Indian Journal of Microbiology

, Volume 59, Issue 2, pp 129–136 | Cite as

Bioinoculants for Bioremediation Applications and Disease Resistance: Innovative Perspectives

  • Twinkle Chaudhary
  • Pratyoosh ShuklaEmail author
Review Article


Soil microbial species that act as PGPR or bioinoculants have the capability of improving plant health and promoting its growth. They facilitate plants for uptake nutrients from their surroundings. They provide resistivity to pathogenic pests and also play many roles in the bioremediation process. Bioremediation is the biological approach for the elimination of toxic contaminants by the approach of beneficial microbes. By the consortium of beneficial microbes and plant, a large number of heavy metal and organic contaminants can be controlled. With this advancement of bioremediation, microbial species that act as bioinoculants also help in the enhancement of induced systemic resistance (ISR) and their consortium triggers it by controlling SA, JA, ET and hormonal signaling pathways. Here, this review discusses the progress made on these areas and how the beneficial microbes that act as bioinoculants towards triggering bioremediation and ISR mechanism.


Bioinoculants Induced systemic resistance (ISR) Bioremediation Phytohormones Signaling pathway 



The author, TC acknowledges Maharshi Dayanand University, Rohtak, India for University Research Scholarship (URS). PS acknowledges Department of Science and Technology, New Delhi, Govt. of India, FIST grant (Grant No. 1196 SR/FST/LS-I/ 2017/4) and Department of Biotechnology, Government of India (Grant no. BT/PR27437/BCE/8/1433/2018). PS acknowledges, Department of Microbiology, Barkatullah University, Bhopal, India for their infrastructural support for D.Sc. work.


