedCrossRefPubMedCentralGoogle Scholar
  38. Bensalim, S., Nowak, J., & Asiedu, S. K. (1998). A plant growth promoting rhizobacterium and temperature effects on performance of 18 clones of potato. American Journal of Potato Research, 75, 145–152.CrossRefGoogle Scholar
  39. Benz, G., Schroder, T., Kurz, J., Wunsche, C., Karl, W., Steffens, G., Pfitzner, J., & Schmidt, D. (1982). Konstitution der Desferriform der Albomycine d1, d2 and e. Angewandte Chemie, 94, 552–553.CrossRefGoogle Scholar
  40. Berdy, J. (2005). Bioactive microbial metabolites. Journal of Antibiotics, 58, 1–26.PubMedCrossRefPubMedCentralGoogle Scholar
  41. Berendsen, R. L., Pieterse, C. M., & Bakker, P. A. (2012). The rhizosphere microbiome and plant health. Trends in Plant Science, 17, 478–486.PubMedCrossRefPubMedCentralGoogle Scholar
  42. Bernstein, H. C., & Carlson, R. P. (2012). Microbial consortia engineering for cellular factories: In vitro to in sili-co systems. Computational and Structural Biotechnology Journal, 3, e20120017.CrossRefGoogle Scholar
  43. Bernstein, H. C., Paulson, S. D., & Carlson, R. P. (2012). Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. Journal of Biotechnology, 157, 159–166.PubMedCrossRefPubMedCentralGoogle Scholar
  44. Bharathi, R., Vivekananthan, R., Harish, S., Ramanathan, A., & Samiyappan, R. (2004). Rhizobacteria-based bioformulations for the management of fruit rot infection in chillies. Crop Protection, 2, 835–843.CrossRefGoogle Scholar
  45. Bharti, N., Pandey, S. S., Barnawal, D., Patel, V. K., & Kalra, A. (2016). Plant growth promoting rhizobacteria Dietzia natronolimnaea modulates the expression of stress responsive genes providing protection of wheat from salinity stress. Scientific Reports, 6, 34768.PubMedCrossRefPubMedCentralGoogle Scholar
  46. Bhattacharyya, P. N., & Jha, D. K. (2012). Plant growth-promoting rhizobacteria (PGPR): Emergence in agriculture. World Journal of Microbiology and Biotechnology, 28, 1327–1350.PubMedCrossRefPubMedCentralGoogle Scholar
  47. Bishop, P. E., & Jorerger, R. D. (1990). Genetics and molecular biology of an alternative nitrogen fixation system. Plant Molecular Biology, 41, 109–125.Google Scholar
  48. Blumer, C., & Haas, D. (2000). Mechanism, regulation, and ecological role of bacterial cyanide biosynthesis. Archives of Microbiology, 173, 170–177.PubMedCrossRefPubMedCentralGoogle Scholar
  49. Boiero, L., Perrig, D., Masciarelli, O., Penna, C., Cassan, F., & Luna, V. (2007). Phytohormone production by three strains of Bradyrhizobium japonicum and possible physiological and technological implications. Applied Microbiology and Biotechnology, 74(4), 874–880.PubMedCrossRefPubMedCentralGoogle Scholar
  50. Borah, P. K., Jindal, J. K., & Verma, J. P. (2000). Biological management of bacterial leaf spot of mungbean caused by Xanthomonas axonopodis pv. vignaeradiatae. Indian Phytopathology, 53, 384–394.Google Scholar
  51. Bouizgarne, B. (2013). Bacteria for plant growth promotion and disease management. In D. K. Maheshwari (Ed.), Bacteria in agrobiology: Disease management. Berlin/Heidelberg: Springer. Scholar
  52. Bowman, J. P. (2000). Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. International Journal of Systematic and Evolutionary Microbiology, 50(5), 1861–1868.PubMedCrossRefPubMedCentralGoogle Scholar
  53. Boyd, R. J., Hildebrant, A. C., & Allen, O. N. (1971). Retardation of crown gall enlargement after bacteriophage treatment. Plant Disease Report, 55, 145–148.Google Scholar
  54. Bresson, J., Varoquaux, F., Bontpart, T., Touraine, B., & Vile, D. (2013). The PGPR strain Phyllobacterium brassicacearum STM196 induces a reproductive delay and physiological changes that result in improved drought tolerance in Arabidopsis. New Phytologist, 200, 558–569.PubMedCrossRefPubMedCentralGoogle Scholar
  55. Burris, R. H. (1991). Nitrogenases. Journal of Biological Chemistry, 226, 9339–9342.Google Scholar
  56. Buyer, J. S., & Leong, J. (1986). Iron transport-mediated antagonism between plant growth-promoting and plantdeleterious Pseudomonas strains. The Journal of Biological Chemistry, 261, 791–794.PubMedPubMedCentralGoogle Scholar
  57. Camerini, S., Senatore, B., Lonardo, E., Imperlini, E., Bianco, C., Moschetti, G., Rotino, G. L., Campion, B., & Defez, R. (2008). Introduction of a novel pathway for IAA biosynthesis to rhizobia alters vetch root nodule development. Archives of Microbiology, 190, 67–77.PubMedCrossRefPubMedCentralGoogle Scholar
  58. Carmichael, W. W. (2001). Health effects of toxin producing cyanobacteria: The CyanoHABs. Human and Ecological Risk Assessment, 7, 1393–1407.CrossRefGoogle Scholar
  59. Casanovas, E. M., Barassi, C. A., & Sueldo, R. J. (2002). Azospirillum inoculation mitigates water stress effects in maize seedlings. Cereal Research Communications, 30, 343–350.Google Scholar
  60. Cassan, F., Maiale, S., Masciarelli, O., Vidal, A., Luna, V., & Ruiz, O. (2009). Cadaverine production by Azospirillum brasilense and its possible role in plant growth promotion and osmotic stress mitigation. European Journal of Soil Biology, 45, 12–19.CrossRefGoogle Scholar
  61. Cattelan, A. J., Hartel, P. G., & Fuhrmann, J. J. (1999). Screening for plant growth—Promoting rhizobacteria to promote early soybean growth. Soil Science Society of America Journal, 63(6), 1670–1680.CrossRefGoogle Scholar
  62. Chabot, R., Beauchamp, C. J., Kloepper, J. W., & Antoun, H. (1998). Effect of phosphorus on root colonization and growth promotion of maize by bioluminescent mutants of phosphate-solubilizing rhizobium leguminosarum biovar phaseoli. Soil Biology and Biochemistry, 30(12), 1615–1618.CrossRefGoogle Scholar
  63. Chakrabarty, A. M., & Roy, S. C. (1964). Effects of trace elements on the production of pigments by a pseudomonad. The Biochemical Journal, 93, 228–231.PubMedPubMedCentralGoogle Scholar
  64. Chaturvedi, P., Prabahar, V., Manorama, R., Pindi, P. K., Bhadra, B., et al. (2008). Exiguobacterium soli sp. nov., a psychrophilic bacterium from the McMurdo dry valleys, Antarctica. International Journal of Systematic and Evolutionary Microbiology, 58(10), 2447–2453.PubMedCrossRefPubMedCentralGoogle Scholar
  65. Chen, M., Wei, H., Cao, J., Liu, R., Wang, Y., & Zheng, C. (2007). Expression of Bacillus subtilis proBA genes and reduction of feedback inhibition of proline synthesis increases proline production and confers osmotolerance in transgenic Arabidopsis. Journal of Biochemistry and Molecular Biology, 40, 396–403.PubMedPubMedCentralGoogle Scholar
  66. Cho, S. M., Kang, B. R., Han, S. H., Anderson, A. J., Park, J. Y., Lee, Y. H., et al. (2008). 2R, 3R-Butanediol, a bacterial volatile produced by Pseudomonas chlororaphis O6, is involved in induction of systemic tolerance to drought in Arabidopsis thaliana. Molecular Plant-Microbe Interactions, 21, 1067–1075.PubMedCrossRefPubMedCentralGoogle Scholar
  67. Chowdhury, S. P., Hartmann, A., Gao, X. W., & Borriss, R. (2015). Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42-a review. Frontiers in Microbiology, 6, 780. Scholar
  68. Chua, A. C., Ingram, H. A., Raymond, K. N., & Baker, E. (2003). Multidentate pyridinones inhibit the metabolism of nontransferrin-bound iron by hepatocytes and hepatoma cells. European Journal of Biochemistry, 270, 1689–1698.PubMedCrossRefPubMedCentralGoogle Scholar
  69. Close, T. J. (1996). Dehydrins: Emergence of a biochemical role of a family of plant dehydration proteins. Physiologia Plantarum, 97, 795–803.CrossRefGoogle Scholar
  70. Cohen, A. C., Bottini, R., & Piccoli, P. N. (2008). Azosprillium brasilense Sp 245 produces ABA in chemically defined culture medium and increases ABA content in Arabidopsis plants. Plant Growth Regulation, 54, 97–103.CrossRefGoogle Scholar
  71. Cohen, A. C., Travaglia, C. N., Bottini, R., & Piccoli, P. N. (2009). Participation of abscisic acid and gibberellins produced by endophytic Azospirillum in the alleviation of drought effects in maize. Botanique, 87, 455–462.CrossRefGoogle Scholar
  72. Coleman-Derr, D., & Tringe, S. G. (2014). Building the crops of tomorrow: Advantages of 29 symbiont-based approaches to improving abiotic stress tolerance. Frontiers in Microbiology, 5, 283.PubMedCrossRefPubMedCentralGoogle Scholar
  73. Compant, S., Duffy, B., Nowak, J., Cle’ment, C., & Barka, E. A. (2005). Use of plant growth-promoting bacteria for biocontrol of plant diseases: Principles, mechanisms of action, and future prospects. Applied and Environmental Microbiology, 71(9), 4951–4959.PubMedCrossRefPubMedCentralGoogle Scholar
  74. Cook, R. J., & Baker, K. F. (1983). Nature and practice of biological control of plant pathogens. St. Paul: American Phytopathological Society.Google Scholar
  75. Creus, C. M., Sueldo, R. J., & Barassi, C. A. (2004). Water relations and yield in Azospirillum-inoculated wheat exposed to drought in the field. Canadian Journal of Botany, 82, 273–281.CrossRefGoogle Scholar
  76. Creus, C. M., Graziano, M., Casanovas, E. M., Pereyra, M. A., Simontacchi, M., Puntarulo, S., Barassi, C. A., & Lamattina, L. (2005). Nitric oxide is involved in the Azospirillum brasilense-induced lateral root formation in tomato. Planta, 221, 297–303.PubMedCrossRefPubMedCentralGoogle Scholar
  77. Crowley, D. E. (2006). Microbial siderophores in the plant rhizospheric. In Iron nutrition in plants and Rhizospheric microorganisms (pp. 169–198). Dordrecht: Springer.CrossRefGoogle Scholar
  78. Cui, X., & Harling, R. (2005). N-acyl-homoserine lactone-mediated quorum sensing blockage, a novel strategy for attenuating pathogenicity of gram-negative bacterial plant pathogens. European Journal of Plant Pathology, 111, 327–339.CrossRefGoogle Scholar
  79. Dardanelli, M. S., Fernández de Córdoba, F. J., Espuny, M. R., Rodríguez Carvajal, M. A., Soria Díaz, M. E., Gil Serrano, A. M., et al. (2008). Effect of Azospirillum brasilense coinoculated with rhizobium on Phaseolus vulgaris flavonoids and nod factor production under salt stress. Soil Biology and Biochemistry, 40, 2713–2721.CrossRefGoogle Scholar
  80. del Amor, F. M., & Cuadra-Crespo, P. (2012). Plant growth-promoting bacteria as a tool to improve salinity tolerance in sweet pepper. Functional Plant Biology, 39, 82–90. Scholar
  81. DelRio, J. C., Marques, G., Rencoret, J., Martinez, A. T., & Gutierrez, A. (2007). Occurrence of naturally acetylated lignin units. Journal of Agricultural and Food Chemistry, 55, 5461–5468.CrossRefGoogle Scholar
  82. Deshmukh, Y., Khare, P., & Patra, D. (2016). Rhizobacteria elevate principal basmati aroma compound accumulation in rice variety. Rhizosphere, 1, 53–57.CrossRefGoogle Scholar
  83. Desikachary, T. V. (1959). Cyanophyta. Indian Council of Agricultural Research: New Delhi, 686 p.Google Scholar
  84. Deslandes, L., & Rivas, S. (2012). Catch me if you can: Bacterial effectors and plant targets. Trends in Plant Science, 17, 644–655.PubMedCrossRefPubMedCentralGoogle Scholar
  85. Dessaux, Y., Grandclement, C., & Faure, D. (2016). Engineering the rhizosphere. Trends in Plant Science, 21, 266–278.PubMedCrossRefPubMedCentralGoogle Scholar
  86. Dimkpa, C., Svatos, A., Merten, D., Büchel, G., & Kothe, E. (2008). Hydroxamate siderophores produced by Streptomyces acidiscabies E13 bind nickel and promote growth in cowpea (Vigna unguiculata L.) under nickel stress. Canadian Journal of Microbiology, 54, 163–172.PubMedCrossRefPubMedCentralGoogle Scholar
  87. Dimkpa, C., Weinand, T., & Asch, F. (2009a). Plant rhizobacteria interactions alleviate abiotic stress conditions. Plant Cell Environment, 32, 1682–1694.CrossRefGoogle Scholar
