Advertisement

Applied Biochemistry and Biotechnology

, Volume 166, Issue 4, pp 903–924 | Cite as

Integrated Perspective for Effective Bioremediation

  • Vasundhara Paliwal
  • Sampada Puranik
  • Hemant J. PurohitEmail author
Article

Abstract

Identification of factors which can influence the natural attenuation process with available microbial genetic capacities can support the bioremediation which has been viewed as the safest procedure to combat with anthropogenic compounds in ecosystems. With the advent of molecular techniques, assimilatory capacity of an ecosystem can be defined with changing community dynamics, and if required, the essential genetic potential can be met through bioaugmentation. At the same time, intensification of microbial processes with nutrient balancing, expressing and enhancing the degradative capacities, could reduce the time frame of restoration of the ecosystem. The new concept of ecosystems biology has added greatly to conceptualize the networking of the evolving microbiota of the niche that helps in effective application of bioremediation tools to manage pollutants as additional carbon source.

Keywords

Bioremediation Bioaugmentation Natural attenuation Microbial community Genomics tool Ecosystem biology 

References

  1. 1.
    Fuhrman, J. A. (2009). Nature, 459, 193–199.CrossRefGoogle Scholar
  2. 2.
    Konopka, A. (2009). The ISME Journal, 3, 1223–1230.CrossRefGoogle Scholar
  3. 3.
    Purohit, H. J., Raje, D. V., Kapley, A., Padmanabhan, P., & Singh, R. N. (2003). Environmental Science and Technology, 37(19), 356A–363A.CrossRefGoogle Scholar
  4. 4.
    Humbert, J. F., Dorigo, U., Cecchi, P., Le Berre, B., Debroas, D., & Bouvy, M. (2009). Environmental Microbiology, 11(9), 2339–2350.CrossRefGoogle Scholar
  5. 5.
    Makadia, T. H., Adetu, E. M., Simons, K. L., Jardine, D., Sheppard, P. J., & Ball, A. S. (2011). Journal of Environmental Management, 92, 866–871.CrossRefGoogle Scholar
  6. 6.
    Kao, C. M., Chien, H. Y., Surampalli, R. Y., Chien, C. C., & Chen, C. Y. (2010). Journal of Environmental Engineering, 136, 54.CrossRefGoogle Scholar
  7. 7.
    Megharaj, M., Ramakrishnan, B., Venkateswarlu, K., Sethunathan, N., & Naidu, R. (2011). Environment International, 37(8), 1362–1375.CrossRefGoogle Scholar
  8. 8.
    Zeigler, D. (2007), in Understanding biodiversity, chapter 7: diversity of ecosystem and ecological interactions, 63-70.Google Scholar
  9. 9.
    Tyson, G. W., & Banfield, J. F. (2005). Trends in Microbiology, 13(9), 411–415.CrossRefGoogle Scholar
  10. 10.
    Brennerova, M., Josefiova, J., Brenner, V., Pieper, D. H., & Junca, H. (2009). Environmental Microbiology, 11(9), 2216–2227.CrossRefGoogle Scholar
  11. 11.
    Kapley, A., De Baere, T., & Purohit, H. J. (2007). Research in Microbiology, 158(6), 494–500.CrossRefGoogle Scholar
  12. 12.
    Rani, A., Porwal, S., Sharma, R., Kapley, A., Purohit, H. J., & Kalia, V. C. (2008). Bioresource Technology, 99(15), 7098–7107.CrossRefGoogle Scholar
  13. 13.
    Kapley, A., Prasad, S., & Purohit, H. J. (2006). Bioresource Technology, 98(13), 2479–2484.CrossRefGoogle Scholar
  14. 14.
