Agricultural Important Microorganisms: From Rhizosphere to Bioformulation as Biological Control Weapons for Sustainable Agriculture

  • Gunjan Mukherjee
  • Pannalal Dey
  • Sunny Dhiman


Fungi are an integral part of the soil ecology. Rhizosphere holds foremost importance as a primitive site for microbial colonization and operation. A significant number of organic compounds including secretions, sloughed off cells, lysates and exudates are secreted by actively growing roots into the rhizosphere. As a matter of fact, the microbial activity in the rhizosphere is reckoned to be upraised and significantly distinctive in comparison to microbes existing in the bulk soil. Over the years agriculturally important microorganisms (AIM) have witnessed a significant utilization in a broad range of agroecosystems including both immanent and artificial circumstances in diverse applications ranging from nutrient supply, bioremediation, biocontrol and rehabilitation of degraded lands. The successful development of AIM in stressed ecosystem poses many challenges. The adverse effect to the environment due to indiscriminate use of chemical pesticides is of great concern, and hence development of alternate control strategies such as biological control as a substitute for chemicals or as a key component in integrated disease management system is gaining momentum. Biological control agents are usually target specific, and by using these agents in conjunction with fungicides, the level of fungicide applied can be reduced. The role of microorganisms to inhibit phytopathogen and possibility of bioformulation of next-generation products for agriculture market has been discussed.


Trichoderma Rhizosphere Agriculturally important microorganisms Bioformulation Next-generation products 


  1. Abd-El-Moity TH, Shatla MN (1981) Biological control of white rot disease of onion (Sclerotium cepivorum) by Trichoderma harzianum. Phytopathol Z 100:29–35CrossRefGoogle Scholar
  2. Ahmed AS, Sanchez CP, Candela ME (2000) Evaluation of induction of systemic resistance in pepper plants (Capsicum annuum) to Phytophthora capsici using Trichoderma harzianum and its relation with capsidiol accumulation. Eur J Plant Pathol 106:817–824CrossRefGoogle Scholar
  3. Ansari AR, Dhirendra P (1986) Rhizosphere and rhizoplane mycoflora of berley infected with Ustilago haordei. Indian Phytophatol 39(3):380–384Google Scholar
  4. Beagle-Ristaino JE, Papavizas GC (1985) Biological control of Rhizoctonia stem canker and black scurf of potato. Phytopathology 75:560–564CrossRefGoogle Scholar
  5. Bliss DE (1951) The destruction of Armillaria mellea in citrus soils. Phytopathology 41:665–683Google Scholar
  6. Bolton B, Fredrickson JK, Elliott FE (1993) Microbial ecology of the rhizosphere. In: Metting FB Jr (ed) Soil microbial ecology: applications in agricultural and environmental management. Marcel Dekker, Inc, New York, pp 27–63Google Scholar
  7. Bowen GD, Rovira AD (1991) The rhizosphere, the hidden half. In: Waisel Y, Eshel A, Kafkafi U (eds) Plant roots – the hidden half. Marcel Dekker Inc, New York, pp 641–649Google Scholar
  8. Caldwell MM, Richards JH (1989) Hydraulic lift – water efflux from upper roots improves effectiveness of water-uptake by deep roots. Oecologia 79:1–5CrossRefPubMedGoogle Scholar
  9. Chakraborty BN, Chakraborty U, Saha A (1995) Defence strategies of tea (Camellia sinensis) against fungal pathogens. In: Daniel M, Purkayastha RP (eds) Handbook of phytoalexin metabolism and action. Marcel Dekker Inc, New York, pp 485–502Google Scholar