  88. Dimkpa, C. O., Merten, D., Svatos, A., Büchel, G., & Kothe, E. (2009b). Siderophores mediate reduced and increased uptake of cadmium by Streptomyces tendae F4 and sunflower (Helianthus annuus), respectively. Journal of Applied Microbiology, 107, 1687–1696.PubMedCrossRefPubMedCentralGoogle Scholar
  89. Dixit, R., Wasiullah, M. D., Pandiyan, K., Singh, U. B., Sahu, A., et al. (2015). Bioremediation of heavy metals from soil and aquatic environment: An overview of principles and criteria of fundamental processes. Sustainability, 7, 2189–2212. Scholar
  90. Dodd, I. C., Belimov, A. A., Sobeih, W. Y., Safronova, V. I., Grierson, D., & Davies, W. J. (2005). Will modifying plant ethylene status improve plant productivity in water-limited environments? In 4th international crop science congress.Google Scholar
  91. Dodd, I. C., Zinovkina, N. Y., Safronova, V. I., & Belimov, A. A. (2010). Rhizobacterial mediation of plant hormone status. The Annals of Applied Biology, 157, 361–379. Scholar
  92. Doke, N., Ramirez, A. V., & Tomiyama, K. (1987). Systemic induction of resistance in potato plants against Phytophthora infestans by local treatment with hyphal wall components of the fungus. Journal of Phytopathology, 119, 232–239.CrossRefGoogle Scholar
  93. Dong, Y.-H., Wang, L., Xu, J.-L., Zhang, H.-B., Zhang, X. F., & Zhang, L. H. (2001). Quenching quorum-sensingdependent bacterial infection by an N-acyl homoserine lactonase. Nature, 411, 813–817.PubMedCrossRefPubMedCentralGoogle Scholar
  94. Dong, Y. H., Wang, L. H., & Zhang, L. H. (2007). Quorum-quenching microbial infections: Mechanisms and implications. Philosophical Transactions of the Royal Society B, 362, 1201–1211.CrossRefGoogle Scholar
  95. Dordas, C. (2008). Role of nutrients in controlling plant diseases in sustainable agriculture: A review. Agronomy for Sustainable Development, 28, 33–46.CrossRefGoogle Scholar
  96. Duffy, B. K., & Défago, G. (1999). Environmental factors modulating antibiotic and siderophore biosynthesis by Pseudomonas fluorescens biocontrol strains. Applied and Environmental Microbiology, 65, 2429–2438.PubMedPubMedCentralGoogle Scholar
  97. Duijff, B. J., Gianinazzi-Pearson, V., & Lemanceau, P. (1997). Involvement of the outer membrane lipopolysaccharides in the endophytic colonization of tomato roots by biocontrol Pseudomonas fluorescens strain WCS417r. New Phytologist, 135, 325–334.CrossRefGoogle Scholar
  98. Duzan, H. M., Zhou, X., Souleimanov, A., & Smith, D. L. (2004). Perception of Bradyrhizobium japonicum nod factor by soybean (Glycine max (L.) Merr.) root hairs under abiotic stress conditions. Journal of Experimental Botany, 55, 2641–2646. Scholar
  99. Edwards, J., et al. (2015). Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences of the United States of America, 112, E911–E920.PubMedCrossRefPubMedCentralGoogle Scholar
  100. Egamberdieva, D., & Kucharova, Z. (2009). Selection for root colonizing bacteria stimulating wheat growth in saline soils. Biol Fert Soil, 45, 561–573.CrossRefGoogle Scholar
  101. El-Afry, M. M., El-Nady, M. F., Abdelmonteleb, E. B., & Metwaly, M. M. S. (2012). Anatomical studies on droughtstressed wheat plants (Triticum aestivum L.) treated with some bacterial strains. Acta Biol Szeged, 56, 165–174.Google Scholar
  102. Elanor W & Rolfes S (2005). Understanding nutrition. Thomson-Wadsworth (10th ed., p. 6).Google Scholar
  103. Elasri, M., et al. (2001). Acyl-homoserine lactone production is more common among plant-associated Pseudomonas spp. than among soilborne Pseudomonas spp. Applied and Environmental Microbiology, 67, 1198–1209.PubMedCrossRefPubMedCentralGoogle Scholar
  104. Fahad, S., & Bano, A. (2012). Effect of salicylic acid on physiological and biochemical characterization of maize grown in saline area. Pakistan Journal of Botany, 44, 1433–1438.Google Scholar
  105. Farmer, E. E. (2001). Surface-to-air signals. Nature, 411, 854–856.PubMedCrossRefPubMedCentralGoogle Scholar
  106. Farrar, K., Bryant, D., & Cope-Selby, N. (2014). Understanding and engineering beneficial plant-microbe interactions: Plant growth promotion in energy crops. Plant Biotechnology Journal, 12, 1193–1206.PubMedCrossRefPubMedCentralGoogle Scholar
  107. Figueiredo, M. V. B., Burity, H. A., Martinez, C. R., & Chanway, C. P. (2008). Alleviation of drought stress in the common bean (Phaseolus vulgaris L.) by co-inoculation with Paenibacillus polymyxa and Rhizobium tropici. Applied Soil Ecology, 40, 182–188. Scholar
  108. Fitter, A. H., & Garbaye, J. (1994). Interactions between mycorrhizal fungi and other soil microorganisms. Plant and Soil, 159, 123–132.CrossRefGoogle Scholar
  109. Fitzpatrick, B. M. (2014). Symbiote transmission and maintenance of extra-genomic associations. Frontiers in Microbiology, 5, 46.PubMedCrossRefPubMedCentralGoogle Scholar
  110. Fitzpatrick, M. C., Keller, S. R., & Vellend, M. (2015). Ecological genomics meets community-level modelling of biodiversity: Mapping the genomic landscape of current and future environmental adaptation. Ecology Letters, 18,(1):1–16.Google Scholar
  111. Flaherty, J. E., Jones, J. B., Harbaugh, B. K., Smoodi, G. C., & Jackson, L. E. (2000). Control of bacterial spot on tomato in the greenhouse and field with H-mutant bacteriophages. Horticultural Science, 35(5), 882–884.Google Scholar
  112. Flaherty, J. E., Harbaugh, B. K., Jones, J. B., Somodi, G. C., & Jackson, L. E. (2001). H-mutant bacteriophages as a potential biocontrol of bacterial blight of geranium. Horticultural Science, 36(1), 98–100.Google Scholar
  113. Fleming, E. D., & Castenholz, R. W. (2007). Effects of periodic desiccation on the synthesis of the UV-screening compound, scytonemin, in cyanobacteria. Environmental Microbiology, 9, 1448–1455.PubMedCrossRefPubMedCentralGoogle Scholar
  114. Foster, K. R., & Wenseleers, T. (2006). A general model for the evolution of mutualisms. Journal of Evolutionary Biology, 19, 1283–1293.PubMedCrossRefPubMedCentralGoogle Scholar
  115. Franche, C., Lindstrom, K., & Elmerich, C. (2009). Nitrogenfixing bacteria associated with leguminous and nonleguminous plants. Plant and Soil, 321, 35–59.CrossRefGoogle Scholar
  116. Franzmann, P., Stackebrandt, E., Sanderson, K., Volkman, J., Cameron, D., et al. (1988). Halobacterium lacusprofundi sp. nov., a halophilic bacterium isolated from Deep Lake, Antarctica. Syst App Microbiol, 11(1), 20–27.CrossRefGoogle Scholar
  117. Friesen, M. L., et al. (2011). Microbially mediated plant functional traits. Annual Review of Ecology, Evolution, and Systematics, 42, 23–46.CrossRefGoogle Scholar
  118. Fujiwara, A., Fujisawa, M., Hamasaki, R., Kawasaki, T., Fujie, M., & Yamada, T. (2011). Biocontrol of Ralstonia solanacearum by treatment with lytic bacteriophages. Applied and Environmental Microbiology, 77(12), 4155–4162.PubMedCrossRefPubMedCentralGoogle Scholar
  119. Gal, M., Preston, G. M., Massey, R. C., Spiers, A. J., & Rainey, P. B. (2003). Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Molecular Ecology, 12, 3109–3121.PubMedCrossRefPubMedCentralGoogle Scholar
  120. Garcion, C., Lamotte, O., & Me’traux, J. P. (2007). In D. R. Walters, A. C. Newton, & G. D. Lyon (Eds.),. Induced resistance for plant defence Mechanisms of defense to pathogens: Biochemistry and physiology (pp. 109–132). Oxford: Blackwell Publishing.Google Scholar
  121. Garland, T., & Rose, M. R. (2009). Experimental evolution. University of California Press.Google Scholar
  122. Garrido-Sanz, D., et al. (2016). Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS One, 11, e0150183.PubMedCrossRefPubMedCentralGoogle Scholar
  123. Gayathri, M., Kumar, P. S., Prabha, A. M. L., & Muralitharan, G. (2015). In vitro regeneration of Arachis hypogaea L. and Moringa oleifera Lam. Using extracellular phytohormones from Aphanothece sp. MBDU 515. Algae Research, 7, 100–105.CrossRefGoogle Scholar
  124. Geitler, L. (1932). Cyanophyceae. Rabenhorst’s Kryptogamen-Flora von Deutschland, Österreich und der Schweiz. Leipzig: Akademische Verlagsgesellschaft.Google Scholar
  125. Gent, D. H., & Schwartz, H. F. (2005). Management of xanthomonas leaf blight of onion with a plant activator, biological control agents, and copper bactericides. Plant Disease, 89, 631–639.PubMedCrossRefPubMedCentralGoogle Scholar
  126. Georgia, F. R., & Poe, C. P. (1931). Study of bacterial fluorescence in various media. 1. Inorganic substances necessary for bacterial fluorescence. Journal of Bacteriology, 22, 349–361.PubMedPubMedCentralGoogle Scholar
  127. Gill, J. J., & Abedon, S. T. (2003). Bacteriophage ecology and plants. APSnet Feature, November. Available at:
  128. Glick, B. R. (2003). Phytoremediation: Synergistic use of plants and bacteria to clean up the environment. Biotechnology Advances, 21, 383–393.PubMedCrossRefPubMedCentralGoogle Scholar
  129. Glick, B. R. (2005). Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase. FEMS Microbiology Letters, 251, 1–7.PubMedCrossRefPubMedCentralGoogle Scholar
  130. Glick, B. R. (2012a). Plant growth-promoting bacteria: Mechanisms and applications. Scientifica (Cairo), 1–15.CrossRefGoogle Scholar
  131. Glick, B. R. (2012b). Plant growth-promoting bacteria: Mechanisms and applications. Scientifica (Cairo), 2012, 963401. Scholar
  132. Glick, B. R., & Pasternak, J. J. (2003). Molecular biotechnology: Principles and application recombinant Dna technology (3rd ed.). Washington: ASM Press.Google Scholar
  133. Glick, B. R., Patten, C. L., Holguin, G., & Penrose, G. M. (1999). Biochemical and genetic mechanisms used by plant growth promoting bacteria. London: Imperial College Press.CrossRefGoogle Scholar
  134. Glick, B. R., Cheng, Z., Czarny, J., & Duan, J. (2007). Promotion of plant growth by ACC deaminase-producing soil bacteria. European Journal of Plant Pathology, 119, 329–339. Scholar
  135. Görke, B., & Stülke, J. (2008). Carbon catabolite repression in bacteria: Many ways to make the most out of nutrients. Nature Reviews. Microbiology, 6, 613–624.PubMedCrossRefPubMedCentralGoogle Scholar
  136. Gosink, J., Herwig, R., & Staley, J. (1997). Octadecabacter arcticus gen. nov., sp. nov., and O. antarcticus, sp. nov., nonpigmented, psychrophilic gas vacuolate bacteria from polar sea ice and water. Systematic and Applied Microbiology, 20(3), 356–365.CrossRefGoogle Scholar
  137. Gou, W., Tian, L., Ruan, Z., Zheng, P., Chen, F., Zhang, L., Cui, Z., Zheng, P., Li, Z., Gao, M., Shi, W., Zhang, L., Liu, J., & Hu, J. (2015). Accumulation of choline and glycinebetaine and drought stress tolerance induced in maize (zea mays) by three plant growth promoting rhizobacteria (pgpr) strains. Pakistan Journal of Botany, 47, 581–586.Google Scholar
  138. Goyer, C. (2005). Isolation and characterization of phages Stsc1 and Stsc3 infecting Streptomyces scabiei and their potential as biocontrol agents. Canadian Journal of Plant Pathology, 27, 210–216.CrossRefGoogle Scholar
  139. Gray, E. J., & Smith, D. L. (2005). Intracellular and extracellular PGPR: Commonalities and distinctions in the plant-bacterium signaling processes. Soil Biology and Biochemistry, 37, 395–412. Scholar
  140. Greer, G. G. (2005). Bacteriophage control of foodborne bacteria. Journal of Food Protection, 68, 1102–1111.PubMedCrossRefPubMedCentralGoogle Scholar
  141. Greppin, H., & Gouda, S. (1965). Action de la lumiere sur le pigment de Pseudomonas fluorescens Migula. Archival Science, 18, 721–725.Google Scholar
