Advertisement

Microbial Interactions and Plant Health

  • Amrita SenguptaEmail author
  • Sunil Kumar Gunri
  • Tapas Biswas
Chapter

Abstract

With augmented population, hasty industrialization, and urbanization worldwide, land for agricultural production is declining faster, and there is a huge demand for ecologically viable and environmentally affable techniques in agriculture, competent of providing adequate sustenance for the increasing human inhabitants and of improving the quality as well as quantity of certain agricultural harvests. A great deal of endeavor focusing on soil biology and the agroecosystem as a whole is required, enabling better perception of the complex processes and communications governing the stability of agricultural lands and plant kingdom. The scientific advances in modern times, researching biodiversity, have revealed that microbial miscellany is of massive potential that can be explored through careful assortment of the same and their booming use may solve critical agricultural and environmental issues. Here, we promote the thought that considering the mechanism by which plants select and interact with their microbiomes may have a direct or indirect effect on plant health that further may lead to establishment of novel microbiome-driven strategies that can embark upon the development of a more sustainable agriculture.

Keywords

Association Biofertilizers Crop production Inoculation Microorganisms PGPR Phyllosphere Rhizosphere Symbiosis 

References

  1. Abreu-Tarazi MF, Navarrete AA, Andreote FD, Almeida CV, Tsai SM, Almeida M (2010) Endophytic bacteria in long-term in vitro cultivated axenic pineapple microplants revealed by PCR DGGE. World J Microbiol Biotechnol 26:555–560CrossRefGoogle Scholar
  2. Ahmad I, Ahmad F, Pichtel H (eds) (2011) Microbes and microbial technology: agricultural and environmental applications doi  10.1007/978-1-4419-7931-5_1
  3. Alabouvette C, Olivain C, Steinberg C (2006) Biological control of plant diseases: the European situation. Eur J Plant Pathol 114:329–341CrossRefGoogle Scholar
  4. Almeida CV, Andreote FD, Yara R, Ossamu FA, Azevedo JL, Almeida M (2009) Bacteriossomes in axenic plants: endohytes as stable symbionts. World J Microbiol Biotechnol 25:1757–1764CrossRefGoogle Scholar
  5. Andreote FD, Gumiere T, Durrer A (2014) Exploring interactions of plant microbiomes. Sci Agric 71(6):528–539CrossRefGoogle Scholar
  6. Andrews JH, Harris RF (2000) The ecology and biogeography of microorganisms on plant surfaces. Annu Rev Phytopathol 38:145–180PubMedCrossRefGoogle Scholar
  7. Araújo WL, Marcon J, Maccheroni W, van Elsas JD, van Vuurde JWL, Azevedo JL (2002) Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants. Appl Environ Microbiol 68:4906–4914PubMedPubMedCentralCrossRefGoogle Scholar
  8. Argueso C, Hansen M, Kieber J (2007) Regulation of ethylene biosynthesis. J Plant Growth Regul 26(2):92–105. doi: 10.1007/s00344-007-0013-5 CrossRefGoogle Scholar
  9. Arshad M, Shaharoona B, Mahmood T (2008) Inoculation with Pseudomonas spp containing ACC-deaminase partially eliminates the effects of drought stress on growth yield and ripening of pea (Pisum sativum L). Pedosphere 18(5):611–620. doi: 10.1016/S1002-0160(08)60055-7 CrossRefGoogle Scholar
  10. Asiegbu FO, Nahalkova JLG (2005) Pathogen-inducible cDNAs from the interaction of the root rot fungus Heterobasidion annosum with scots pine (Pinus sylvestris L). Plant Sci 168:365372CrossRefGoogle Scholar
  11. Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32(6):666–681. doi: 10.1111/j1365-3040200901926x. PMID: 19143988PubMedCrossRefGoogle Scholar
  12. Badri DV, Loyola-Vargas VM, Broeckling CD, De-la-Pena C, Jasinski M, Santelia D, Martinoia E, Sumner LW, Banta LM, Stermitz F, Vivanco JM (2008) Altered profile of secondary metabolites in the root exudates of Arabidopsis ATP-binding cassette transporter mutants. Plant Physiol 146(2):762–771. doi:10.1104/pp107109587 PMID:18065561 PubMedPubMedCentralCrossRefGoogle Scholar
  13. Badri DV, Quintana N, El Kassis EG, Kim HK, Choi YH, Sugiyama A, Verpoorte R, Martinoia E, Manter DK, Vivanco JM (2009) An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiol 151(4):2006–2017. doi: 10.1104/pp109147462. PMID:19854857PubMedPubMedCentralCrossRefGoogle Scholar