  10. Chakraborty BN, Chakraborty U, Saha A, Sunar K, Dey PL (2010a) Evaluation of phosphate solubilizers from soils of North Bengal and their diversity analysis. World J Agri Sci 6(2):195–200Google Scholar
  11. Chakraborty BN, Chakraborty U, Saha A, Dey PL, Sunar K (2010b) Molecular characterization of Trichoderma viride and Trichoderma harzianum isolated from soils of North Bengal based on rDNA markers and analysis of their PCR-RAPD profiles. Global J Biochem Biotechnol 5(1):55–61Google Scholar
  12. Chakraborty BN, Chakraborty U, Dey PL, Sunar K (2010c) Phylogenetic relationship of Trichoderma isolates of North Bengal based on sequence analysis of ITS region of rDNA. J Appl Sci Res 6(10):1477–1482Google Scholar
  13. Chet I (1987) Trichoderma- application, mode of action and potential as a biocontrol agent of soilborne plant pathogenic fungi. In: Chet I (ed) Innovative approaches to plant disease control. Wiley, New York, pp 137–160Google Scholar
  14. Cook RJ (1993) Making greater use of introduced microorganisms for biological-control of plant-pathogens. Annu Rev Phytopathol 31:53–80CrossRefPubMedGoogle Scholar
  15. Corke ATK, Hunter T (1979) Biocontrol of Nectria galligena infection of pruning wounds on apple shoots. J Hortic Sci 54:47–55CrossRefGoogle Scholar
  16. Cutler HG, Hill RA (1994) Natural fungicides and their delivery systems as alternatives to synthetics. In: Wilson CL, Wisniewski ME (eds) Biological control of post harvest disease. Theory and practice. CRC Press Inc, Boca Raton, pp 135–152Google Scholar
  17. De Meyer G, Bigirimana J, Elad Y, Hofte M (1998) Induced systemic resistance in Trichoderma harzianum T39 biocontrol of Botrytis cinerea. Eur J Plant Pathol 104:79–286CrossRefGoogle Scholar
  18. Delgado De Kallman L, Arbelaez Torres G (1990) Control of Sclerotinia clerotiorum (Lib) deary in Chrysanthemum and snapbean with different isolates of Trichoderma and with fungicides. Agronomia Colombiana 7:33–39Google Scholar
  19. Domsch KH, Gams W, Anderson TH (1980) Compendium of soil fungi, vol I. Academic, LondonGoogle Scholar
  20. Dubos B, Ricard JL (1974) Curative treatment of peach trees against silver leaf disease(Stereum purpureum) with Trichoderma viride preparations. Plant Dis Rep 58:147–150Google Scholar
  21. Elad Y, Chet I, Karan J (1980) Trichoderma harzianum: A biocontrol agent effective against Sclerorium rotfsii and Rhizoctonia solani. Phytopathology 70:119–121CrossRefGoogle Scholar
  22. Elad Y, Zvieli Y, Chet I (1986) Biological control of Macrophomina phaseolina (Tassi) Goid by Trichoderma harzianum. Crop Prot 5:288–292CrossRefGoogle Scholar
  23. Gopinath A, Shekhar SH and Prakash HS (1987) Colonization of Fusarium species in sorghum seeds and their significance. Indian Phytopathology 40:181–185.Google Scholar
  24. Grondona I, Perez de Algaba A, Monte E, Garcia-Acha I (1992) Biological control of sugarbeet diseases caused by Phoma betae: greenhouse and field tests. Brlerin Organisation Internationale de Lutte Biologique contre les Animaux et les Plantes Nuisiblesl Section Regionale Ouest Palearctique 15:39–41Google Scholar
  25. Hanhong B (2011) Trichoderma species as abiotic and biotic stress quenchers in plants. Res J Biotechnol 6(3):73–79Google Scholar
  26. Hawksworth DL, Sutton BC, Ainsworth GC (1983) Ainsworth and Bisby’s dictionary of fungi, 7th edn. Commonwealth Mycological Institute, KewGoogle Scholar
  27. Hayes CK, Harman GE, Woo SL, Gullino ML, Lorito M (1993) Methods of electrophoretic karyotyping of filamentous fungi in the genus Trichoderma. Anal Biochem 209:176–182CrossRefPubMedGoogle Scholar