  142. Grosskopf, T., & Soyer, O. S. (2014a). Synthetic microbial communities. Current Opinion in Microbiology, 18, 72–77.PubMedCrossRefPubMedCentralGoogle Scholar
  143. Grosskopf, T., & Soyer, O. S. (2014b). Synthetic microbial communities. Current Opinion in Microbiology, 18, 72–77.PubMedCrossRefPubMedCentralGoogle Scholar
  144. Gupta, K., Dey, A., & Gupta, B. (2013). Plant polyamines in abiotic stress responses. Acta Physiologiae Plantarum, 35, 2015–2036. Scholar
  145. Gurusaravanan, P., Vinoth, S., Kumar, M. S., Thajuddin, N., & Jayabalan, N. (2013). Effect of cyanobacteria extracellular products on high-frequency in vitro induction and elongation of Gossypium hirsutum L. organs through shoot apex explants. Journal of Genetic Engineering and Biotechnology, 11, 9–16.CrossRefGoogle Scholar
  146. Gusain, Y. S., Singh, U. S., & Sharma, A. K. (2015). Bacterial mediated amelioration of drought stress in drought tolerant and susceptible cultivars of rice (Oryza sativa L.). African Journal of Biotechnology, 14, 764–773.CrossRefGoogle Scholar
  147. Gysin, J., Crenn, Y., Pereira da silva, L., & Breton, C. (1991). Siderophores as antiparasitic agents. US Patent 5, 192–807.Google Scholar
  148. Haas, D., & Défago, G. (2005). Biological control of soil-borne pathogens by fluorescent pseudomonads. Nature Reviews. Microbiology, 3, 307–319.PubMedCrossRefGoogle Scholar
  149. Han, J., Sun, L., Dong, X., Cai, Z., Sun, X., Yang, H., & Song, W. (2005). Characterization of a novel plant growth-promoting bacteria strain Delftia tsuruhatensis HR4 both as a diazotroph and a potential biocontrol agent against various plant pathogens. Systematic and Applied Microbiology, 28(1), 66–76.PubMedCrossRefPubMedCentralGoogle Scholar
  150. Hardoim, P. R., Van Overbeek, L. S., & Van Elsas, J. D. (2008). Properties of bacterial endophytes and their proposed role in plant growth. Trends in Microbiol, 16, 463–471.CrossRefGoogle Scholar
  151. Hartmann, A., Rothballer, M., & Schmid, M. (2008). Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant and Soil, 312, 7–14.CrossRefGoogle Scholar
  152. Heath, K. D., & Stinchcombe, J. R. (2014). Explaining mutualism variation: A new evolutionary paradox. Evolution, 68, 309–314.PubMedCrossRefPubMedCentralGoogle Scholar
  153. Heckman, D. S., Geiser, D. M., Eidell, B. R., Stauffer, R. L., Kardos, N. L., & Hedges, S. B. (2001). Molecular evidence for the early colonization of land by fungi and plants. Science, 293, 30 1129–30 1133.CrossRefGoogle Scholar
  154. Hedin, L. O., Brookshire, E. N. J., Menge, D. N. L., & Barron, A. R. (2009). The nitrogen paradox in tropical forest ecosystems. Annual Review of Ecology, Evolution and Systematics, 40, 613–635.CrossRefGoogle Scholar
  155. Heidari, M., & Golpayegani, A. (2011). Effects of water stress and inoculation with plant growth promoting rhizobacteria (PGPR) on antioxidant status and photosynthetic pigments in basil (Ocimum basilicum L.). Journal of the Saudi Society of Agricultural Sciences, 11, 57–61.CrossRefGoogle Scholar
  156. Hellebust, J. A. (1974). Extracellular products. In W. D. P. Stewart (Ed.), Algal physiology and biochemistry (pp. 838–863). Oxford: Blackwell Scientific Publications.Google Scholar
  157. Henry, G., Thonart, P., & Ongena, M. (2012). PAMPs, MAMPs, DAMPs and others: An update on the diversity of plant immunity elicitors. Biotechnologie, Agronomie, Société et Environnement, 16, 257–268.Google Scholar
  158. Himmel, M. E., et al. (2007). Biomass recalcitrance: Engineering plants and enzymes for biofuels production. Science, 315, 804–807.PubMedCrossRefPubMedCentralGoogle Scholar
  159. Hinsa, S. M., Espinosa-Urgel, M., Ramos, J. L., & O’Toole, G. A. (2003). Transition from reversible to irreversible attachment during biofilm formation by Pseudomonas fluorescens WCS365 requires an ABC transporter and a large secreted protein. Molecular Microbiology, 49, 905–918.PubMedCrossRefPubMedCentralGoogle Scholar
  160. Hirsch, P., Ludwig, W., Hethke, C., Sittig, M., Hoffmann, B., et al. (1998). Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antarctic soils and sandstone: Bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Systematic and Applied Microbiology, 21(3), 374–383.PubMedCrossRefPubMedCentralGoogle Scholar
  161. Hofte, M. (1993). Classes of microbial siderophores. In L. L. Barton (Ed.), Iron chelation in plants and soil microorganisms (pp. 3–26). San Diego: BC Hemming in Academic Press.CrossRefGoogle Scholar
  162. Huang, J., Wei, Z., Tan, S., Mei, X., Yin, S., Shen, Q., & Xu, Y. (2013). The rhizosphere soil of diseased tomato plants as a source for novel microorganisms to control bacterial wilt. Applied Soil Ecology, 72, 79–84.CrossRefGoogle Scholar
  163. Hugenholtz, P. (2002). Exploring prokaryotic diversity in the genomic era. Genome Biology, 3, REVIEWS0003.PubMedCrossRefPubMedCentralGoogle Scholar
  164. Hui, L. J., & Kim, S. D. (2013). Induction of drought stress resistance by multifunctional PGPR Bacillus licheniformis K11 in pepper. Plant Pathology Journal, 29, 201–208.CrossRefGoogle Scholar
  165. Humphry, D. R., George, A., Black, G. W., & Cummings, S. P. (2001). Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. International Journal of Systematic and Evolutionary Microbiology, 51(4), 1235–1243.PubMedCrossRefPubMedCentralGoogle Scholar
  166. Hussain, M. B., Zahir, Z. A., Asghar, H. N., & Asghar, M. (2014). Exopolysaccharides producing rhizobia ameliorate drought stress in wheat. International Journal of Agriculture and Biology, 16, 3–13.Google Scholar
  167. Ings, J., Mur, L. A., Robson, P. R., & Bosch, M. (2013). Physiological and growth responses to water deficit in the bioenergy crop Miscanthus x giganteus. Frontiers in Plant Science, 4, 468.PubMedCrossRefPubMedCentralGoogle Scholar
  168. Iriarte, F. B., Balogh, B., Momol, M. T., & Jones, J. B. (2007). Factors affecting survival of bacteriophage on tomato leaf surfaces. Applied and Environmental Microbiology, 73(6), 1704–1711.PubMedCrossRefPubMedCentralGoogle Scholar
  169. Jafra, S., et al. (2006). Detection and characterization of bacteria from the potato rhizosphere degrading N-acyl-homoserine lactone. Canadian Journal of Microbiology, 52, 1006–1015.PubMedCrossRefPubMedCentralGoogle Scholar
  170. Jagadeesh, K. S. (2000). Selection of rhizobacteria antagonistic to Ralstonia solanacearum causing bacterial wilt in tomato and their biocontrol mechanisms. PhD Thesis. University of Agricultural Sciences, Dharwad.Google Scholar
  171. Jamil, M., Zeb, S., Anees, M., Roohi, A., Ahmed, I., Rehman, S. U., & Rha, E. S. (2014). Role of Bacillus Licheniformis in phytoremediation of nickel contaminated soil cultivated with Rice. International Journal of Phytoremediation, 16, 554–571.PubMedCrossRefPubMedCentralGoogle Scholar
  172. Jones, J. D., & Dang, J. L. (2006). The plant immune system. Nature, 444, 323–329.PubMedCrossRefPubMedCentralGoogle Scholar
  173. Jones, J. B., Lacy, G. H., Bouzar, H., Minsavage, G. V., Stall, R. E., & Schaad, N. W. (2005). Bacterial spot-worldwide distribution, importance and review. Acta Horticulturae, (695), 27–33.Google Scholar
  174. Julian, G., Cameron, H. J., & Olsen, R. A. (1983). Role of chelation by ortho dihydroxy phenols in iron absorption by plant roots. Journal of Plant Nutrition, 6, 163–175.CrossRefGoogle Scholar
  175. Kang, S. M., Radhakrishnan, R., Khan, A. L., Kim, M. J., Park, J. M., Kim, B. R., Shin, D. H., & Lee, I. J. (2014a). Gibberellin secreting rhizobacterium, Pseudomonas putida H-2-3 modulates the hormonal and stress physiology of soybean to improve the plant growth under saline and drought conditions. Plant Physiology and Biochemistry, 84, 115–124.PubMedCrossRefPubMedCentralGoogle Scholar
  176. Kang, S.-M., Khan, A. L., Waqas, M., You, Y.-H., Kim, J.-H., Kim, J.-G., et al. (2014b). Plant growth-promoting rhizobacteria reduce adverse effects of salinity and osmotic stress by regulating phytohormones and antioxidants in Cucumis sativus. Journal of Plant Interactions, 9, 673–682. Scholar
  177. Kang, S. M., Khan, A. L., Waqas, M., You, Y. H., Kim, J. H., Kim, J. G., Hamayun, M., & Lee, I. J. (2014c). Plant growth-promoting rhizobacteria reduce adverse effects of salinity and osmotic stress by regulating phytohormones and antioxidants in Cucumis sativus. Journal of Plant Interactions, 9, 673–682.CrossRefGoogle Scholar
  178. Kang, Y., Shen, M., Wang, H., & Zhao, Q. (2015). Complete genome sequence of Bacillus pumilus strain WP8, an efficient plant growth-promoting rhizobacterium. Genome Announcements, 3(1), e01452–e01414.PubMedCrossRefPubMedCentralGoogle Scholar
  179. Karen, A. S., Grimplet, J., Cushman, J., & Cramer, G. R. (2010). Transcriptomics analysis methods: Microarray data processing, analysis and visualization using the Affymetrix Genechip® Vitis Vinifera genome array. Method Results Grapevine Research, 317–334.Google Scholar
  180. Kasim, W. A., Osman, M. E., Omar, M. N., Abd El-Daim, I. A., Bejai, S., & Meijer, J. (2013). Control of drought stress in wheat using plant growth promoting bacteria. Journal of Plant Growth Regulation, 32, 122–130.CrossRefGoogle Scholar
  181. Kaur, G., & Reddy, M. S. (2014). Influence of P-solubilizing bacteria on crop yield and soil fertility at multilocational sites. European Journal of Soil Biology, 61, 35–40.CrossRefGoogle Scholar
  182. Kaushal, M., & Wani, S. P. (2015). Plant-growth-promoting rhizobacteria: Drought stress alleviators to ameliorate crop production in drylands. Annales de Microbiologie, 1–8.Google Scholar
  183. Kempf, B., & Bremer, E. (1998). Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Archives of Microbiology, 170, 319–330. Scholar
  184. Keshavan, N. D., Chowdhary, P. K., Haines, D. C., & Gonzalez, J. E. (2005). L-Canavanine made by Medicago sativa interferes with quorum sensing in Sinorhizobium meliloti. Journal of Bacteriology, 187, 8427–8436.PubMedCrossRefPubMedCentralGoogle Scholar
  185. Khalid, A., Akhtar, M. J., Mahmood, M. H., & Arshad, M. (2006). Effect of substrate-dependent microbial ethylene production on plant growth. Microbiology, 75, 231–236.CrossRefGoogle Scholar
  186. Khan, M. S., Zaidi, A., & Wani, P. A. (2006). Role of phosphate-solubilizing microorganisms in sustainable agriculture—A review. Agronomy for Sustainable Development, 27, 29–43.CrossRefGoogle Scholar
  187. Kim, S. B., & Timmusk, S. (2013). A simplified method for gene knockout and direct screening of recombinant clones for application in Paenibacillus polymyxa. PLoS One, 8.Google Scholar
  188. Kim, K. Y., Jordan, D., & McDonald, G. A. (1998). Enterobacter agglomerans, phosphate solubilizing bacteria, and microbial activity in soil: Effect of carbon sources. Soil Biology and Biochemistry, 30(8), 995–1003.CrossRefGoogle Scholar
  189. Kim, S. J., Shin, S. C., Hong, S. G., Lee, Y. M., Choi, I. G., et al. (2012a). Genome sequence of a novel member of the genus Psychrobacter isolated from Antarctic soil. Journal of Bacteriology, 194(9), 2403.PubMedCrossRefPubMedCentralGoogle Scholar
  190. Kim, S., Lowman, S., Hou, G., Nowak, J., Flinn, B., & Mei, C. (2012b). Growth promotion and colonization of switchgrass (Panicum virgatum) cv. Alamo by bacterial endophyte Burkholderia phytofirmans strain PsJN. Biotechnology for Biofuels, 5, 37.PubMedCrossRefPubMedCentralGoogle Scholar
  191. Kim, K., Jang, Y.-J., Lee, S.-M., Oh, B.-T., Chae, J.-C., & Lee, K.-J. (2014). Alleviation of salt stress by Enterobacter sp. EJ01 in tomato and Arabidopsis is accompanied by up-regulation of conserved salinity responsive factors in plants. Molecules and Cells, 37, 109–117. Scholar