  14. Badri DV, Chaparro JM, Zhang R, Shen Q, Vivanco JM (2013a) Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chem 288(7):4502–4512. doi: 10.1074/jbcM112433300. PMID:23293028PubMedPubMedCentralCrossRefGoogle Scholar
  15. Badri DV, Zolla G, Bakker MG, Manter DK, Vivanco JM (2013b) Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior. New Phytol 198(1):264–273. doi: 10.1111/nph12124. PMID: 23347044PubMedCrossRefGoogle Scholar
  16. Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57(1):233–266. doi: 10.1146/annurevarplant57032905105159. PMID:16669762PubMedCrossRefGoogle Scholar
  17. Banerjee M, Yesmin L (2002) Sulfur-oxidizing plant growth promoting Rhizobacteria for enhanced canola performance US Patent 20080070784Google Scholar
  18. Barriuso J, Ramos-Solabo B, Guierrez M (2008a) Protection against pathogen and salt stress by four plant growth promoting rhizobacteria isolated from Pinus sp on Arabidopsis thaliana. Biol Control 98(6):666–672Google Scholar
  19. Barriuso J, Solano BR, Lucas JA, Lobo AP, Villaraco AG, Mañero FJG (2008b) In: Ahmad I, Pichtel J, Hayat S (eds) Ecology genetic diversity and screening strategies of Plant Growth Promoting Rhizobacteria (PGPR). WILEY-VCH Verlag GmbH, Co KGaA, Weinheim, pp 1–17Google Scholar
  20. Beattie GA, Lindow SE (1995) The secret life of foliar bacterial pathogens on leaves. Annu Rev Phytopathol 33:145–172PubMedCrossRefGoogle Scholar
  21. Berg G (2009) Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84:11–18PubMedCrossRefGoogle Scholar
  22. Bloemberg GV, Lugtenberg BJJ (2001) Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr Opin Plant Biol 4:343–350PubMedCrossRefGoogle Scholar
  23. Bokulich NA, Thorngate JH, Richardson PM, Mills DA (2014) Microbial biogeography of wine grapes is conditioned by cultivar vintage and climate. Proc Natl Acad Sci USA 111:E139–E148PubMedCrossRefGoogle Scholar
  24. Brandl MT, Quinones B, Lindow SE (2001) Heterogeneous transcription of an indoleacetic acid biosynthetic gene in Erwinia herbicola on plant surfaces. Proc Natl Acad Sci USA 98:3454–3459PubMedPubMedCentralCrossRefGoogle Scholar
  25. Brimecombe MJ, De Leij FAAM, Lynch JM (2007) Rhizodeposition and microbial populations. In: Pinton R, Veranini Z, Nannipieri P (eds) The rhizosphere biochemistry and organic substances at the soil-plant interface. Taylor, Francis Group, New YorkGoogle Scholar
  26. Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM (2008) Root exudates regulate soil fungal community composition and diversity. Appl Environ Microbiol 74(3):738–744. doi: 10.1128/AEM02188-07 PubMedCrossRefGoogle Scholar
  27. Buchanan R, Gruissem W, Jones RL (2000) Biochemistry and molecular biology of plants. American Society of Plant Biologists, RockvilleGoogle Scholar
  28. Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64(1):807–838PubMedCrossRefGoogle Scholar
  29. Buysens S, Heungens K, Poppe J, Höfte M (1996) Involvement of pyochelin and pyoverdin in suppression of Pythium induced damping off of tomato by Pseudomonas aeruginosa 7NSK2. Appl Environ Microbiol 62:865–871PubMedPubMedCentralGoogle Scholar
  30. Cassán F, García Salamone I (2008) Azospirillum sp: cell physiology plant response agronomic and environmental research in Argentina. Asociacion Argentina de Microbiologia, Buenos AiresGoogle Scholar
  31. Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, Vivanco JM (2013) Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One 8(2):e55731. doi:10.1371/journalpone 0055731. PMID:23383346PubMedPubMedCentralCrossRefGoogle Scholar
  32. Chet I, Chernin L (2002) Biocontrol microbial agents in soil. In: Bitton G (ed) Encyclopedia of environmental microbiology. Willey, New York, pp 450–465Google Scholar
  33. Chin-A-Woeng TFC, Bloemberg GV, Lugtenberg BJ (2003) Phenazines and their role in biocontrol by Pseudomonas bacteria. New Phytol 157:503–523CrossRefGoogle Scholar
  34. Compant S, Duffy B, Nowak J, Clement C, Barka EA (2005) Use of plant growth promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 71:4951–4959PubMedPubMedCentralCrossRefGoogle Scholar
  35. Cook JH, Beyea J, Keeler KH (1991) Potential impacts of biomass production in the United States on biological diversity. Annu Rev Energ Environ 16:401–431CrossRefGoogle Scholar
