Emerging Significance of Rhizospheric Probiotics and Its Impact on Plant Health: Current Perspective Towards Sustainable Agriculture

  • Gaurav Yadav
  • Kanchan Vishwakarma
  • Shivesh SharmaEmail author
  • Vivek Kumar
  • Neha Upadhyay
  • Nitin Kumar
  • Rishi Kumar Verma
  • Rohit Mishra
  • Durgesh Kumar Tripathi
  • R. G. Upadhyay


Plants act as a shelter for vast numbers of microorganisms known as plant microbiome which is the key to plant health. Microbial population residing in plants interacts with plants through a series of complex mechanism. The plant microbe interactions can be beneficial, neutral or detrimental depending upon the nature of microbiome in the plant. Plant roots and rhizosphere are the most populated regions of plant where microbial activity is highest due to the secretion of bioactive compounds from roots. The beneficial soil microorganisms are also known as plant probiotics and have the potential to improve plant health and fitness both in natural and adverse environmental conditions. The microorganism which acts as potential probiotics utilized for the manufacturing of biofertilizers because they serve in promoting plant growth and it is now possible to formulate any type of probiotics, because of their common physiological characters. In the present chapter, the main focus is given to the rhizospheric microbiome which functions as plant probiotics and the importance of rhizospheric probiotics in plant growth promotion during stressed conditions. The chapter also includes the details for the delivery of successful biofertilizers by combining various probiotics and guidelines for their registration for providing a safe and efficient biofertilizer in the market.



Authors are thankful to Director MNNIT Allahabad for providing necessary facilities for execution of this work. The support rendered by MHRD sponsored project “Design and Innovation Centre” is also acknowledged.


  1. Adeleke RA, Cloete TE, Bertrand A, Khasa DP (2012) Iron ore weathering potentials of ectomycorrhizal plants. Mycorrhiza 22:535–544PubMedCrossRefGoogle Scholar
  2. Bailly A, Weisskopf L (2012) The modulating effect of bacterial volatiles on plant growth. Plant Signal Behav 7:1–7CrossRefGoogle Scholar
  3. Bardi L, Malusà E (2012) Drought and nutritional stresses in plant: alleviating role of rhizospheric microorganisms. In: Haryana N, Punj S (eds) Abiotic stress: new research. Nova Science Publishers Inc, Hauppauge, pp 1–57Google Scholar
  4. Barka EA, Nowak J, Clement C (2006) Enhancement of chilling resistance of inoculated grapevine plantlets with a plant growth-promoting rhizobacterium, Burkholderia phytofirmans strain PsJN. Appl Environ Microbiol 72:7246–7252CrossRefGoogle Scholar
  5. Barr M, East AK, Leonard M, Mauchline TH, Poole PS (2008) In vivo expression technology (IVET) selection of genes of Rhizobium leguminosarum biovar viciae A34 expressed in the rhizosphere. FEMS Microbiol Lett 282:219–227PubMedCrossRefGoogle Scholar
  6. Barret M, Morrissey JP, O’Gara F (2011) Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence. Biol Fertil Soils 47:729–743CrossRefGoogle Scholar
  7. Bashan Y (1998) Inoculants for plant growth promoting bacteria for use in agriculture. Adv Biotechnol 16:729–770CrossRefGoogle Scholar
  8. Belimov AA, Kojemiakov AP, Chuvarliyeva CV (1995) Interaction between barley and mixed cultures of nitrogen fixing and phosphate-solubilizing bacteria. Plant Soil 173:29–37CrossRefGoogle Scholar
  9. Bennett PC, Rogers JR, Choi WJ (2001) Silicates, silicate weathering, and microbial ecology. Geomicrobiol J 18:3–19CrossRefGoogle Scholar
  10. Berendsen RL, Pieterse CMJ, Bakker P (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486PubMedCrossRefGoogle Scholar