    Ciric, L., Griffiths, R. I., Philp, J. C., & Whiteley, A. S. (2010). Bioresource Technology, 101, 5235–5241.CrossRefGoogle Scholar
  15. 15.
    Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, C., Jones, R., Robeson, M., Edwards, R. A., Felts, B., Rayhawk, S., Knight, R., Rohwer, F., & Jackson, R. B. (2007). Applied and Environmental Microbiology, 73(21), 7059–7066.CrossRefGoogle Scholar
  16. 16.
    Xie, Q., Lin, J., Qin, Y., Zhou, J., & Bu, W. (2011). Protein & Cell, 2(2), 161–170.CrossRefGoogle Scholar
  17. 17.
    Roeselers, G., Zippel, B., Staal, M., van Loosdrecht, M., & Muyzer, G. (2006). FEMS Microbiology Ecology, 58(2), 169–178.CrossRefGoogle Scholar
  18. 18.
    Reid, N. M., Bowers, T. H., & Lloyd-Jones, G. (2008). Applied Microbiology and Biotechnology, 79, 285–292.CrossRefGoogle Scholar
  19. 19.
    Hazen, T. C., et al. (2009). Archives of Microbiology, 191, 221–232.CrossRefGoogle Scholar
  20. 20.
    Sul, W. J., Park, J., Quensen, J. F., 3rd, Rodrigues, J. L., Seliger, L., Tsoi, T. V., Zylstra, G. J., & Tiedje, J. M. (2009). Applied and Environmental Microbiology, 75(17), 5501–5506.CrossRefGoogle Scholar
  21. 21.
    Uhlík, O., Jecna, K., Leigh, M. B., Mackova, M., & Macek, T. (2009). The Science of the Total Environment, 407, 3611–3619.CrossRefGoogle Scholar
  22. 22.
    Vishnevetsky, S., & Steinberger, Y. (1997). Journal of Arid Environments, 37, 83–90.CrossRefGoogle Scholar
  23. 23.
    Kapley, A., & Purohit, H. J. (2009). Indian Journal of Microbiology, 49, 108–113.CrossRefGoogle Scholar
  24. 24.
    El Azhari, N., Devers-Lamrani, M., Chatagnier, G., Rouard, N., & Martin-Laurent, F. (2010). Journal of Hazardous Materials, 177, 593–601.CrossRefGoogle Scholar
  25. 25.
    Moharikar, A., Kapley, A., & Purohit, H. J. (2003). Environmental Science and Pollution Research International, 10(6), 373–378.CrossRefGoogle Scholar
  26. 26.
    Ward, B. B., & Bouskill, N. J. (2011). Methods in Enzymology, 496, 373–396.CrossRefGoogle Scholar
  27. 27.
    Frias-Lopez, J., Shi, Y., Tyson, G. W., Coleman, M. L., Schuster, S. C., Chisholm, S. W., & Delong, E. F. (2008). PNAS, 105, 3805–3810.CrossRefGoogle Scholar
  28. 28.
    Chauhan, N. S., Ranjan, R., Purohit, H. J., Kalia, V. C., & Sharma, R. (2009). FEMS Microbiology Ecology, 67(1), 130–139.CrossRefGoogle Scholar
  29. 29.
    Selvakumaran, S., Kapley, A., Kalia, V. C., & Purohit, H. J. (2008). Bioresource Technology, 99, 1189–1195.CrossRefGoogle Scholar
  30. 30.
    Purohit, H. J., Raje, D. V., & Kapley, A. (2003). BMC Bioinformatics, 4, 19.CrossRefGoogle Scholar
  31. 31.
    Raje, D. V., Purohit, H. J., Badhe, Y. P., Tambe, S. S., & Kulkarni, B. D. (2010). Journal of Biosciences, 35(4), 617–627.CrossRefGoogle Scholar
  32. 32.
    Pandey, J., Chauhan, A., & Jain, R. K. (2009). FEMS Microbiology Reviews, 33, 324–375.CrossRefGoogle Scholar
  33. 33.
    Tyagi, M., da Fonseca, M. M., & de Carvalho, C. C. (2011). Biodegradation, 22, 231–241.CrossRefGoogle Scholar
  34. 34.
    Mills, S. A., & Frankenberger, W. T., Jr. (1994). Bulletin of Environmental Contamination and Toxicology, 53(2), 280–284.CrossRefGoogle Scholar
  35. 35.
