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Methods for Detecting Biocontrol and Plant Growth-Promoting Traits in Rhizobacteria

  • Gustavo SantoyoEmail author
  • Juan M. Sánchez-Yáñez
  • Sergio de los Santos-Villalobos
Chapter
Part of the Rhizosphere Biology book series (RHBIO)

Abstract

The field of agriculture requires new strategies to control the damage caused by phytopathogens and to effectively promote plant growth and production. Until recently, one of the best alternatives was the application of microorganisms exhibiting biocontrol and plant growth-promoting traits. Therefore, to select the best microorganisms, it is essential to analyse these beneficial activities based on reliable search methods and to ensure the greatest extent possible and their successful application in the field. In this chapter, we have summarized and compared different methods to detect direct and indirect activities that promote plant growth, with an emphasis on rhizobacteria. Moreover, we have compiled a detailed description of the methods that could be of interest for analysing bacterial isolates that exhibit potential plant growth-promoting activities.

Keywords

Plant growth-promoting mechanisms Biological control ACC deaminase Siderophores Auxins Rhizosphere colonization Volatiles Antifungal compounds 

Notes

Acknowledgements

G.S. thanks the Coordinación de la InvestigaciónCientífica of the Universidad Michoacana de San Nicolás de Hidalgo for the financial support to research projects.