  11. Bonfante P, Anca I-A (2009) Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu Rev Microbiol 63:363–383PubMedCrossRefGoogle Scholar
  12. Bonkowski M, Villenave C, Griffiths B (2009) Rhizosphere fauna: the functional and structural diversity of intimate interactions of soil fauna with plant roots. Plant Soil 321:213–233CrossRefGoogle Scholar
  13. Brakhage AA, Schroeckh V (2011) Fungal secondary metabolites – strategies to activate silent gene clusters. Fungal Genet Biol 48:15–22PubMedCrossRefGoogle Scholar
  14. Buckling A, Harrison F, Vos M, Brockhurst MA, Gardner A, West SA, Griffin A (2007) Siderophore-mediated cooperation and virulence in Pseudomonas Aeruginosa. FEMS Microbiol Ecol 62:135–141PubMedCrossRefGoogle Scholar
  15. Buee M, De Boer W, Martin F, van Overbeek L, Jurkevitch E (2009) The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors. Plant Soil 321:189–212CrossRefGoogle Scholar
  16. Bulgarelli D, Rott M, Schlaeppi K et al (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95PubMedCrossRefGoogle Scholar
  17. Calvaruso C, Turpault MP, Leclerc E, Frey-Klett P (2007) Impact of ectomycorrhizosphere on the functional diversity of soil bacterial and fungal communities from a forest stand in relation to nutrient mobilization processes. Microbial Ecol 54:567–577CrossRefGoogle Scholar
  18. Cartieaux F, Contesto C, Gallou A et al (2008) Simultaneous interaction of Arabidopsis thaliana with Bradyrhizobium sp. strain ORS278 and Pseudomonas syringae pv. Tomato DC3000 leads to complex transcriptome changes. Mol Plant-Microbe Interact 21:244–259PubMedCrossRefGoogle Scholar
  19. Cavagnaro TR, Smith FA, Smith SE, Jakobsen I (2005) Functional diversity in arbuscular mycorrhizas: exploitation of soil patches with different phosphate enrichment differs among fungal species. Plant Cell Environ 28:642–650CrossRefGoogle Scholar
  20. Chelius MK, Triplett EW (2001) The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb Ecol 41:252–263PubMedCrossRefGoogle Scholar
  21. Chernin L, Toklikishvili N, Ovadis M, Kim S, Ben-Ari J, Khmel I, Vainstein A (2011) Quorum-sensing quenching by rhizobacterial volatiles. Environ Microbiol Rep 3:698–704PubMedCrossRefGoogle Scholar
  22. Collignon C, Uroz S, Turpault MP, Frey-Klett P (2011) Seasons differently impact the structure of mineral weathering bacterial communities in beech and spruce stands. Soil Biol Biochem 43:2012–2022CrossRefGoogle Scholar
  23. Cook RJ, Thomashow LS, Weller DM, Fujimoto D, Mazzola M, Bangera G, Kim DS (1995) Molecular mechanisms of defense by rhizobacteria against root disease. Proc Natl Acad Sci U S A 92:4197PubMedPubMedCentralCrossRefGoogle Scholar
  24. Cruz-Hernandez A, Tomasini-Campocosio A, Perez-Flores L, Fernandez-Perrino F, Gutierrez-Rojas M (2012) Inoculation of seed-borne fungus in the rhizosphere of Festuca arundinacea promotes hydrocarbon removal and pyrene accumulation in roots. Plant Soil 363:261–270Google Scholar
  25. De Freitas JR, Gupta VVS, Germida JJ (1993) Influence of Pseudomonas syringae R 25 and P. putida R 105 on the growth and N2 fixation (ARA) of pea (Pisum sativum L.) and field bean (Phaseolus vulgaris L.) Biol Fertil Soils 16:215–220CrossRefGoogle Scholar
  26. De Vleesschauwer D, Hofte M (2009) Rhizobacteria-induced systemic resistance. Adv Bot Res 51:223–281CrossRefGoogle Scholar
  27. DeAngelis KM, Ji PS, Firestone MK, Lindow SE (2005) Two novel bacterial biosensors for detection of nitrate availability in the rhizosphere. Appl Environ Microbiol 71:8537–8547PubMedPubMedCentralCrossRefGoogle Scholar
  28. DeAngelis KM, Brodie EL, DeSantis TZ, Andersen GL, Lindow SE, Firestone MK (2009) Selective progressive response of soil microbial community to wild oat roots. ISME J 3:168–178PubMedCrossRefGoogle Scholar