  1. 1.
    Abou-Shanab RA, El-Sheekh MM, Sadowsky MJ (2019). Role of rhizobacteria in phytoremediation of metal-impacted sites. In: Bharagava R, Chowdhary P (eds) Emerging and eco-friendly approaches for waste management. Springer, Singapore, pp 299–328.
  2. 2.
    Barnawal D, Singh R, Singh RP (2019). Role of plant growth promoting rhizobacteria in drought tolerance: regulating growth hormones and osmolytes. In: Singh AK, Kumar A, Singh PK (eds) PGPR amelioration in sustainable agriculture. Woodhead Publishing, pp. 107–128.
  3. 3.
    Basu S, Rabara RC, Negi S, Shukla P (2018) Engineering PGPMOs through gene editing and systems biology: a solution for phytoremediation? Trends Biotechnol. CrossRefPubMedGoogle Scholar
  4. 4.
    Beneduzi A, Ambrosini A, Passaglia LM (2012) Plant growth-promoting rhizobacteria (PGPR): their potential as antagonists and biocontrol agents. Genet Mol Biol 35:1044–1051. CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Bhardwaj D, Ansari MW, Sahoo RK, Tuteja N (2014) Biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity. Microb Cell Fact 13:66. CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Bouizgarne B (2013). Bacteria for plant growth promotion and disease management. In: Maheshwari D (ed) Bacteria in agrobiology: disease management. Springer, Berlin, pp. 15–47.
  7. 7.
    Chaudhary K, Agarwal S, Khan S (2018). Role of Phytochelatins (PCs), Metallothioneins (MTs), and Heavy Metal ATPase (HMA) Genes in heavy metal tolerance. In: Prasad R (ed) Mycoremediation and environmental sustainability. Springer, Cham, pp 39–60.
  8. 8.
    Compant S, Duffy B, Nowak J, Clément C, Barka A (2005) Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 71:4951–4959. CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Cycon M, Zmijowska A, Wojcik M, Piotrowska-Seget Z (2013) Biodegradation and bioremediation potential of diazinon-degrading Serratia marcescens to remove other organophosphorus pesticides from soils. J Environ Econ Manag 117:7–16. CrossRefGoogle Scholar
  10. 10.
    Dangi AK, Sharma B, Khangwal I, Shukla P (2018) Combinatorial interactions of biotic and abiotic stresses in plants and their molecular mechanisms: systems biology approach. Mol Biotechnol. CrossRefPubMedGoogle Scholar
  11. 11.
    Dangi AK, Sharma B, Hill RT, Shukla P (2019) Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 39:79–98CrossRefGoogle Scholar
  12. 12.
    Dixit R, Malaviya D, Pandiyan K, Singh U, Sahu A, Shukla R, Singh B, Rai J, Sharma P, Lade H, Paul D (2015) Bioremediation of heavy metals from soil and aquatic environment: an overview of principles and criteria of fundamental processes. Sustainability 7:2189–2212. CrossRefGoogle Scholar
  13. 13.
    Ebadi A, Sima NAK, Olamaee M, Hashemi M, Nasrabadi RG (2018) Remediation of saline soils contaminated with crude oil using the halophyte Salicornia persica in conjunction with hydrocarbon-degrading bacteria. J Environ Econ Manag 219:260–268. CrossRefGoogle Scholar
  14. 14.
    Estrada-De Los Santos P, Rojas-Rojas FU, Tapia-Garcia EY (2016) To split or not to split: an opinion on dividing the genus Burkholderia. Ann Microbiol 66:1303–1314. CrossRefGoogle Scholar
  15. 15.
    Fahad S, Nie L, Chen Y, Wu C, Xiong D, Saud S, Hongyan L, Cui K, Huang J (2015). Crop plant hormones and environmental stress. In: Lichtfouse E (ed) Sustainable agriculture reviews. Springer, Cham, pp 371-400.
  16. 16.
    Gouda S, Kerry RG, Das G, Paramithiotis S, Shin HS, Patra JK (2018) Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture. Microbiol Res 206:131–140. CrossRefGoogle Scholar
  17. 17.
    Gupta SK, Shukla P (2017) Gene editing for cell engineering: trends and applications. Crit Rev Biotechnol 37:672–684. CrossRefPubMedGoogle Scholar
  18. 18.
    Haldar S, Sengupta S (2016). Microbial ecology at rhizosphere: bioengineering and future prospective. In: Choudhary D, Varma A, Tuteja N (ed) Plant–microbe interaction: an approach to sustainable agriculture. Springer, Singapore, pp 63–96.
  19. 19.
    Hirsch AM, Valdes M (2010) Micromonospora: an important microbe for biomedicine and potentially for biocontrol and biofuels. Soil Biol Biochem 42:536–542. CrossRefGoogle Scholar
  20. 20.
    Hussain I, Aleti G, Naidu R, Puschenreiter M, Mahmood Q, Rahman MM, Wang F, Shaheen S, Syed JH, Reichenauer TG (2018) Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: a review. Sci Total Environ 628:1582–1599. CrossRefPubMedGoogle Scholar
  21. 21.
