Plant Growth Promotion and Biocontrol Mediated by Plant-Associated Bacteria

  • Miguel A. MatillaEmail author
  • Tino Krell
Part of the Microorganisms for Sustainability book series (MICRO, volume 5)


The rhizosphere, defined as the volume of soil under the physical, chemical and biological influences of plant roots, is a region of enormous microbial diversity and activity. This microbial activity is essential for plant nutrition and health since it favours the uptake of nutrients by the plant and offers resistance against a wide range of plant pathogens. Bacteria are the main microbial representatives in the rhizosphere, and plant growth-promoting rhizobacteria (PGPR) stimulate plant growth by multiple mechanisms. In this chapter, we present an overview of the strategies employed by PGPR to exert their beneficial effects on the colonized plants. The direct effects of PGPR on plant growth are mainly derived from their capacity to improve the nutritional status of plants and the production of phytohormones. Alternatively, beneficial rhizospheric bacteria can also promote plant health by protecting plants against pathogens mainly through the induction of systemic resistance and the production of exoenzymes and multiple antagonistic metabolites. Here, special attention has been given to the biosynthesis and biological activities of bioactive volatiles, non-ribosomal peptides and polyketides by PGPR. Finally, the promising use of PGPR-based products as sustainable agricultural practices is discussed.


Plant growth-promoting rhizobacteria Phytohormones Biocontrol Induced systemic resistance Bioactive secondary metabolites 



Miguel A. Matilla was supported by the Spanish Ministry of Economy and Competitiveness Postdoctoral Research Program, Juan de la Cierva (JCI-2012-11815). The Tino Krell laboratory is supported by FEDER funds and Fondo Social Europeo through grants from the Junta de Andalucía (grant CVI-7335) and the Spanish Ministry for Economy and Competitiveness (grant BIO2013-42297). We thank Angel J. Matilla (Department of Plant Physiology, University of Santiago de Compostela, Spain) for the critical review of this chapter and for his advice on the phytohormone section.


  1. Abdel-Lateif K, Bogusz D, Hocher V (2012) The role of flavonoids in the establishment of plant roots endosymbioses with arbuscular mycorrhiza fungi, rhizobia and Frankia bacteria. Plant Signal Behav 7:636–641PubMedPubMedCentralCrossRefGoogle Scholar
  2. Adie BA, Pérez-Pérez J, Pérez-Pérez MM, Godoy M, Sánchez-Serrano JI, Schmelz EA (2007) ABA is an essential signal for plant resistance to pathogens affecting JA biosynthesis and the activation of defenses in Arabidopsis. Plant Cell 19:1665–1681PubMedPubMedCentralCrossRefGoogle Scholar
  3. Aguado-Santacruz GAA, Moreno-Gómez BA, Jiménez-Francisco BB, García-Moya EB, Preciado-Ortiz RE (2012) Impact of the microbial siderophores and phytosiderophores on the iron assimilation by plants: a synthesis. Rev Fitotec Mex 35:9–21Google Scholar
  4. Ahemad M, Kribet M (2014) Mechanisms and applications of plant growth promoting rhizobacteria: current perspective. J King Saud Univ-Sci 26:1–20CrossRefGoogle Scholar
  5. Ahirwar N (2015) PGPR current and future prospects for development of sustainable agriculture. J Microbiol Biotechnol 7:96–102Google Scholar
  6. Ahmed E, Homlströn SJM (2014) Siderophores in environmental research: roles and applications. Microb Biotechnol 7:196–208PubMedPubMedCentralCrossRefGoogle Scholar
  7. Aira M, Gómez-Brandón M, Lazcano C, Baath E, Domínguez E (2010) Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities. Soil Biol Biochem 42:2276–2281CrossRefGoogle Scholar
  8. Alström S (1991) Induction of disease resistance in common bean susceptible to halo blight bacterial pathogen after seed bacterization with rhizosphere pseudomonads. J Gen Appl Microbiol 37:495–501CrossRefGoogle Scholar
  9. Andreote F, Mendes R, Dini-Andreote F, Rossetto PB, Labate CA, Pizzirani-Kleiner AA, Van Elsas JD, Azevedo JL, Araújo WL (2008) Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development. Antonie Van Leeuwenhoek 93:415–424PubMedCrossRefGoogle Scholar
  10. Antoun H, Prevost D (2006) Ecology of plant growth promoting rhizobacteria. In: Siddiqui ZAS (ed) PGPR: biocontrol and biofertilization. Springer, Dordrecht, pp 1–38Google Scholar
  11. Arkhipova TN, Veselov SU, Melentiev AI, Martynenko EV, Kudoyarova GR (2005) Ability of bacterium Bacillus subtilis to produce cytokinins and to influence the growth and endogenous hormone content of lettuce plants. Plant Soil 272:201–209CrossRefGoogle Scholar
  12. Asselbergh B, Achuo AE, Hofte M, Van Gijsegem F (2008) Abscisic acid deficiency leads to rapid activation of tomato defense responses upon infection with Erwinia chrysanthemi. Mol Plant Pathol 9:11–24PubMedGoogle Scholar
  13. Audrain B, Farag MA, Ryu CM, Ghigo JM (2015) Role of bacterial volatile compounds in bacterial biology. FEMS Microbiol Rev 39:222–233PubMedCrossRefGoogle Scholar
  14. Aznar A, Dellagi A (2015) New insights into the role of siderophores as triggers of plant immunity: what can we learn from animals? J Exp Bot 66:3001–3010PubMedCrossRefGoogle Scholar
  15. Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32:666–681PubMedCrossRefGoogle Scholar
  16. 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 151:2006–2017PubMedPubMedCentralCrossRefGoogle Scholar
  17. Badri DV, Chaparro JM, Zhang R, Shen Q, Vivanco JM (2013) 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 288:4502–4512PubMedPubMedCentralCrossRefGoogle Scholar
  18. Baez U, Martinoia E (2013) Root exudates: the hidden part of plant defense. Trends Plant Sci 19:90–97Google Scholar
  19. Bailly A, Weisskopf L (2012) The modulating effect of bacterial volatiles on plant growth: current knowledge and future challenges. Plant Signal Behav 7:79–85PubMedPubMedCentralCrossRefGoogle Scholar
  20. 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 57:233–266PubMedCrossRefGoogle Scholar
  21. Bakker AW, Schippers B (1987) Microbial cyanide production in the rhizosphere in relation to potato yield reduction and Pseudomonas SPP-mediated plant growth-stimulation. Soil Biol Biochem 19:451–457CrossRefGoogle Scholar
  22. Bakker PA, Berendsen RL, Doornbos RL, Wintermans PC, Pieterse CM (2013) The rhizosphere revisited: root microbiomics. Front Plant Sci 165:1–7Google Scholar
  23. Bakker MG, Schlatter DC, Otto-Hanson L, Kinkel LL (2014) Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome. Mol Ecol 23:1571–1583PubMedCrossRefGoogle Scholar
  24. Bari R, Jone JDG (2009) Role of plant hormones in plant defence responses. Plant Mol Biol 69:473–488PubMedCrossRefGoogle Scholar
  25. Bashan Y, de-Bashan LE, Prabhu SR, Hernández JP (2014) Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013). A review. Plant Soil 378:1–33CrossRefGoogle Scholar
  26. Belimov AA, Dodd IC, Safronova VI, Dumova VA, Shaposhnikov AI, Ladatko AG, Davies WJ (2014) Abscisic acid metabolizing rhizobacteria decrease ABA concentrations in planta and alter plant growth. Plant Physiol Biochem 74:84–91PubMedCrossRefGoogle Scholar
  27. Berendsen RL, Pieterse CMJ, Bakker PAHM (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486PubMedCrossRefGoogle Scholar
  28. Berg G (2009) Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. App Microbiol Biotech 14:11–18CrossRefGoogle Scholar
  29. Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1–13PubMedCrossRefGoogle Scholar
  30. Bishop PE, Jorerger RD (1990) Genetics and molecular biology of an alternative nitrogen fixation system. Plan Mol Biol 41:109–125Google Scholar
  31. Bitas V, Kim HS, Bennett JW, Kang S (2013) Sniffing on microbes: diverse roles of microbial volatile organic compounds in plant health. Mol Plant-Microbe Interact 26:835–843PubMedCrossRefGoogle Scholar
  32. Blom D, Fabbri C, Connor E, Schiestl F, Klauser D, Boller T et al (2011) Production of plant growth modulating volatiles is widespread among rhizosphere bacteria and strongly depends on culture conditions. Environ Microbiol 13:3047–3058PubMedCrossRefGoogle Scholar