  36. Coronado C, Zuanazzi J, Sallaud C, Quirion JC, Esnault R, Husson HP, Kondorosi A, Ratet P (1995) Alfalfa root flavonoid production is nitrogen regulated. Plant Physiol 108(2):533–542. doi:10.1104/pp1082533 PMID:12228491PubMedPubMedCentralCrossRefGoogle Scholar
  37. Crowley TJ (2000) Causes of climate change over the past 1000 years. Science 289:270–277PubMedCrossRefGoogle Scholar
  38. Davey ME, O’Toole GA (2000) Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev 64:847–867PubMedPubMedCentralCrossRefGoogle Scholar
  39. Davidson IA, Robson MJ (1986) Effect of contrasting patterns of nitrate application on the nitrate uptake N2-fixation nodulation and growth of white clover. Ann Bot 57(3):331–338CrossRefGoogle Scholar
  40. De Bary A (1866) Morphologie und Physiologie Pilze Flechten und Myxomyceten Hofmeister’s handbook of physiological botany Engelmann Leipzig GermanyGoogle Scholar
  41. De Vleeschauwer D, Höfte M (2007) Using Serratia plymuthica to control fungal pathogens of plants. CAB Rev 2:4–6CrossRefGoogle Scholar
  42. De Werra P, Péchy T, Keel C, Maurhofer M (2009) Role of gluconic acid production in the regulation of biocontrol traits of Pseudomonas fluorescens CHA0. Appl Environ Microbiol 75:4162–4174PubMedPubMedCentralCrossRefGoogle Scholar
  43. DeFlaun MF, Gerba CP (1993) Monitoring recombinant DNA microorganisms and viruses in soil. In: Metting FBJ (ed) Soil microbial ecology: application in agricultural and environmental management. Marcel Dekker, Washington, DC, pp 131–150Google Scholar
  44. Diener AC, Gaxiola RA, Fink GR (2001) Arabidopsis ALF5 a multidrug efflux transporter gene family member confers resistance to toxins. Plant Cell. Online 13(7):1625–1638. doi: 10.1105/tpc1371625 PubMedPubMedCentralCrossRefGoogle Scholar
  45. Dini-Andreote F, van Elsas JD (2013) Back to the basics: the need for ecophysiological insights to enhance our understanding of microbial behaviour in the rhizosphere. Plant Soil 373:1–15CrossRefGoogle Scholar
  46. Dini-Andreote F, Andreote FD, Araújo WL, Trevors JT, van Elsas JD (2012) Bacterial genomes: habitat specificity and uncharted organisms. Microbial Ecol 64:1–7CrossRefGoogle Scholar
  47. Dobbelaere S, Okon Y (2007) The plant growth promoting effects and plant responses In: Elmerich C, Newton WE (eds) Associative and endophytic nitrogen fixing bacteria and cyanobacterial associations (Nitrogen fixation: origins applications and research progress) Heidelberg. Springer, VerlagGoogle Scholar
  48. Dobbelare S, Vanderleyden J, Okon Y (2003) Plant growth promoting effects of diazotrophs in the rhizosphere. Crit Rev Plant Sci 22:107–149CrossRefGoogle Scholar
  49. Doornbos R, Loon L, Bakker PHM (2012) Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere A review. Agron Sust Dev 32(1):227–243. doi: 10.1007/s13593–011-0028-y CrossRefGoogle Scholar
  50. Dunne C, Moenne Loccoz Y, de Bruijn FJ, O’Gara F (2000) Overproduction of an inducible extracellular serine protease improves biological control of Pythium ultimum by Stenotrophomonas maltophilia strain W81. Microbiology 146:2069–2078PubMedCrossRefGoogle Scholar
  51. Emmert EAB, Handelsman J (1999) Biocontrol of plant disease: a (gram) positive perspective. FEMS Microbiol Lett 171:1–9PubMedCrossRefGoogle Scholar
  52. Ferrara FIS, Oliveira ZM, Gonzales HHS, Floh EIS, Barbosa HR (2012) Endophytic and rhizospheric enterobacteria isolated from sugar cane have different potentials for producing plant growth-promoting substances. Plant Soil 353:409–417CrossRefGoogle Scholar
  53. Franks A, Ryan RP, Abbas A, Mark GL, O’Gara F (2006) Molecular tools for studying plant growth promoting rhizobacteria. In: Cooper JE, Rao JR (eds) Molecular approaches to soil rhizosphere and plant microorganisms analysis. Biddes Ltd Kings, Lynn, pp 116–131CrossRefGoogle Scholar
  54. Fransson PMA, Johansson EM (2010) Elevated CO2 and nitrogen influence exudation of soluble organic compounds by ectomycorrhizal root systems. FEMS Microbiol Ecol 71(2):186–196. doi: 10.1111/j1574-6941200900795x. PMID:19889031PubMedCrossRefGoogle Scholar
  55. Freiberg E (1998) Microclimatic parameters influencing nitrogen fixation in the phyllosphere in a Costa Rican premontane rain forest. Oecologia 117:9–18PubMedCrossRefGoogle Scholar