  29. Demoling F, Figueroa D, Baath E (2007) Comparison of factors limiting bacterial growth in different soils. Soil Biol Biochem 39:2485–2495CrossRefGoogle Scholar
  30. Desai S (2016) Challenges in regulation and registration of biopesticides: an overview. In: Microbial inoculants in sustainable agricultural productivity. Springer, India, pp 301–308CrossRefGoogle Scholar
  31. Dodd IC, Perez-Alfocea F (2012) Microbial amelioration of crop salinity stress. J Exp Bot 63:3415–3428PubMedCrossRefGoogle Scholar
  32. Effmert U, Kalderas J, Warnke R, Piechulla B (2012) Volatile mediated interactions between bacteria and fungi in the soil. J Chem Ecol 38:665–703PubMedCrossRefGoogle Scholar
  33. El-Komy HMA (2005) Co-immobilization of A. lipoferum and B. megaterium for plant nutrition. Food Technol Biotechnol 43(1):19–27Google Scholar
  34. Fages J (1992) An industrial view of Azospirillum inoculants: formulation and application technology. Symbiosis 13:15–26Google Scholar
  35. FAO (1988) Guidelines on the registration of biological pest control agent. Food and Agriculture Organization of the United Nations, RomeGoogle Scholar
  36. Ferluga S, Venturi V (2009) OryR is a LuxR-family protein involved in inter kingdom signaling between pathogenic Xanthomonas oryzae pv. Oryzae and rice. J Bacteriol 191:890–897PubMedCrossRefGoogle Scholar
  37. Franche C, Lindström K, Elmerich C (2009) Nitrogen fixing bacteria associated with leguminous and non leguminous pants. Plant Soil 321:35–59CrossRefGoogle Scholar
  38. Frey-Klett P, Garbaye J, Tarkka M (2007) The mycorrhiza helper bacteria revisited. New Phytol 176:22–36PubMedCrossRefGoogle Scholar
  39. Gaby JC, Buckley DH (2011) A global census of nitrogenase diversity. Environ Microbiol 13:1790–1799PubMedCrossRefGoogle Scholar
  40. Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390PubMedCrossRefGoogle Scholar
  41. Geurts R, Lillo A, Bisseling T (2012) Exploiting an ancient signalling machinery to enjoy a nitrogen fixing symbiosis. Curr Opin Plant Biol 15:438–443PubMedCrossRefGoogle Scholar
  42. Gianinazzi S, Gollotte A, Binet MN, van Tuinen D, Redecker D, Wipf D (2010) Agroecology: the key role of arbuscular mycorrhizas in ecosystem services. Mycorrhiza 20:519–530PubMedCrossRefGoogle Scholar
  43. Grichko VP, Glick BR (2001) Amelioration of flooding stress by ACC deaminase-containing plant growth-promoting bacteria. Plant Physiol Biochem 39:11–17CrossRefGoogle Scholar
  44. Guimarães AA, Jaramillo PMD, Nóbrega RSA, Florentino LA, Silva KB, de Souza Moreira FM (2012) Genetic and symbiotic diversity of nitrogen-fixing bacteria isolated from agricultural soils in the western Amazon by using cowpea as the trap plant. Appl Environ Microbiol 78(18):6726–6733CrossRefGoogle Scholar
  45. Gupta AK (2004) The complete technology book on biofertilizers and organic farming. National Institute of Industrial Research Press, IndiaGoogle Scholar
  46. Hawkes CV, DeAngelis KM, Firestone MK (2007) Root interactions with soil microbial communities and processes. In: Cardon Z, Whitbeck J (eds) The Rhizosphere. Elsevier, New York, pp 1–3Google Scholar
  47. Hayat R, Ali S, Amara U, Khalid R, Ahmed I (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 60:579–598CrossRefGoogle Scholar
  48. He Z, Gentry TJ, Schadt CW et al (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1:67–77PubMedCrossRefGoogle Scholar
  49. Herron PM, Gage DJ, Cardon ZG (2010) Micro-scale water potential gradients visualized in soil around plant root tips using microbiosensors. Plant Cell Environ 33:199–210PubMedCrossRefGoogle Scholar
  50. Hider RC, Kong X (2010) Chemistry and biology of siderophores. Nat Prod Rep 27:637–657PubMedCrossRefGoogle Scholar
  51. Hinsinger P, Marschner P (2006) Rhizosphere– perspectives and challenges – a tribute to Lorenz Hiltner. Plant Soil 283:vii–viiiCrossRefGoogle Scholar