  33. Blumer C, Haas D (2000) Mechanism, regulation, and ecological role of bacterial cyanide biosynthesis. Arch Microbiol 173:170–177PubMedCrossRefGoogle Scholar
  34. Boller T, Felix G (2009) A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu Rev Plant Biol 60:379–406PubMedCrossRefGoogle Scholar
  35. Brandl H, Lehmann S, Faramarzi MA, Martinell D (2008) Biomobilization of silver, gold, and platinum from solid waste materials by HCN-forming microorganisms. Hydrometallurgy 94:14–17CrossRefGoogle Scholar
  36. Bulgarelli D, Schlaeppi K, Spaeten S, Ver Loren Van Themaat E, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838PubMedCrossRefGoogle Scholar
  37. Burdon JJ, Thrall PH (2009) Coevolution of plants and their pathogens in natural habitats. Science 324:755–756PubMedPubMedCentralCrossRefGoogle Scholar
  38. Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, Vivanco JM (2013a) Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One 8:e55731PubMedPubMedCentralCrossRefGoogle Scholar
  39. Chaparro JM, Badri DV, Vivanco JM (2013b) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790–803PubMedPubMedCentralCrossRefGoogle Scholar
  40. Chen XH, Vater J, Piel J, Franke P, Scholz R, Schneider K, Koumoutsi A, Hitzeroth G, Grammel N, Strittmatter AW, Gottschalk G, Süssmuth RD, Borriss R (2006) Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amyloliquefaciens FZB 42. J Bacteriol 188:4024–4036PubMedPubMedCentralCrossRefGoogle Scholar
  41. Chen XH, Koumoutsi A, Scholz R, Borriss R (2009a) More than anticipated – production of antibiotics and other secondary metabolites by Bacillus amyloliquefaciens FZB42. J Mol Microbiol Biotechnol 16:14–24PubMedCrossRefGoogle Scholar
  42. Chen XH, Scholz R, Borriss M, Junge H, Mögel G, Kunz S, Borriss R (2009b) Difficidin and bacilysin produced by plant-associated Bacillus amyloliquefaciens are efficient in controlling fire blight disease. J Biotechnol 140:38–44PubMedCrossRefGoogle Scholar
  43. Chernin L, Chet I (2002) Microbial enzymes in biocontrol of plant pathogens and pests. In: Burns RG, Dick RP (eds) Enzymes in the environment: activity, ecology, and applications. Marcel Dekker, New York, pp 171–225Google Scholar
  44. Cho SM, Kang BR, Han SH, Anderson AJ, Park JY, Lee YH, Cho BH, Yang KY, Ryu CM, Kim YC (2008) 2R,3R-butanediol, a bacterial volatile produced by Pseudomonas chlororaphis O6, is involved in induction of systemic tolerance to drought in Arabidopsis thaliana. Mol Plant-Microbe Interact 21:1067–1075PubMedCrossRefGoogle Scholar
  45. Chowdhury SP, Hartmann A, Gao X, Borriss R (2015a) Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42 – a review. Front Microbiol 6:780PubMedPubMedCentralCrossRefGoogle Scholar
  46. Chowdhury SP, Uhl J, Grosch R, Alquéres S, Pittroff S, Dietel K, Schmitt-Kopplin P, Borriss R, Hartmann A (2015b) Cyclic Lipopeptides of Bacillus amyloliquefaciens subsp. plantarum colonizing the lettuce rhizosphere enhance plant defense responses toward the bottom rot pathogen Rhizoctonia solani. Mol Plant-Microbe Interact 28:984–995PubMedCrossRefGoogle Scholar
  47. Chung J, Song GC, Ryu CM (2016) Sweet scents from good bacteria: case studies on bacterial volatile compounds for plant growth and immunity. Plant Mol Biol 90:677–687PubMedCrossRefGoogle Scholar
  48. Cohen AC, Bottini R, Piccoli P (2008) Azospirillum brasilense Sp 245 produces ABA in chemically-defined culture medium and increases ABA content in Arabidopsis plants. Plant Growth Regul 54:97–103CrossRefGoogle Scholar
  49. Cohen AC, Bottini R, Pontin M, Berli FJ, Moreno D, Boccanlandro H, Travaglia CN, Piccoli PN (2015) Azospirillum brasilense ameliorates the response of Arabidopsis thaliana to drought mainly via enhancement of ABA levels. Physiol Plant 153:79–90PubMedCrossRefGoogle Scholar
  50. Compant S, Duffy B, Nowak J, Clément 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
  51. Conrath U, Beckers GJM, Flors V, García-Agustín P, Jakab G et al (2006) Priming: getting ready for battle. Mol Plant-Microbe Interact 19:1062–1071PubMedCrossRefGoogle Scholar
  52. Contesto C, Milesi S, Mantelin S, Zancarini A, Desbrosses G, Varoquaux F (2010) The auxin-signaling pathway is required for the lateral root response of Arabidopsis to the rhizobacterium Phyllobacterium brassicacearum. Planta 232:1455–1470PubMedCrossRefGoogle Scholar
  53. Corral-Lugo A, De la Torre J, Matilla MA, Fernández M, Morel B, Espinosa-Urgel M, Krell T (2016) Assessment of the contribution of chemoreceptor-based signalling to biofilm formation. Environ Microbiol 18:3355–3372PubMedCrossRefGoogle Scholar
  54. Cronin D, Moenne-Loccoz Y, Fenton A, Dunne C, Dowling DN, O’gara F (1997) Role of 2,4-Diacetylphloroglucinol in the Interactions of the biocontrol Pseudomonad strain F113 with the potato cyst nematode Globodera rostochiensis. Appl Environ Microbiol 63:1357–1361PubMedPubMedCentralGoogle Scholar
  55. D’Alessandro M, Erb M, Ton J, Brandenburg A, Karlen D, Zopfi J, Turlings TC (2014) Volatiles produced by soil-borne endophytic bacteria increase plant pathogen resistance and affect tritrophic interactions. Plant Cell Environ 37:813–826PubMedCrossRefGoogle Scholar
  56. Dandurishvili N, Toklikishvili N, Ovadis M, Eliashvili P, Giorgobiani N, Keshelava R, Tediashvili M, Vainstein A, Khmel I, Szegedi E, Chernin L (2011) Broad-range antagonistic rhizobacteria Pseudomonas fluorescens and Serratia plymuthica suppress Agrobacterium crown gall tumours on tomato plants. J Appl Microbiol 110:341–352PubMedCrossRefGoogle Scholar
  57. Danhorn T, Fuqua C (2007) Biofilm formation by plant-associated bacteria. Annu Rev Microbiol 61:401–422PubMedCrossRefGoogle Scholar
  58. De García Salamone IE, Hynes RK, Nelson LM (2001) Cytokinin production by plant growth promoting rhizobacteria and selected mutants. Can J Microbiol 47:404–411CrossRefGoogle Scholar
  59. De la Peña C, Lei Z, Watson BS, Sumner LW, Vivanco JM (2008) Root-microbe communication through protein secretion. J Biol Chem 283:25247–25255CrossRefGoogle Scholar
  60. de Souza JT, Arnould C, Deulvot C, Lemanceau P, Gianinazzi-Pearson V, Raaijmakers JM (2003) Effect of 2,4-diacetylphloroglucinol on Pythium: cellular responses and variation in sensitivity among propagules and species. Phytopathology 93:966–975PubMedCrossRefGoogle Scholar
  61. de Torres Zabala M, Bennett MH, Truman WH, Grant MR (2009) Antagonism between salicylic and abscisic acid reflects early host pathogen conflict and moulds plant defence responses. Plant J 59:375–386PubMedCrossRefGoogle Scholar
  62. de Torres-Zabala M, Truman W, Bennett MH, Lafforgue G, Mansfield JW, Rodriguez Egea P, Bogre L, Grant M (2007) Pseudomonas syringae pv. tomato hijacks the Arabidopsis abscisic acid signalling pathway to cause disease. EMBO J 26:1434–1443PubMedPubMedCentralCrossRefGoogle Scholar
  63. De Vleesschauwer D, Höfte M (2007) Using Serratia plymuthica to control fungal pathogens of plants. CAB Rev Perspect Agric Vet Sci Nutr Nat Resour 2:1–12Google Scholar
  64. De Vleesschauwer D, Höfte M (2009) Rhizobacteria-induced systemic resistance. Adv Bot Res 51:223–281CrossRefGoogle Scholar
  65. De Vrieze M, Pandey P, Bucheli TD, Varadarajan AR, Ahrens CH, Weisskopf L, Bailly A (2015) Volatile organic compounds from native potato-associated Pseudomonas as potential anti-oomycete agents. Front Microbiol 6:1295PubMedPubMedCentralCrossRefGoogle Scholar
  66. Debois D, Jourdan E, Smargiasso N, Thonart P, De Pauw E, Ongena M (2014) Spatiotemporal monitoring of the antibiome secreted by Bacillus biofilms on plant roots using MALDI mass spectrometry imaging. Anal Chem 86:4431–4438PubMedCrossRefGoogle Scholar
  67. Denancé N, Sánchez-Vallet A, Goffner D, Molina A (2013) Disease resistance or growth: the role of plant hormones in balancing immune responses and fitness costs. Front Plant Sci 4:155PubMedPubMedCentralCrossRefGoogle Scholar
  68. Dickschat JS, Martens R, Brinkhoff T, Simon M, Schulz S (2005) Volatiles released by a Streptomyces species isolated from the North Sea. Chem Biodivers 2:837–865PubMedCrossRefGoogle Scholar