  56. Fuentes-Ramirez LE, Caballero-Mellado J (2005) Bacterial biofertilizers. In: Siddiqui ZA (ed) PGPR: biocontrol and biofertilization. Springer, Dordrecht, pp 143–172Google Scholar
  57. Furukawa J, Yamaji N, Wang H, Mitani N, Murata Y, Sato K, Katsuhara M, Takeda K, Ma JF (2007) An aluminum-activated citrate transporter in barley. Plant Cell Physiol 48(8):1081–1091. doi: 10.1093/pcp/pcm091. PMID: 17634181PubMedCrossRefGoogle Scholar
  58. Glick BR (2005) Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase. FEMS Microbiol Lett 251(1):1–7. doi:10.1016/jfemsle2005 07030. PMID:16099604PubMedCrossRefGoogle Scholar
  59. Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169:30–39PubMedCrossRefGoogle Scholar
  60. Glick BR, Cheng Z, Czarny J, Duan J (2007) Promotion of plant growth by ACC deaminase-producing soil bacteria. In: Bakker PAHM, Raaijmakers JM, Bloemberg G, Hofte M, Lemanceau P, Cooke BM (eds) New perspectives and approaches in plant growth-promoting rhizobacteria research. Springer, Dordrecht, pp 329–339CrossRefGoogle Scholar
  61. Gottschalk G (1986) Bacterial metabolism. Springer, Berlin/Heidelberg/New YorkCrossRefGoogle Scholar
  62. Griffin GJ, Hale MG, Shay FJ (1976) Nature and quantity of sloughed organic matter produced by roots of axenic peanut plants. Soil Biol Biochem 8:29–32CrossRefGoogle Scholar
  63. Haas D, Défago G (2005) Biological control of soilborne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 3:307–319PubMedCrossRefGoogle Scholar
  64. Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43:895–914CrossRefGoogle Scholar
  65. Hardoim P, van Overbeek L, van Elsas J (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16:463–471PubMedCrossRefGoogle Scholar
  66. Harman GE, Howell CR, Viterbo A, Chet I, Lorito M (2004) Trichoderma species – opportunistic, avirulent plant symbionts. Nat Rev Microbiol 2:43–56PubMedCrossRefGoogle Scholar
  67. Hartmann A, Rothballer M, Schmid M (2008) Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant Soil 312(1-2):7–14CrossRefGoogle Scholar
  68. Heath MC (1981) A generalized concept of host-parasite specificity. Phytopathology 7:1121–1123CrossRefGoogle Scholar
  69. Hiltner L (1904) Uber neuere Erfahrungen und Probleme auf dem Gebiet der Bodenbakteriologie und unter besonderer Berücksichtigung der Gründüngung und Brachte. Arbeiten der Deutschen Landwirtschaftlichen Gesellschaft 98:59–78Google Scholar
  70. Hirsch PR, Mauchline TH (2012) Who’s who in the plant root microbiome? Nat Biotechnol 30:961–962PubMedCrossRefGoogle Scholar
  71. Ishimaru Y, Kakei Y, Shimo H, Bashir K, Sato Y, Sato Y, Uozumi N, Nakanishi H, Nishizawa NK (2011) A rice phenolic efflux transporter is essential for solubilizing precipitated apoplasmic iron in the plant stele. J Biol Chem 286(28):24649–24655. doi: 10.1074/jbcM111221168. PMID: 21602276PubMedPubMedCentralCrossRefGoogle Scholar
  72. Jackson T (1999) Renewable energy Summary paper for the renewables series. Energy Policy 20:861–883CrossRefGoogle Scholar
  73. Jacobsen BJ, Zidack NK, Larson BJ (2004) The role of Bacillus-based biological control agents in integrated pest management systems: plant diseases. Phytopathology 94:1272–1275PubMedCrossRefGoogle Scholar
  74. Jones K (1970) Nitrogen fixation in phyllosphere of Douglas Fir Pseudotsuga-Douglasii. Ann Bot 34:239–244CrossRefGoogle Scholar
  75. Jones DL, Hodge A, Kuzyakov Y (2004) Plant and mycorrhizal regulation of rhizodeposition. New Phytol 163(3):459–480. doi:10.1111/j1469–81372004 01130x CrossRefGoogle Scholar
  76. Kamilova F, Validov S, Azarova T, Mulders I, Lugtenberg B (2005) Enrichment for enhanced competitive plant root tip colonizers selects for a new class of biocontrol bacteria. Environ Microbiol 7:1809–1817PubMedCrossRefGoogle Scholar
  77. Kang SM, Khan AL, Waqs M, You YH, Kim JH, Kim GK, Hamayun M, Lee IJ (2014) Plant growth promoting rhizobacteria reduce adverse effects of salinity and osmotic stress by regulating phytohormones and antioxidants in Cucumis sativus. J Plant Interact 9:673–682CrossRefGoogle Scholar
  78. Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Ann Rev Microbiol 56:211–236CrossRefGoogle Scholar