References

  1. Ahemad M, Kibret M (2014) Mechanisms and applications of plant growth promoting rhizobacteria: current perspective. J King Saud Univ Sci 26:1–20CrossRefGoogle Scholar
  2. Ahmad F, Ahmad I, Khan MS (2008) Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol Res 163:173–181CrossRefGoogle Scholar
  3. Arora NK, Verma M (2017) Modified microplate method for rapid and efficient estimation of siderophore produced by bacteria. 3 Biotech 7:381CrossRefGoogle Scholar
  4. Badri DV, Weir TL, van der Lelie D, Vivanco JM (2009) Rhizosphere chemical dialogues: plant–microbe interactions. Curr Opin Biotechnol 20:642–650CrossRefGoogle Scholar
  5. Bashan Y, De-Bashan LE, Prabhu SR, Hernandez J-P (2014) The quantitative relationship between nitrogen fixation and the acetylene-reduction assay. Aust J Biol Sci 23:1015–1026Google Scholar
  6. 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 26:835–843CrossRefGoogle Scholar
  7. Bloemberg GV, Lugtenberg BJ (2001) Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr Opin Plant Biol 4:343–350CrossRefGoogle Scholar
  8. Brink SC (2016) Unlocking the secrets of the rhizosphere. Trends Plant Sci 21:169–170CrossRefGoogle Scholar
  9. Burris RH, Wilson PW (1957) Methods for measurement of nitrogen fixation. Methods Enzymol 4:355–366CrossRefGoogle Scholar
  10. Cattelan AJ, Hartel PG, Fuhrmann JJ (1999) Screening for plant growth–promoting rhizobacteria to promote early soybean growth. Soil Sci Soc Am J 63:1670–1680CrossRefGoogle Scholar
  11. de los Santos Villalobos S, Parra Cota FI, Herrera Sepúlveda A, Valenzuela Aragón B, Estrada Mora JC (2018) Colección de microorganismosedáficos y endófitosnativosparacontribuira la seguridadalimentarianacional. Rev Mex Cienc Agríc 9:191–202Google Scholar
  12. de los Santos-Villalobos S, Barrera-Galicia GC, Miranda-Salcedo MA, Peña-Cabriales JJ (2012) Burkholderiacepacia XXVI siderophore with biocontrolcapacity against Colletotrichumgloeosporioides. World J Microbiol Biotechnol 28:2615–2623CrossRefGoogle Scholar
  13. de los Santos-Villalobos S, de Folter S, Délano-Frier JP, Gómez-Lim MA, Guzmán-Ortiz DA, Peña-Cabriales JJ (2013) Growth promotion and flowering induction in mango by Burkholderia and Rhizobium inoculation: morphometric, biochemical and molecular events. J Plant Growth Regul 32:615–627CrossRefGoogle Scholar
  14. Dekkers LC, Mulders IH, Phoelich CC, Chin-A-Woeng TFC, Wijfjes AHM, Lugtenberg BJJ (2000) The sss colonization gene of the tomato–Fusariumoxysporumf.sp. radicislycopersicibiocontrol strain Pseudomonas fluorescens WCS365 can improve root colonization of other wild-type Pseudomonas spp. bacteria. Mol Plant-Microbe Interact 13:1177–1183CrossRefGoogle Scholar
  15. Domingo JL (2016) Safety assessment of GM plants: an updated review of the scientific literature. Food Chem Toxicol 95:12–18CrossRefGoogle Scholar
  16. Elad Y, Baker R (1985) Influence of trace amounts of cations and siderophore-producing pseudomonads on chlamydospore germination of Fusariumoxysporum. Phytopathology 75:1047–1052CrossRefGoogle Scholar
  17. Fahad S et al (2015) Phytohormones and plant responses to salinity stress: a review. J Plant Growth Regul 75:391–404CrossRefGoogle Scholar
  18. Fernando WGD, Nakkeeran S, Zhang Y (2005) Biosynthesis of antibiotics by PGPR and its relation in biocontrol of plant diseases. In: Siddiqui ZA (ed) PGPR: biocontrol and biofertilization. Springer, Dordrecht, pp 67–109Google Scholar
  19. Fett WF, Osman SF, Dunn MF (1987) Auxin production by plant-pathogenic pseudomonads and xanthomonads. Appl Environ Microbiol 53:1839–1845PubMedPubMedCentralGoogle Scholar
  20. Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, Shinozaki K (2006) Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol 9:436–442CrossRefGoogle Scholar
  21. Fukuhara H, Minakawa Y, Akao S, Minamisawa K (1994) The involvement of indole-3-acetic acid produced by Bradyrhizobium elkanii in nodule formation. Plant Cell Physiol 35:1261–1265Google Scholar