  192. Kloepper, J. W., & Beauchamp, C. J. (1992). A review of issues related to measuring of plant roots by bacteria. Canadian Journal of Microbiology, 38, 1219–1232.CrossRefGoogle Scholar
  193. Kloepper, J. W., & Schroth, M. N. (1978). Plant growth promoting rhizobacteria on radishes. In: Proceedings of the fourth international conference on plant pathogen bacteria, INRA, Gilbert-Clarey, Tours, France 2, pp. 879–882.Google Scholar
  194. Kloepper, J. W., & Schroth, M. N. (1981a). Plant growth-promoting Rhizobacteria and PlantGrowth under Gnotobiotic conditions. Phytopathology, 71, 642–644.CrossRefGoogle Scholar
  195. Kloepper, J. W., & Schroth, M. N. (1981b). Relationship of in vitro antibiosis of plant growth promoting rhizobacteria to plant growth and the displacement of root microflora. Phytopathology, 71, 1020–1024.CrossRefGoogle Scholar
  196. Kloepper, J. W., Leong, J., Teintze, M., & Schroth, M. N. (1980). Enhancing plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature, 286, 885–886.CrossRefGoogle Scholar
  197. Kloepper, J. W., Gutierrez-Estrada, A., & McInroy, J. A. (2007). Photoperiod regulates elicitation of growth promotion but not induced resistance by plant growth-promoting rhizobacteria. Canadian Journal of Microbiology, 53(2), 159–167.PubMedCrossRefPubMedCentralGoogle Scholar
  198. Knief, C. (2014). Analysis of plant microbe interactions in the era of next generation sequencing technologies. Frontiers in Plant Science, 5.Google Scholar
  199. Knoester, M., Pieterse, C. M., Bol, J. F., & Van Loon, L. C. (1999). Systemic resistance in Arabidopsis induced by rhizobacteria requires ethylene-dependent signaling at the site of application. Molecular Plant-Microbe Interactions, 12(8), 720–727.PubMedCrossRefPubMedCentralGoogle Scholar
  200. Köberl, M., Ramadan, E. M., Adam, M., Cardinale, M., Hallmann, J., Heuer, H., Smalla, K., & Berg, G. (2013). Bacillus and Streptomyces were selected as broad-spectrum antagonists against soilborne pathogens from arid areas in Egypt. FEMS Microbiology Letters, 342, 168–178.PubMedCrossRefPubMedCentralGoogle Scholar
  201. Köberl, M., White, R. A., III, Erschen, S., El-Arab, T. F., Jansson, J. K., & Berg, G. (2015). Draft genome sequence of Streptomyces sp. strain Wb2n-11, a desert isolate with broad-spectrum antagonism against soilborne phytopathogens. Genome Announcements, 3(4).Google Scholar
  202. Koch, H., & Schmid-Hempel, P. (2011). Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. Proceedings of the National Academy of Sciences of the United States of America, 108, 19288–19292.PubMedCrossRefPubMedCentralGoogle Scholar
  203. Koch, B., Liljefors, T., Persson, T., Nielsen, J., Kjelleberg, S., & Givskov, M. (2005). The LuxR receptor: The sites of interaction with quorum-sensing signals and inhibitors. Microbiology, 151, 3589–3602.PubMedCrossRefPubMedCentralGoogle Scholar
  204. Koehn, F. E., Lomgley, R. E., & Reed, J. K. (1992). Microcolins A and B, new immunosuppressive peptide from the blue-green algae Lyngbya majuscule. Journal of Natural Products, 55, 613–619.PubMedCrossRefPubMedCentralGoogle Scholar
  205. Kohler, J., Caravaca, F., Carrasco, L., & Roldan, A. (2006). Contribution of Pseudomonas mendocina and Glomus intraradices to aggregate stabilization and promotion of biological fertility in rhizosphere soil of lettuce plants under field conditions. Soil Use and Management, 22, 298–304. Scholar
  206. Kohler, J., Herna’ndez, J. A., Caravaca, F., & Rolda’n, A. (2008). Plant-growth promoting rhizobacteria and arbuscular mycorrhizal fungi modify alleviation biochemical mechanisms in water stressed plants. Functional Plant Biology, 35, 141–151.CrossRefGoogle Scholar
  207. Konnova, S. A., Brykova, O. S., Sachkova, O. A., Egorenkova, I. V., & Ignatov, V. V. (2001). Protective role of the polysaccharide containing capsular components of Azospirillum brasilense. Microbiol, 70, 436–440.CrossRefGoogle Scholar
  208. Kuan, K. B., Othman, R., Abdul Rahim, K., & Shamsuddin, Z. H. (2016). Plant growth-promoting rhizobacteria inoculation to enhance vegetative growth, nitrogen fixation and nitrogen remobilisation of maize under greenhouse conditions. PLoS One, 11, e0152478. Scholar
  209. Kulik, M. M. (1995). The potential for using cyanobacteria (blue-green algae) and algae in the biological control of plant pathogenic bacteria and fungi. European Journal of Plant Pathology, 101, 585–599.CrossRefGoogle Scholar
  210. Kumar, V., Behl, R. K., & Narula, N. (2001). Establishment of phosphate solubilizing strains of Azotobacter chroococcum in the rhizosphere and their effect on wheat cultivars under greenhouse conditions. Microbiological Research, 156, 87–93.PubMedCrossRefPubMedCentralGoogle Scholar
  211. Kutter, E. (1997). Phage therapy: Bacteriophages as antibiotics Olympia. Washington: Accessed Apr 2014.
  212. Lang, J. M., Gent, D. H., & Schwartz, H. F. (2007). Management of Xanthomonas leaf blight of onion with bacteriophages and a plant activator. Plant Disease, 91(7), 871–878.PubMedCrossRefPubMedCentralGoogle Scholar
  213. Lau, J. A., & Lennon, J. T. (2012). Rapid responses of soil microorganisms improve plant fitness in novel environments. Proceedings of the National Academy of Sciences of the United States of America, 109, 14058–14062.PubMedCrossRefPubMedCentralGoogle Scholar
  214. Lee, Y. M., Hwang, C. Y., Lee, I., Jung, Y. J., Cho, Y., et al. (2014). Lacinutrix jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment and emended description of the genus Lacinutrix. Antonie Van Leeuwenhoek, 106(3), 527–533.PubMedCrossRefPubMedCentralGoogle Scholar
  215. Leeman, M., DenOuden, E. M., VanPelt, J. A., Dirkx, F. P. M., Steijl, H., Bakker, P. A. H. M., & Schippers, B. (1996). Iron availability affects induction of systemic resistance to Fusarium wilt of radish by Pseudomonas fluorescens. Phytopathology, 86, 149–155.CrossRefGoogle Scholar
  216. Lenhoff, H. M. (1963). An inverse relationship of the effects of oxygen and iron on the production of fluorescin and cytochrome C by Pseudomonas fluorescens. Nature, 199, 601–602.PubMedCrossRefPubMedCentralGoogle Scholar
  217. Lifshitz, R., Kloepper, J. W., Scher, F. M., Tipping, E. M., & Laliberte, M. (1986). Nitrogen-fixing pseudomonads isolated from roots of plants grown in the Canadian high arctic. Applied and Environmental Microbiology, 51, 251–255.PubMedPubMedCentralGoogle Scholar
  218. Lim, J. H., & Kim, S. D. (2013). Induction of drought stress resistance by multi-functional PGPR Bacillus licheniformis K11 in pepper. Plant Pathology Journal, 29, 201–208.PubMedCrossRefPubMedCentralGoogle Scholar
  219. Linderman, R. G. (1994). Role of AM fungi in biocontrol. In F. L. Pfleger & R. G. Linderman (Eds.), Mycorrhizae and plant health (pp. 1–25). St. Paul: APS Press.Google Scholar
  220. Liu, B., Wu, S., Song, Q., Zhang, X., & Xie, L. (2006). Two novel bacteriophages of thermophilic bacteria isolated from deep-sea hydrothermal fields. Current Microbiology, 53, 163–166.PubMedCrossRefPubMedCentralGoogle Scholar
  221. Liu, F. C., Xing, S. J., Ma, H. L., Du, Z. Y., & Ma, B. Y. (2013). Cytokinin-producing, plant growthpromoting rhizobacteria that confer resistance to drought stress in Platycladus orientalis container seedlings. Applied Microbiology and Biotechnology, 97, 9155–9164.PubMedCrossRefPubMedCentralGoogle Scholar
  222. Loper, J. E., & Buyer, J. S. (1991). Siderophores in microbial interactions on plant surfaces. Molecular Plant-Microbe Interactions, 4, 5–13.CrossRefGoogle Scholar
  223. Loper, J. E., & Henkels, M. D. (1999). Utilization of heterologous siderophores enhances levels of iron available to Pseudomonas putida in the rhizosphere. Applied and Environmental Microbiology, 65(12), 5357–5363.PubMedPubMedCentralGoogle Scholar
  224. Loper, J. E., Kobayashi, D. Y., & Paulsen, I. T. (2007). The genomic sequence of Pseudomonas fluorescens Pf-5: Insights into biological control. Phytopathology, 97(2), 233–238.PubMedCrossRefPubMedCentralGoogle Scholar
  225. López, N. I., Pettinari, M. J., Stackebrandt, E., Tribelli, P. M., Põtter, M., et al. (2009). Pseudomonas extremaustralis sp. nov., a poly (3-hydroxybutyrate) producer isolated from an Antarctic environment. Current Microbiology, 59(5), 514–519.PubMedCrossRefPubMedCentralGoogle Scholar
  226. Lu, X. (2010). A perspective: Photosynthetic production of fatty acid-based biofuels in genetically engineered cyanobacteria. Biotechnology Advances, 28, 742–746.PubMedCrossRefPubMedCentralGoogle Scholar
  227. Lugtenberg, B., & Kamilova, F. (2009a). Plant-growth-promoting rhizobacteria. Annual Review of Microbiology, 63, 541–556.PubMedCrossRefPubMedCentralGoogle Scholar
  228. Lugtenberg, B., & Kamilova, F. (2009b). Plant-growth-promoting rhizobacteria. Annual Review of Microbiology, 63, 541–555.PubMedCrossRefPubMedCentralGoogle Scholar
  229. Lugtenberg, B. J., Dekkers, L., & Bloemberg, G. V. (2001). Molecular determinants of rhizosphere colonization by Pseudomonas. Annual Review of Phytopathology, 39, 461–490.PubMedCrossRefPubMedCentralGoogle Scholar
  230. Lugtenberg, B. J., Malfanova, N., Kamilova, F., & Berg, G. (2013). Plant growth promotion by microbes. Molecular Microbial Ecology of the Rhizosphere, 1(2), 559–573.CrossRefGoogle Scholar
  231. Mackelprang, R., et al. (2011). Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature, 480, 368–371.PubMedCrossRefPubMedCentralGoogle Scholar
  232. Maffei, M. E., Arimura, G. I., & Mithofer, A. (2012). Natural elicitors, effectors and modulators of plant responses. Natural Product Reports, 29(11), 1288–1303.PubMedCrossRefPubMedCentralGoogle Scholar
  233. Mahmood, S., Daur, I., Al-Solaimani, S. G., Ahmad, S., Madkour, M. H., Yasir, M., Hirt, H., Ali, S., & Ali, Z. (2016). Plant growth promoting rhizobacteria and silicon synergistically enhance salinity tolerance of Mung bean. Frontiers in Plant Science, 7.Google Scholar
  234. Manefield, M., et al. (2002). Halogenated furanones inhibit quorum sensing through accelerated LuxR turnover. Microbiology, 148, 1119–1127.PubMedCrossRefPubMedCentralGoogle Scholar
  235. Mantelin, S., & Touraine, B. (2004). Plant growth-promoting rhizobacteria and nitrate availability: Impacts on root development and nitrate uptake. Journal of Experimental Botany, 55, 27–34.PubMedCrossRefPubMedCentralGoogle Scholar
  236. Margesin, R., Zhang, D. C., Frasson, D., & Brouchkov, A. (2016). Glaciimonas frigoris sp. nov., a psychrophilic bacterium isolated from ancient Siberian permafrost sediment, and emended description of the genus Glaciimonas. International Journal of Systematic and Evolutionary Microbiology, 66(2), 744–748.PubMedCrossRefPubMedCentralGoogle Scholar
  237. Mariano, R. L. R., Silveira, E. B., Assis, S. M. P., Gomes, A. M. A., Oliveira, I. S., & Nascimento, A. R. P. (2001). Diagnose e manejo de fitobacterioses de importância no Nordeste Brasileiro. In S. J. Michereff & R. Barros (Eds.), Proteção de Plantas na Agricultura Sustentável (pp. 141–169). Brasil: UFRPE, Recife.Google Scholar
  238. Marulanda, A., Azcon, R., Chaumont, F., Ruiz-Lozano, J. M., & Aroca, R. (2010). Regulation of plasma membrane aquaporins by inoculation with a Bacillus megaterium strain in maize (Zea mays L.) plants under unstressed and salt-stressed conditions. Planta, 232, 533–543. Scholar