  79. Kiers ET, Duhamel M, Beesetty Y, Mensah JA, Franken O, Verbruggen E, Fellbaum CR, Kowalchuk GA, Hart MM, Bago A, Palmer TM, West SA, Vandenkoornhuyse P, Jansa J, Bucking H (2011) Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science 333(6044):880–882. doi: 10.1126/science1208473. PMID:21836016PubMedCrossRefGoogle Scholar
  80. Kinkel LL, Wilson M, Lindow SE (2000) Plant species and plant incubation conditions influence variability in epiphytic bacterial population size. Microb Ecol 39:1–11PubMedCrossRefGoogle Scholar
  81. Kishore GK, Pande S, Podile AR (2005) Biological control of late leaf spot of peanut (Arachis hypogaea) with chitinolytic bacteria. Phytopathology 95:1157–1165PubMedCrossRefGoogle Scholar
  82. Kloepper JW, Schroth MN (1978) Plant growth promoting rhizobacteria on radishes In: Proceedings of the IVth international conference on plant pathogenic bacteria Argers France:Station de Pathologie Vegetale et Phytobacteriologyie INRA, pp 879–882Google Scholar
  83. Lambais MR, Crowley DE, Cury JC, Bull RC, Rodrigues RR (2006) Bacterial diversity in tree canopies of the Atlantic forest. Science 312:1917–1917PubMedCrossRefGoogle Scholar
  84. Leyval C, Berthelin J (1993) Rhizodeposition and net release of soluble organic compounds by pine and beech seedlings inoculated with rhizobacteria and ectomycorrhizal fungi. Biol Fertil Soils 15(4):259–267. doi:10.1007/ bf00337210 CrossRefGoogle Scholar
  85. Li L, He Z, Pandey GK, Tsuchiya T, Luan S (2002) Functional cloning and characterization of a plant efflux carrier for multidrug and heavy metal detoxification. J Biol Chem 277(7):5360–5368. doi: 10.1074/jbcM108777200. PMID:11739388PubMedCrossRefGoogle Scholar
  86. Lindow SE, Brandl MT (2003) Microbiology of the phyllophere. Appl Environ Microbiol 69:1875–1883PubMedPubMedCentralCrossRefGoogle Scholar
  87. Liu J, Magalhaes JV, Shaff J, Kochian LV (2009) Aluminum-activated citrate and malate transporters from the MATE and ALMT families function independently to confer Arabidopsis aluminum tolerance. Plant J 57(3):389–399. doi: 10.1111/j1365-313X200803696x. PMID:18826429PubMedCrossRefGoogle Scholar
  88. Long SR (2001) Genes and signals in the Rhizobium-legume symbiosis. Plant Physiol 125:69–72PubMedPubMedCentralCrossRefGoogle Scholar
  89. Loper JE (1988) Role of fluorescent siderophore production in biological control of Pythium ultirnum by a Pseudomonas fluorescens strain. Phytopathology 78:166–172CrossRefGoogle Scholar
  90. Loper JE, Gross H (2007) Genomic analysis of antifungal metabolite production by Pseudomonas fluorescens Pf5. Eur J Plant Pathol 119:265–278CrossRefGoogle Scholar
  91. Loper JE, Henkels MD (1997) Availability of iron to Pseudomonas fluorescens in rhizosphere and bulk soil evaluated with an ice nucleation reporter gene. Appl Environ Microbiol 63:99–105PubMedPubMedCentralGoogle Scholar
  92. Loyola-Vargas V, Broeckling C, Badri D, Vivanco J (2007) Effect of transporters on the secretion of phytochemicals by the roots of Arabidopsis thaliana. Planta 225(2):301–310. doi: 10.1007/s00425–006–0349-2. PMID:16868775PubMedCrossRefGoogle Scholar
  93. Lucy M, Reed E, Glick BR (2004) Applications of free living plant growth-promoting rhizobacteria. Antonie van Leeuwenhoek 86(1):1–25PubMedCrossRefGoogle Scholar
  94. Lugtenberg BJJ, Dekkers LC (1999) What makes Pseudomonas bacteria rhizosphere competent. Environ Microbiol 1:9–13PubMedCrossRefGoogle Scholar
  95. Lugtenberg BJJ, Chin A, TFC W, Bloemberg GV (2002) Microbe plant interactions: principles and mechanisms. Antonie Van Leeuwenhoek 81:373–383PubMedCrossRefGoogle Scholar
  96. Magalhaes JV, Liu J, Guimaraes CT, Lana UGP, Alves VMC, Wang Y-H, Schaffert RE, Hoekenga OA, Pineros MA, Shaff JE, Klein PE, Carneiro NP, Coelho CM, Trick HN, Kochian LV (2007) A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum. Nat Genet 39(9):1156–1161. doi: 10.1038/ng2074. PMID: 17721535PubMedCrossRefGoogle Scholar
  97. Matilla MA, Ramos JL, Bakker PAHM, Doornbos R, Badri DV, Vivanco JM, Ramos-Gonzalez MI (2010a) Pseudomonas putida KT2440 causes induced systemic resistance and changes in Arabidopsis root exudation. Environ Microbiol 2(3):381–382Google Scholar