  22. Gershenzon J, Dudareva N (2007) The function of terpene natural products in the natural world. Nat Chem Biol 3:408–414CrossRefGoogle Scholar
  23. Ghosh S, Sengupta C, Maiti TK, Basu PS (2008) Production of 3-indolylacetic acid in root nodules and culture by a Rhizobium species isolated from root nodules of the leguminous pulse Phaseolusmungo. Folia Microbiol 53:351CrossRefGoogle Scholar
  24. Glick BR (2012) Plant growth-promoting bacteria: mechanisms and applications. Scientifica 2012:963401Google Scholar
  25. Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169:30–39CrossRefGoogle Scholar
  26. Gordon SA, Weber RP (1951) Colorimetric estimation of indoleacetic acid. Plant Physiol 26:192–195CrossRefGoogle Scholar
  27. Halda-Alija L (2003) Identification of indole-3-acetic acid producing freshwater wetland rhizosphere bacteria associated with Juncuseffusus L. Can J Microbiol 49:781–787CrossRefGoogle Scholar
  28. Hernández-León R et al (2015) Characterization of the antifungal and plant growth-promoting effects of diffusible and volatile organic compounds produced by Pseudomonas fluorescens strains. Biol Control 81:83–92CrossRefGoogle Scholar
  29. Hernández-Salmerón JE, Prieto-Barajas CM, Valencia-Cantero E, Moreno-Hagelsieb G, Santoyo G (2014) Isolation and characterization of genetic variability in bacteria with β-hemolytic and antifungal activity isolated from the rhizosphere of Medicagotruncatula plants. Gen Mol Res 13:4967–4975CrossRefGoogle Scholar
  30. Hoffman BM, Lukoyanov D, Yang ZY, Dean DR, Seefeldt LC (2014) Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem Rev 114:4041–4062CrossRefGoogle Scholar
  31. Höfte M, Altier N (2010) Fluorescent pseudomonads as biocontrol agents for sustainable agricultural systems. Res Microbiol 161:464–471CrossRefGoogle Scholar
  32. Honma M, Shimomura T (1978) Metabolism of 1-aminocyclopropane-1-carboxylic acid. Agric Biol Chem 42:1825–1831Google Scholar
  33. Hsieh FC, Li MC, Lin TC, Kao SS (2004) Rapid detection and characterization of surfactin-producing Bacillus subtilis and closely related species based on PCR. Curr Microbiol 49:186–191Google Scholar
  34. Jackson ML (2005) Soil chemical analysis: advanced course. UW-Madison Libraries Parallel Press.Google Scholar
  35. Kai M, Haustein M, Molina F, Petri A, Scholz B, Piechulla B (2009) Bacterial volatiles and their action potential. Appl Microbiol Biotechnol 81:1001–1012CrossRefGoogle Scholar
  36. Karadeniz A, Topcuoğlu ŞF, Inan S (2006) Auxin, gibberellin, cytokinin and abscisic acid production in some bacteria. World J Microbiol Biotechnol 22:1061–1064CrossRefGoogle Scholar
  37. Kloepper JW, Leong J, Teintze M, Schroth MN (1980) Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature 286:885–886CrossRefGoogle Scholar
  38. Leclère V et al (2005) Mycosubtilin overproduction by Bacillus subtilis BBG100 enhances the organism’s antagonistic and biocontrol activities. Appl Environ Microbiol 71:4577–4584CrossRefGoogle Scholar
  39. Levy-Booth DJ, Prescott CE, Grayston SJ (2014) Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems. Soil Biol Biochem 75:11–25CrossRefGoogle Scholar
  40. Liu K, Newman M, McInroy JA, Hu CH, Kloepper JW (2017) Selection and assessment of plant growth-promoting rhizobacteria for biological control of multiple plant diseases. Phytopathology 107:928–936CrossRefGoogle Scholar
  41. Lopez-Lozano NE, Carcaño-Montiel MG, Bashan Y (2016) Using native trees and cacti to improve soil potential nitrogen fixation during long-term restoration of arid lands. Plant Soil 403:317–329CrossRefGoogle Scholar
  42. Mabit L, Zapata F, Dercon G, Benmansour M, Bernard C, Walling DE (2014) Assessment of soil erosion and sedimentation: the role of fallout radionuclides. Iaea Tecdoc Series 3.Google Scholar
  43. Maget-Dana R, Peypoux F (1994) Iturins, a special class of pore-forming lipopeptides: biological and physicochemical properties. Toxicology 87:151–174CrossRefGoogle Scholar