  239. Mauchline, T. H., et al. (2015). An analysis of Pseudomonas genomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota. Environmental Microbiology, 17, 4764–4778.PubMedCrossRefPubMedCentralGoogle Scholar
  240. Maurhofer, M., Hase, C., Meuwly, P., Metraux, J. P., & Défago, G. (1994). Induction of systemic resistance of tobacco to tobacco necrosis virus by the root-colonizing Pseudomonas fluorescens strain CHA0: Influence of the gacA gene and of pyoverdine production. Phytopathology, 84, 139–146.CrossRefGoogle Scholar
  241. Mayak, S., Tirosh, T., & Glick, B. R. (2004). Plant growth-promoting bacteria that confer resistance to water stress in tomatoes and peppers. Plant Science, 166, 525–530.CrossRefGoogle Scholar
  242. Mazzola, M., Cook, R. J., Thomashow, L. S., Weller, D. M., & Pierson, L. S., 3rd. (1992). Contribution of phenazine antibiotic biosynthesis to the ecological competence of fluorescent pseudomonads in soil habitats. Applied and Environmental Microbiology, 58, 2616–2624.PubMedPubMedCentralGoogle Scholar
  243. McGrath, S. P., Chaudri, A. M., & Giller, K. E. (1995). Long-term effects of metals in sewage sluge on soils, microorganisms and plants. Journal of Industrial Microbiology, 14(2), 94–104.PubMedCrossRefPubMedCentralGoogle Scholar
  244. McMillan, V. E., Hammond-Kosack, K. E., & Gutteridge, R. J. (2011). Evidence that wheat cultivars differin their ability to build up inoculum of the take-all fungus, Gaeumannomyces graminis var. tritici, under a first wheat crop. Plant Pathology, 60, 200–206.CrossRefGoogle Scholar
  245. McNear, D. H. Jr. (2013). The Rhizosphere – Roots, soil and everything in between. Nature Education Knowledge, 4, 1.Google Scholar
  246. McNeil, D. L., Romero, S., Kandula, J., Stark, C., Stewart, A., & Larsen, S. (2001). Bacteriphages: A potential biocontrol agent against walnut blight (Xanthomonas campestris pv. juglandis). New Zealand Plant Protection, 54, 220–224.CrossRefGoogle Scholar
  247. Mehrabi, Z., et al. (2016). Pseudomonas spp. diversity is negatively associated with suppression of the wheat take-all pathogen. Scientific Reports, 6, 29905.PubMedCrossRefPubMedCentralGoogle Scholar
  248. Miernik, A. (2003). Occurrence of bacteria and coli bacteriophages as potential indicators of fecal pollution of vistula river and zegrze reservoir. Polish Journal of Environmental Studies, 13(1), 79–84.Google Scholar
  249. Miethke, M., & Marahiel, M. A. (2007). Siderophore-based Iron acquisition and pathogen control. Microbiology and Molecular Biology Reviews, 71, 413–445.PubMedCrossRefPubMedCentralGoogle Scholar
  250. Miransari, M., & Smith, D. L. (2009). Alleviating salt stress on soybean (Glycine max (L.) Merr.) – Bradyrhizobium japonicumsymbiosis, using signal molecule genistein. European Journal of Soil Biology, 45, 146–152. Scholar
  251. Mirshad, P. P., and Puthur, J. T. (2017). Drought tolerance of bioenergy grass Saccharum spontaneum L. enhanced by arbuscular mycorrhizae. Rhizosphere 3, Part 1, 1–1, 8.CrossRefGoogle Scholar
  252. Mitri, S., et al. (2011). Social evolution in multispecies biofilms. Proceedings of the National Academy of Sciences of the United States of America, 108, 10839–41086.PubMedCrossRefPubMedCentralGoogle Scholar
  253. Miyawaki, K., Tarkowski, P., Matsumoto-Kitano, M., Kato, T., Sato, S., Tarkowska, D., Tabata, S., Sandberg, G., & Kakimoto, T. (2006). Roles of Arabidopsis ATP/ADP 32 isopentenyltransferases and tRNA isopentenyltransferases in cytokinin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America, 103, 16598–16603.PubMedCrossRefPubMedCentralGoogle Scholar
  254. Moran, N. A. (2015). Genomics of the honey bee microbiome. Current Opinion in Insect Science, 10, 22–28.PubMedCrossRefPubMedCentralGoogle Scholar
  255. Morgan, P. W., & Drew, M. C. (1997). Ethylene and plant responses to stress. Physiologia Plantarum, 100, 620–630. Scholar
  256. Morris, P. F., & Ward, E. W. R. (1992). Chemoattraction of zoospores of the plant soybean pathogen, Phytophthora sojae, by isoflavones. Physiological and Molecular Plant Pathology, 40, 17–22.CrossRefGoogle Scholar
  257. Morton, J. B., & Benny, G. L. (1990). Revised classification of arbuscular mycorrhizal fungi (zygomycetes): A new order glomales, two new suborders, glomineae and gigasporineae and gigasporaceae, with an amendation of glomaceae. Mycotaxon, 37, 471–491.Google Scholar
  258. Mulkidjanian, A. Y., Koonin, E. V., Makarova, K. S., Mekhedov, S. L., Sorokin, A., Wolf, Y. I., Dufresne, A., et al. (2006). The cyanobacterial genome core and the origin of photosynthesis. Proceedings of National Academy of Science USA, 103, 13126–13131.CrossRefGoogle Scholar
  259. Munsch, P., & Olivier, J. M. (1995). Biocontrol of bacterial blotch of the cultivated mushroom with lytic phages: Some practical considerations. In T. J. Elliott (Ed.), Science and cultivation of edible fungi. Proceedings of the 14th international congress (Vol. II, pp. 595–602). Rotterdam: Balkema, AA.Google Scholar
  260. Nadeem, S. M., Zahir, Z. A., Naveed, M., & Arshad, M. (2009). Rhizobacteria containing ACC-deaminase confer salt tolerance in maize grown on salt-affected fields. Canadian Journal of Microbiology, 55, 1302–1309. Scholar
  261. Nakkeeran, S., & Fernando, W. G. D. (2005). Plant growth promoting rhizobacteria formulations and its scope in commercialization for the management of pests and diseases. In Z. A. Siddiqui (Ed.), PGPR: biocontrol and biofertilization (pp. 257–296). Dordrecht: Springer.Google Scholar
  262. Nandakumar, R., Babu, S., Viswanathan, R., Raguchander, T., & Samiyappan, R. (2001). Induction of systemic resistance in rice against sheath blight disease by Pseudomonas fluorescens. Soil Biology and Biochemistry, 33, 603–612.CrossRefGoogle Scholar
  263. Nardi, S., Concheri, G., Pizzeghello, D., Sturaro, A., Rella, R., & Parvoli, G. (2000). Soil organic matter mobilization by root exudates. Chemosphere, 41, 653–658.PubMedCrossRefPubMedCentralGoogle Scholar
  264. Narula, N., Kothe, E., & Behl, R. K. (2009). Role of root exudates in plant-microbe interactions. Journal of Applied Botany and Food Quality Angewandte Botanik, 82, 122–130.Google Scholar
  265. Naseem, H., & Bano, A. (2014). Role of plant growth-promoting rhizobacteria and their exopolysaccharide in drought tolerance of maize. Journal of Plant Interactions, 9, 689–701.CrossRefGoogle Scholar
  266. Nautiyal, C. S., Srivastava, S., Chauhan, P. S., Seem, K., Mishra, A., & Sopory, S. K. (2013). Plant growth-promoting bacteria Bacillus amyloliquefaciens NBRISN13 modulates gene expression profile of leaf and rhizosphere community in rice during salt stress. Plant Physiology and Biochemistry, 66, 1–9. Scholar
  267. Nayak, S., Prasanna, R., Prasanna, B. M., & Sahoo, D. B. (2007). Analysing diversity among Indian isolates of Anabaena (Nostocales, Cyanophyta) using morphological, physiological and biochemical characters. World Journal of Microbiology and Biotechnology, 23, 1575–1584.CrossRefGoogle Scholar
  268. Negi, S., Ivanchenko, M. G., & Muday, G. K. (2008). Ethylene regulates lateral root formation and auxin transport in Arabidopsis thaliana. The Plant Journal, 55, 175–187.PubMedCrossRefPubMedCentralGoogle Scholar
  269. Negrao, S., Schmockel, S. M., & Tester, M. (2017). Evaluating physiological responses of plants to salinity stress. Annals of Botany, 119, 1–11.PubMedCrossRefPubMedCentralGoogle Scholar
  270. Neil, D. L., Romero, S., Kandula, J., Stark, C., Stewart, A., & Larsen, S. (2001). Bacteriophages: A potential biocontrol agent against walnut blight (Xanthomonas campestris pv. juglandis). New Zealand Plant Protection, 54, 220–224.CrossRefGoogle Scholar
  271. Newman, M. A., Sundelin, T., Nielsen, J. T., & Erbs, G. (2013). MAMP (microbe associated molecular pattern) triggered immunity in plants. Frontiers in Plant Science, 4, 139.PubMedCrossRefPubMedCentralGoogle Scholar
  272. Nguyen, D. D., et al. (2016). Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nature Microbiology, 2, 16197.PubMedCrossRefPubMedCentralGoogle Scholar
  273. Niu, B., Vater, J., Rueckert, C., Blom, J., Lehmann, M., Ru, J., Chen, X., Wang, Q., & Borriss, R. (2013). Polymyxin P is the active principle in suppressing phytopathogenic Erwinia spp. by the biocontrol rhizobacterium Paenibacillus polymyxa M-1. BMC Microbiology, 13, 137.PubMedCrossRefPubMedCentralGoogle Scholar
  274. Niu, S. Q., Li, H. R., Pare, P. W., Aziz, M., Wang, S. M., Shi, H. Z., et al. (2016). Induced growth promotion and higher salt tolerance in the halophyte grass Puccinellia tenuiflora by beneficial rhizobacteria. Plant and Soil, 407, 217–230. Scholar
  275. Noble, A. D., Ruaysoongern, S., Penning de Vries, F. W. T. et al. (2004) Enhancing the agronomic productivity of degraded soils in Northeast Thailand through clay-based interventions. In V. Seng, E. Craswell, S. Fukai, & K. Fischer (Eds.), Water and agriculture (Vol. 116, pp. 147–160, ACIAR Proceedings 2004). ACIAR, Canberra.Google Scholar
  276. Nowak, J., & Shulaev, V. (2003). Priming for transplant stress resistance in vitro propagation. In vitro Cellular and Developmental Biology—Plant, 39, 107–124.CrossRefGoogle Scholar
  277. O’Callaghan, M. (2016). Microbial inoculation of seed for improved crop performance: Issues and opportunities. Applied Microbiology and Biotechnology, (13), 5729–5746.PubMedCrossRefPubMedCentralGoogle Scholar
  278. Obradovic, A., Jones, J. B., Momel, M. T., & Olson, S. M. (2004). Management of tomato bacterial spot in the field by foliar applications of bacteriophages and SAR inducers. Plant Disease, 88, 736–740.PubMedCrossRefPubMedCentralGoogle Scholar
  279. Obradovic, A., Jones, J. B., Balogh, B., & Momol, M. T. (2008). Integrated management of tomato bacterial spot. In A. Ciancio & K. G. Mukerji (Eds.), Integrated management of disease caused by fungi, phytoplasma and bacteria (pp. 211–221). Dordrecht: Springer.CrossRefGoogle Scholar
  280. Oldroyd, G. E. (2013). Speak, friend, and enter: Signalling systems that promote beneficial symbiotic associations in plants. Nature Reviews. Microbiology, 11, 252–263. Scholar
  281. Ongena, M., Henry, G., Adam, A., Jourdan, E., & Thonart, P. (2009). Plant defense reactions stimulated following perception of Bacillus lipopeptides. In 8th International PGPR Workshop, USA, p. 43.Google Scholar
  282. Ovadis, M., Liu, X., Gavriel, S., Ismailov, Z., Chet, I., & Chernin, L. (2004). The global regulator genes from biocontrol strain Serratia plymuthica IC1270: Cloning, sequencing, and functional studies. Journal of Bacteriology, 186, 4986–4993.PubMedCrossRefPubMedCentralGoogle Scholar
  283. Park, C. S., Paulitz, T. C., & Baker, R. (1988). Biocontrol of Fusarium wilt of cucumber resulting from interactions between Pseudomonas putida and non pathogenic isolates of Fusarium oxysporum. Phytopathology, 78, 190–194.CrossRefGoogle Scholar
  284. Paul, M. J., Primavesi, L. F., Jhurreea, D., & Zhang, Y. (2008). Trehalose metabolism and signaling. Annual Review of Plant Biology, 59, 417–441.PubMedCrossRefPubMedCentralGoogle Scholar
  285. Peay, K. G., Bidartondo, M. I., & Arnold, A. E. (2010). Not every fungus is everywhere: Scaling to the biogeography of fungal–plant interactions across roots, shoots and ecosystems. New Phytologist, 185, 878–882.PubMedCrossRefPubMedCentralGoogle Scholar
  286. Peiffer, J. A., et al. (2013). Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences of the United States of America, 110, 6548–6553.PubMedCrossRefPubMedCentralGoogle Scholar