  52. Hinsinger P, Bengough AG, Vetterlein D, Young IM (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil 321:117–152CrossRefGoogle Scholar
  53. Hitbold AE, Thurlow N, Skipper HD (1980) Evaluation of commercial soybean inoculants by various techniques. Agron J 72:675–681CrossRefGoogle Scholar
  54. Hoffmeister D, Keller NP (2007) Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat Prod Rep 24:393–416PubMedCrossRefGoogle Scholar
  55. Hol WHG, de Boer W, Termorshuizen AJ et al (2010) Reduction of rare soil microbes modifies plant-herbivore interactions. Ecol Lett 13:292–301PubMedCrossRefGoogle Scholar
  56. Insam H, Seewald MSA (2010) Volatile organic compounds (VOCs) in soils. Biol Fertil Soils 46:199–213CrossRefGoogle Scholar
  57. Jamalizadeh M, Etebarian HR, Aminian H et al (2010) Biological control of Botrytis mali on apple fruit by use of Bacillus bacteria, isolated from the rhizosphere of wheat. Arch Phytopathol Plant Protect 43:1836–1845CrossRefGoogle Scholar
  58. Jensen LE, Nybroe O (1999) Nitrogen availability to Pseudomonas fluorescens DF57 is limited during decomposition of barley straw in bulk soil and in the barley rhizosphere. Appl Environ Microbiol 65:4320–4328PubMedPubMedCentralGoogle Scholar
  59. Jha B, Gontia I, Hartmann A (2012) The roots of the halophyte Salicornia Brachiata are a source of new halotolerant diazotrophic bacteria with plant growth-promoting potential. Plant Soil 356:265–277CrossRefGoogle Scholar
  60. Jogler C, Waldmann J, Huang XL, Jogler M, Glockner FO, Mascher T, Kolter R (2012) Identification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in Planctomycetes by comparative genomics. J Bacteriol 194:6419–6430PubMedPubMedCentralCrossRefGoogle Scholar
  61. Johnson NC, Graham JH (2013) The continuum concept remains a useful framework for studying mycorrhizal functioning. Plant Soil 363:411–419CrossRefGoogle Scholar
  62. Jones D, Hinsinger P (2008) The rhizosphere: complex by design. Plant Soil 312:1–6CrossRefGoogle Scholar
  63. Jorquera MA, Shaharoona B, Nadeem SM, de la Luz Mora M, Crowley DE (2012) Plant growth-promoting rhizobacteria associated with ancient clones of creosote bush (Larrea tridentata). Microb Ecol 64:1008–1017PubMedCrossRefGoogle Scholar
  64. Kawasaki A, Watson ER, Kertesz MA (2012) Indirect effects of polycyclic aromatic hydrocarbon contamination on microbial communities in legume and grass rhizospheres. Plant Soil 358:169–182CrossRefGoogle Scholar
  65. Knief C, Delmotte N, Chaffron S et al (2011) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6:1378–1390PubMedPubMedCentralCrossRefGoogle Scholar
  66. Koch B, Worm J, Jensen LE, Hojberg O, Nybroe O (2001) Carbon limitation induces sigma(S)-dependent gene expression in Pseudomonas fluorescens in soil. Appl Environ Microbiol 67:3363–3370PubMedPubMedCentralCrossRefGoogle Scholar
  67. Kogel KH, Franken P, Hückelhoven R (2006) Endophyte or parasite – what decides? Curr Opin Plant Biol 9:358–363PubMedCrossRefGoogle Scholar
  68. Kragelund L, Hosbond C, Nybroe O (1997) Distribution of metabolic activity and phosphate starvation response of lux-tagged Pseudomonas fluorescens reporter bacteria in the barley rhizosphere. Appl Environ Microbiol 63:4920–4928PubMedPubMedCentralGoogle Scholar
  69. Kuiper I, Lagendijk EL, Bloemberg GV, Lugtenberg BJJ (2004) Rhizoremediation: a beneficial plant–microbe interaction. Mol Plant-Microbe Interact 17:6–15PubMedCrossRefGoogle Scholar
  70. Kulakova AN, Kulakov LA, McGrath JW, Quinn JP (2009) The construction of a whole-cell biosensor for phosphonoacetate, based on the LysR-like transcriptional regulator PhnR from Pseudomonas fluorescens 23F. Microb Biotechnol 2:234–240PubMedPubMedCentralCrossRefGoogle Scholar