  69. Domik D, Thürmer A, Weise T, Brandt W, Daniel R, Piechulla B (2016) A terpene synthase is involved in the synthesis of the volatile organic compound sodorifen of Serratia plymuthica 4Rx13. Front Microbiol 7:737PubMedPubMedCentralCrossRefGoogle Scholar
  70. Doornbos L, Van Loon L, Bakker PAHM (2012) Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review. Agron Sustain Dev 32:227–243CrossRefGoogle Scholar
  71. Drogue B, Combes-Meynet E, Moënne-Loccoz Y, Wisniewski-Dyé F, Prigent-Combaret C (2013) Control of the cooperation between plant growth-promoting rhizobacteria and crops by rhizosphere signals. de Bruijn, F.J. Molecular microbial ecology of the rhizosphere. 1 and 2. Wiley, Hoboken, 281–294Google Scholar
  72. Du L, Shen B (2001) Biosynthesis of hybrid peptide-polyketide natural products. Curr Opin Drug Discov Devel 4:215–228PubMedGoogle Scholar
  73. Duca D, Lorv J, Patten CL, Rose D, Glick BR (2014) Indole-3-acetic acid in plant-microbe interactions. Antonie Van Leeuwenhoek 106:85–125PubMedCrossRefGoogle Scholar
  74. Dudareva N, Klempien A, Muhlemann JK, Kaplan I (2013) Biosynthesis, function and metabolic engineering of plant volatile organic compounds. New Phytol 198:16–32PubMedCrossRefGoogle Scholar
  75. Dunne C, Moënne-Loccoz Y, McCarthy J, Higgins P, Powell J, Dowling DN et al (1998) Combining proteolytic and phloroglucinol-producing bacteria for improved biocontrol of Pythium-mediated damping-off of sugar beet. Plant Pathol 47:299–307CrossRefGoogle Scholar
  76. Dutta S, Podile AR (2010) Plant growth promoting rhizobacteria (PGPR): the bugs to debug the root zone. Crit Rev Microbiol 36:232–244PubMedCrossRefGoogle Scholar
  77. Effmert U, Kalderas JJ, Warnke R, Piechulla B (2012) Volatile mediated interactions between bacteria and fungi in the soil. J Chem Ecol 36:665–703CrossRefGoogle Scholar
  78. Elshafie HS, Camele I, Racioppi R, Scrano L, Iacobellis NS, Bufo SA (2012) In vitro antifungal activity of Burkholderia gladioli pv. agaricicola against some phytopathogenic fungi. Int J Mol Sci 13:16291–16302PubMedPubMedCentralCrossRefGoogle Scholar
  79. Fan B, Carvalhais LC, Becker A, Fedoseyenko D, von Wirén N, Borriss R (2012) Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates. BMC Microbiol 12:116PubMedPubMedCentralCrossRefGoogle Scholar
  80. Farag MA, Zhang H, Ryu CM (2013) Dynamic chemical communication between plants and bacteria through airborne signals: induced resistance by bacterial volatiles. J Chem Ecol 39:1007–1018PubMedPubMedCentralCrossRefGoogle Scholar
  81. Fenton AM, Stephens PM, Crowley J, O’Callaghan M, O’Gara F (1992) Exploitation of gene(s) involved in 2,4-diacetylphloroglucinol biosynthesis to confer a new biocontrol capability to a Pseudomonas strain. Appl Environ Microbiol 58:3873–3878PubMedPubMedCentralGoogle Scholar
  82. Fernando WGD, Ramarathnam R, Krishnamoorthy AS, Savchuk SC (2005) Identification and use of potential bacterial organic antifungal volatiles in biocontrol. Soil Biol Biochem 37:955–964CrossRefGoogle Scholar
  83. Finkelstein R (2013) Abscisic acid synthesis and response. Arabidopsis Book 11:e0166PubMedPubMedCentralCrossRefGoogle Scholar
  84. Fisch KM (2013) Biosynthesis of natural products by microbial iterative hybrid PKS–NRPS. RSC Adv 3:18228–18247CrossRefGoogle Scholar
  85. Fischbach MA, Walsh CT (2009) Antibiotics for emerging pathogens. Science 325:1089–1093PubMedPubMedCentralCrossRefGoogle Scholar
  86. Flaishman M, Eyal Z, Zilberstein A, Voisard C, Haas D (1996) Suppression of Septoria tritici leaf blotch and leaf and rust of wheat by recombinant cyanide-producing strains of Pseudomonas putida. Mol Plant-Microbe Interact 9:642–645CrossRefGoogle Scholar
  87. Frankenberger WT, Arshad M (1995) Phytohormones in soils: production and function. Marcel Dekker, New YorkGoogle Scholar
  88. Frapolli M, Défago G, Moënne-Loccoz Y (2010) Denaturing gradient gel electrophoretic analysis of dominant 2,4-diacetylphloroglucinol biosynthetic phlD alleles in fluorescent Pseudomonas from soils suppressive or conducive to black root rot of tobacco. Soil Biol Biochem 42:649–656CrossRefGoogle Scholar
  89. Frapolli M, Pothier JF, Défago G, Moënne Y (2012) Evolutionary history of synthesis pathway genes for phloroglucinol and cyanide antimicrobials in plant-associated fluorescent pseudomonads. Mol Phylogen Evol 63:877–890CrossRefGoogle Scholar
  90. Frébort I, Kowalska M, Hluska T, Frébortová J, Galuszka P (2011) Evolution of cytokinin biosynthesis and degradation. J Exp Bot 62:2431–2452PubMedCrossRefGoogle Scholar
  91. Gamalero E, Glick BR (2011) Mechanisms used by plant growth-promoting bacteria. In: Maheshwari DK (ed) Bacteria in agrobiology: plant nutrient management. Springer, Berlin, pp 17–46CrossRefGoogle Scholar
  92. Gamalero E, Glick BR (2012) Ethylene and abiotic stress tolerance in plants. In: Ahmad P, Prassad MNV (eds) Environmental adaptations and stress tolerance on plants in the era of climatic change. Springer, New York, pp 395–412CrossRefGoogle Scholar
  93. Gamalero E, Glick BR (2015) Bacterial modulation of plant ethylene levels. Plant Physiol 169:13–22PubMedPubMedCentralCrossRefGoogle Scholar
  94. Glare T, Caradus J, Gelernter W, Jackson T, Keyhani N, Köhl J, Marrone P, Morin L, Stewart A (2012) Have biopesticides come of age? Trends Biotechnol 30:250–258PubMedCrossRefGoogle Scholar
  95. Glick BR (2012) Plant growth promoting-rhizobacteria: mechanisms and applications. Hindawi Publishing Corporation, Scientifica: 963401Google Scholar
  96. Glick BR, Cheng Z, Czarny J, Duan J (2007) Promotion of plant growth by ACC deaminase-producing soil bacteria. Eur J Plant Pathol 119:329–339CrossRefGoogle Scholar
  97. Gong L, Tan H, Chen F, Li T, Zhu J, Jian Q, Yuan D, Xu L, Hu W, Jiang Y, Duan X (2016) Novel synthesized 2, 4-DAPG analogues: antifungal activity, mechanism and toxicology. Sci Rep 6:32266PubMedPubMedCentralCrossRefGoogle Scholar
  98. Graner G, Persson P, Meijer J, Alstrom S (2003) A study on microbial diversity in different cultivars of Brassica napus in relation to its wilt pathogen, Verticillium longisporum. FEMS Microbiol Lett 29:269–276CrossRefGoogle Scholar
  99. Gray EJ, Smith DL (2005) Intracellular and extracellular PGPR: commonalities and distinctions in the plant-bacterium signaling processes. Soil Biol Biochem 37:395–412CrossRefGoogle Scholar
  100. Groenhagen U, Baumgartner R, Bailly A, Gardiner A, Eberl L, Schulz S, Weisskopf L (2013) Production of bioactive volatiles by different Burkholderia ambifaria strains. J Chem Ecol 39:892–906PubMedCrossRefGoogle Scholar
  101. Gross H, Loper JE (2009) Genomics of secondary metabolite production by Pseudomonas spp. Nat Prod Rep 26:1408–1446PubMedCrossRefGoogle Scholar
  102. Großkinsky DK, Tafner R, Moreno MV, Stenglein SA, García de Salamone IE, Nelson LM, Novák O, Strnad M, van der Graaff E, Roitsch T (2016) Cytokinin production by Pseudomonas fluorescens G2018 determines biocontrol activity against Pseudomonas syringae in Arabidopsis. Sci Rep 6:23310PubMedPubMedCentralCrossRefGoogle Scholar
  103. Grossmann K (2010) Auxin herbicides: current status of mechanism and mode of action. Pest Manag Sci 66:113–120PubMedGoogle Scholar
  104. Gulick AM (2016) Structural insight into the necessary conformational changes of modular nonribosomal peptides synthetases. Curr Opin Chem Biol 35:89–96PubMedPubMedCentralCrossRefGoogle Scholar
  105. Gurney R, Thomas CM (2011) Mupirocin: biosynthesis, special features and applications of an antibiotic from a gram-negative bacterium. Appl Microbiol Biotechnol 90:11–21PubMedCrossRefGoogle Scholar
  106. Gutierrez-Luna FM, Lopez-Bucio J, Tamirano-Hernandez J, Valencia-Cantero E, de la Cruz HR, Andias-Rodriguez L (2010) Plant growth-promoting rhizobacteria modulate root system architecture in Arabidopsis thaliana through volatile organic compound emission. Symbiosis 51:75–83CrossRefGoogle Scholar
  107. Ha S, Vankova R, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS (2012) Cytokinins: metabolism and function in plant adaptation to environmental stresses. Trends Plant Sci 17:172–179PubMedCrossRefGoogle Scholar
  108. Haas D, Defago G (2005) Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 3:307–319PubMedCrossRefGoogle Scholar
