Rhizocompetence of Applied Bioinoculants

  • Chandandeep Kaur
  • G. SelvakumarEmail author
  • A. N. Ganeshamurthy


Concomitant with the demand for chemical free food, the demand for bioinoculants for plant growth promotion and protection against pests and disease causing organisms has also seen a phenomenal increase. This has led to the mushrooming of several products in the market that have met with varying degrees of success. Very often it has been observed that inoculant strains that perform exceedingly well under laboratory conditions fail under field conditions. This can be primarily attributed to the utilization of non-rhizocompetent strains. Since the inoculated strain has to compete with a multitude of native microbes in the rhizospheric region, strains lacking rhizocompetence traits often fail to establish and perform in the rhizosphere. Rhizocompetence traits such as biofilm formation, siderophore production, antagonism, ability to utilize root exudates, motility, and protease activity can prove to be game changers under field conditions. This chapter attempts to highlight the importance of rhizocompetence traits in inoculant selection and development, in order to harness the benefit of applied inoculants.


Bioinoculants Rhizosphere Rhizocompetence Root colonization Traits 



Chandandeep Kaur was supported by a grant from the Department of Science and Technology, Ministry of Science and Technology, Government of India, under the WOS-A scheme.


  1. Abbott LK, Murphy DV (2003) Soil biological fertility: a key to sustainable land use in agriculture. Kluwer Academic Publishers, Dordrecht, pp 1–15Google Scholar
  2. Ahmad JS, Baker R (1987) Rhizosphere competence of Trichoderma harzianum. Phytopathology 77:182–189CrossRefGoogle Scholar
  3. Alnahdi HS (2012) Isolation and screening of extracellular proteases produced by new isolated Bacillus sp. J Appl Pharma Sci 2:071–074Google Scholar
  4. Ames P, Bergman K (1981) Competitive advantage provided by bacterial motility in the formation of nodules by Rhizobium meliloti. J Bacteriol 148:728–729PubMedPubMedCentralGoogle Scholar
  5. Bais HP, Weir TL, Perry LG et al (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266CrossRefPubMedGoogle Scholar
  6. Banerjee R, Agnihotri R, Bhattacharyya BC (1993) Purification of alkaline protease of Rhizopus oryzae by foam fractionation. Bioprocess Biosyst Eng 9(6):245–248Google Scholar
  7. Barbour WM, Hattermann DR, Stacey G (1991) Chemotaxis of Bradyrhizobium japonicum to soybean exudates. Appl Environ Microbiol 57:2635–2639PubMedPubMedCentralGoogle Scholar
  8. Barraquio WL, Segubre EM, Gonzalez MS et al (2000) Diazotrophic enterobacteria: what is their role in the rhizosphere? In: Ladha JK, Reddy PM (eds) The quest for nitrogen fixation in rice. IRRI, Manila, pp 93–118Google Scholar
  9. Bauer WD, Caetano-Anollés G (1990) Chemotaxis, induced gene expression and competitiveness in the rhizosphere. Plant Soil 129:45–52CrossRefGoogle Scholar
  10. Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486CrossRefPubMedGoogle Scholar
  11. Bowen GD, Rovira AD (1999) The rhizosphere and its management to improve plant growth. Adv Agron 66:1–02CrossRefGoogle Scholar
  12. Burns RG (1982) Enzyme activity in soil: location and a possible role in microbial ecology. Soil Biol Biochem 14:423–427CrossRefGoogle Scholar
  13. Caetano-Anolles G, Crist-Estes DK, Bauer WD (1988) Chemotaxis of Rhizobium meliloti to the plant flavone luteolin requires functional nodulation genes. J Bacteriol 170:3164–3169CrossRefPubMedPubMedCentralGoogle Scholar
  14. Cardinale M (2015) Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy. Front Microbiol