  71. Leahy J, Mendelsohn M, Kough J, Jones R, Berckes N (2014) Biopesticide oversight and registration at the U.S. Environmental Protection Agency. In: Coats JR et al (eds) Biopesticides: state of the art and future opportunities. ACS Symposium Series, American Chemical Society, WashingtonGoogle Scholar
  72. Leininger S, Urich T, Schloter M et al (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809PubMedCrossRefGoogle Scholar
  73. Lemanceau P, Expert D, Gaymard F, Bakker P, Briat JF (2009) Role of iron in plant–microbe interactions. Adv Bot Res 51:491–549CrossRefGoogle Scholar
  74. Leveau JHJ, Uroz S, de Boer W (2010) The bacterial genus Collimonas: mycophagy, weathering and other adaptive solutions to life in oligotrophic soil environments. Environ Microbiol 12:281–292PubMedCrossRefGoogle Scholar
  75. Liu D, Lian B, Dong H (2012) Isolation of Paenibacillus sp. and assessment of its potential for enhancing mineral weathering. Geomicrobiol J 29:413–421CrossRefGoogle Scholar
  76. Loh J, Pierson EA, Pierson LS, Stacey G, Chatterjee A (2002) Quorum sensing in plant-associated bacteria. Curr Opin Plant Biol 5:285–290PubMedCrossRefGoogle Scholar
  77. Lucy M, Reed E, Glick BR (2004) Application of free living plant growth-promoting rhizobacteria. Antonie Van Leeuwenhoek 86:1–25PubMedCrossRefGoogle Scholar
  78. Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556PubMedCrossRefGoogle Scholar
  79. Lundberg DS, Lebeis SL, Paredes SH et al (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86PubMedPubMedCentralCrossRefGoogle Scholar
  80. Lupwayi NZ, Olsen PE, Sonde ES et al (2000) Inoculant quality and its evaluation. Field Crop Res 65:259–270CrossRefGoogle Scholar
  81. Lynch JM (1990) The Rhizosphere. John Wiley, Sons, New YorkGoogle Scholar
  82. Mapelli F, Marasco R, Balloi A, Rolli E, Cappitelli F, Daffonchio D, Borin S (2012) Mineral-microbe interactions: biotechnological potential of bioweathering. J Biotechnol 157:473–481PubMedCrossRefGoogle Scholar
  83. Mark GL, Dow JM, Kiely PD et al (2005) Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe–plant interactions. Proc Natl Acad Sci U S A 102:17454–17459PubMedPubMedCentralCrossRefGoogle Scholar
  84. Marschner P, Crowley D, Rengel Z (2011) Rhizosphere interactions between microorganisms and plants govern iron and phosphorus acquisition along the root axis – model and research methods. Soil Biol Biochem 43:883–894CrossRefGoogle Scholar
  85. Mayak S, Tirosh T, Glick BR (2004a) Plant growth-promoting bacteria that confer resistance to water stress in tomatoes and peppers. Plant Sci 166:525–530CrossRefGoogle Scholar
  86. Mayak S, Tirosh T, Glick BR (2004b) Plant growth-promoting bacteria confer resistance in tomato plants to salt stress. Plant Physiol Biochem 42:565–572PubMedCrossRefGoogle Scholar
  87. Meeting FB (1992) Soil microbial ecology: applications in agricultural and environmental management. Marcel Dekker, New YorkGoogle Scholar
  88. Mendes R, Kruijt M, de Bruijn I et al (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100PubMedCrossRefGoogle Scholar
  89. Mendes R, Paolina G, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37(5):634–663PubMedCrossRefGoogle Scholar
  90. Miller RM, Jastrow JD (2000) Mycorrhizal fungi influence soil structure. In: Kapulnik Y, Douds DD Jr (eds) Arbuskular mycorrhizas: physiology and function. Kluwer Academic Publishers, London, pp 3–18CrossRefGoogle Scholar
  91. Miransari M (2011) Arbuscular mycorrhizal fungi and nitrogen uptake. Arch Microbiol 193:77–81PubMedCrossRefGoogle Scholar
  92. Mohammadi K, Ghalavand A, Aghaalikhani M, Sohrabi Y, Heidari GR (2010) Impressibility of chickpea seed quality from different systems of increasing soil fertility. Electron J Crop Prod 3(1):103–119Google Scholar