  109. Haas D, Keel C (2003) Regulation of antibiotic production in root-colonizing Pseudomonas spp and relevance for biological control of plant disease. Annu Rev Phytopathol 41:117–153PubMedCrossRefGoogle Scholar
  110. Haichar FE, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2:1221–1230PubMedCrossRefGoogle Scholar
  111. Hamley IW (2015) Lipopeptides: from self-assembly to bioactivity. Chem Commun 51:8574–8583CrossRefGoogle Scholar
  112. Hartung W, Sauter A, Turner NC, Fillery I, Heilmeier H (1996) Abscisic acid in soils: what is its function and which factors and mechanisms influence its concentration? Plant Soil 184:105–110CrossRefGoogle Scholar
  113. Hawes MC, Curlango-Rivera G, Xiong Z, Kessler JO (2012) Roles of root border cells in plant defense and regulation of rhizosphere microbial population by extracellular DNA “trapping”. Plant Soil 355:1–16CrossRefGoogle Scholar
  114. 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
  115. Heeb S, Haas D (2001) Regulatory roles of the GacS/GacA two-component system in plant-associated and other Gram-negative bacteria. Mol Plant-Microbe Interact 14:1351–1363PubMedCrossRefGoogle Scholar
  116. Helfrich EJ, Piel J (2016) Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 33:231–316PubMedCrossRefGoogle Scholar
  117. Hellberg JE, Matilla MA, Salmond GP (2015) The broad-spectrum antibiotic, zeamine, kills the nematode worm Caenorhabditis elegans. Front Microbiol 6:137PubMedPubMedCentralCrossRefGoogle Scholar
  118. Hertweck C (2009) The biosynthetic logic of polyketide diversity. Angew Chem Int Ed Engl 48:4688–4716PubMedCrossRefGoogle Scholar
  119. Hider RC, Kong X (2010) Chemistry and biology of siderophores. Nat Prod Rep 27:637–657PubMedCrossRefGoogle Scholar
  120. Hiltner L (1904) Uber neuere Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie unter besonderden berucksichtigung und Brache. Arb Dtsch Landwirtsch Gesellschaft 98:59–78Google Scholar
  121. Höfte M, Bakker PAHM (2007) Competition for iron and induced systemic resistance by siderophores of plant growth-promoting rhizobacteria. In: Varma A, Chincholkar SB (eds) Microbial siderophores. Springer, Berlin, pp 121–134CrossRefGoogle Scholar
  122. Houlden A, Timms-Wilson TM, Day MJ, Bailey MJ (2008) Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops. FEMS Microbiol Ecol 65:193–201PubMedCrossRefGoogle Scholar
  123. Huang X-F, Chaparro JM, Reardon KF, Zhang R, Shen Q, Vivanco JM (2014) Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 92:267–275CrossRefGoogle Scholar
  124. Hutsch BW, Augustin J, Merbach W (2000) Plant rhizodeposition an important source for carbon turnover in soils. J Plant Nutr Soil Sci 165:397e407Google Scholar
  125. Iavicoli A, Boutet E, Buchala A, Métraux JP (2003) Induced systemic resistance in Arabidopsis thaliana in response to root inoculation with Pseudomonas fluorescens CHA0. Mol Plant-Microbe Interact 16:851–858PubMedCrossRefGoogle Scholar
  126. Inceoglu Ö, Overbeek LS, Salles JF, Elsas JD (2013) Normal operating range of bacterial communities in soil used for potato cropping. Appl Environ Microbiol 79:1160–1170PubMedPubMedCentralCrossRefGoogle Scholar
  127. Jiang CJ, Shimono M, Sugano S, Kojima M, Yazawa K, Yoshida R et al (2010) Abscisic acid interacts antagonistically with salicylic acid signaling pathway in rice- Magnaporthe grisea interaction. Mol Plant-Microbe Interact 23:791–798PubMedCrossRefGoogle Scholar
  128. Jiang F, Chen L, Belimov AA, Shaposhnikov AI, Gong F, Meng X, Hartung W, Jeschke DW, Davies WJ, Dodd IC (2012) Multiple impacts of the plant growth-promoting rhizobacterium Variovorax paradoxus 5C-2 on nutrient and ABA relations of Pisum sativum. J Exp Bot 63:6421–6430PubMedPubMedCentralCrossRefGoogle Scholar
  129. Jiang CJ, Shimono M, Sugano S, Kojima M, Liu X, Inoue H, Sakakibara H, Takatsuji H (2013) Cytokinins act synergistically with salicylic acid to activate defense gene expression in rice. Mol Plant-Microbe Interact 26:287–296PubMedCrossRefGoogle Scholar
  130. Jones DL, Nguyen C, Finlay RD (2009) Carbon flow in the rhizosphere: carbon trading at the soil-root interface. Plant Soil 321:5–33CrossRefGoogle Scholar
  131. Kai M, Effmert U, Berg G, Piechulla B (2007) Volatiles of bacterial antagonists inhibit mycelial growth of the plant pathogen Rhizoctonia solani. Arch Microbiol 187:351–360PubMedCrossRefGoogle Scholar
  132. Kai M, Haustein M, Molina F, Petri A, Scholz B, Piechulla B (2009) Bacterial volatiles and their action potential. Appl Microbiol Biotech 81:1001–1012CrossRefGoogle Scholar
  133. Kai M, Crespo E, Cristescu SM, Harren FJ, Francke W, Piechulla B (2010) Serratia odorifera: analysis of volatile emission and biological impact of volatile compounds on Arabidopsis thaliana. Appl Microbiol Biotechnol 88:965–976PubMedCrossRefGoogle Scholar
  134. Kamensky M, Ovadis M, Chet I, Chernin L (2003) Soil-borne strain IC14 of Serratia plymuthica with multiple mechanisms of antifungal activity provides biocontrol of Botrytis cinerea and Sclerotinia sclerotiorum diseases. Soil Biol Biochem 35:323–331CrossRefGoogle Scholar
  135. Kamilova F, Kravchenko LV, Shaposhnikov AI, Azarova T, Makarova N, Lugtenberg B (2006) Organic acids, sugars and L-tryptophane in exudates of vegetables growing on stonewool and their effects on activities of rhizosphere bacteria. Mol Plant-Microbe Interact 9:250–256CrossRefGoogle Scholar
  136. Kanchiswamy CN, Malnoy M, Maffei ME (2015) Chemical diversity of microbial volatiles and their potential for plant growth and productivity. Front Plant Sci 6:151PubMedPubMedCentralCrossRefGoogle Scholar
  137. Karadeniz A, Topcuoglu SF, Inan S (2006) Auxin, gibberellin, cytokinin and abscisic acid production in some bacteria. World J Microbiol Biotechnol 22:1061–1064CrossRefGoogle Scholar
  138. Keel C, Schenider U, Maurhofer M, Voisard C, Laville J, Burger U, Wirthener P, Haas D, Défago G (1992) Suppression of root diseases by Pseudomonas fluorescens CHA0: importance of the bacterial secondary metabolite 2,4-diacetylphloroglucinol. Mol. Plant Microbe Interact 5:4–13CrossRefGoogle Scholar
  139. Khan MS, Zaidi A, Ahmad E (2014) Mechanism of phosphate solubilization and physiological functions of phosphate-solubilizing microorganisms. In: Khan et al (eds) Phosphate solubilizing microorganisms. Springer, Cham, pp 31–62Google Scholar
  140. Kim YC, Leveau J, Gardener BB, Pierson EA, Pierson LS, Ryu C-M (2011) The multifactorial basis for plant health promotion by plant-associated bacteria. Appl Environ Microbiol 77:1548–1555PubMedPubMedCentralCrossRefGoogle Scholar
  141. Kloepper JW, Gutiérrez-Estrada A, McInroy JA (2007) Photoperiod regulated elicitation of growth promotion but not induced resistance by plant growth-promoting rhizobacteria. Can J Microbiol 53:159–167PubMedCrossRefGoogle Scholar
  142. Koga H, Dohi K, Mori M (2004) Abscisic acid and low temperatures suppress the whole plant-specific resistance reaction of rice plants to the infection of Magnaporthe grisea. Physiol Mol Plant Pathol 65:3–9CrossRefGoogle Scholar
  143. Kwak YS, Han S, Thomashow LS, Rice JT, Paulitz TC, Kim D, Weller DM (2011) Saccharomyces cerevisiae genome-wide mutant screen for sensitivity to 2,4-diacetylphloroglucinol, an antibiotic produced by Pseudomonas fluorescens. Appl Environ Microbiol 77:1770–1776PubMedCrossRefGoogle Scholar
  144. Kyselková M, Moënne-Loccoz Y (2012) Pseudomonas and other microbes in disease-suppressive soils. In: Lichtfouse E (ed) Sustainable agriculture reviews: organic fertilisation, soil quality and human health, vol 9. Springer, Dordrecht, pp 93–140CrossRefGoogle Scholar
  145. Lanteigne C, Gadkar VJ, Wallon T, Novinscak A, Filion M (2012) Production of DAPG and HCN by Pseudomonas sp. LBUM300 contributes to the biological control of bacterial canker of tomato. Phytopathology 102:967–973PubMedCrossRefGoogle Scholar
  146. Lee B, Farag MA, Park HB, Kloepper JW, Lee SH, Ryu CM (2012) Induced resistance by a long-chain bacterial volatile: elicitation of plant systemic defense by a C13 volatile produced by Paenibacillus polymyxa. PLoS One 7:e48744PubMedPubMedCentralCrossRefGoogle Scholar