  15. Chowdhury SP, Dietel K, Rändler M et al (2013) Effects of Bacillus amyloliquefaciens FZB42 on lettuce growth and health under pathogen pressure and its impact on the rhizosphere bacterial community. PLoS One 8:68818CrossRefGoogle Scholar
  16. Crosa JH (1989) Genetics and molecular biology of siderophore-mediated iron transport in bacteria. Microbiol Rev 53:517–530PubMedPubMedCentralGoogle Scholar
  17. Davey ME, O’Toole GA (2000) Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev 64:847–867CrossRefPubMedPubMedCentralGoogle Scholar
  18. Dharmatilake AJ, Bauer WD (1992) Chemotaxis of Rhizobium meliloti towards nodulation gene-inducing compounds from alfalfa roots. Appl Environ Microbiol 58:1153–1158PubMedPubMedCentralGoogle Scholar
  19. Dudeja SS, Suneja S, Khurana AL (1997) Iron acquisition system and its role in legume-Rhizobium symbiosis. Indian J Microbiol 37:1–2Google Scholar
  20. Glick BR, Bashan Y (1997) Genetic manipulation of plant growth-promoting bacteria to enhance biocontrol of phytopathogens. Biotechnol Adv 15:353–378CrossRefPubMedGoogle Scholar
  21. Gulash M, Ames P, Larosiliere RC et al (1984) Rhizobia are attracted to localized sites on legume roots. Appl Environ Microbiol 48:149–152PubMedPubMedCentralGoogle Scholar
  22. Gupta R, Beg Q, Lorenz P (2002) Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbiol Biotechnol 59:15–32CrossRefPubMedGoogle Scholar
  23. Gupta A, Roy I, Khare SK et al (2005) Purification and characterization of a solvent stable protease from Pseudomonas aeruginosa PseA. J Chromatogr A1069(2):155–161CrossRefGoogle Scholar
  24. Haggag WM, Timmusk S (2008) Colonization of peanut roots by biofilm forming Paenibacillus polymyxa initiates biocontrol against crown rot disease. J Appl Microbiol 4:961–969Google Scholar
  25. Heinrich D, Hess D (1985) Chemotactic attraction of Azospirillum lipoferum by wheat roots and characterization of some attractants. Can J Microbiol 31:26–31CrossRefGoogle Scholar
  26. Henrichsen J (1972) Gliding and twitching motility of bacteria unaffected by cytochalasin B. Acta Pathol Microbiol Scand Sect B Microbiol Immunol 80:623–624Google Scholar
  27. Hiltner L (1904) Überneuere Erfahrungen und Probleme auf demGebiete der BodenbakteriologieunterbesondererBerücksichtigung der Gründüngung und Brache. Arb DLG 98:59–78Google Scholar
  28. Jayasinghearachchi HS, Seneviratne GA (2004) Bradyrhizobial-Penicillium spp. biofilm with nitrogenase activity improves N2 fixing symbiosis of soybean. Biol Fert Soils 40:432–434Google Scholar
  29. Jones DL, Darrah PR (1995) Influx and efflux of organic acids across the soil-root interface of Zea mays L. and its implications in rhizosphere C flow. Plant Soil 173:103–109CrossRefGoogle Scholar
  30. Kearns DB (2010) A field guide to bacterial swarming motility. Nature Rev Microbiol 8:634–644CrossRefGoogle Scholar
  31. Kloepper JW, Beauchamp CJ (1992) A review of issues related to measuring colonization of plant roots by bacteria. Can J Microbiol 12:1219–1232CrossRefGoogle Scholar
  32. Kloepper JW, Schroth MN (1978) Plant growth promoting rhizobacteria on radishes. Proc 4th Int Conf Plant Pathogenic Bacteria 2:879–882Google Scholar
  33. Kloepper JW, Scher FM, Laliberte M et al (1985) Measuring the spermosphere colonizing capacity (spermosphere competence) of bacterial inoculants. Can J Microbiol 1:926–929CrossRefGoogle Scholar
  34. Kumar CG, Takagi H (1999) Microbial alkaline proteases: from a bioindustrial viewpoint. Biotechnol Adv 17(7):561–594CrossRefPubMedGoogle Scholar
  35. Kumar R, Bhatia R, Kukreja K et al (2007) Establishment of Azotobacter on plant roots: chemotactic response, development and analysis of root exudates of cotton (Gossypium hirsutum L.) and wheat (Triticum aestivum L.) J Basic Microbiol 47:436–439CrossRefPubMedGoogle Scholar
  36. Ladd JN, Foster RC, Nannipieri P et al (1996) Soil structure and biological activity. Soil Biol Biochem 9:23–78Google Scholar