  98. Matilla MA, Ramos JL, Bakker PAHM, Doornbos R, Badri DV, Vivanco JM, Ramos-Gonzalez MI (2010b) Pseudomonas putida KT2440 causes induced systemic resistance and changes in Arabidopsis root exudation. Environ Microbiol Rep 2(3):381–388. doi:10.1111/j1758–22292009 00091x. PMID:23766110PubMedCrossRefGoogle Scholar
  99. Mayak S, Tirosh T, Glick BR (2004) Plant growth-promoting bacteria confer resistance in tomato plants to salt stress. Plant Physiol Biochem 42(6):565–572. doi: 10.1016/jplaphy200405009. PMID:15246071PubMedCrossRefGoogle Scholar
  100. Meier IC, Avis PG, Phillips RP (2013) Fungal communities influence root exudation rates in pine seedlings. FEMS Microbiol Ecol 83(3):585–595. doi: 10.1111/1574–694112016. PMID:23013386PubMedCrossRefGoogle Scholar
  101. Mendes R, Pizzirani-Kleiner AA, Araujo WL, Raaijmakers JM (2007) Diversity of cultivated endophytic bacteria from sugarcane: genetic and biochemical characterization of Burkholderia cepacia complex isolates. Appl Environ Microbiol 73(22):7259–7267PubMedPubMedCentralCrossRefGoogle Scholar
  102. Mercado-Blanco J, Bakker P (2007) Interactions between plants and beneficial Pseudomonas spp: exploiting bacterial traits for crop protection. Antonie van Leeuwenhoek 92(4):367–389. doi: 10.1007/s10482–007–9167-1 PubMedCrossRefGoogle Scholar
  103. Micallef SA, Channer S, Shiaris MP, Colon-Carmona A (2009a) Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere. Plant Signal Behav 4(8):777–780. doi: 10.4161/psb489229. PMID:19820328PubMedPubMedCentralCrossRefGoogle Scholar
  104. Micallef SA, Shiaris MP, Colon-Carmona A (2009b) Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot 60(6):1729–1742. doi: 10.1093/jxb/erp053. PMID:19342429PubMedPubMedCentralCrossRefGoogle Scholar
  105. Mitter B, Petric A, Shin MW, Chain PSG, Hauberg-Lotte L, Reinhold-Hurek B, Nowak J, Sessitsch A (2013) Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Front Plant Sci 4:120PubMedPubMedCentralCrossRefGoogle Scholar
  106. Morgan JAW (2005) Biological costs and benefits to plant-microbe interactions in the rhizosphere. J Exp Bot 56(417):1729–1739PubMedCrossRefGoogle Scholar
  107. Morris CE, Kinkel LL (2002) Fifty years of phyllosphere microbiology: significant contributions to research in related fields. In: Lindow SE, Hecht-Poinar EI, Elliott V (eds) Phyllosphere microbiology. APS Press, St Paul, pp 365–375Google Scholar
  108. Müller H, Westendorf C, Leitner E, Chernin L, Riedel K, Schmidt S, Eberl L, Berg G (2009) Quorumsensing effects in the antagonistic rhizosphere bacterium Serratia plymuthica HROC48 FEMS. Microbiol Ecol 67:468–478. doi: 10.1111/j.1574-6941.2008.00635.x. PMID: 19220861 CrossRefGoogle Scholar
  109. Narasimhan K, Basheer C, Bajic VB, Swarup S (2003) Enhancement of plant–microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiol 132(1):146–153. doi: 10.1104/pp102016295. PMID:12746520PubMedPubMedCentralCrossRefGoogle Scholar
  110. Nelson E (1990) Exudate molecules initiating fungal responses to seeds and roots. Plant Soil 129:61–73Google Scholar
  111. Newton AC, BDL F, Atkins SD, Walters DR, Daniell TJ (2010) Pathogenesis parasitism and mutualism in the trophic space of microbe–plant interactions. Trends Microbiol 18(8):365–373. doi: 10.1016/jtim201006002. PMID:20598545PubMedCrossRefGoogle Scholar
  112. Nguyen C (2003) Rhizodeposition of organic C by plants:mechanisms and controls. Agronomie 23:375–396CrossRefGoogle Scholar
  113. O’Brien RD, Lindow SE (1989) Effect of plant species and environmental conditions on epiphytic population sizes of Pseudomonas syringae and other bacteria. Phytopathology 79:619–627CrossRefGoogle Scholar
  114. Odum EP (1971) Fundamentals of ecology. Saunders, PhiladelphiaGoogle Scholar
  115. Olubukola O, Babalola O, Glick BR (2012) The use of microbial inoculants in African agriculture. Food Agric Environ 10:540–549Google Scholar
  116. Ongena M, Thonart P (2006) Resistance induced in plants by nonpathogenic microorganisms: elicitation and defense responses. In: Teixeira da Silva JA (ed) Floriculture ornamental and plant biotechnology: advances and topical issues. Global Science Books, London, pp 447–463Google Scholar
  117. Penrose DM, Glick BR (2003) Methods for isolating and characterizing ACC deaminase containing plant growth-promoting rhizobacteria. Physiol Plant 118:10–15.Google Scholar