  147. Lehr P (2010) Biopesticides: the global market. Report code CHM029B. BCC Research, LondonGoogle Scholar
  148. Lemanceau P, Expert D, Gaymard F, Bakker P, Briat JF (2009) Role of iron in plant-microbe interactions. Plant Innate Immun 51:491–549Google Scholar
  149. Lemfack MC, Nickel J, Dunkel M, Preissner R, Piechulla B (2014) mVOC: a database of microbial volatiles. Nucleic Acids Res 42:D744–D748PubMedCrossRefGoogle Scholar
  150. Lesuffleur F, Liquet JBC (2010) Characterisation of root amino acid exudation in white clover (Trifolium repens L.) Plant Soil 333:191–201CrossRefGoogle Scholar
  151. Li X, Rui J, Mao Y, Yannarell A, Mackie R (2014a) Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar. Soil Biol Biochem 68:392–401CrossRefGoogle Scholar
  152. Li B, Li Q, Xu Z, Zhang N, Shen Q, Zhang R (2014b) Responses of beneficial Bacillus amyloliquefaciens SQR9 to different soilborne fungal pathogens through the alteration of antifungal compounds production. Front Microbiol 5:636PubMedPubMedCentralGoogle Scholar
  153. Li J, Liu W, Luo L, Dong D, Liu T, Zhang T, Lu C, Liu D, Zhang D, Wu H (2015) Expression of Paenibacillus polymyxa β-1,3-1,4-glucanase in Streptomyces lydicus A01 improves its biocontrol effect against Botrytis cinerea. Biol Control 90:141–147CrossRefGoogle Scholar
  154. Liu Y, Chen L, Zhang N, Li Z, Zhang G, Xu Y, Shen Q, Zhang R (2016) Plant-microbe communication enhances auxin biosynthesis by a root-associated bacterium, Bacillus amyloliquefaciens SQR9. Mol Plant-Microbe Interact 29:324–330PubMedCrossRefGoogle Scholar
  155. Llamas MA, Imperi F, Visca P, Lamont IL (2014) Cell-surface signalling in Pseudomonas: stress responses, iron transport, and pathogenicity. FEMS Microbiol Rev 38:569–597PubMedCrossRefGoogle Scholar
  156. Loper JE, Kobayashi DY, Paulsen IT (2007) The genomic sequence of Pseudomonas fluorescens Pf-5: insights into biological control. Phytopathology 97:233–238PubMedCrossRefGoogle Scholar
  157. Lugtenberg BJJ, Bloemberg GV (2004) Life in the rhizosphere. In: Ramos JL (ed) Pseudomonas: genomics, life style and molecular architecture, vol 1. Kluwer Acad/Plenum, New York, pp 403–430CrossRefGoogle Scholar
  158. Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556PubMedCrossRefGoogle Scholar
  159. Ma JF (2005) Plant root responses to three abundant soil minerals: silicon, aluminum and iron. Crit Rev Plant Sci 24:267–281CrossRefGoogle Scholar
  160. Marilley L, Hartwig UA, Aragno M (1999) Influence of an elevated atmospheric CO2 content on soil and rhizosphere bacterial communities beneath Lolium perenne and Trifolium repens under field conditions. Microb Ecol 38:39–49PubMedCrossRefGoogle Scholar
  161. Mark GL, Dow JM, Kiely PD, Higgins H, Haynes J, Baysse C, Abbas A, Foley T, Franks A, Morrissey J 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
  162. Maróti G, Kondorosi E (2014) Nitrogen-fixing Rhizobium-legume symbiosis: are polyploidy and host peptide-governed symbiont differentiation general principles of endosymbiosis? Front Microbiol 5:326PubMedPubMedCentralGoogle Scholar
  163. Matilla MA, Espinosa-Urgel M, Rodríguez-Herva JJ, Ramos JL, Ramos-González MI (2007a) Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere. Genome Biol 8:R179PubMedPubMedCentralCrossRefGoogle Scholar
  164. Matilla MA, Ramos JL, Duque E, de Dios Alché J, Espinosa-Urgel M, Ramos-González MI (2007b) Temperature and pyoverdine-mediated iron acquisition control surface motility of Pseudomonas putida. Environ Microbiol 9:1842–1850PubMedCrossRefGoogle Scholar
  165. Matilla MA, Ramos JL, Bakker PAHM, Doornbos RD, Badri DV, Vivanco JM, Ramos-González MI (2010) Pseudomonas putida KT2440 causes induced systemic resistance and changes in Arabidopsis root exudation. Environ Microb Rep 2:381–388CrossRefGoogle Scholar
  166. Matilla MA, Pizarro-Tobías P, Roca A, Fernández M, Duque E, Molina L, Wu X, Van der Lelie D, Gómez MJ, Segura A, Ramos JL (2011a) Complete genome of the plant growth promoting rhizobacterium Pseudomonas putida BIRD-1. J Bacteriol 193:1290PubMedCrossRefGoogle Scholar
  167. Matilla MA, Travieso ML, Ramos JL, Ramos-González MI (2011b) Cyclic diguanylate turnover mediated by the sole GGDEF/EAL response regulator in Pseudomonas putida: its role in the rhizosphere and an analysis of its target processes. Environ Microbiol 13:1745–1766PubMedCrossRefGoogle Scholar
  168. Matilla MA, Stöckmann H, Leeper FJ, Salmond GPC (2012) Bacterial biosynthetic gene clusters encoding the anti-cancer haterumalide class of molecules: biogenesis of the broad spectrum antifungal and antioomycete compound, oocydin A. J Biol Chem 287:39125–39138PubMedPubMedCentralCrossRefGoogle Scholar
  169. Matilla MA, Leeper FJ, Salmond GP (2015) Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq. Environ Microbiol 17:2993–3008PubMedPubMedCentralCrossRefGoogle Scholar
  170. Matilla MA, Nogellova V, Morel B, Krell T, Salmond GP (2016a) Biosynthesis of the acetyl-CoA carboxylase-inhibiting antibiotic, andrimid in Serratia is regulated by Hfq and the LysR-type transcriptional regulator, AdmX. Environ Microbiol 18:3635–3650PubMedPubMedCentralCrossRefGoogle Scholar
  171. Matilla MA, Drew A, Udaondo Z, Krell T, Salmond GPC (2016b) Genome sequence of Serratia plymuthica A153, a model rhizobacterium for the investigation of the synthesis and regulation of haterumalides, zeamine, and andrimid. Genome Announc 4:e00373–e00316PubMedPubMedCentralCrossRefGoogle Scholar
  172. Matilla-Vázquez MA, Matilla AJ (2014) Ethylene: role in plants under environmental stress. In: Ahmad P, Wani MR (eds) Physiological mechanisms and adaptation strategies in plants under changing environment, vol 2. Springer, New York, pp 189–222CrossRefGoogle Scholar
  173. Matilla MA, Udaondo Z, Krell T, Salmond GPC (2017) Genome sequence of MSU97, a plant-associated bacterium that makes multiple antibiotics. Genome Announc 5(9):e01752–16PubMedPubMedCentralCrossRefGoogle Scholar
  174. Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100PubMedCrossRefGoogle Scholar
  175. Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663PubMedCrossRefGoogle Scholar
  176. Meyer SL, Halbrendt JM, Carta LK, Skantar AM, Liu T, Abdelnabby HM, Vinyard BT (2009) Toxicity of 2,4-diacetylphloroglucinol (DAPG) to plant-parasitic and bacterial-feeding nematodes. J Nematol 41:274–280PubMedPubMedCentralGoogle Scholar
  177. Meziane H, Van der Sluis I, Van Loon LC, Höfte M, Bakker PAHM (2005) Determinants of Pseudomonas putida WCS358 involved in inducing systemic resistance in plants. Mol Plant Pathol 6:177–185PubMedCrossRefGoogle Scholar
  178. Micallef SA, Shiaris MP, Colón-Carmona A (2009) Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot 60:1729–1742PubMedPubMedCentralCrossRefGoogle Scholar
  179. Miller BR, Gulick AM (2016) Structural biology of nonribosomal peptide synthetases. In: Bradley, Evans (eds) Nonribosomal peptide and polyketide biosynthesis: methods and protocols. Methods in molecular biology, vol 1401. Springer, New York, pp 3–29CrossRefGoogle Scholar
  180. Miller SA, Beed FD, Harmon CL (2009) Plant disease diagnostic capabilities and networks. Annu Rev Phytopathol 47:15–38PubMedCrossRefGoogle Scholar
  181. Milling A, Smalla K, Xaver F, Maidl K, Schloter M, Munch JC (2004) Effects of transgenic potatoes with an altered starch composition on the diversity of soil and rhizosphere bacteria and fungi. Plant Soil 266:23–39CrossRefGoogle Scholar
  182. Mohammadi K (2012) Phosphorus solubilizing bacteria: occurrence, mechanisms and their role in crop production. Resour Environ 2:80–85Google Scholar
  183. Mohr PG, Cahill DM (2003) Abscisic acid influences the susceptibility of Arabidopsis thaliana to Pseudomonas syringae pv. tomato and Peronospora parasitica. Funct Plant Biol 30:461–469CrossRefGoogle Scholar
  184. Mougel C, Offre P, Ranjard L, Corberand T, Gamalero E, Robin C, Lemanceau P (2006) Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5. New Phytol 170:165–175PubMedCrossRefGoogle Scholar
  185. Mousa WK, Raizada MN (2015) Biodiversity of genes encoding anti-microbial traits within plants associated microbes. Front Plant Sci 6:231PubMedPubMedCentralGoogle Scholar