  37. Leong SA, Neilands JB (1981) Relationship of siderophore-mediated iron assimilation to virulence in crown gall disease. J Bacteriol 147:482–491PubMedPubMedCentralGoogle Scholar
  38. Li XG, Zhang TL, Wang XX et al (2013) The composition of root exudates from two different resistant peanut cultivars and their effects on the growth of soil-borne pathogen. J Biol Sci 9(2):164–173Google Scholar
  39. Loper JE, Henkels MD (1999) Utilization of heterologous siderophores enhances levels of iron available to Pseudomonas putida in the rhizosphere. Appl Environ Microbiol 65:5357–5363PubMedPubMedCentralGoogle Scholar
  40. Lottmann J, Heuer H, de Vries J et al (2000) Establishment of introduced antagonistic bacteria in the rhizosphere of transgenic potatoes and their effect on the bacterial community. FEMS Microbiol Ecol 1:41–49CrossRefGoogle Scholar
  41. Macnab RM (2003) How bacteria assemble flagella. Annu Rev Microbiol 57:77–100CrossRefPubMedGoogle Scholar
  42. Macnab RM, Aizawa SI (1984) Bacterial motility and the bacterial flagellar motor. Annu Rev Biophys Bioeng 13(1):51–83CrossRefPubMedGoogle Scholar
  43. Mager DM, Thomas AD (2011) Extracellular polysaccharides from cyanobacterial soil crusts: a review of their role in dryland soil processes. J Arid Environ 75(2):91–97CrossRefGoogle Scholar
  44. Mandimba G, Heulin T, Bally R et al (1986) Chemotaxis of free-living nitrogen-fixing bacteria towards maize mucilage. Plant Soil 90:129–139CrossRefGoogle Scholar
  45. Nelson LM (2004) Plant growth promoting rhizobacteria (PGPR): prospects for new inoculants. Crop Manag 3(1)0–0Google Scholar
  46. Neumann G, Bott S, Ohler MA et al (2014) Root exudation and root development of lettuce (Lactuca sativa L. cv. Tizian) as affected by different soils. Front Microbiol 5:82–92Google Scholar
  47. Nogales J, Pérez-Mendoza D, Gallegos MT et al (2016) Importance of motile and biofilm lifestyles of rhizobia for the establishment of symbiosis with legumes. Beneficial Plant-microbial Interactions: Ecology and Applications. (in press) p 47–69Google Scholar
  48. O’Toole GA, Pratt LA, Watnick PI et al (1999) Genetic approaches to study of biofilms. Methods Enzymol 310:91–109CrossRefPubMedGoogle Scholar
  49. Owen D, Williams AP, Griffith GW et al (2015) Use of commercial bio-inoculants to increase agricultural production through improved phosphorus acquisition. Appl Soil Ecol 86:41–54CrossRefGoogle Scholar
  50. Pinton R, Varanini Z, Nannipieri P (2007) The rhizosphere: biochemistry and organic substances at the soil-plant interface. Marcel-Dekker, New YorkCrossRefGoogle Scholar
  51. Prasanna R, Joshi M, Rana A et al (2012) Influence of co-inoculation of bacteria-cyanobacteria on crop yield and C–N sequestration in soil under rice crop. World J Microbiol Biotechnol 28(3):1223–1235CrossRefPubMedGoogle Scholar
  52. Prasanna R, Chaudhary V, Gupta V et al (2013) Cyanobacteria mediated plant growth promotion and bioprotection against Fusarium wilt in tomato. Eur J Plant Pathol 136(2):337–353CrossRefGoogle Scholar
  53. Raja P, Uma S, Gopal H et al (2006) Impact of bio inoculants consortium on rice root exudates, biological nitrogen fixation and plant growth. J Biol Sci 6:815–823CrossRefGoogle Scholar
  54. Rao NSS (1993) Biofertilizers in agriculture and forestry. International Science Publishers, New DelhiGoogle Scholar
  55. Robinson JB, Bauer WD (1993) Relationships between C4 dicarboxylic acid transport and chemotaxis in Rhizobium meliloti. J Bacteriol 175:2284–2291CrossRefPubMedPubMedCentralGoogle Scholar
  56. Rossi F, Roberto De P (2015) Role of cyanobacterial exopolysaccharides in phototrophic biofilms and in complex microbial mats. Life 5(2):1218–1238CrossRefPubMedPubMedCentralGoogle Scholar