  93. Mohammadi K, Ghalavand A, Aghaalikhani M, Heidari GR, Sohrabi Y (2011) Introducing the sustainable soil fertility system for chickpea (Cicer arietinum L). Afr J Biotechnol 10(32):6011–6020Google Scholar
  94. Nelson EB (2004) Microbial dynamics and interactions in the spermosphere. Annu Rev Phytopathol 42:271–309PubMedCrossRefGoogle Scholar
  95. OECD (1996) Date requirements for registration of biopesticides in OECD member countries: survey results, environment monograph no. 106. Organization for Economic Cooperation and Development, ParisGoogle Scholar
  96. OECD (2002) Consensus document on information used in assessment of environmental applications involving baculoviruses. Series on harmonisation of regulatory oversight in biotechnology no. 20. ENV/JM/MONO (2002)1 OECD. Organization for Economic Cooperation and Development, ParisGoogle Scholar
  97. Owen D, Williams AP, Griffi th GW, Withers PJA (2015) Use of commercial bio-inoculants to increase agricultural production through improved phosphorus acquisition. Appl Soil Ecol 86:41–54CrossRefGoogle Scholar
  98. Pineda A, Zheng S-J, van Loon JJA, Pieterse CMJ, Dicke M (2010) Helping plants to deal with insects: the role of beneficial soil-borne microbes. Trends Plant Sci 15:507–514PubMedCrossRefGoogle Scholar
  99. Pozo MJ, Azcon-Aguilar C (2007) Unraveling mycorrhiza-induced resistance. Curr Opin Plant Biol 10:393–398PubMedCrossRefGoogle Scholar
  100. Prabakaran J, Ravi KB (1991) Interaction effect of A. Brasilense and Pseudomonas sp. A phosphate solubilizer on the growth of Zea mays. In: Microbiology Abstracts, XXXI Annual Conference of the Association of Microbiologists of India, TNAU, Coimbatore, January 23–26, p 109Google Scholar
  101. Qiang X, Weiss M, Kogel KH, Schafer P (2012) Piriformospora indica a mutualistic basidiomycete with an exceptionally large plant host range. Mol Plant Pathol 13:508–518PubMedCrossRefGoogle Scholar
  102. Raaijmakers J, Mazzola M (2012) Diversity and natural functions of antibiotics produced by beneficial and pathogenic soil bacteria. Annu Rev Phytopathol 50:403–424PubMedCrossRefGoogle Scholar
  103. Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361CrossRefGoogle Scholar
  104. Radhakrishnan KC (1996) Role of biofertilizers in cotton productivity. In: National seminar biofertilizer production problem and constraints, TNAU, Coimbatore, January 24–25, p 17Google Scholar
  105. Rainey PB (1999) Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1:243–257PubMedCrossRefGoogle Scholar
  106. Ramos C, Molbak L, Molin S (2000) Bacterial activity in the rhizosphere analyzed at the single-cell level by monitoring ribosome contents and synthesis rates. Appl Environ Microbiol 66:801–809PubMedPubMedCentralCrossRefGoogle Scholar
  107. Raudales RE, Stone E, McSpadden Gardener BB (2009) Seed treatment with 2,4-diacetylphloroglucinol-producing pseudomonads improves crop health in low-pH soils by altering patterns of nutrient uptake. Phytopathology 99:506–511PubMedCrossRefGoogle Scholar
  108. Richardson AE, Barea JM, McNeill AM, Prigent-Combaret C (2009) Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant Soil 321:305–339CrossRefGoogle Scholar
  109. Rochat L, Pechy-Tarr M, Baehler E, Maurhofer M, Keel C (2010) Combination of fluorescent reporters for simultaneous monitoring of root colonization and antifungal gene expression by a biocontrol pseudomonad on cereals with flow cytometry. Mol Plant-Microbe Interact 23:949–961PubMedCrossRefGoogle Scholar
  110. Rodríguez H, Fraga R (1999) Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv 17:319–339PubMedCrossRefGoogle Scholar
  111. Roesch LFW, Fulthorpe RR, Riva A et al (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290PubMedPubMedCentralGoogle Scholar