  287. Peret, B., De Rybel, B., Casimiro, I., Benkova, E., Swarup, R., Laplaze, L., Beeckman, T., & Bennett, M. J. (2009). Arabidopsis lateral root development: An emerging story. Trends in Plant Science, 14, 399–408.PubMedCrossRefPubMedCentralGoogle Scholar
  288. Pereyra, M. A., Zalazar, C. A., & Barassi, C. A. (2006). Root phospholipids in Azospirillum-inoculated wheat seedlings exposed to water stress. Plant Physiology and Biochemistry, 44, 873–879.PubMedCrossRefPubMedCentralGoogle Scholar
  289. Philippot, L., Raaijmakers, J. M., Lemanceau, P., & van der Putten, W. H. (2013). Going back to the roots: The microbial ecology of the rhizosphere. Nature Reviews. Microbiology, 11, 789–799.PubMedCrossRefPubMedCentralGoogle Scholar
  290. Pieterse, C. M. J., Van Wees, S. C. M., Hoffland, E., Vanpelt, J. A., & Vanloon, L. C. (1996). Systemic resistance in Arabidopsis induced by biocontrol bacteria is independent of salicylic acid accumulation and pathogenesis-related gene expression. Plant Cell, 8, 1225–1237.PubMedPubMedCentralGoogle Scholar
  291. Pieterse, C. M., Van Wees, S. C. M., van Pelt, J. A., Knoester, M., Lann, R., Gerrits, H., Weisbeek, P. J., & van Loon, L. C. (1998). A novel signaling pathway controlling induced systemic resistance in Arabidopsis. Plant Cell, 10, 1571–1580.PubMedCrossRefPubMedCentralGoogle Scholar
  292. Pietrangelo, A. (2002). Mechanism of iron toxicity. In C. Hershko (Ed.), Iron chelation theraphy (Vol. 509, 1st ed., pp. 19–43). New York: Kluwer Academic/Plenum Publishers.CrossRefGoogle Scholar
  293. Pii, Y., Mimmo, T., Tomasi, N., Terzano, R., Cesco, S., & Crecchio, C. (2015). Microbial interactions in the rhizosphere: Beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process- a review. Biology and Fertility of Soils, 51, 403–415.CrossRefGoogle Scholar
  294. Pinedo, I., Ledger, T., Greve, M., & Poupin, M. J. (2015). Burkholderia phytofirmans PsJN induces long-term metabolic and transcriptional changes involved in Arabidopsis thaliana salt tolerance. Frontiers in Plant Science, 6, 466. Scholar
  295. Powell, P. E., Cline, G. R., Reid, C. P. P., & Szaniszlo, P. J. (1980). Occurrence of hydroxamate siderophore iron chelators in soils. Nature, 287, 833–834.CrossRefGoogle Scholar
  296. Pradhan, D., Mishra, D., Kim, D. J., Jong, G. A., Chaudhury, G. R., & Lee, S. W. (2010). Bioleaching kinetics and multivariate analysis of spent petroleum catalyst dissolution using two acidophiles. Journal of Hazardous Materials, 175, 267–273.PubMedCrossRefPubMedCentralGoogle Scholar
  297. Press, C. M., Wilson, M., Tuzun, S., & Kloepper, J. W. (1997). Salicylic acid produced by Serratia marcescens 90-166 is not the primary determinant of induced systemic resistance in cucumber or tobacco. Molecular Plant-Microbe Interactions, 10, 761–768.CrossRefGoogle Scholar
  298. Provorov, N. A., & Tikhonovich, I. A. (2003). Genetic resources for improving nitrogen fixation in legume–rhizobia symbiosis. Genetic Resources and Crop Evolution, 50, 89–99.CrossRefGoogle Scholar
  299. Provorov, N. A., Saimnazarov, U. B., Bahromov, I. U., Pulatova, D. Z., Kozhemyakov, A. P., & Kurbanov, G. A. (1998). Effect of rhizobia inoculation on the seed (herbage) production of mungbean (Phaseolus aureus Roxb.) grown at Uzbekistan. Journal of Arid Environments, 39, 569–575.CrossRefGoogle Scholar
  300. Qurashi, A. W., & Sabri, A. N. (2012). Bacterial exopolysaccharide and biofilm formation stimulate chickpea growth and soil aggregation under salt stress. Brazilian Journal of Microbiology, 43, 1183–1191.PubMedCrossRefPubMedCentralGoogle Scholar
  301. Ramamoorthy, V., & Samiyappan, R. (2001). Induction of defence related genes in Pseudomonas fluorescens treated chilli plants in response to infection by Colletotrichum capsici. Journal of Mycology and Plant Pathology, 31, 146–155.Google Scholar
  302. Ravel, J., & Cornelis, P. (2003). Genomics of pyoverdine-mediated iron uptake in pseudomonads. Trends in Microbiology, 11, 195–200.PubMedCrossRefPubMedCentralGoogle Scholar
  303. Ravensdale, M., Blom, T. J., Gracia-Garza, J. A., Svircev, A. M., & Smith, R. J. (2007). Bacteriophages and the control of Erwinia carotovora subsp. carotovora. Canadian Journal of Plant Pathology, 29, 121–130.CrossRefGoogle Scholar
  304. Reddy, N., & Yang, Y. (2005). Biofibers from agricultural byproducts for industrial applications. Trends Biotechnology, 23, 22–27.CrossRefGoogle Scholar
  305. Reddy, G., Pradhan, S., Manorama, R., & Shivaji, S. (2010). Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil. International Journal of Systematic and Evolutionary Microbiology, 60(4), 866–870.PubMedCrossRefPubMedCentralGoogle Scholar
  306. Reguera, M., Peleg, Z., & Blumwald, E. (2012). Targeting metabolic pathways for genetic engineering abiotic stress-tolerance in crops. Biochimica et Biophysica Acta, 1819, 186–194.PubMedCrossRefPubMedCentralGoogle Scholar
  307. Rivero, R. M., Kojima, M., Gepstein, A., Sakakibara, H., Mittler, R., Gepstein, S., & Blumwald, E. (2007). Delayed leaf senescence induces extreme drought tolerance in a flowering plant. Proceedings of the National Academy of Sciences of the United States of America, 104, 19631–19636.PubMedCrossRefPubMedCentralGoogle Scholar
  308. Roberson, E. B., & Firestone, M. K. (1992). Relationship between desiccation and exopolysaccharide production in soil Pseudomonas sp. Applied and Environmental Microbiology, 58, 1284–1291.PubMedPubMedCentralGoogle Scholar
  309. Rodriguez, S. J., Suarez, R., Caballero, M. J., & Itturiaga, G. (2009). Trehalose accumulation in Azospirillum brasilense improves drought tolerance and biomass in maize plants. FEMS Microbiology Letters, 296, 52–59.CrossRefGoogle Scholar
  310. Rojas-Tapias, D., Moreno-Galván, A., Pardo-Díaz, S., Obando, M., Rivera, D., & Bonilla, R. (2012). Effect of inoculation with plant growth-promoting bacteria (PGPB) on amelioration of saline stress in maize (Zea mays). Applied Soil Ecology, 61, 264–272.CrossRefGoogle Scholar
  311. Rolli, E., Marasco, R., Vigani, G., Ettoumi, B., Mapelli, F., Deangelis, M. L., Gandolfi, C., Casati, E., Previtali, F., Gerbino, R., Pierotti Cei, F., Borin, S., Sorlini, C., Zocchi, G., & Daffonchio, D. (2015). Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait. Environmental Microbiology, 17, 316–331.PubMedCrossRefPubMedCentralGoogle Scholar
  312. Ruggiero, C. E., Neu, M. P., Matonic, J. H., & Reilly, S. D. (2000). Interactions of Pu with desferrioxamine siderophores can affect bioavailability and mobility. Actinide Research Quarterly, 2000, 16–18.Google Scholar
  313. Ryan, P. R., Delhaize, E., & Jones, D. L. (2001). Function and mechanism of organic anion exudation from plant roots. Annual Review of Plant Physiology and Plant Molecular Biology, 52, 527–560.PubMedCrossRefPubMedCentralGoogle Scholar
  314. Ryan, R. P., Germaine, K., Franks, A., Ryan, D. J., & Dowling, D. N. (2008). Bacterial endophytes: Recent developments and applications. FEMS Microbiology Letters, 278, 1–9.PubMedCrossRefPubMedCentralGoogle Scholar
  315. Ryan, P. R., Dessaux, Y., Thomashow, L. S., & Weller, D. M. (2009a). Rhizosphere engineering and management for sustainable agriculture. Plant and Soil, 321, 363–383.CrossRefGoogle Scholar
  316. Ryan, P. R., Dessaux, Y., Thomashow, L. S., & Weller, D. M. (2009b). Rhizosphere engineering and management for sustainable agriculture. Plant and Soil, 321, 363–383.CrossRefGoogle Scholar
  317. Ryu, C. M., Farag, M. A., Hu, C. H., Reddy, M. S., Kloepper, J. W., & Pare, P. W. (2004a). Bacterial volatiles induce systemic resistance in Arabidopsis. Plant Physiology, 134, 1017–1026.PubMedCrossRefPubMedCentralGoogle Scholar
  318. Ryu, C. M., Murphy, J. F., Mysore, K. S., & Kloepper, J. W. (2004b). Plant growth-promoting rhizobacterial systemically protect Arabidopsis thaliana against cucumber mosaic virus by a salicylic acid and NPR1- independent and jasmonic acid-dependent signaling pathway. The Plant Journal, 39, 381–392.PubMedCrossRefPubMedCentralGoogle Scholar
  319. Saleem, M., Arshad, M., Hussain, S., & Bhatti, A. S. (2007). Perspective of plant growth promoting rhizobacteria (PGPR) containing ACC deaminase in stress agriculture. Journal of Industrial Microbiology & Biotechnology, 34, 635–648.CrossRefGoogle Scholar
  320. Saleh, S. S., & Glick, B. R. (2001). Involvement of gacS and rpoS in enhancement of the plant growth-promoting capabilities of Enterobacter cloacae CAL2 and Pseudomonas putida UW4. Canadian Journal of Microbiology, 47, 698–705.PubMedCrossRefPubMedCentralGoogle Scholar
  321. Sandhya, V., Ali, S. Z., Grover, M., Reddy, G., & Venkateswarlu, B. (2009). Alleviation of drought stress effects in sunflower seedlings by the exopolysaccharides producing Pseudomonas putida strain GAP-P45. Biology and Fertility of Soils, 46, 17–26.CrossRefGoogle Scholar
  322. Sandhya, V., Ali, S. Z., Grover, M., Reddy, G., & Venkateswaralu, B. (2010). Effect of plant growth promoting Pseudomonas spp. on compatible solutes antioxidant status and plant growth of maize under drought stress. Plant Growth Regulation, 62, 21–30.Google Scholar
  323. Sang-Mo, K., Radhakrishnan, R., Khan, A. L., Min-Ji, K., Jae-Man, P., Bo-Ra, K., Dong-Hyun, S., & In-Jung, L. (2014). Gibberellin secreting rhizobacterium, Pseudomonas putida H-2-3 modulates the hormonal and stress physiology of soybean to improve the plant growth under saline and drought conditions. Plant Physiology and Biochemistry, 84, 115–124.CrossRefGoogle Scholar
  324. Saxena, A. K., Yadav, A. N., Rajawat, M. V. S., Kaushik, R., Kumar, R., et al. (2016). Microbial diversity of extreme regions: An unseen heritage and wealth. Indian Journal of Plant Genetics Resources, 29(3), 246–248.CrossRefGoogle Scholar
  325. Schnabel, E. L., & Jones, A. L. (2001). Isolation and characterization of five Erwinia amylovora bacteriophages and assessment of phage resistance in strains of Erwinia amylovora. Applied and Environmental Microbiology, 67(1), 59–64.PubMedCrossRefPubMedCentralGoogle Scholar
  326. Seaton, S. C., & Silby, M. W. (2014). Genetics and functional genomics of the Pseudomonas fluorescens group. Genomics of Plant Associated Bacteria, ed al (pp. 99–125). DCGe. Berlin/Heidelberg: Springer.Google Scholar
  327. Selvakumar, G., Panneerselvam, P., & Ganeshamurthy, A. N. (2012). Bacterial mediated alleviation of abiotic stress in crops. In D. K. Maheshwari (Ed.), Bacteria in agrobiology: Stress management (pp. 205–224). Berlin/Heidelberg: Springer.CrossRefGoogle Scholar
  328. Sessitsch, A., Reiter, B., & Berg, G. (2004). Endophytic bacterial communities of field-grown potato plants and their plant growth-promoting and antagonistic abilities. Canadian Journal of Microbiology, 50, 239–249.PubMedCrossRefPubMedCentralGoogle Scholar
  329. Shakir, M. A., Asghari, B., & Arshad, M. (2012). Rhizosphere bacteria containing ACC deaminase conferred drought tolerance in wheat grown under semi-arid climate. Soil Environment, 31, 108–112.Google Scholar
  330. Shao, H. B., Chu, L. Y., Jaleel, C. A., Manivannan, P., Panneerselvam, R., & Shao, M. A. (2009). Understanding water deficit stress-induced changes in the basic metabolism of higher plants - biotechnologically and sustainably improving agriculture and the ecoenvironment in arid regions of the globe. Critical Reviews in Biotechnology, 29, 131–151.PubMedCrossRefPubMedCentralGoogle Scholar
  331. Shen, L., Liu, Y., Gu, Z., Xu, B., Wang, N., et al. (2015). Massilia eurypsychrophila sp. nov. a facultatively psychrophilic bacteria isolated from ice core. International Journal of Systematic and Evolutionary Microbiology, 65(7), 2124–2129.PubMedCrossRefPubMedCentralGoogle Scholar