  57. Rovira AD, Campbell R (1975) A scanning electron microscope study of interactions between microorganisms and Gaeumannomyces graminis (Syn. Ophiobolus graminis) on wheat roots. Microb Ecol 2(3):177–185Google Scholar
  58. Sampedro I, Parales RE, Krell T et al (2015) Pseudomonas chemotaxis. FEMS Microbiol Rev 39:17–46PubMedGoogle Scholar
  59. 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
  60. Scherwinski K, Grosch R, Berg G (2008) Effect of bacterial antagonists on lettuce: active biocontrol of Rhizoctonia solani and negligible, short-term effects on non-target microorganisms. FEMS Microbial Ecol 1:106–116CrossRefGoogle Scholar
  61. Schreiter S, Sandmann M, Smalla K et al (2014) Soil type dependent rhizosphere competence and biocontrol of two bacterial inoculant strains and their effects on the rhizosphere microbial community of field-grown lettuce. PLoS One 9:103726CrossRefGoogle Scholar
  62. Seneviratne CJ, Jin L, Samaranayake LP (2008) Biofilm lifestyle of Candida: a mini review. Oral Dis 14:582–590CrossRefPubMedGoogle Scholar
  63. Sharma A, Johri BN (2003) Growth promoting influence of siderophore producing Pseudomonas strains GRP3A and PRS9 in maize (Zea mays L.) under iron limiting conditions. Microbiol Res 158:243–248Google Scholar
  64. Sharma A, Johri BN, Sharma AK et al (2003) Plant growth-promoting bacterium Pseudomonas sp. strain GRP 3 influences iron acquisition in mung bean (Vigna radiata L. Wilzcek). Soil Biol Biochem 35:887–894CrossRefGoogle Scholar
  65. Singh G, Mukerji KG (2006) Root exudates as determinant of rhizospheric microbial biodiversity. In: Mukerji KG, Manoharachary C, Singh J (eds) Soil biology: microbial activity in the rhizosphere. Springer, Berlin/Heidelberg, pp 39–53CrossRefGoogle Scholar
  66. Sivan A, Chet I (1989) Degradation of fungal cell walls by lytic enzymes of Trichoderma harzianum. Microbiology 135:675–682CrossRefGoogle Scholar
  67. Tabatabai MA (1982) Soil enzymes – methods of soil analysis. Part 2 Chemical and microbiological properties. Agronomy monograph no. 9, 2nd edn. American Society of Agronomy, Madison, pp 903–947Google Scholar
  68. Timmusk S, Wagner EG (1999) The plant-growth-promoting rhizobacterium Paenibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: a possible connection between biotic and abiotic stress responses. Mol Plant-Microbe Interact 12:951–959CrossRefPubMedGoogle Scholar
  69. Timmusk S, Grantcharova N, Wagner EG (2005) Paenibacillus polymyxa invades plant roots and forms biofilms. Appl Environ Microbiol 71:7292–7300CrossRefPubMedPubMedCentralGoogle Scholar
  70. Timmusk S, Van West P, Gow NA et al (2009) Paenibacillus polymyxa antagonizes oomycete plant pathogens Phytophthora palmivora and Pythium aphanidermatum. J Appl Microbiol 106:1473–1481CrossRefPubMedGoogle Scholar
  71. Ude S, Arnold DL, Moon CD et al (2006) Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates. Environ Microbiol 8:1997–2011CrossRefPubMedGoogle Scholar
  72. Van Loon LC (2007) Plant responses to plant growth-promoting rhizobacteria. Eur J Plant Pathol 119:243–254CrossRefGoogle Scholar
  73. Van Veen JA, Van Overbeek LS, Van Elsas JD (1997) Fate and activity of microorganisms introduced into soil. Microbiol Mol Biol Rev 61:121–135PubMedPubMedCentralGoogle Scholar
  74. Weitere M, Bergfeld T, Rice SA et al (2005) Grazing resistance of Pseudomonas aeruginosa biofilms depends on type of protective mechanism, developmental stage and protozoan feeding mode. Environ Microbiol 7:1593–1601CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Chandandeep Kaur
    • 1
  • G. Selvakumar
    • 1
    Email author
  • A. N. Ganeshamurthy
    • 1
  1. 1.ICAR- Indian Institute of Horticultural Research, Hessaraghatta Lake PostBengaluruIndia

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