  112. Rousk J, Baath E (2007) Fungal and bacterial growth in soil with plant materials of different C/N ratios. FEMS Microbiol Ecol 62:258–267PubMedCrossRefGoogle Scholar
  113. Sahu PK, Brahmaprakash GP (2016) Formulations of biofertilizers–approaches and advances. In: Microbial inoculants in sustainable agricultural productivity. Springer, India, pp 179–198CrossRefGoogle Scholar
  114. Salvioli A, Bonfante P (2013) Systems biology and “omics” tools: a cooperation for next-generation mycorrhizal studies. Plant Sci 203:107–114PubMedCrossRefGoogle Scholar
  115. Shirley M, Avoscan L, Bernaud E, Vansuyt G, Lemanceau P (2011) Comparison of iron acquisition from Fe-pyoverdine by strategy I and strategy II plants. Botany 89:731–735CrossRefGoogle Scholar
  116. Siddikee M, Chauhan P, Anandham R, Han GH, Sa T (2010) Isolation, characterization, and use for plant growth promotion under salt stress, of ACC deaminase-producing halotolerant bacteria derived from coastal soil. J Microbiol Biotechnol 20:1577–1584PubMedCrossRefGoogle Scholar
  117. Smith SE, Read DJ (2008) Mycorrhizal symbiosis, 3rd edn. Elsevier/Academic, New York/London/Burlington/San Diego, p 605Google Scholar
  118. Smyth SJ, McHughen A (2012) Regulation of genetically modified crops in USA and Canada: Canadian overview. In: Woznaik CA, McHughen A (eds) Regulation of agricultural biotechnology: the United States and Canada. Springer, Dordrecht, pp 15–34CrossRefGoogle Scholar
  119. Steindler L, Venturi V (2007) Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors. FEMS Microbiol Lett 266:1–9PubMedCrossRefGoogle Scholar
  120. Supanjani Han HS, Jung SJ, Lee KD (2006) Rock phosphate potassium and rock solubilizing bacteria as alternative sustainable fertilizers. Agron Sustain Dev 26:233–240CrossRefGoogle Scholar
  121. Tawaraya K, Naito M, Wagatsuma T (2006) Solubilization of insoluble inorganic phosphate by hyphal exudates of arbuscular mycorrhizal fungi. J Plant Nutr 29:657–665CrossRefGoogle Scholar
  122. Teixeira LCRS, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J, Rosado AS (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 4:989–1001PubMedCrossRefGoogle Scholar
  123. Tringe SGC, von Mering A, Kobayashi AA et al (2005) Comparative metagenomics of microbial communities. Science 308:554–557PubMedCrossRefGoogle Scholar
  124. Trivedi P, He Z, Van Nostrand JD, Albrigo G, Zhou J, Wang N (2011) Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J 6:363–383PubMedPubMedCentralCrossRefGoogle Scholar
  125. Ullrich MS, Schergaut M, Boch J, Ullrich B (2000) Temperature-responsive genetic loci in the plant pathogen Pseudomonas syringae pv. Glycinea. Microbiology 146:2457–2468PubMedCrossRefGoogle Scholar
  126. Upadhyay SK, Singh DP, Saikia R (2009) Genetic diversity of plant growth promoting rhizobacteria isolated from rhizospheric soil of wheat under saline condition. Curr Microbiol 59:489–496PubMedCrossRefGoogle Scholar
  127. Uroz S, Buee M, Murat C, Frey-Klett P, Martin F (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2:281–288PubMedCrossRefGoogle Scholar
  128. van de Mortel JE, de Vos RCH, Dekkers E et al (2012) Metabolic and transcriptomic changes induced in Arabidopsis by the rhizobacterium Pseudomonas fluorescens SS101. Plant Physiol 160:2173–2188PubMedPubMedCentralCrossRefGoogle Scholar
  129. van der Heijden MGA, Sanders IR (2002) Mycorrhizal ecology. Springer, New YorkGoogle Scholar
  130. Vansuyt G, Robin A, Briat JF, Curie C, Lemanceau P (2007) Iron acquisition from Fe-pyoverdine by Arabidopsis thaliana. Mol Plant-Microbe Interact 20:441–447PubMedCrossRefGoogle Scholar
  131. Vespermann A, Kai M, Piechulla B (2007) Rhizobacterial volatiles affect the growth of fungi and Arabidopsis thaliana. Appl Environ Microbiol 73:5639–5641PubMedPubMedCentralCrossRefGoogle Scholar