    Yang, J., Kloepper, J. W., & Ryu, C. M. (2009). Trends in Plant Science, 14(1), 1–4.CrossRefGoogle Scholar
  36. 36.
    Keasling, J. D., Van Dien, S. J., Trelstad, P., Renninger, N., & McMahon, K. (2000). Biochemistry (Moscow), 65(3), 324–331.Google Scholar
  37. 37.
    Basu, A., Das, D., Bapat, P., Wangikar, P. P., & Phale, P. S. (2009). Microbiology Research, 164(4), 429–437.CrossRefGoogle Scholar
  38. 38.
    Samanta, S. K., Bhushan, B., & Jain, R. K. (2001). Applied Microbiology and Biotechnology, 55(5), 627–631.CrossRefGoogle Scholar
  39. 39.
    Ostberga, T. L., Jonsson, A. P., Bylund, D., & Lundstrom, U. S. (2007). International Biodeterioration & Biodegradation, 60, 334–341.CrossRefGoogle Scholar
  40. 40.
    Blagodatskaya, E., & Kuzyakov, Y. (2008). Biology and Fertility of Soils, 45, 115–131.CrossRefGoogle Scholar
  41. 41.
    Mouser, P. J., N' Guessan, A. L., Elifantz, H., Holmes, D. E., Williams, K. H., Wilkins, M. J., Long, P. E., & Lovley, D. R. (2009). Environmental Science and Technology, 43, 4386–4392.CrossRefGoogle Scholar
  42. 42.
    Kwapisz, E., Wszelaka, J., Marchut, O., & Bielecki, S. (2008). International Biodeterioration & Biodegradation, 61, 214–222.CrossRefGoogle Scholar
  43. 43.
    Ruberto, L., Dias, R., Lo Balbo, A., Vazquez, S. C., Hernandez, E. A., & Mac Cormack, W. P. (2009). Journal of Applied Microbiology, 106(4), 1101–10.CrossRefGoogle Scholar
  44. 44.
    K. N. Timmis (ed.), Handbook of hydrocarbon and lipid microbiology, DOI  10.1007/978-3-540-77587-4_355,
  45. 45.
    Vinas, M., Sabate, J., Espuny, M. J., & Solanas, A. M. (2005). Applied and Environmental Microbiology, 71, 7008–7018.CrossRefGoogle Scholar
  46. 46.
    Chaineau, C. H., Yepremian, C., Vidalie, J. F., Ducreux, J., & Ballerini, D. (2003). Water, Air, and Soil Pollution, 144, 419–440.CrossRefGoogle Scholar
  47. 47.
    Vidali, M. (2001). Pure and Applied Chemistry, 73(7), 1163–1172.CrossRefGoogle Scholar
  48. 48.
    da Silva, A. C., de Oliveira, F. J., Bernardes, D. S., & de França, F. P. (2009). Applied Biochemistry and Biotechnology, 153(1–3), 58–66.CrossRefGoogle Scholar
  49. 49.
    Janssen, P. H. (2006). Applied and Environmental Microbiology, 72(3), 1719–1728.CrossRefGoogle Scholar
  50. 50.
    Purohit, H. J. (2003). Journal of Cleaner Production, 11, 293–301.CrossRefGoogle Scholar
  51. 51.
    Martínez-Lavanchy, P. M., Muller, C., Nijenhuis, I., Kappelmeyer, U., Buffing, M., McPherson, K., & Heipieper, H. J. (2010). Applied and Environmental Microbiology, 76(20), 6715–6723.CrossRefGoogle Scholar
  52. 52.
    Ono, A., Miyazaki, R., Sota, M., Ohtsubo, Y., Nagata, Y., & Tsuda, M. (2007). Applied Microbiology and Biotechnology, 74(2), 501–510.CrossRefGoogle Scholar
  53. 53.
    Khardenavis, A. A., Kapley, A., & Purohit, H. J. (2010). Applied Biochemistry and Biotechnology, 160, 704–718.CrossRefGoogle Scholar
  54. 54.
    Schweigert, N., Hunziker, R. W., Escher, B. I., & Eggen, R. I. (2001). Environmental Toxicology and Chemistry, 20(2), 239–247.Google Scholar
  55. 55.
    Guerin, T. F. (2008). Journal of Hazardous Materials, 154, 9–20.CrossRefGoogle Scholar
  56. 56.