  118. Petrini O (1991) Fungal endophytes of tree leaves. In: Fokkema NJ, van den Heuvel (eds) Microbial ecology of the leaves. Cambridge University Press, Cambridge, pp 185–187Google Scholar
  119. Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799PubMedCrossRefGoogle Scholar
  120. Pierik R, Tholen D, Poorter H, Visser EJW, Laurentius ACJ, Voesenek (2006) The Janus face of ethylene: growth inhibition and stimulation. Trends Plant Sci 11:176–183PubMedCrossRefGoogle Scholar
  121. Pinton R, Veranini Z, Nannipieri P (2007) The rhizosphere biochemistry and organic substances at the soil plant interface. Taylor, Francis Group LLC, New YorkCrossRefGoogle Scholar
  122. Quecine MC, Araujo WL, Tsui S, Parra JRP, Azevedo JL, Pizzirani-Kleiner AA (2014) Control of Diatraea saccharalis by the endophytic Pantoea agglomerans 331 expressing cry1Ac7. Arch Microbiol 196:227–234PubMedCrossRefGoogle Scholar
  123. Raaijmakers JM, Vlami M, de Souza JT (2002) Antibiotic production by bacterial biocontrol agents. Antonie Van Leeuwenhoek 81:537–547PubMedCrossRefGoogle Scholar
  124. Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, van Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361CrossRefGoogle Scholar
  125. Rastogi G, Sbodio A, Tech JJ, Suslow TV, Coaker GL, Leveau JHJ (2012) Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce. ISME J 6:1812–1822PubMedPubMedCentralCrossRefGoogle Scholar
  126. Reddy VS, Shlykov MA, Castillo R, Sun EI, Saier MH (2012) The major facilitator superfamily (MFS) revisited. FEBS J 279(11):2022–2035. doi:10.1111/ j1742-4658201208588x. PMID:22458847PubMedPubMedCentralCrossRefGoogle Scholar
  127. Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N (2010) The ecology of the phyllosphere: geographic and phyllogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 12:2885–2893PubMedPubMedCentralCrossRefGoogle Scholar
  128. Rizzo DM, Garbelotto M, Hansen EA (2005) Phytophthora ramorum: integrative research and management of an emerging pathogen in California and Oregon forests. Annu Rev Phytopathol 43:309–335PubMedCrossRefGoogle Scholar
  129. Rosenblueth M, Martinez-Romero E (2006) Bacterial endophytes and their interactions with hosts molecular plant-microbe interactions 19:827–837PubMedCrossRefGoogle Scholar
  130. Rosling A, Lindahl BD, AFS T, Finlay RD (2004) Mycelial growth and substrate acidification of ectomycorrhizal fungi in response to different minerals. FEMS Microbiol Ecol 47(1):31–37. doi: 10.1016/S0168–6496(03)00222–8. PMID:19712344PubMedCrossRefGoogle Scholar
  131. Ryan RP, Monchy S, Cardinale M, Taghavi S, Crossman L, Avison MB, Berg G, van der Lelie D, Dow JM (2009) Versatility and adaptation of bacteria from the genus Stenotrophomonas. Nat Microbiol Rev 7:514–525CrossRefGoogle Scholar
  132. Saikkonen K, Faeth SH, Helander M, Sullivan TJ (1998) Fungal endophytes: a continuum of interactions with host plants. Ann Rev Ecol Syst 29:319–343CrossRefGoogle Scholar
  133. Salisbury FB (1994) The role of plant hormones. In: Wilkinson RE (ed) Plant-environment interaction. Dekker, New York, pp 39–81Google Scholar
  134. Schrey SD, Tarkka MT (2008) Friends and foes:streptomycetes as modulators of plant disease and symbiosis. Antonie Van Leeuwenhoek 94:11–19PubMedCrossRefGoogle Scholar
  135. Schroth MN, Hildebrand DC (1964) Influence of plant exudates on root infecting fungi. Annu Rev Phytopathol 2(10):11–32Google Scholar
  136. Sengupta A, Gunri S (2015) Microbial intervention in agriculture: an overview. Afr J Microbiol Res 9(18):1215–1226CrossRefGoogle Scholar
  137. Shoda M (2000) Bacterial control of plant diseases. J Biosci Bioeng 89:515–521PubMedCrossRefGoogle Scholar
  138. Sivakumar PV, Thamizhiniyan P (2012) Enhancement in growth and yield of tomato by using AM fungi and Azospirillum. Int J Environ Biol 2(3):137–141Google Scholar
  139. Stearns JC, Woody OZ, McConkey BJ, Glick BR (2012) Effects of bacterial ACC deaminase on Brassica napus gene expression. Mol Plant Microb Interact 25(5):668–676. doi: 10.1094/MPMI-08-11-0213. PMID:22352713CrossRefGoogle Scholar
  140. Steenhoudt O, Vanderleyden J (2000) Azospirillum a free-living nitrogen-fixing bacterium closely associated with grasses: genetic biochemical and ecological aspects. FEMS Microbiol Rev 24:487–506PubMedCrossRefGoogle Scholar