  44. Martínez-Absalón S et al (2014) Potential use and mode of action of the new strain Bacillus thuringiensis UM96 for the biological control of the grey mould phytopathogenBotrytis cinerea. Biocontrol Sci Tech 24:1349–1362CrossRefGoogle Scholar
  45. Meena VS, Bahadur I, Maurya BR, Kumar A, Meena RK, Meena SK, Verma JP (2016) Potassium-solubilizing microorganism in evergreen agriculture: an overview. In: Potassium solubilizing microorganisms for sustainable agriculture. Springer, New Delhi, pp 1–20CrossRefGoogle Scholar
  46. Mehta S, Nautiyal CS (2001) An efficient method for qualitative screening of phosphate-solubilizing bacteria. Curr Microbiol 43:51–56CrossRefGoogle Scholar
  47. Meyer JA, Abdallah MA (1978) The fluorescent pigment of Pseudomonas fluorescens: biosynthesis, purification and physicochemical properties. Microbiology 107:319–328Google Scholar
  48. Mus F et al (2016) Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Appl Environ Microbiol 82:3698–3710CrossRefGoogle Scholar
  49. Nautiyal CS (1999) An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol Lett 170:265–270CrossRefGoogle Scholar
  50. Nesme J et al (2016) Back to the future of soil metagenomics. Front Microbiol 7:73CrossRefGoogle Scholar
  51. Orozco-Mosqueda MC, Velázquez-Becerra C, Macías-Rodríguez LI, Santoyo G, Flores-Cortez I, Alfaro-Cuevas R, Valencia-Cantero E (2013) Arthrobacteragilis UMCV2 induces iron acquisition in Medicagotruncatula (strategy I plant) in vitro via dimethylhexadecylamine emission. Plant Soil 362:51–66CrossRefGoogle Scholar
  52. Orozco-Mosqueda MC, del Carmen Rocha-Granados M, Glick BR, Santoyo G (2018) Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol Res.  https://doi.org/10.1016/j.micres.2018.01.005
  53. Parnell JJ, Berka R, Young HA, Sturino JM, Kang Y, Barnhart DM, DiLeo MV (2016) From the lab to the farm: an industrial perspective of plant beneficial microorganisms. Front Plant Sci 7:1110CrossRefGoogle Scholar
  54. Penrose DM, Glick BR (2003) Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. Physiol Plant 118:10–15CrossRefGoogle Scholar
  55. Phinney BO (1983) The history of gibberellins. In: Crozier A (ed) The biochemistry and physiology of gibberellins, vol 1, pp 19–52Google Scholar
  56. Pikovskaya RI (1948) Mobilization of phosphorus in soil in connection with the vital activity of some microbial species. Mikrobiologiya 17:362–370Google Scholar
  57. Rainey PB (1999) Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1:243–257CrossRefGoogle Scholar
  58. Reich A, Schibli A (2006) High performance thin-layer chromatography for the analysis of medicinal plants. Thieme, New York/StuttgartGoogle Scholar
  59. Rodríguez H, Fraga R (1999) Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv 17:319–339CrossRefGoogle Scholar
  60. Rojas-Solís D, Hernández-Pacheco CE, Santoyo G (2016) Evaluation of Bacillus and Pseudomonas to colonize the rhizosphere and their effect on growth promotion in tomato (Physalis ixocarpa Brot. ex Horm.). Rev Chapingo Ser Hortic 22:45–57Google Scholar
  61. Rojas-Solís D, Zetter-Salmón E, Contreras-Pérez M, Rocha-Granados MC, Macías-Rodríguez L, Santoyo G (2018) Pseudomonas stutzeri E25 and Stenotrophomonas maltophilia CR71 endophytes produce antifungal volatile organic compounds and exhibit additive plant growth-promoting effects. Biocatal Agric Biotechnol 13:46–52Google Scholar
  62. 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 USA 100:4927–4932CrossRefGoogle Scholar
  63. Ryu CM, Farag MA, Hu CH, Reddy MS, Kloepper JW, Paré PW (2004) Bacterial volatiles induce systemic resistance in Arabidopsis. Plant Physiol 134:1017–1026CrossRefGoogle Scholar
  64. Saha M, Sarkar S, Sarkar B, Sharma BK, Bhattacharjee S, Tribedi P (2016) Microbial siderophores and their potential applications: a review. Environ Sci Pollut Res 23:3984–3999CrossRefGoogle Scholar