    Vazquez, S., Nogales, B., Ruberto, L., Hemandez, E., Christie-Oleza, J., Balbo, A. L., Bosch, R., Lalucat, J., & Cormack, W. M. (2009). Microbial Ecology, 57, 598–610.CrossRefGoogle Scholar
  57. 57.
    Zhou, Y. Y., Chen, D. Z., Zhu, R. Y., & Chen, J. M. (2011). Bioresource Technology. doi: 10.1016/j.biortech.2011.03.076.
  58. 58.
    Burgess, J. E., Quarmby, J., & Stephenson, T. (1999). Biotechnology Advances, 17(1), 49–70.CrossRefGoogle Scholar
  59. 59.
    Liebeg, E. W., & Cutright, T. J. (1999). International Biodeterioration & Biodegradation, 44, 55–64.CrossRefGoogle Scholar
  60. 60.
    Jean, J. S., Lee, M. K., Wang, S. M., Chattopadhyay, P., & Maity, J. P. (2008). Bioresource Technology, 99(16), 7807–7815.CrossRefGoogle Scholar
  61. 61.
    Ronen, Z., Visnovsky, S., & Nejidat, A. (2005). Soil Biology and Biochemistry, 37, 1640–1647.CrossRefGoogle Scholar
  62. 62.
    Wu, R. R., Dang, Z., Yi, X. Y., Yang, C., Lu, G. N., Guo, C. L., & Liu, C. Q. (2011). Journal of Hazardous Materials, 186, 978–983.CrossRefGoogle Scholar
  63. 63.
    Morel, F. M., (2000). in Opportunities For Environmental Applications Of Marine Biotechnology Google Scholar
  64. 64.
    Alcalde, M., Ferrer, M., Plou, F. J., & Ballesteros, A. (2006). Trends in Biotechnology, 24(6), 281–287.CrossRefGoogle Scholar
  65. 65.
    Mancini, G., Lanciotti, E., & Bruno, M. (2010). Chemical Engineering Transactions, 20, 271–278.Google Scholar
  66. 66.
    Scott, C., et al. (2008). Indian Journal of Microbiology, 48, 65–79.CrossRefGoogle Scholar
  67. 67.
    Chauhan, A., Fazlurrahman, Oakeshott, J. G., & Jain, R. K. (2008). Indian Journal of Microbiology, 48, 95–113.CrossRefGoogle Scholar
  68. 68.
    Joo, H., Lin, Z., & Arnold, F. H. (1999). Nature, 399(6737), 670–673.CrossRefGoogle Scholar
  69. 69.
    Tortella, G. R., Rubilar, O., Gianfreda, L., Valenzuela, E., & Diez, M. C. (2008). World Journal of Microbiology and Biotechnology, 24, 2805–2818.CrossRefGoogle Scholar
  70. 70.
    Diaz, E., & Prieto, M. A. (2000). Current Opinion in Biotechnology, 11(5), 467–475.CrossRefGoogle Scholar
  71. 71.
    Cao, B., Nagarajan, K., & Loh, K. C. (2009). Applied Microbiology and Biotechnology, 85, 207–228.CrossRefGoogle Scholar
  72. 72.
    Govantes, F., Garcia-González, V., Porrua, O., Platero, A. I., Jimenez-Fernandez, A., & Santero, E. (2010). FEMS Microbiology Letters, 310, 1–8.CrossRefGoogle Scholar
  73. 73.
    Smith, C. J., & Osborn, A. M. (2008). FEMS Microbiology Ecology, 67, 6–20.CrossRefGoogle Scholar
  74. 74.
    Peng, J. J., Cai, C., Qiao, M., Li, H., & Zhu, Y. G. (2010). Environmental Pollution, 158, 2872–2879.CrossRefGoogle Scholar
  75. 75.
    Shi, Y., Tyson, G. W., & DeLong, E. F. (2009). Nature, 459(7244), 266–269.CrossRefGoogle Scholar
  76. 76.
    Ng, W. L., & Bassler, B. L. (2009). Annual Review of Genetics, 43, 197–222.CrossRefGoogle Scholar
  77. 77.
    Horswill, A. R., Stoodley, P., Stewart, P. S., & Parsek, M. R. (2007). Analytical and Bioanalytical Chemistry, 387(2), 371–380.CrossRefGoogle Scholar
  78. 78.
    Kalia, V. C., Raju, S. C., & Purohit, H. J. (2010). The Open Microbiology Journal, 4, 1–13.CrossRefGoogle Scholar
  79. 79.