  141. Steinkellner S, Lendzemo V, Langer I, Schweiger P, Khaosaad T, Toussaint JP, Vierheilig H (2007) Flavonoids and strigolactones in root exudates as signals in symbiotic and pathogenic plant–fungus interactions. Molecules 12(7):1290–1306. doi: 10.3390/12071290. PMID:17909485PubMedCrossRefGoogle Scholar
  142. Sugiyama A, Shitan N, Yazaki K (2008) Signaling from soybean roots to Rhizobium:an ATP-binding cassette-type transporter mediates genistein secretion. Plant Signal Behav 3(1):38–40. doi: 10.4161/psb314819. PMID:19704765PubMedPubMedCentralCrossRefGoogle Scholar
  143. Tournas VH, Katsoudas E (2005) Mould and yeast flora in fresh berries grapes and citrus fruits. Int J Food Microbiol 105:1117CrossRefGoogle Scholar
  144. Unno Y, Okubo K, Wasaki J, Shinano T, Osaki M (2005) Plant growth promotion abilities and microscale bacterial dynamics in the rhizosphere of lupin analysed by phytate utilization ability. Environ Microbiol 7:396–404PubMedCrossRefGoogle Scholar
  145. Uren NC (2000) Types amounts and possible functions of compounds released into the rhizosphere by soil-grown plants. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere: biochemistry and organic substances at the soil–plant interface. Marcel Dekker, New York, pp 19–40Google Scholar
  146. van Etten HD, Mansfield JW, Bailey JA, Farmer EE (1994) Two classes of plant antibiotics: phytoalexins versus phytoanticipins. Plant Cell 6:1191–1192CrossRefGoogle Scholar
  147. Van Loon LC (2007) Plant responses to plant growth promoting bacteria. Eur J Plant Pathol 119:243–254CrossRefGoogle Scholar
  148. van Veen JA, van Overbeek LS, van Elisas JD (1997) Fate and activity of microorganisms introduced into soil. Microbiol Mol Biol Rev 61:121–135PubMedPubMedCentralGoogle Scholar
  149. Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255:571–586CrossRefGoogle Scholar
  150. Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev 10:828–840Google Scholar
  151. Weger LA, van Arendonk JJCM, Recourt K, van der Hofstad GAJM, Weisbeek PJ, Lugtenberg B (1988) Siderophore mediated uptake of Fe3+ by the plant growth stimulating Pseudomonas putida strain WCS358 and by other rhizosphere microorganisms. J Bacteriol 170:4693–4698PubMedPubMedCentralCrossRefGoogle Scholar
  152. Weller DM (1988) Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annu Rev Phytopathol 26:379–407CrossRefGoogle Scholar
  153. Weston LA, Ryan PR, Watt M (2012) Mechanisms for cellular transport and release of allelochemicals from plant roots into the rhizosphere. J Exp Bot 63(9):3445–3454PubMedCrossRefGoogle Scholar
  154. Whipps JM (2001) Microbial interactions and biocontrol in the rhizosphere. J Exp Bot 52:487–511PubMedCrossRefGoogle Scholar
  155. Yang J, Kloepper JW, Ryu CM (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14(1):1–4. doi:10.1016/jtplants2008 10004. PMID:19056309PubMedCrossRefGoogle Scholar
  156. Yazaki K (2005) Transporters of secondary metabolites. Curr Opin Plant Biol 8(3):301–307. doi: 10.1016/jpbi200503011. PMID: 15860427PubMedCrossRefGoogle Scholar
  157. Zahran HH (1999) Rhizobium–legume symbiosis and nitrogen fixation under severe conditions and in an arid climate. Microbiol Mol Biol Rev 63(4):968–989. PMID: 10585971PubMedPubMedCentralGoogle Scholar
  158. Zhang J, Subramanian S, Stacey G, Yu O (2009) Flavones and flavonols play distinct critical roles during nodulation of Medicago truncatula by Sinorhizobium meliloti. Plant J 57(1):171–183. doi:10.1111/j1365-313X2008 03676x. PMID:18786000PubMedCrossRefGoogle Scholar
  159. Zolla G, Badri DV, Bakker MG, Manter DK, Vivanco JM (2013) Soil microbiomes vary in their ability to confer drought tolerance to Arabidopsis. Appl Soil Ecol 68:1–9. doi: 10.1016/japsoil201303007 CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Amrita Sengupta
    • 1
    Email author
  • Sunil Kumar Gunri
    • 1
  • Tapas Biswas
    • 2
  1. 1.Department of Agronomy, Faculty of AgricultureBidhan Chandra Krishi ViswavidyalayaMohanpur, NadiaIndia
  2. 2.Department of Agricultural Chemistry and Soil Science, Faculty of AgricultureBidhan Chandra Krishi ViswavidyalayaMohanpur, NadiaIndia

Personalised recommendations