  28. Hee R (1991) Selection and identification on antagonistic rhizobacteria for controlling soil borne diseases of vegetables. Res Rep Rural Dev. ADM (Suweon) 33 (Icrop prot): 10–19Google Scholar
  29. Hermosa R, Viterbo A, Chet I, Monte E (2012) Plant-beneficial effects of Trichoderma and of its genes. Microbiology 158(1):17–25CrossRefPubMedGoogle Scholar
  30. Hiltner L (1904) Uber neuere Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie unter besonderer Berücksichtigung der Gründüngung und Brache. Arb DLG 98:59–78Google Scholar
  31. Hinsinger P, Plassard C, Tang C, Jaillard B (2003) Origins of root mediated pH changes in the rhizosphere and their environment constraints – a review. Plant Soil 248:43–59CrossRefGoogle Scholar
  32. Hoitink HAJ, Boehm J (1999) Biocontrol within the context of soil microbial communities: A substrate-dependent phenomenon. In: Webster RK (ed) Annual review of phytopathology, vol 37. Annual Reviews Inc, Palo Alto, pp 427–446Google Scholar
  33. Kallurmath RS, Rajasab AH (2000) Rhizosphere Mycoflora of onion. Indian J Mycol Plant Pathol 30(3):339–342Google Scholar
  34. Koike N (2001) Induction of systemic resistance in cucumber against several diseases by plant growth-promoting fungi: lignification and superoxide generation. Eu J Plant Pathol 107:523–533CrossRefGoogle Scholar
  35. Kumar NR, Arasu TV, Gunasekaran P (2002) Genotyping of antifungal compounds producing plant growth promoting rhizobacteria, Pseudomonas fluorescens. Curr Sci 82(12):1463–1466Google Scholar
  36. Latunde-Dada AO (1993) Biological control of southern blight disease of tomato caused by Sclerotium rolfsii with simplified mycelial formulations of Trichoderma koningii. Plant Pathol 42:522–529CrossRefGoogle Scholar
  37. Lewis JA, Papvizas GC (1980) Integrated control of Rhizoctonia fruit rot of cucumber. Phytopathology 70:85–89CrossRefGoogle Scholar
  38. Lo CT, Nelson EB, Hayes CK, Harman GE (1998) G. E. Ecological studies of transformed Trichoderma harzianum strain 1295-22 in the rhizosphere and on the phylloplane of creeping bentgrass. Phytopathology 88:129–136CrossRefPubMedGoogle Scholar
  39. Lynch JM, Whipps JM (1990) Substrate flow in the rhizosphere. Plant Soil 129:1–10CrossRefGoogle Scholar
  40. Marois JJ, Mitchell DJ, Sonoda RM (1981) Biological control of Fusarium crown rot of tomato under field conditions. Phyropathology 71:1257–1260Google Scholar
  41. Mathivannan N, Manibhushanrao K, Murugesan K (2006) Biological control of Plant pathogens. In: Anand N (ed) Recent trends in biochemical research. University of Madras, Chennai, pp 275–323Google Scholar
  42. Mathur K, Gurjar RBS, Jhamaria SL (2004) Rhizosphere Mycoflora of Chilli crop. Infected with Rhizoctonia solani. Indian J Mycol Plant Pathol 34(2):312–313Google Scholar
  43. Meyer RJ, Plaskowitz JS (1989) Scanning electron microscopy of conidia and conidial matrix of Trichoderma. Mycologia 81:312–317CrossRefGoogle Scholar
  44. Mishra PK, Mukhopadhyay AN, Fox RTV (2005) Integrated and biological control of gladiolus corm rot and wilt caused by Fusarium oxysporum f.sp. gladioli. Ann App Biol 137(3):361–364CrossRefGoogle Scholar
  45. Mukherjee PK, Horwitz BA, Herrera-Estrella A, Schmoll M, Kenerley CM (2013) Trichoderma research in the genome era. Annu Rev Phytopathol 51:105–129CrossRefPubMedGoogle Scholar
  46. Mukhopadhyay AN (1992) Integrated control of Chickpea wilt complex by Trichoderma and chemical methods in India. Int J Pest Management 38(4):372–375Google Scholar