  332. Shintu, P. V., & Jayaram, K. M. (2015). Phosphate solubilising bacteria (Bacillus polymyxa) - an effective approach to mitigate drought in tomato (Lycopersicon esculentum Mill.). Tropical Plant Research, 2, 17–22.Google Scholar
  333. Shinwari, K. I., Shah, A. U., Afridi, M. I., Zeeshan, M., Hussain, H., Hussain, J., & Ahmad, O. (2015). Application of plant growth promoting rhizobacteria in bioremediation of heavy metal polluted soil. Asian Journal of Multidisciplinary Studies, 3, 179–185.Google Scholar
  334. Shivaji, S., Ray, M., Rao, N. S., Saisree, L., Jagannadham, M., et al. (1992). Sphingobacterium antarcticus sp. nov., a psychrotrophic bacterium from the soils of Schirmacher oasis, Antarctica. International Journal of Systematic and Evolutionary Microbiology, 42(1), 102–106.Google Scholar
  335. Shtark, O. Y., Borisov, A. Y., Zhukov, V. A., Provorov, N. A., & Tikhonovich, I. A. (2010). Intimate associations of beneficial soil microbes with host plants. In R. Dixon & E. Tilston (Eds.), Soil microbiology and sustainable crop production (pp. 119–196). Berlin/Heidelberg: Springer.CrossRefGoogle Scholar
  336. Shukla, P. S., Agarwal, P. K., & Jha, B. (2012). Improved salinity tolerance of Arachis hypogaea (L.) by the interaction of Halotolerant plant-growth-promoting Rhizobacteria. Journal of Plant Growth Regulation, 31, 195–206.CrossRefGoogle Scholar
  337. Shunmugam, S., Hinttala, R., Lehtimäki, N., Mittinen, M., Uusimaa, J., Majamma, K., Sivonen, K., et al. (2013). Nodularia spumigena extract induces upregulation of mitochondrial respiratory chain complexes in spinach (Spinacia oleracea L.). Acta Physiologiae Plantarum, 35, 969–974.CrossRefGoogle Scholar
  338. Shunmugam, S., Jokela, J., Wahlsten, M., Battchikova, N., Rehman, A. U., Vass, I., Karonen, M., et al. (2014). Secondary metabolite from Nostoc XPORK14A inhibits photosynthesis and growth of Synechocystis PCC 6803. Plant, Cell and Environment, 37, 1371–1381.PubMedCrossRefPubMedCentralGoogle Scholar
  339. Singh, S., & Kapoor, K. K. (1999). Inoculation with phosphate-solubilizing microorganisms and a vesicular-arbuscular mycorrhizal fungus improves dry matter yield and nutrient uptake by wheat grown in a sandy soil. Biology and Fertility of Soils, 28(2), 139–144.CrossRefGoogle Scholar
  340. Sizer, F., & Whitney, E. (2007). Nutrition: Concepts and controversies. Cengage Learning, 26.Google Scholar
  341. Somerville, C., & Briscoe, L. (2001). Genetic engineering and water. Science, 292, 2217–2217.PubMedCrossRefPubMedCentralGoogle Scholar
  342. Spaepen, S., & Vanderleyden, J. (2011a). Auxin and plant-microbe interactions. Cold Spring Harbor Perspectives in Biology, 3(4), a001438.PubMedCrossRefPubMedCentralGoogle Scholar
  343. Spaepen, S., & Vanderleyden, J. (2011b). Auxin and plant-microbe interactions. Cold Spring Harbor Perspectives in Biology, 3, a001438. Scholar
  344. Spaepen, S., Vanderleyden, J., & Remans, R. (2007). Indole- 3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiology Reviews, 31, 425–448.PubMedCrossRefPubMedCentralGoogle Scholar
  345. Stevenson, J. R., Villoria, N., Byerlee, D., Kelley, T., & Maredia, M. (2013). Green revolution research saved an estimated 18 to 27 million hectares from being brought into agricultural production. Proceedings of the National Academy of Sciences of the United States of America, 110, 8363–8368.PubMedCrossRefPubMedCentralGoogle Scholar
  346. Stockwell, V. O., Johnson, K. B., Sugar, D., & Loper, J. E. (2010). Control of fire blight by Pseudomonas fluorescens A506 and Pantoea vagans C9-1 applied as single strains and mixed inocula. Phytopathology, 100, 1330–1339.PubMedCrossRefPubMedCentralGoogle Scholar
  347. Suarez, R., Wong, A., Ramirez, M., Barraza, A., OrozcoMdel, C., Cevallos, M. A., et al. (2008). Improvement of drought tolerance and grain yield in common bean by over expressing trehalose-6-phosphate synthase in rhizobia. Molecular Plant-Microbe Interactions, 21, 958–966.PubMedCrossRefPubMedCentralGoogle Scholar
  348. Subramanian, K. S., & Tarafdar, J. C. (2011). Prospects of nanotechnology in Indian farming. Indian Journal of Agricultural Sciences, 8, 887–893.Google Scholar
  349. Subramanian, S., Ricci, E., Souleimanov, A., & Smith, D. L. (2016a). A proteomic approach to lipo-chitooligosaccharide and thuricin 17 effects on soybean germinationunstressed and salt stress. PLoS One, 11, e0160660. Scholar
  350. Subramanian, S., Souleimanov, A., & Smith, D. L. (2016b). Proteomic studies on the effects of lipo-chitooligosaccharide and thuricin 17 under unstressed and salt stressed conditions in Arabidopsis thaliana. Frontiers in Plant Science, 7, 1314. Scholar
  351. Sueldo, R. J., Invernati, A., Plaza, S. G., & Barassi, C. A. (1996). Osmotic stress in wheat seedlings: Effects on fatty acid composition and phospholipid turnover in coleoptiles. Cereal Research Communications, 24, 77–84.Google Scholar
  352. Sulakvelidze, A., & Barrow, P. (2005). Phage therapy in animals and agribusiness, in bacteriophages: Biology and applications. In E. Kutter & A. Sulakvelidze (Eds.), Bacteriophage: Biology and applications (pp. 335–380). Boca Raton: CRC Press.Google Scholar
  353. Summers, W. C. (2001). Bacteriophage therapy. Annual Reviews Microbiology, 55, 437–451.CrossRefGoogle Scholar
  354. Sun, H., Tao, J., Gu, P., Xu, G., & Zhang, Y. (2016). The role of strigolactones in root development. Plant Signaling & Behavior, 11(1).Google Scholar
  355. Swarup, R., Perry, P., Hagenbeek, D., Van Der Straeten, D., Beemster, G. T. S., Sandberg, G., Bhalerao, R., Ljung, K., & Bennett, M. J. (2007). Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation. Plant Cell, 19, 2186–2196.PubMedCrossRefPubMedCentralGoogle Scholar
  356. Tak, H. I., Ahmad, F., & Babalola, O. O. (2013). Advances in the application of plant GrowthPromoting Rhizobacteria in phytoremediation of heavy metals. Reviews of Environmental Contamination and Toxicology, 223(223), 33–52.PubMedGoogle Scholar
  357. Tank, N., & Saraf, M. (2010). Salinity-resistant plant growth promoting rhizobacteria ameliorates sodium chloride stress on tomato plants. Journal of Plant Interactions, 5, 51–58.CrossRefGoogle Scholar
  358. Teale, W. D., Paponov, I. A., & Palme, K. (2006). Auxin in action: Signalling, transport and the control of plant growth and development. Nature Reviews. Molecular Cell Biology, 7, 847–859. Scholar
  359. Thiel, T., & Pratte, B. (2001). Effect on heterocyst differentiation of nitrogen fixation in vegetative cells of the cyanobacterium Anabaena variabilis ATCC 29413. Journal of Bacteriology, 183, 280–286.PubMedCrossRefPubMedCentralGoogle Scholar
  360. Thomas, C. A. (1965). Effect of photoperiod and nitrogen on reaction of sesame to pseudomonas sesame and Xanthomonas sesami. Plant Disease Report, 49, 119–120.Google Scholar
  361. Timmusk, S., & Wagner, E. G. (1999). The plant-growth-promoting rhizobacterium Paenibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: A possible connection between biotic and abiotic stress responses. Molecular Plant-Microbe Interactions, 12, 951.PubMedCrossRefPubMedCentralGoogle Scholar
  362. Timmusk, S., Islam, A., Abd El, D., Lucian, C., Tanilas, T., Ka nnaste, A., et al. (2014). Drought-tolerance of wheat improved by rhizosphere bacteria from harsh environments: Enhanced biomass production and reduced emissions of stress volatiles. PLoS One, 9, 1–13.CrossRefGoogle Scholar
  363. Upadhyay, S. K., Singh, J. S., Saxena, A. K., & Singh, D. P. (2011a). Impact of PGPR inoculation on growth and antioxidant status of wheat under saline conditions. Plant Biology, 14, 605–611.PubMedCrossRefPubMedCentralGoogle Scholar
  364. Upadhyay, S. K., Singh, J. S., & Singh, D. P. (2011b). Exopolysaccharide-producing plant growth-promoting rhizobacteria under salinity condition. Pedosphere, 21, 214–222. Scholar
  365. Vaishnav, A., Kumari, S., Jain, S., Varma, A., & Choudhary, D. K. (2015a). Putative bacterial volatile-mediated growth in soybean (Glycine max L. Merrill) and expression of induced proteins under salt stress. Journal of Applied Microbiology, 119, 539–551. Scholar
  366. Vaishnav, A., Kumari, S., Jain, S., Varma, A., & Choudhary, D. K. (2015b). Putative bacterial volatile-mediated growth in soybean (Glycine max L. Merrill) and expression of induced proteins under salt stress. Journal of Applied Microbiology, 119, 539–551.PubMedCrossRefPubMedCentralGoogle Scholar
  367. Van Loon, C. (1997). Induced resistance in plants and the role of pathogenesis related proteins. European Journal of Plant Pathology, 103, 753–765.CrossRefGoogle Scholar
  368. Van Loon, L. C., Bakker, P. A. H., & Pieterse, C. M. J. (1998). Systemic resistance induced by rhizosphere bacteria. Annual Review of Phytopathology, 36, 453–483.PubMedCrossRefPubMedCentralGoogle Scholar
  369. Van Maris, A. J., Winkler, A. A., Kuyper, M., de Laat, W. T., van Dijken, J. P., & Pronk, J. T. (2007). Development of efficient xylose fermentation in Saccharomyces cerevisiae: Xylose isomerase as a key component. Advances in Biochemical Engineering/Biotechnology, 108, 179–204.Google Scholar
  370. Van Peer, R., Niemann, G. J., & Schippers, B. (1991). Induced resistance and phytoalexin accumulation in biological control of Fusarium wilt of carnation by Pseudomonas sp. strain WCS417r. Phytopathology, 81, 728–734.CrossRefGoogle Scholar
  371. Van Trappen, S., Vandecandelaere, I., Mergaert, J., & Swings, J. (2005). Flavobacterium fryxellicola sp. nov. and Flavobacterium psychrolimnae sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes. International Journal of Systematic and Evolutionary Microbiology, 55(2), 769–772.PubMedCrossRefPubMedCentralGoogle Scholar
  372. Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A., & Dufresne, A. (2015). The importance of the microbiome of the plant holobiont. New Phytologist, 206, 1196–1206.PubMedCrossRefPubMedCentralGoogle Scholar
  373. Vanni, M. (2002). Nutrient cycling by animals in freshwater ecosystems. Annual Review of Ecology and Systematics, 33, 341–370.CrossRefGoogle Scholar
  374. Vardharajula, S., Zulfikar Ali, S., Grover, M., Reddy, G., & Bandi, V. (2011). Drought-tolerant plant growth promoting Bacillus spp., effect on growth, osmolytes, and antioxidant status of maize under drought stress. Journal of Plant Interactions, 6, 1–14.CrossRefGoogle Scholar
  375. Vargas, L., Santa Brigida, A. B., Mota Filho, J. P., de Carvalho, T. G., Rojas, C. A., et al. (2014). Drought tolerance conferred to sugarcane by association with gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways. PLoS ONE, 9(12), e114744. eCollection.CrossRefPubMedPubMedCentralGoogle Scholar
  376. Venturi, V., & Fuqua, C. (2013). Chemical signaling between plants and plant-pathogenic bacteria. Annual Review of Phytopathology, 51, 17–37.PubMedCrossRefPubMedCentralGoogle Scholar
  377. Verma, P., Yadav, A. N., Khannam, K. S., Panjiar, N., Kumar, S., et al. (2015). Assessment of genetic diversity and plant growth promoting attributes of psychrotolerant bacteria allied with wheat (Triticum aestivum) from the northern hills zone of India. Annales de Microbiologie, 65(4), 1885–1899.CrossRefGoogle Scholar
  378. Verslues, P. E. (2017). Time to grow: Factors that control plant growth during mild to moderate drought stress. Plant Cell and Environment, 40, 177–179.CrossRefGoogle Scholar