  186. Moynihan JA, Morrissey JP, Coppoolse ER, Stiekema WJ, O’Gara F, Boyd EF (2009) Evolutionary history of the phl gene cluster in the plant-associated bacterium Pseudomonas fluorescens. Appl Environ Microbiol 75:2122–2131PubMedPubMedCentralCrossRefGoogle Scholar
  187. Nagpure A, Choudhary B, Gupta RK (2014) Chitinases: in agriculture and human healthcare. Crit Rev Biotechnol 34:215–232PubMedCrossRefGoogle Scholar
  188. Nandi M, Selin C, Brassinga AKC, Belmonte MF, Fernando WGD, Loewen PC, Kievit TR (2015) Pyrrolnitrin and hydrogen cyanide production by Pseudomonas chlororaphis strain PA23 exhibits nematicidal and repellent activity against Caenorhabditis elegans. PLoS One 10:e0123184PubMedPubMedCentralCrossRefGoogle Scholar
  189. Nascimento FX, Vicente CSL, Barbosa P, Espada M, Glick BR, Oliveira S, Mota M (2013) The use of the ACC deaminase producing bacterium Pseudomonas putida UW4 as a biocontrol agent for pine wilt disease. BioControl 58:427–433CrossRefGoogle Scholar
  190. Naseem M, Kaltdorf M, Dandekar T (2015) The nexus between growth and defence signalling: auxin and cytokinin modulate plant immune response pathways. J Exp Bot 66:4885–4896PubMedCrossRefGoogle Scholar
  191. Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26:1362–1384PubMedPubMedCentralCrossRefGoogle Scholar
  192. Neumann G, Römheld V (2007) The release of root exudates as affected by the plant physiological status. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere: biochemistry and organic substances at the soil-plant interface. CRC Press, New York, pp 23–72CrossRefGoogle Scholar
  193. Newmann G, Römheld V (2007) The release of root exudates as affected by the plant physiological status. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere: biochemistry and organic substances at the soil-plant interface. CRC Press, New York, pp 23–72CrossRefGoogle Scholar
  194. Nihorimbere V, Cawoy H, Seyer A, Brunelle A, Thonart P, Ongena M (2012) Impact of rhizosphere factors on cyclic lipopeptide signature from the plant beneficial strain Bacillus amyloliquefaciens S499. FEMS Microbiol Ecol 79:176–191PubMedCrossRefGoogle Scholar
  195. Oerke EC, Dehne HW (2004) Safeguarding production – losses in major crops and the role of crop protection. Crop Prot 23:275–285CrossRefGoogle Scholar
  196. Oliver KL, Hamelin RC, Hintz WE (2008) Effects of transgenic hybrid aspen over-expressing polyphenol oxidase on rhizosphere diversity. Appl Environ Microb 74:5340–5348CrossRefGoogle Scholar
  197. Ongena M, Jourdan E, Adam A, Paquot M, Brans A, Joris B et al (2007a) Surfactin and fengycin lipopeptides of Bacillus subtilis as elicitors of induced systemic resistance in plants. Environ Microbiol 9:1084–1090PubMedCrossRefGoogle Scholar
  198. Ongena M, Jourdan E, Adam A, Paquot M, Brans A, Joris B, Arpigny JL, Thonart P (2007b) Surfactin and fengycin lipopeptides of Bacillus subtilis as elicitors of induced systemic resistance in plants. Environ Microbiol 9:1084–1090PubMedCrossRefGoogle Scholar
  199. Ovadis M, Liu X, Ismailov Z, Chet I, Chernin L (2004) The global regulator genes from biocontrol strain Serratia plymuthica IC270: cloning, sequencing, and functional studies. J Bacteriol 186:4983–4993CrossRefGoogle Scholar
  200. Parray JA, Jan S, Kamili AN, Qadri RA, Egamberdieva D, Ahmad P (2016) Current perspectives on plant growth-promoting rhizobacteria. J Plant Growth Regul 35:877–902CrossRefGoogle Scholar
  201. Partida-Martinez LP, Hertweck C (2007) A gene cluster encoding rhizoxin biosynthesis in Burkholderia rhizoxina, the bacterial endosymbiont of the fungus Rhizopus microsporus. Chembiochem 8:41–45PubMedCrossRefGoogle Scholar
  202. Patten CL, Blakney AJC, Coulson TJD (2013) Activity, distribution and function of indole-3-acetic acid biosynthetic pathways in bacteria. Crit Rev Microbiol 39:395–415PubMedCrossRefGoogle Scholar
  203. Peberdy JF (1990) Fungal cell wall – a review. In: Kuhn PJ, Trinci APJ, Jung MJ, Goosey MM, Cooping IG (eds) Biochemistry of cell walls and membranes in fungi. Springer, Heidelberg, pp 5–24CrossRefGoogle Scholar
  204. Perrig D, Boiero ML, Masciarelli OA, Penna C, Ruiz OA, Cassan FD, Luna MV (2007) Plant-growth-promoting compounds produced by two agronomically important strains of Azospirillum brasilense, and implications for inoculants formulation. Appl Microbiol Biotech 75:1143–1150CrossRefGoogle Scholar
  205. Perry LG, Alford ER, Horiuchi J, Paschke MW, Vivanco JM (2007) Chemical signals in the rhizosphere: root-root and root-microbe communication. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere: biochemistry and organic substances at the soil-plant interface, 2nd edn. CRC Press, New York, pp 297–330Google Scholar
  206. Pidot SJ, Coyne S, Kloss F, Hertweck C (2014) Antibiotics from neglected bacterial sources. Int J Med Microbiol 304:14–22PubMedCrossRefGoogle Scholar
  207. Pieterse CMJ, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SCM (2012) Hormonal modulation of plant immunity. Annu Rev Cell Develop Biol 28:489–521CrossRefGoogle Scholar
  208. Pieterse CM, Zamioudis C, Berendsen RL, Weller DM, Van Wees SC, Bakker PA (2014) Induced systemic resistance by beneficial microbes. Annu Rev Phytopathol 52:347–375PubMedCrossRefGoogle Scholar
  209. Pimentel D (2005) Environmental and economic costs of the application of pesticides primarily in the United States. Environ Dev Sustain 7:229–252CrossRefGoogle Scholar
  210. Prathap M, Ranjitha-Kumari BD (2015) A critical review on plant growth promoting rhizobacteria. J Plant Pathol Micro 6:1000266Google Scholar
  211. Quecine MC, Araujo WL, Marcon J, Gai CS, Azevedo JL, Pizzirani-Kleiner AA (2008) Chitinolytic activity of endophytic Streptomyces and potential for biocontrol. Lett Appl Microbiol 47:486–491PubMedCrossRefGoogle Scholar
  212. Quintana-Rodriguez E, Morales-Vargas AT, Molina-Torres J, Ádame-Alvarez RM, Acosta-Gallegos JA, Heil M (2015) Plant volatiles cause direct, induced and associational resistance in common bean to the fungal pathogen Colletotrichum lindemuthianum. J Ecol 103:250–260CrossRefGoogle Scholar
  213. Raaijmakers JM, Leeman M, MMP VO, Van der Sluis I, Schippers B, PAHM B (1995) Dose–response relationships in biological control of fusarium wilt of radish by Pseudomonas spp. Phytopathology 85:1075–1081CrossRefGoogle Scholar
  214. Raaijmakers JM, Paulitz TC, Steinberg CH, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361CrossRefGoogle Scholar
  215. Raaijmakers JM, De Bruijn I, Nybroe O, Ongena M (2010) Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics. FEMS Microbiol Rev 34:1037–1062PubMedCrossRefGoogle Scholar
  216. Ramaekers L, Remans R, Rao IM, Blair MW, Vanderleyden J (2010) Strategies for improving phosphorus acquisition efficiency of crop plants. Field Crops Res 117:169–176CrossRefGoogle Scholar
  217. Reed MLE, Glick BR (2013) Applications of plant growth-promoting bacteria for plant and soil systems. Gupta, V.K, Schmoll, M., Maki, M., Tuohy, M., Mazutti, M.A., Applications of microbial engineering. Taylor and Francis, Enfield, 181–229CrossRefGoogle Scholar
  218. Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T (2015) Roots shaping their microbiome: global hotspots for microbial activity. Annu Rev Phytopathol 53:403–424PubMedCrossRefGoogle Scholar
  219. Reyes-Darias JA, García V, Rico-Jiménez M, Corral-Lugo A, Lesouhaitier O, Juárez-Hernández D, Yang Y, Bi S, Feuilloley M, Muñoz-Rojas J, Sourjik V, Krell T (2015) Specific gamma-aminobutyrate chemotaxis in pseudomonads with different lifestyle. Mol Microbiol 97:488–501PubMedCrossRefGoogle Scholar
  220. Rezzonico F, Zala M, Keel C, Duffy B, Moënne-Loccoz Y, Défago G (2007) Is the ability of biocontrol fluorescent pseudomonads to produce the antifungal metabolite 2,4-diacetylphloroglucinol really synonymous with higher plant protection? New Phytol 173:861–872PubMedCrossRefGoogle Scholar
  221. Richardson AE, Barea JM, McNeil 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