  47. Mukhopadhyay AN (2009) Challenges, changes and choices before Trichoderma based biopesticides. J Mycol Plant Pathol 39(3):542Google Scholar
  48. Munnecke DE (1972) Factors affecting the efficacy of fungicides in soil. Annu Rev Phytopathol 10:375–398CrossRefGoogle Scholar
  49. Pandey KK, Upadhyay JP (2000) Microbial population from rhizosphere and non-rhizosphere soil of pigeon pea. J Mycol Plant Pathol 30(1):7–10Google Scholar
  50. Papendick RI, Campbell GS (1975) Water potential in the rhizosphere and plant and methods of measurement and experimental control. In: Bruehl GW (ed) Biology and control of soil-born plant pathogens. American Phytopathological Society, St. Paul, pp 34–49Google Scholar
  51. Parveen S, Vijay RK (2004) Antagonism by Trichoderma viride against leaf blight pathogen of wheat. J Mycol Plant Pathol 34(2):220–222Google Scholar
  52. Seaman A (2003) Efficacy of OMRI-approved products for tomato foliar disease control. N Y State Integr Pest Manag Program Publ 129:164–167Google Scholar
  53. Shaik I, Nusrath M (1987) Vertical variation in the rhizosphere and rhizosphere mycoflora of Cajanus cajan with special reference to wilt diseases. Ind J Bot 10:126–129Google Scholar
  54. Sharma M, Gupta SK (2003) Ecofriendly methods for the management of root-rot and web blight of French bean. J Mycol Plant Pathol 33(3):345–361Google Scholar
  55. Sharma RN, Champawat RS, Gaur RB (2004) Efficacy of Rhizospheric and Rhizoplane microflora on spore germination in Fusarium oxysporum, the luciant of Jojoba wilt. J Mycol Plant Pathol 34(2):579–580Google Scholar
  56. Singh F, Hooda I, Sindhan GS (2004) Biological control of tomato wilt caused by Fusarium oxysporum f. sp. lycopersici. J Mycol Plant Pathol 34(2):568–570Google Scholar
  57. Sivan A (1987) Biological control of Fusarium crown rot of tomato by Trichoderma harzianum under field conditions. Plant Dis 71:587–592CrossRefGoogle Scholar
  58. Sorensen J (1997) The rhizosphere as a habitat for soil microorganisms. In: van Elsas JD, Trevors JT, EMH W (eds) Modern soil microbiology. Marcel-Dekker, Inc, New York, pp 21–45Google Scholar
  59. Stephan A, Meyer AH, Schmid B (2000) Plant diversity affects culturable soil bacteria in experimental grassland communities. J Ecol 88:988–998CrossRefGoogle Scholar
  60. Sutton JC, Peng G (1993) Biocontrol of Botrytis cinerea in strawberry leaves. Phytopathology 83:615–621CrossRefGoogle Scholar
  61. Tiwari RKS, Singh A (2004) Efficacy of fungicides of Rhizoctonia solani and Sclerotium rolfsii and their effect on Trichoderma harzianum and Rhizobium leguminosarum. J Mycol Plant Pathol 34(2):212–224Google Scholar
  62. Tronsmo A, Raa I (1977) Antagonistic action of Trichoderma pseudokoningii against the apple pathogen Botrytis cinerea. Phytopathol Z 89:216–220CrossRefGoogle Scholar
  63. Upadhyay JP, Mukhopadhyay AN (1986) Biological control of Sclerotium rolfsii by Trichoderma harzianum in sugarbeet. Trop Pest Manag 32(21):5–220Google Scholar
  64. Vinale F, Sivasithamparam K, Ghisalberti EL, Marra R, Woo SL, Lorito M (2008) Review Trichoderma- plant pathogen interactions. Soil Biol Biochem 40:1–10CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Gunjan Mukherjee
    • 1
    • 2
  • Pannalal Dey
    • 2
  • Sunny Dhiman
    • 3
  1. 1.Department of BiotechnologyChandigarh UniversityMohaliIndia
  2. 2.The Energy and Resources Institute, India Habitat CentreNew DelhiIndia
  3. 3.Department of BiotechnologyUniversity Institute of Biotechnology, Chandigarh UniversityMohaliIndia

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