  379. Vértesy, L., Aretz, W., Fehlhaber, H. W., & Kogler, H. (1995). Salimycin A-D, Antibiotoka aus Streptomyces violaveus, DSM 8286, mit Siderophor- Aminoglycosid-Struktur. Helvetica Chimica Acta, 78, 46–60.CrossRefGoogle Scholar
  380. Vessey, J. K. (2003). Plant growth-promoting rhizobacteria as biofertilizers. Plant and Soil, 255, 571–586.CrossRefGoogle Scholar
  381. Vidhyasekaran, P., Kamala, N., Ramanathan, A., Rajappan, K., Paranidharan, V., & Velazhahan, R. (2001). Induction of systemic resistance by Pseudomonas fluorescens Pf1 against Xanthomonas oryzae pv. oryzae in rice leaves. Phytoparasitica, 29(2), 155–166.CrossRefGoogle Scholar
  382. Viikari, L., Alapuranen, M., Puranen, T., Vehmaanpera, J., & Siika-Aho, M. (2007). Thermostable enzymes in lignocellulose hydrolysis. Advances in Biochemical Engineering/Biotechnology, 108, 121–145.PubMedCrossRefPubMedCentralGoogle Scholar
  383. Viswanathan, R., & Samiyappan, R. (1999). Induction of systemic resistance by plant growth-promoting rhizobacteria against red rot disease caused by Colletotrichum falcatum went in sugarcane. In Proceedings of the Sugar Technology Association of India (Vol. 61, pp. 24–39). New Delhi: Sugar Technology Association.Google Scholar
  384. Vivekananthana, R., Ravia, M., SaravanaKumara, D., Kumarb, N., Prakasama, V., & Samiyappan, R. (2004). Microbially induced defense related proteins against postharvest anthracnose infection in mango. Crop Protection, 23, 1061–1067.CrossRefGoogle Scholar
  385. Vurukonda, S. S. K. P., Vardharajula, S., Shrivastava, M., & SkZ, A. (2016). Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria. Microbiological Research, 184, 13–24.PubMedCrossRefPubMedCentralGoogle Scholar
  386. Walters, D. R., Ratsep, J., & Havis, N. D. (2013). Controlling crop diseases using induced resistance: Challenges for the future. Journal of Experimental Botany, 64, 1263–1280.PubMedCrossRefPubMedCentralGoogle Scholar
  387. Wang, H. R., Wang, M. Z., & Yu, L. H. (2009a). Effects of dietary protein sources on the rumen microorganisms and fermentation of goats. Journal of Animal and Veterinary Advances, 7, 1392–1401.Google Scholar
  388. Wang, Z., Gerstein, M., & Snyder, M. (2009b). RNA-Seq: A evolutionary tool for transcriptomics. Nature Reviews. Genetics, 10, 57–63.PubMedCrossRefPubMedCentralGoogle Scholar
  389. Wang, C. J., Yang, W., Wang, C., Gu, C., Niu, D. D., Liu, H. X., et al. (2012). Induction of drought tolerance in cucumber plants by a consortium of three plant growth-promoting Rhizobacterium strains. PLoS One, 7, 1–10.Google Scholar
  390. Wei, G., Kloepper, J. W., & Tuzun, S. (1996). Induced systemic resistance to cucumber diseases and increased plant growth by plant growth-promoting rhizobacteria under field conditions. Phytopathology, 86, 221–224.CrossRefGoogle Scholar
  391. Weisbeek, P. J., Van der Hofstad, G. A. J. M., Schippers, B., & Marugg, J. D. (1986). Genetic analysis of the iron uptake system of two plant growth promoting Pseudomonas strains. NATO ASI Series A, 117, 299–313.Google Scholar
  392. Weller, D. M. (1988). Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annual Review of Phytopathology, 26, 379–407.CrossRefGoogle Scholar
  393. Werner, D. (2005). Production and biological nitrogen fixation of tropical legumes. In Nitrogen fixation in agriculture, forestry, ecology, and the environment (pp. 1–13). Springer.Google Scholar
  394. Weyens, N., Beckers, B., Schellingen, K., Ceulemans, R., Van der Lelie, D., Newman, L., et al. (2015). The potential of the Ni-resistant TCE-degrading Pseudomonas putida W619-TCE to reduce phytotoxicity and improve phytoremediation efficiency of poplar cuttings on a Ni-TCE Co-contamination. International Journal of Phytoremediation, 17, 40–48. Scholar
  395. Whilmotte, A. (1994). Molecular evolution and taxonomy of the cyanobacteria. In D. A. Bryant (Ed.), The molecular biology of cyanobacteria (pp. 1–25). Dordrecht: Kluwer Academic Publishers.Google Scholar
  396. Whipps, J. M. (2001). Microbial interactions and biocontrol in the rhizosphere. Journal of Experimental Botany, 52(1), 487–511.PubMedCrossRefPubMedCentralGoogle Scholar
  397. Whitehead, N. A., Barnard, A., Slater, M. L., Simpson, H. N. J. L., & Salmond, G. P. C. (2001). Quorum-sensing in Gram-negative bacteria. FEMS Microbiology Reviews, 25, 365–404.PubMedCrossRefPubMedCentralGoogle Scholar
  398. Wintermans, P. C., Bakker, P. A., & Pieterse, C. M. (2016). Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria. Plant Molecular Biology, 90, 623–634. Scholar
  399. Wiszniewska, A., Hanus-Fajerska, E., Grabski, K., & Tukaj, Z. (2013). Promoting effects of organic medium supplements on the micropropagation of promising ornamental Daphne species (Thymelaeaceae). In Vitro Cellular and Developmental Biology-Plant, 49, 51–59.CrossRefGoogle Scholar
  400. Xiong, L., Wang, R.-G., Mao, G., & Koczan, J. M. (2006). Identification of drought tolerance determinants by genetic analysis of root response to drought stress and abscisic acid. Plant Physiology, 142, 1065–1074.PubMedCrossRefPubMedCentralGoogle Scholar
  401. Yadav, A. N. (2015). Bacterial diversity of cold deserts and mining of genes for low temperature tolerance. Ph.D Thesis- IARI, New Delhi, India, p. 234.Google Scholar
  402. Yadav, A. N., Sachan, S. G., Verma, P., & Saxena, A. K. (2015a). Prospecting cold deserts of north western Himalayas for microbial diversity and plant growth promoting attributes. Journal of Bioscience and Bioengineering, 119(6), 683–693.PubMedCrossRefPubMedCentralGoogle Scholar
  403. Yadav, A. N., Sachan, S. G., Verma, P., Tyagi, S. P., Kaushik, R., et al. (2015b). Culturable diversity and functional annotation of psychrotrophic bacteria from cold desert of Leh Ladakh (India). World Journal of Microbiology and Biotechnology, 31(1), 95–108.PubMedCrossRefPubMedCentralGoogle Scholar
  404. Yakimov, M. M., Giuliano, L., Gentile, G., Crisafi, E., Chernikova, T. N., et al. (2003). Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water. International Journal of Systematic and Evolutionary Microbiology, 53(3), 779–785.PubMedCrossRefPubMedCentralGoogle Scholar
  405. Yang, H., Knapp, J., Koirala, P., Rajagopal, D., Peer, W. A., Silbart, L. K., Murphy, A., & Gaxiola, R. A. (2007). Enhanced phosphorus nutrition in monocots and dicots overexpressing a phosphorus-responsive type IH+-pyrophosphatase. Plant Biotechnology Journal, 5, 735–745.PubMedCrossRefPubMedCentralGoogle Scholar
  406. Yang, J., Kloepper, J. W., & Ryu, C. M. (2009a). Rhizosphere bacteria help plants tolerate abiotic stress. Trends in Plant Science, 14, 1–4.PubMedCrossRefPubMedCentralGoogle Scholar
  407. Yang, J., Kloepper, J. W., & Ryu, C. M. (2009b). Rhizosphere bacteria help plants tolerate abiotic stress. Trends in Plant Science, 14, 1–4. Scholar
  408. Yang, S., Vanderbeld, B., Wan, J., & Huang, Y. (2010). Narrowing down the targets, towards successful genetic engineering of drought-tolerant crops. Molecular Plant, 3, 469–490.PubMedCrossRefPubMedCentralGoogle Scholar
  409. Yang, M. M., et al. (2011). Biological control of take-all by fluorescent Pseudomonas spp. from Chinese wheat fields. Phytopathology, 101, 1481–1491.PubMedCrossRefPubMedCentralGoogle Scholar
  410. Yao, L. X., Wu, Z. S., Zheng, Y. Y., Kaleem, I., & Li, C. (2010). Growth promotion and protection against salt stress by Pseudomonas putida Rs-198 on cotton. European Journal of Soil Biology, 46, 49–54. Scholar
  411. Yin, H. F., Chen, C. J., Yang, J., Weston, D. J., Chen, J. G., Muchero, W., Ye, N., Tschaplinski, T. J., Wullschleger, S. D., Cheng, Z. M., Tuskan, G. A., & Yang, X. H. (2014). Functional genomics of drought tolerance in bioenergy crops. Critical Reviews in Plant Sciences, 33, 205–224.CrossRefGoogle Scholar
  412. Yuwono, T., Handayani, D., & Soedarsono, J. (2005). The role of osmotolerant rhizobacteria in rice growth under different drought conditions. Australian Journal of Agricultural Research, 56, 715–721.CrossRefGoogle Scholar
  413. Zaccardelli, M., Saccardi, A., Gambin, E., & Mazzuchi, U. (1992). Xanthomonas campestris pv. Pruni bacteriophages on peach trees and their potential use for biological control. Phytopathol. Méditerranée, 31, 133–140.Google Scholar
  414. Zachariah, S., Kumari, P., & Das, S. K. (2016). Psychrobacter pocilloporae sp. nov., isolated from a coral, Pocillopora eydouxi. International Journal of Systematic and Evolutionary Microbiology, 66(12), 5091–5098.PubMedCrossRefPubMedCentralGoogle Scholar
  415. Zahir, Z. A., Munir, A., Asghar, H. N., Shaharoona, B., & Arshad, M. (2008). Effectiveness of rhizobacteria containing ACC-deaminase for growth promotion of pea (Pisum sativum) under drought conditions. Journal of Microbiology and Biotechnology, 18, 958–963.PubMedPubMedCentralGoogle Scholar
  416. Zahran, H. H. (1999). Rhizobium-legume symbiosis and nitrogen fixation under severe conditions and in an arid climate. Microbiology and Molecular Biology Reviews, 63, 968–989.PubMedPubMedCentralGoogle Scholar
  417. Zahran, H. H. (2001). Rhizobia from wild legumes: Diversity, taxonomy, ecology, nitrogen fixation and biotechnology. Journal of Biotechnology, 91, 143–153.PubMedCrossRefPubMedCentralGoogle Scholar
  418. Zaidi, A., Khan, M. S., Ahemad, M., & Oves, M. (2009). Plant growth promotion by phosphate solubilizing bacteria. Acta Microbiologica et Immunologica Hungarica, 56, 263–284.PubMedCrossRefPubMedCentralGoogle Scholar
  419. Zhang, H., Kim, M. S., Sun, Y., Dowd, S. E., Shi, H., & Paré, P. W. (2008). Soil bacteria confer plant salt tolerance by tissue-specific regulation of the sodium transporter HKT1. Molecular Plant-Microbe Interactions, 21, 737–744. Scholar
  420. Zhang, H., Murzello, C., Sun, Y., Kim, M. S., Xie, X., Jeter, R. M., Zak, J. C., Dowd, S. E., & Pare, P. W. (2010a). Choline and osmotic-stress tolerance induced in Arabidopsis by the soil microbe bacillus subtilis (GB03). Molecular Plant-Microbe Interactions, 23, 1097–1104.PubMedCrossRefPubMedCentralGoogle Scholar
  421. Zhang, H. M., Murzello, C., Sun, Y., Kim, M. S., Xie, X. T., Jeter, R. M., Zak, J. C., Dowd, S. E., & Pare, P. W. (2010b). Choline and osmotic-stress tolerance induced in arabidopsis by the soil microbe Bacillus subtilis (GB03). Molecular Plant-Microbe Interactions, 23, 1097–1104.PubMedCrossRefPubMedCentralGoogle Scholar
  422. Zhang, D. C., Busse, H. J., Liu, H. C., Zhou, Y. G., Schinner, F., et al. (2011). Sphingomonas glacialis sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite. International Journal of Systematic and Evolutionary Microbiology, 61(3), 587–591.PubMedCrossRefPubMedCentralGoogle Scholar
  423. Zhou, Z., Jiang, F., Wang, S., Peng, F., Dai, J., et al. (2012). Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil. International Journal of Systematic and Evolutionary Microbiology, 62(8), 1963–1969.PubMedCrossRefPubMedCentralGoogle Scholar
  424. Zhou, C., Ma, Z., Zhu, L., Xiao, X., Xie, Y., Zhu, J., et al. (2016). Rhizobacterial strain Bacillus megaterium BOFC15 induces cellular polyamine changes that improve plant growth and drought resistance. International Journal of Molecular Sciences, 17, 976. Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Javid Ahmad Parray
    • 1
  • Mohammad Yaseen Mir
    • 2
  • Nowsheen Shameem
    • 3
  1. 1.Department of Environmental ScienceGovernment SAM Degree CollegeBudgamIndia
  2. 2.Centre of Research for DevelopmentUniversity of KashmirSrinagarIndia
  3. 3.Department of Environmental ScienceCluster UniversitySrinagarIndia

Personalised recommendations