  222. Roca A, Pizarro-Tobías P, Udaondo Z, Fernández M, Matilla MA, Molina-Henares MA, Molina L, Segura A, Duque E, Ramos JL (2013) Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1. Environ Microbiol 15:780–794Google Scholar
  223. Rodríguez H, Fraga R (1999) Phosphate solubilizing bacteria and their role in plant growth promotion. Biotech Adv 17:319–339CrossRefGoogle Scholar
  224. Rodríguez H, Fraga R, González T, Bashan Y (2006) Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria. Plant Soil 287:15–21CrossRefGoogle Scholar
  225. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SH, Camargo FA, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290PubMedPubMedCentralCrossRefGoogle Scholar
  226. Rosas SB, Andres JA, Rovera M, Correa NS (2006) Phosphate-solubilizing Pseudomonas putida can influence the rhizobia-legume symbiosis. Soil Biol Biochem 38:3502–3505CrossRefGoogle Scholar
  227. Roselló-Mora R, Amann R (2001) The species concept of prokaryotes. FEMS Microbiol Rev 25:39–67CrossRefGoogle Scholar
  228. Rossolini GM, Shippa S, Riccio ML, Berlutti F, Macaskie LE, Thaller MC (1998) Bacterial nonspecific acid phosphatases: physiology, evolution and use as tools in microbial biotechnology. Cell Mol Life Sci 54:833–850PubMedCrossRefGoogle Scholar
  229. Rudrappa T, Splaine RE, Biedrzycki ML, Bais HP (2008) Cyanogenic pseudomonads influence multitrophic interactions in the rhizosphere. PLoS One 3:e2073PubMedPubMedCentralCrossRefGoogle Scholar
  230. Rudrappa T, Biedrzycki ML, Kunjeti SG, Donofrio NM, Czymmek KJ, Paré PW et al (2010) The rhizobacterial elicitor acetoin induces systemic resistance in Arabidopsis thaliana. Commun Integr Biol 3:130–138PubMedPubMedCentralCrossRefGoogle Scholar
  231. Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, Paré PW, Kloepper JW (2003) Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci U S A 100:4927–4932PubMedPubMedCentralCrossRefGoogle Scholar
  232. Ryu CM, Farag MA, Hu CH, Reddy MS, Kloepper JW, Paré PW (2004) Bacterial volatiles induce systemic resistance in Arabidopsis. Plant Physiol 134:1017–1026PubMedPubMedCentralCrossRefGoogle Scholar
  233. Saha R, Saha N, Donofrio RS, Bestervelt LL (2013) Microbial siderophores: a mini review. J Basic Microbiol 53:303–317PubMedCrossRefGoogle Scholar
  234. Saha M, Sarkar S, Sarkar B, Kumar B, Sharma BK, Bhattacharjee S, Tribedi P (2016) Microbial siderophores and their potential applications: a review. Environ Sci Pollut Res 23:3984–3999CrossRefGoogle Scholar
  235. Saharan BS, Nehra V (2011) Plant growth promoting rhizobacteria: a critical review. Life Sci Med Res 21:1–30Google Scholar
  236. Salomon MV, Bottini R, de Souza Filho GA, Cohen AC, Moreno D, Gil M, Piccoli P (2014) Bacteria isolated from roots and rhizosphere of Vitis vinifera retard water losses, induce abscisic acid accumulation and synthesis of defense-related terpenes in in vitro cultured grapevine. Physiol Plant 151:359–374PubMedCrossRefGoogle Scholar
  237. Sashidhar B, Podile AR (2010) Mineral phosphate solubilization by rhizosphere bacteria and scope for manipulation of the direct oxidation pathway involving glucose dehydrogenase. J App Microb 109:1–2Google Scholar
  238. Sattely ES, Fischbach MA, Walsh CT (2008) Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways. Nat Prod Rep 25:757–793PubMedCrossRefGoogle Scholar
  239. Schalk IJ, Hannauer M, Braud A (2011) New roles of bacterial siderophores in metal transport and tolerance. Environ Microbiol 13:2844–2854PubMedCrossRefGoogle Scholar
  240. Schenk PM, Carvalhais LC, Kazan K (2012) Unraveling plant–microbe interactions: can multi-species transcriptomics help? Trends Biotechnol 30:177–184PubMedCrossRefGoogle Scholar
  241. Scherlach K, Graupner K, Hertweck C (2013) Molecular bacteria-fungi interactions: effects on environment, food, and medicine. Annu Rev Microbiol 67:375–397PubMedCrossRefGoogle Scholar
  242. Schöller CEG, Gürtler H, Petersen R, Molin S, Wilkins K (2002) Volatile metabolites from actinomycetes. J Agric Food Chem 50:2615–2621PubMedCrossRefGoogle Scholar
  243. Scott JC, Greenhut IV, Leveau JHJ (2013) Functional characterization of the bacterial iac genes for degradation of the plant hormone indole-3-acetic acid. J Chem Ecol 39:942–951PubMedCrossRefGoogle Scholar
  244. Sgroy V, Cassan F, Masciarelli O, Del Papa MF, Lagares A, Luna V (2009) Isolation and characterization of endophytic plant growth-promoting (PGPB) or stress homeostasis-regulating (PSHB) bacteria associated to the halophyte Prosopisstrom bulifera. Appl Microbiol Biotech 85:371–381CrossRefGoogle Scholar
  245. Shigenaga AM, Arqueso CT (2016) No hormone to rule them all: interactions of plant hormones during the responses of plants to pathogens. Semin Cell Dev Biol 56:174–189PubMedCrossRefGoogle Scholar
  246. Singh RP, Shelke GM, Kumar A, Jha PN (2015) Biochemistry and genetics of ACC deaminase: a weapon to “stress ethylene” produced in plants. Front Microbiol 6:937PubMedPubMedCentralGoogle Scholar
  247. Soares-Gomes E, Schuch V, Macedo-Lemos EG (2013) Biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. Braz J Microbiol 44:1007–1034CrossRefGoogle Scholar
  248. Somers E, Vanderleyden J, Srinivasan M (2004) Rhizosphere bacterial signalling: a love parade beneath our feet. Crit Rev Microbiol 30:205–240PubMedCrossRefGoogle Scholar
  249. Spaepen S, Vanderleyden J (2011) Auxin and plant-microbe interaction. Cold Spring Harb Perspect Biol 3:a001438PubMedPubMedCentralCrossRefGoogle Scholar
  250. Spaepen S, Vanderleyden J, Remans R (2007) Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol Rev 31:425–448PubMedCrossRefGoogle Scholar
  251. Spoel SH, Dong X (2012) How do plants achieve immunity? Defence without specialized immune cells. Nat Rev Immunol 12:89–100PubMedCrossRefGoogle Scholar
  252. Srivastava S, Chaudhry V, Mishra A, Chauhan PS, Rehman A, Yadav A, Tuteja N, Nautiyal CS (2012) Gene expression profiling through microarray analysis in Arabidopsis thaliana colonized by Pseudomonas putida MTCC5279, a plant growth promoting rhizobacterium. Plant Signal Behav 7:235–245PubMedPubMedCentralCrossRefGoogle Scholar
  253. 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
  254. Strieker M, Tanović A, Marahiel MA (2010) Nonribosomal peptide synthetases: structures and dynamics. Curr Opin Struct Biol 20:234–240PubMedCrossRefGoogle Scholar
  255. Thakore Y (2006) The biopesticide market for global agricultural use. Ind Biotechnol 2:194–208CrossRefGoogle Scholar
  256. Till M, Race PR (2014) Progress challenges and opportunities for the re-engineering of trans-AT polyketide synthases. Biotechnol Lett 36:877–888PubMedCrossRefGoogle Scholar
  257. Trapet P, Avoscan L, Klinguer A, Pateyron S, Citerne S, Chervin C, Mazurier S, Lemanceau P, Wendehenne D, Besson-Bard A (2016) The Pseudomonas fluorescens siderophore pyoverdine weakens Arabidopsis thaliana defense in favor of growth in iron-deficient conditions. Plant Physiol 171:675–693PubMedPubMedCentralCrossRefGoogle Scholar
  258. Tripathi AK, Khanuja SPS, Kumar S (2002) Chitin synthesis inhibitors as insect-pest control agents. J Med Arom Plant Sci 24:104–122Google Scholar
  259. Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W et al (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci U S A 104:10376–10381PubMedPubMedCentralCrossRefGoogle Scholar
  260. Uren NC (2007) Types, amounts and possible functions of compounds released into rhizosphere by soil-grown plants. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere: biochemistry and organic substances at the soil-plant interface. CRC Press, New York, pp 1–21Google Scholar
  261. Vacheron J, Desbrosses G, Bouffaud ML, Touraine B, Moënne-Loccoz Y, Muller D, Legendre L, Wisniewski-Dyé F, Prigent-Combaret C (2013) Plant growth-promoting rhizobacteria and root system functioning. Front Plant Sci 4:356PubMedPubMedCentralCrossRefGoogle Scholar
  262. van de Mortel JE, de Vos RC, Dekker E, Pineda A, Guillod L, Bouwmeester K et al (2012) Metabolic and transcriptomic changes induced in Arabidopsis by the rhizobacterium Pseudomonas fluorescens SS101. Plant Physiol 160:2173–2188PubMedPubMedCentralCrossRefGoogle Scholar