    Imam J, Variar M, Shukla P (2013). Role of enzymes and proteins in plant–microbe interaction: a study of M. oryzae versus rice, in advances. In: Shukla P, Pletschke B (ed) Enzyme biotechnol, Springer India, 137–145.
  22. 22.
    Imam J, Singh PK, Shukla P (2016) Plant microbe interactions in post genomic era: perspectives and applications. Front Microbiol 7:1488. CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Imam J, Shukla P, Prasad Mandal N, Variar M (2017) Microbial interactions in plants: perspectives and applications of proteomics. Curr Protein Pept Sci 18:956–965. CrossRefPubMedGoogle Scholar
  24. 24.
    Kahlon RS (2016). Biodegradation and bioremediation of organic chemical pollutants by Pseudomonas. In: Kahlon R (ed) Pseudomonas: molecular and applied biology. Springer, Cham, pp 343–417.
  25. 25.
    Kang SM, Radhakrishnan R, Khan AL, Kim MJ, Park JM, Kim BR, Shin DH, Lee IJ (2014) Gibberellin secreting rhizobacterium, Pseudomonas putida H-2-3 modulates the hormonal and stress physiology of soybean to improve the plant growth under saline and drought conditions. Plant Physiol Biochem 84:115–124. CrossRefPubMedGoogle Scholar
  26. 26.
    Kaushal M (2019). Portraying rhizobacterial mechanisms in drought tolerance: a way forward toward sustainable agriculture. In: Singh AK, Kumar A, Singh PK (ed) PGPR amelioration in sustainable agriculture. Woodhead Publishing, pp 195–216.
  27. 27.
    Kloepper JW, Ryu CM, Zhang S (2004) Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology 94:1259–1266. CrossRefPubMedGoogle Scholar
  28. 28.
    Kumar A, Verma JP (2019). The role of microbes to improve crop productivity and soil health. In: Achal V, Mukherjee A (eds) Ecological wisdom inspired restoration engineering. Springer, Singapore, pp 249–265.
  29. 29.
    Kumar V, Baweja M, Singh PK, Shukla P (2016) Recent developments in systems biology and metabolic engineering of plant–microbe interactions. Front Plant Sci 7:1421PubMedPubMedCentralGoogle Scholar
  30. 30.
    Le Xu CW, Oelmüller R, Zhang W (2018) Role of Phytohormones in Piriformospora indica-induced growth promotion and stress tolerance in plants: more questions than answers. Front Microbiol. CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Lim JH, Kim SD (2013) Induction of drought stress resistance by multi-functional PGPR Bacillus licheniformis K11 in pepper. Plant pathol J 29:201. CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Mishra J, Fatima T, Arora N K (2018). Role of secondary metabolites from plant growth-promoting rhizobacteria in combating salinity stress. In: Egamberdieva D, Ahmad P (ed) Plant microbiome: stress response. Springer, Singapore, pp 127–163.
  33. 33.
    Myresiotis CK, Vryzas Z, Papadopoulou-Mourkidou E (2012) Biodegradation of soil-applied pesticides by selected strains of plant growth-promoting rhizobacteria (PGPR) and their effects on bacterial growth. Biodegradation 23:297–310. CrossRefPubMedGoogle Scholar
  34. 34.
    Narasimhan K, Basheer C, Bajic VB, Swarup S (2003) Enhancement of plant–microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiol 2003:146–153. CrossRefGoogle Scholar
  35. 35.
    Ndeddy Aka RJ, Babalola OO (2016) Effect of bacterial inoculation of strains of Pseudomonas aeruginosa, Alcaligenes feacalis and Bacillus subtilis on germination, growth and heavy metal (Cd, Cr, and Ni) uptake of Brassica juncea. Int J Phytoremediat 18:200–209. CrossRefGoogle Scholar
  36. 36.
    Ortíz I, Velasco A, Le Borgne S, Revah S (2013) Biodegradation of DDT by stimulation of indigenous microbial populations in soil with cosubstrates. Biodegradation 24:215–225. CrossRefPubMedGoogle Scholar
  37. 37.
    Pandotra P, Raina M, Salgotra R K, Ali S, Mir Z A, Bhat J A, Tyagi A, Upadhahy D (2018). Plant-bacterial partnership: a major pollutants remediation approach. In: Oves M, Zain Khan M, M I Ismail I (ed) Modern age environmental problems and their remediation. Springer, Cham, pp 169–200.
  38. 38.
    Pangesti N, Pineda A, Dicke M, Van Loon JJA (2015) Variation in plant-mediated interactions between rhizobacteria and caterpillars: potential role of soil composition. Plant Biol 17:474–483. CrossRefPubMedGoogle Scholar
  39. 39.
    Parewa HP, Meena VS, Jain LK, Choudhary A (2018). Sustainable crop production and soil health management through plant growth-promoting rhizobacteria. In: Meena V (ed) Role of rhizospheric microbes in soil. Springer, Singapore, pp 299–329.
  40. 40.