    Nusrat, H., Shankar, P., Kushwah, J., Bhushan, A., Joshi, J., Mukherjee, T., Raju, S. C., Purohit, H. J., & Kalia, V. C. (2011). Journal of Microbiology and Biotechnology, 21(10), 1001–1011.CrossRefGoogle Scholar
  80. 80.
    Kang, Y. S., & Park, W. (2010). Journal of Applied Microbiology, 109(5), 1650–1659.Google Scholar
  81. 81.
    Singh, R., Paul, D., & Jain, R. K. (2006). Trends in Microbiology, 14(9), 389–397.CrossRefGoogle Scholar
  82. 82.
    Ron, E. Z., & Rosenberg, E. (2002). Current Opinion in Biotechnology, 13(3), 249–252.CrossRefGoogle Scholar
  83. 83.
    Atkinson, S., & Williams, P. (2009). Journal of the Royal Society, Interface, 6(40), 959–978.CrossRefGoogle Scholar
  84. 84.
    Desai, C., Pathak, H., & Madamwar, D. (2010). Bioresource Technology, 101, 1558–1569.CrossRefGoogle Scholar
  85. 85.
    Chauhan, A., & Jain, R. K. (2010). Biodegradation, 21, 861–879.CrossRefGoogle Scholar
  86. 86.
    Trigo, A., Valencia, A., & Cases, I. (2009). FEMS Microbiology Reviews, 33, 98–108.CrossRefGoogle Scholar
  87. 87.
    Ellis, L. B., Roe, D., & Wackett, L. P. (2006). Nucleic Acids Research, 34, D517–D521.CrossRefGoogle Scholar
  88. 88.
    Pazos, F., Guijas, D., Valencia, A., & De Lorenzo, V. (2005). Nucleic Acids Research, 33, D588–D592.CrossRefGoogle Scholar
  89. 89.
    Carbajosa, G., Trigo, A., Valencia, A., & Cases, I. (2009). Nucleic Acids Research, 37, D598–D602.CrossRefGoogle Scholar
  90. 90.
    Domde, P., Kapley, A., & Purohit, H. J. (2006). Environmental Science and Pollution Research, 5, 1–5.Google Scholar
  91. 91.
    Byss, M., Elhottova, D., Triska, J., & Baldrian, P. (2008). Chemosphere, 73(9), 1518–1523.CrossRefGoogle Scholar
  92. 92.
    Dalby, A. P., Kormas, K. A., Christaki, U., & Karayanni, H. (2008). Environmental Microbiology, 10(1), 47–56.Google Scholar
  93. 93.
    Behzadian, F., Barjeste, H., Hosseinkhani, S., & Zarei, A. R. (2011). Current Microbiology, 62(2), 690–696.CrossRefGoogle Scholar
  94. 94.
    Lee, J. H., Mitchell, R. J., Kim, B. C., Cullen, D. C., & Gu, M. B. (2005). Biosensors & Bioelectronics, 21(3), 500–507.CrossRefGoogle Scholar
  95. 95.
    Liao, V. H., Chien, M. T., Tseng, Y. Y., & Ou, K. L. (2006). Environmental Pollution, 142(1), 17–23.CrossRefGoogle Scholar
  96. 96.
    Hynninen, A., Tonismann, K., & Virta, M. (2010). Bioengineered Bugs, 1(2), 132–138.CrossRefGoogle Scholar
  97. 97.
    Roling, W. F., Milner, M. G., Jones, D. M., Fratepietro, F., Swannell, R. P., Daniel, F., & Head, I. M. (2004). Applied and Environmental Microbiology, 70(5), 2603–13.CrossRefGoogle Scholar
  98. 98.
    Diplock, E. E., Mardlin, D. P., Killham, K. S., & Paton, G. I. (2009). Environmental Pollution, 15, 1831–1840.CrossRefGoogle Scholar
  99. 99.
    Gemende, B., Gerbeth, A., Muller, G., Hose, C., Siedel, J., Lange, R., & Muller, R. H. (2006). Land Contamination and Reclamation, 14(2), 252–257.CrossRefGoogle Scholar
  100. 100.
    Couto, M. N., Monteiro, E., & Vasconcelos, M. T. (2010). Environmental Science and Pollution Research International, 17(7), 1339–1346.CrossRefGoogle Scholar
  101. 101.