  132. Vishwakarma K, Sharma S, Kumar N, Upadhyay N, Devi S, Tiwari A. (2016) Contribution of Microbial Inoculants to Soil Carbon Sequestration and Sustainable Agriculture. In: Microbial Inoculants in Sustainable Agricultural Productivity. pp. Springer India. 101–113Google Scholar
  133. Vishwakarma K, Upadhyay N, Kumar N, Yadav G, Singh J, Mishra R.K., Kumar V, Verma R, Upadhyay R.G., Pandey M, Sharma S, (2017) Abscisic Acid Signaling and Abiotic Stress Tolerance in Plants: A Review on Current Knowledge and Future Prospects. Frontiers in Plant Science 08Google Scholar
  134. Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840PubMedCrossRefGoogle Scholar
  135. Wagner GM (1997) Azolla. A review of its biology and utilisation. Bot Rev 63:1–26CrossRefGoogle Scholar
  136. Walker EL, Connolly EL (2008) Time to pump iron: iron-deficiency-signaling mechanisms of higher plants. Curr Opin Plant Biol 11:530–535PubMedCrossRefGoogle Scholar
  137. Wang HB, Zhang ZX, Li H et al (2011) Characterization of metaproteomics in crop rhizospheric soil. J Proteome Res 10:932–940PubMedCrossRefGoogle Scholar
  138. Weinert N, Piceno Y, Ding GC et al (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol 75:497–506PubMedCrossRefGoogle Scholar
  139. Whipps JM (2001) Ecological and biotechnological considerations in enhancing disease biocontrol. In: Vurro M, Gressel J, Butt T, Harman GE, Pilgeram A, St. Leger RJ, Nuss DL (eds) Enhancing biocontrol agents and handling risks, vol 339. IOP Press, Amsterdam, pp 43–51Google Scholar
  140. Wu L, Wang H, Zhang Z, Lin R, Lin W (2011) Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil. PLoS One 6:e20611PubMedPubMedCentralCrossRefGoogle Scholar
  141. Yehuda Z, Shenker M, Hadar Y, Chen YN (2000) Remedy of chlorosis induced by iron deficiency in plants with the fungal siderophore rhizoferrin. J Plant Nutr 23:1991–2006CrossRefGoogle Scholar
  142. Zaddy E, Perevolosky A, Okon Y (1993) Promotion of plant growth by inoculation with aggregated and single cell suspension by Azospirillum brasilense. Soil Biol Biochem 25:819–823CrossRefGoogle Scholar
  143. Zamioudis C, Pieterse CMJ (2012) Modulation of host immunity by beneficial microbes. Mol Plant-Microbe Interact 25:139–150PubMedCrossRefGoogle Scholar
  144. Zhang F, Lynch DH, Smith DL (1995) Impact of low root temperatures in soybean [Glycine max (L.) Merr.] on nodulation and nitrogen fixation. Environ Exp Bot 35:279–285CrossRefGoogle Scholar
  145. Zhang F, Dashti N, Hynes R, Smith DL (1996) Plant growth promoting rhizobacteria and soybean [Glycine max (L.) Merr.] nodulation and nitrogen fixation at suboptimal root zone temperatures. Ann Bot 77:453–460CrossRefGoogle Scholar
  146. Zhang H, Sun Y, Xie X, Kim MS, Dowd SE, Par_e PW (2009) A soil bacterium regulates plant acquisition of iron via deficiency-inducible mechanisms. Plant J 58:568–577PubMedCrossRefGoogle Scholar
  147. Zou C-S, Mo M-H, Y-Q G, Zhou J-P, Zhang K-Q (2007) Possible contributions of volatile-producing bacteria to soil fungistasis. Soil Biol Biochem 39:2371–2379CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Gaurav Yadav
    • 1
    • 2
  • Kanchan Vishwakarma
    • 1
  • Shivesh Sharma
    • 1
    • 2
    Email author
  • Vivek Kumar
    • 3
  • Neha Upadhyay
    • 1
  • Nitin Kumar
    • 1
  • Rishi Kumar Verma
    • 1
  • Rohit Mishra
    • 2
  • Durgesh Kumar Tripathi
    • 2
  • R. G. Upadhyay
    • 4
  1. 1.Department of Biotechnology, Motilal Nehru National Institute of Technology AllahabadAllahabadIndia
  2. 2.Centre for Medical Diagnostic and Research, MNNIT AllahabadAllahabadIndia
  3. 3.Amity Institute of Microbial TechnologyAmity UniversityNoidaIndia
  4. 4.V.C.S.G. Uttarakhand University of Horticulture and ForestryTehri GarhwalIndia

Personalised recommendations