    Pereira PM, Teixeira R SS, Oliveira MALD, Silva MD, Leitao VSF (2013). Optimized atrazine degradation by Pleurotus ostreatus INCQS 40310: an alternative for impact reduction of herbicides used in sugarcane crops. J Microb Biochem Technol S12:006.
  41. 41.
    Phieler R, Merten D, Roth M, Buchel G, Kothe E (2015) Phytoremediation using microbially mediated metal accumulation in Sorghum bicolor. Environ Sci Pollut Res 22:19408–19416. CrossRefGoogle Scholar
  42. 42.
    Pieterse CM, Zamioudis C, Berendsen RL, Weller DM, Van Wees SC, Bakker PA (2014) Induced systemic resistance by beneficial microbes. Annu Rev Phytopathol 52:347–375. CrossRefPubMedGoogle Scholar
  43. 43.
    Plangklang P, Reungsang A (2010) Bioaugmentation of carbofuran by Burkholderia cepacia PCL3 in a bioslurry phase sequencing batch reactor. Process Biochem 45:230–238. CrossRefGoogle Scholar
  44. 44.
    Prabhu AA, Chityala S, Jayachandran D, Naik N, Dasu VV (2017). Rhizoremediation of environmental contaminants using microbial. Plant–Microbe Interactions. In: Singh D, Singh H, Prabha R (ed) Agro-ecological perspectives: volume 2: microbial interactions and agro-ecological impacts, p 433.
  45. 45.
    Qin S, Zhang YJ, Yuan B, Xu PY, Xing K, Wang J (2014) Isolation of ACC deaminase-producing habitat-adapted symbiotic bacteria associated with halophyte Limonium sinense (Girard) Kuntze and evaluating their plant growth-promoting activity under salt stress. Plant Soil 374:753–766. CrossRefGoogle Scholar
  46. 46.
    Ramjegathesh R, Samiyappan R, Raguchander T, Prabakar K, Saravanakumar D (2013). Plant–PGPR interactions for pest and disease resistance in sustainable agriculture. In: Maheshwari D (ed) Bacteria in agrobiology: disease management. Springer, Berlin, pp 293–320.
  47. 47.
    Rashid M, Chung YR (2017) Induction of systemic resistance against insect herbivores in plants by beneficial soil microbes. Front Plant Sci 8:1816. CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Saha R, Saha N, Donofrio RS, Bestervelt LL (2013) Microbial siderophores. J Basic Microbiol 53:303–317. CrossRefPubMedGoogle Scholar
  49. 49.
    Sharma B, Dangi AK, Shukla P (2018) Contemporary enzyme based technologies for bioremediation: a review. J Environ Manag 210:10–22. CrossRefGoogle Scholar
  50. 50.
    Shrivastava P, Kumar R (2015) Soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation. Saudi J Biol Sci 22:123–131. CrossRefPubMedGoogle Scholar
  51. 51.
    Swissa N, Nitzan Y, Langzam Y, Cahan R (2014) Atrazine biodegradation by a monoculture of Raoultella planticola isolated from a herbicides wastewater treatment facility. Int Biodeterior Biodegrad 92:6–11. CrossRefGoogle Scholar
  52. 52.
    Toussaint JP, Pham TTM, Barriault D, Sylvestre M (2012) Plant exudates promote PCB degradation by a rhodococcal rhizobacteria. Appl Microbiol Biotechnol 95:1589–1603. CrossRefPubMedGoogle Scholar
  53. 53.
    Turan M, Esitken A, Sahin F (2012). Plant growth promoting rhizobacteria as alleviators for soil degradation. In: Maheshwari D (ed) Bacteria in agrobiology: stress management. Springer, Berlin, pp 41–63.
  54. 54.
    Tyagi S, Mulla SI, Lee KJ, Chae JC, Shukla P (2018) VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes. Crit Rev Biotechnol 38:1277–1296CrossRefPubMedGoogle Scholar
  55. 55.
    Ullah A, Heng S, Munis MFH, Fahad S, Yang X (2015) Phytoremediation of heavy metals assisted by plant growth promoting (PGP) bacteria: a review. Environ Exp Bot 117:28–40. CrossRefGoogle Scholar
  56. 56.
    Verma JP, Jaiswal DK, Sagar R (2014) Pesticide relevance and their microbial degradation: a-state-of-art. Rev Rev Environ Sci Bio 13:429–466. CrossRefGoogle Scholar
  57. 57.
    Vurukonda SSKP, Vardharajula S, Shrivastava M, SkZ A (2016) Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria. Microbiol Res 184:13–24. CrossRefPubMedGoogle Scholar
  58. 58.
    Ye S, Zeng G, Wu H, Zhang C, Dai J, Liang J, Yu J, Ren X, Yi H, Cheng M, Zhang C (2017) Biological technologies for the remediation of co-contaminated soil. Crit Rev Biotechnol 37:1062–1076. CrossRefPubMedGoogle Scholar
  59. 59.
    Zehnder GW, Murphy JF, Sikora EJ, Kloepper JW (2009) Application of rhizobacteria for induced resistance. Euro J Plant Pathol 107:39–50. CrossRefGoogle Scholar

Copyright information

© Association of Microbiologists of India 2019

Authors and Affiliations

  1. 1.Enzyme Technology and Protein Bioinformatics Laboratory, Department of MicrobiologyMaharshi Dayanand UniversityRohtakIndia

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