  65. Santoyo G, Orozco-Mosqueda MC, Govindappa M (2012) Mechanisms of biocontrol and plant growth-promoting activity in soil bacterial species of Bacillus and Pseudomonas: a review. Biocontrol Sci Tech 22:855–872CrossRefGoogle Scholar
  66. Santoyo G, Moreno-Hagelsieb G, Orozco-Mosqueda MC, Glick BR (2016) Plant growth-promoting bacterial endophytes. Microbiol Res 183:92–99CrossRefGoogle Scholar
  67. Sasaki T, Suzaki T, Soyano T, Kojima M, Sakakibara H, Kawaguchi M (2014) Shoot-derived cytokinins systemically regulate root nodulation. Nat Commun 5:4983CrossRefGoogle Scholar
  68. Scher FM, Ziegle JS, Kloepper JW (1984) A method for assessing the root-colonizing capacity of bacteria on maize. Can J Microbiol 30:151–157CrossRefGoogle Scholar
  69. Schoenborn L, Yates PS, Grinton BE, Hugenholtz P, Janssen PH (2004) Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Appl Environ Microbiol 70:4363–4366CrossRefGoogle Scholar
  70. Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56CrossRefGoogle Scholar
  71. Stotzky G, Schenk S (1976) Volatile organic compounds and microorganisms. CRC Crit Rev Microbiol 4:333–382CrossRefGoogle Scholar
  72. Swain MR, Naskar SK, Ray RC (2007) Indole-3-acetic acid production and effect on sprouting of yam (Dioscorearotundata L.) minisetts by Bacillus subtilis isolated from culturablecowdungmicroflora. Pol J Microbiol 56:103PubMedGoogle Scholar
  73. Taylor KG, Konhauser KO (2011) Iron in Earth surface systems: a major player in chemical and biological processes. Elements 7:83–88CrossRefGoogle Scholar
  74. Terakado-Tonooka J, Ohwaki Y, Yamakawa H, Tanaka F, Yoneyama T, Fujihara S (2008) Expressed nifH genes of endophytic bacteria detected in field-grown sweet potatoes (Ipomoea batatas L.). Microbes Environ 23:89–93CrossRefGoogle Scholar
  75. Thaweenut N, Hachisuka Y, Ando S, Yanagisawa S, Yoneyama T (2011) Two seasons’ study on nifH gene expression and nitrogen fixation by diazotrophicendophytes in sugarcane (Saccharum spp. hybrids): expression of nifH genes similar to those of rhizobia. Plant Soil 338:435–449CrossRefGoogle Scholar
  76. Tilman D, Cassman KG, Matson PA, Naylor R, Polasky S (2002) Agricultural sustainability and intensive production practices. Nature 418:671–677CrossRefGoogle Scholar
  77. Timmusk S, Paalme V, Pavlicek T, Bergquist J, Vangala A, Danilas T, Nevo E (2011) Bacterial distribution in the rhizosphere of wild barley under contrasting microclimates. PLoS One 6:e17968CrossRefGoogle Scholar
  78. Verma V, Ravindran P, Kumar PP (2016) Plant hormone-mediated regulation of stress responses. BMC Plant Biol 16:86CrossRefGoogle Scholar
  79. Villarreal-Delgado MF, Villa-Rodríguez ED, Cira-Chávez LA, Estrada-Alvarado MI, Parra-Cota FI, de los Santos-Villalobos S (2018) The genus Bacillus as a biological control agent and its implications in the agricultural biosecurity. Rev Mex Fitopatol 36:95–130Google Scholar
  80. Widmer F, Shaffer BT, Porteous LA, Seidler RJ (1999) Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon Cascade Mountain range. Appl Environ Microbiol 65:374–380PubMedPubMedCentralGoogle Scholar
  81. Wilson EO (2003) The future of life. Vintage Books, New YorkGoogle Scholar
  82. Zehr JP, Mellon MT, Zani S (1998) New nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifH) genes. Appl Environ Microbiol 64:3444–3450PubMedPubMedCentralGoogle Scholar
  83. Zhang Y, Fernando WG, Kievit TRD, Berry C, Daayf F, Paulitz TC (2006) Detection of antibiotic-related genes from bacterial biocontrol agents with polymerase chain reaction. Can J Microbiol 52:476–481CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Gustavo Santoyo
    • 1
    Email author
  • Juan M. Sánchez-Yáñez
    • 1
  • Sergio de los Santos-Villalobos
    • 2
  1. 1.Instituto de Investigaciones Químico BiológicasUniversidad Michoacana de San Nicolás de HidalgoMoreliaMexico
  2. 2.CONACYT-Instituto Tecnológico de SonoraCiudad ObregónMexico

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