    Jorgensen, K. S., Salminen, J. M., & Bjorklof, K. (2010). Methods in Molecular Biology, 599, 217–233.CrossRefGoogle Scholar
  102. 102.
    Walter, M., Boyd-Wilson, K., Boul, L., Ford, C., McFadden, D., Chong, B., & Pinfold, J. (2005). International Biodeterioration & Biodegradation, 56, 51–57.CrossRefGoogle Scholar
  103. 103.
    Hazen, T. C. (2010). Peer Reviewed. Berkeley, California USA: Lawrence Berkeley National Laboratory.Google Scholar
  104. 104.
    Singh, J.S., Abhilash, P.C., Singh, H.B., Singh, R.P. & Singh, D.P. (2011). Gene doi: 10.1016/j.gene.2011.03.001.
  105. 105.
    Hansel, C. M., Fendorf, S., Jardine, P. M., & Francis, C. A. (2008). Applied and Environmental Microbiology, 74(5), 1620–1633.CrossRefGoogle Scholar
  106. 106.
    Diplock, E. E., Alhadrami, H. A., & Paton, G. I. (2009). Advances in Biochemical Engineering/Biotechnology, 118, 189–209.CrossRefGoogle Scholar
  107. 107.
    Ohtsubo, Y., Shimura, M., Delawary, M., Kimbara, K., Takagi, M., Kudo, T., et al. (2003). Applied and Environmental Microbiology, 69(1), 146–53.CrossRefGoogle Scholar
  108. 108.
    Fernandez-Luqueno, F., Valenzuela-Encinas, C., Marsch, R., Martinez-Suarez, C., Vazquez-Nunez, E., & Dendooven, L. (2011). Environmental Science and Pollution Research, 18, 12–30.CrossRefGoogle Scholar
  109. 109.
    Rojas, L. A., Yanez, C., Gonzalez, M., Lobos, S., Smalla, K., & Seeger, M. (2011). PLoS One, 6(3), 17555.CrossRefGoogle Scholar
  110. 110.
    Khardenavis, A. A., Kapley, A., & Purohit, H. J. (2008). International Biodeterioration & Biodegradation, 62, 38–45.CrossRefGoogle Scholar
  111. 111.
    Wu, Z., Dong, H., Zou, L., Lu, D., & Liu, Z. (2011). Applied Biochemistry and Biotechnology. doi: 10.1007/s12010-011-9195-1.
  112. 112.
    Kitano, H. (2002). Science, 295, 1662–1664.CrossRefGoogle Scholar
  113. 113.
    Raes, J., & Bork, P. (2008). Nature Reviews Microbiology, 6, 693–699.CrossRefGoogle Scholar
  114. 114.
    Lorenzo, V. (2008). Current Opinion in Biotechnology, 19(6), 579–589.CrossRefGoogle Scholar
  115. 115.
    Fredrickson, J. K., Romine, M. F., Beliaev, A. S., Auchtung, J. M., Driscoll, M. E., Gardner, T. S., et al. (2008). Nature Reviews Microbiology, 6, 693–699.CrossRefGoogle Scholar
  116. 116.
    Loreau, M. (2010). Philosophical Transaction of the Royal Society B, 365, 49–60.CrossRefGoogle Scholar
  117. 117.
    Matthews, B., Narwani, A., Hausch, S., Nonaka, E., Peter, H., Yamamichi, M., Sullam, K.E., Bird, K.C., Thomas, M.K., Torrance C., Hanley & Turner, C.B.,(2011). Ecology Letters, doi:  10.1111/j.1461-0248.2011.01627.x.
  118. 118.
    Loreau, M. (2010). in From populations to ecosystems: monographs in population biology- 46.Google Scholar
  119. 119.
    Vergara, P. M., Pizarro, J., & Castro, S. A. (2011). Ecological Modelling, 222, 1964–1971.CrossRefGoogle Scholar
  120. 120.
    Pascual, M. (2005). PLoS Computational Biology, 1(2), e18.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Vasundhara Paliwal
    • 1
  • Sampada Puranik
    • 1
  • Hemant J. Purohit
    • 1
    Email author
  1. 1.Environmental Genomics Division, National Environmental Engineering Research InstituteCSIRNagpurIndia

Personalised recommendations