  263. Van Der Voort M, Meijer HJ, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmaker JM (2015) Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds. Front Microbiol 6:693Google Scholar
  264. Van Loon LC (2007) Plant responses to plant growth-promoting bacteria. Eur J Plant Pathol 119:243–254CrossRefGoogle Scholar
  265. van Loon LC, Bakker PA, Pieterse CM (1998) Systemic resistance induced by rhizosphere bacteria. Annu Rev Phytopathol 36:453–483PubMedCrossRefGoogle Scholar
  266. Van Peer R, Niemann GJ, Schippers B (1991) Induced resistance and phytoalexin accumulation in biological control of Fusarium wilt of carnation by Pseudomonas sp. strain WCS417r. Phytopathology 81:728–734CrossRefGoogle Scholar
  267. Vansuyt G, Robi A, Briat JF, Curie C, Lemanceau P (2007) Iron acquisition from Fe-pyoverdine by Arabidopsis thaliana. Mol Plant-Microbe Interact 20:441–447PubMedCrossRefGoogle Scholar
  268. Vassilev N, Vassileva M, Nicolaeva I (2006) Simultaneous P-solubilizing and biocontrol activity of microorganisms: potentials and future trends. Appl Microb Biotech 71:137–144CrossRefGoogle Scholar
  269. Vejan P, Abdullah R, Khadiran T, Ismail S, Boyce AN (2016) Role of plant growth promoting rhizobacteria in agricultural sustainability – a review. Molecules 21:3–17CrossRefGoogle Scholar
  270. Velivelli SL, De Vos P, Kromann P, Declerck S, Prestwich BD (2014) Biological control agents: from field to market, problems, and challenges. Trends Biotechnol 32:493–496PubMedCrossRefGoogle Scholar
  271. Venugopalan A, Srivastava S (2015) Endophytes as in vitro production platforms of high value plant secondary metabolites. Biotechnol Adv 33:873–887PubMedCrossRefGoogle Scholar
  272. Verhagen BW, Glazebrook J, Zhu T, Chang HS, van Loon LC, Pieterse CM (2004) The transcriptome of rhizobacteria-induced systemic resistance in Arabidopsis. Mol Plant-Microbe Interact 17:895–908PubMedCrossRefGoogle Scholar
  273. Vespermann A, Kai M, Piechulla B (2007) Rhizobacterial volatiles affect the growth of fungi and Arabidopsis thaliana. Appl Environ Microbiol 73:5639–5641PubMedPubMedCentralCrossRefGoogle Scholar
  274. Vincent MN, Harrison LA, Brackin JM, Kovacevich PA, Mukerji P, Weller DM, Pierson EA (1991) Genetic analysis of the antifungal activity of a soilborne Pseudomonas aureofaciens strain. Appl Environ Microbiol 57:2928–2934PubMedPubMedCentralGoogle Scholar
  275. Visca P, Imperi F, Lamont IL (2007) Pyoverdine siderophores: from biogenesis to biosignificance. Trends Microbiol 15:22–30PubMedCrossRefGoogle Scholar
  276. Vlot AC, Dempsey DA, Klessig DF (2009) Salicylic acid, a multifaceted hormone to combat disease. Annu Rev Phytopathol 47:177–206PubMedCrossRefGoogle Scholar
  277. Voisard C, Keel C, Haas D, Défago G (1989) Cyanide production by Pseudomonas fluorescens helps suppress black root rot of tobacco under gnotobiotic conditions. EMBO J 8:351–358PubMedPubMedCentralGoogle Scholar
  278. Walker TS, Bais HP, Grotewold E, Vivanco JM (2003) Root exudation and rhizosphere biology. Plant Physiol 132:44–51PubMedPubMedCentralCrossRefGoogle Scholar
  279. Walters DR, Ratsep J, Havis ND (2013) Controlling crop diseases using induced resistance: challenges for the future. J Exp Bot 64:1263–1280PubMedCrossRefGoogle Scholar
  280. Wang H, Fewer DP, Holm L, Rouhiainen L, Sivonen K (2014) Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes. Proc Natl Acad Sci U S A 111:9259–9264PubMedPubMedCentralCrossRefGoogle Scholar
  281. Webb BA, Helm RF, Scharf BE (2016) Contribution of individual chemoreceptors to Sinorhizobium meliloti chemotaxis towards amino acids of host and non-host seed exudates. Mol Plant-Microbe Interact 29:231–239PubMedCrossRefGoogle Scholar
  282. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0 – acomprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:W237–W243PubMedPubMedCentralCrossRefGoogle Scholar
  283. Wei G, Kloepper JW, Tuzun S (1991) Induction of systemic resistance of cucumber to Colletotrichum orbiculare by select strains of plant-growth promoting rhizobacteria. Phytopathology 81:1508–1512CrossRefGoogle Scholar
  284. Weingart H, Ullrich H, Geider K, Völksch B (2001) The Role of Ethylene Production in Virulence of Pseudomonas syringae pvs. glycinea and phaseolicola. Phytopathology 91:511–518PubMedCrossRefGoogle Scholar
  285. Weller DM (2007) Pseudomonas biocontrol agents of soilborne pathogens: looking back over 30 years. Phytopathology 97:250–256PubMedCrossRefGoogle Scholar
  286. Weller DM, Mavrodi DV, van Pelt JA, Pieterse CMJ, van Loon LC, Bakker PAHM (2012) Induced systemic resistance in Arabidopsis thaliana against Pseudomonas syringae pv. tomato by 2,4- diacetylphloroglucinol-producing Pseudomonas fluorescens. Phytopathology 102:403–412PubMedCrossRefGoogle Scholar
  287. Wen F, Van Etten HD, Tsaprailis G, Hawes MC (2007) Extracellular proteins in pea root tip and border cell exudates. Plant Physiol 143:773–783PubMedPubMedCentralCrossRefGoogle Scholar
  288. Wenke K, Weise T, Warnke R, Valverde C, Wanke D, Kai M, Piechulla B (2012) Bacterial volatiles mediating information between bacteria and plants. In: Witzany J, Baluška F (eds) Biocommunication of plants, vol 14. Springer, Berlin, pp 327–347CrossRefGoogle Scholar
  289. Wheatley RE (2002) The consequences of volatile organic compound mediated bacterial and fungal interactions. Antonie Van Leeuwenhoek 81:357–336PubMedCrossRefGoogle Scholar
  290. Workentine ML, Chang L, Ceri H, Turner RJ (2009) The GacS-GacA two-component regulatory system of Pseudomonas fluorescens: a bacterial two-hybrid analysis. FEMS Microbiol Lett 292:50–56PubMedCrossRefGoogle Scholar
  291. Xie X, Zhang H, Pare PW (2009) Sustained growth promotion in Arabidopsis with long-term exposure to the beneficial soil bacterium Bacillus subtilis (GB03). Plant Signal Behav 4:948–953PubMedPubMedCentralCrossRefGoogle Scholar
  292. Xu J, Audenaert K, Hofte M, De Vleesschauwer D (2013) Abscisic acid promotes susceptibility to the rice leaf blight pathogen Xanthomonas oryzae pv. oryzae by suppressing salicylic acid-mediated defenses. PLoS One 8:e67413PubMedPubMedCentralCrossRefGoogle Scholar
  293. Yang J, Kloepper JW, Ryu CM (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14:1–4PubMedCrossRefGoogle Scholar
  294. Yasuda M, Ishikawa A, Jikumaru Y, Seki M, Umezawa T, Asami T, Maruyama-Nakashita A, Kudo T, Shinozaki K, Yoshida S, Nakashita H (2008) Antagonistic interaction between systemic acquired resistance and the abscisic acid-mediated abiotic stress response in Arabidopsis. Plant Cell 20:1678–1692PubMedPubMedCentralCrossRefGoogle Scholar
  295. Yu X, Ai C, Xin L, Zhou G (2011) The siderophore-producing bacterium, Bacillus subtilis CAS15, has a biocontrol effect on Fusarium wilt and promotes the growth of pepper. Eur J Soil Biol 47:138–145CrossRefGoogle Scholar
  296. Yuan J, Zhang N, Huang Q, Raza W, Li R, Vivanco JM, Shen Q (2015) Organic acids from root exudates of banana help root colonization of PGPR strain Bacillus amyloliquefaciens NJN-6. Sci Rep 25:13438CrossRefGoogle Scholar
  297. Zdor RE (2015) Bacterial cyanogenesis: impact on biotic interactions. J Appl Microbiol 118:267–274PubMedCrossRefGoogle Scholar
  298. Zhang H, Kim MS, Krishnamachari V et al (2007) Rhizobacterial volatile emissions regulate auxin homeostasis and cell expansion in Arabidopsis. Planta 226:839–851PubMedCrossRefGoogle Scholar
  299. Zhang H, Xie X, Kim MS, Kornyeyev DA, Holaday S, Paré PW (2008) Soil bacteria augment Arabidopsis photosynthesis by decreasing glucose sensing and abscisic acid levels in planta. Plant J 56:264–273PubMedCrossRefGoogle Scholar
  300. Zúñiga A, Poupin MJ, Donoso R, Ledger T, Guiliani N, Gutierrez RA, González B (2013) Quorum sensing and indole-3-acetic acid degradation play a role in colonization and plant growth promotion of Arabidopsis thaliana by Burkholderia phyto Firmans PsJN. Mol Plant-Microbe Interact 26:546–553PubMedCrossRefGoogle Scholar

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© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Department of Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain

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