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Integrated Perspective for Effective Bioremediation

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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.

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References

  1. Fuhrman, J. A. (2009). Nature, 459, 193–199.

    Article  CAS  Google Scholar 

  2. Konopka, A. (2009). The ISME Journal, 3, 1223–1230.

    Article  Google Scholar 

  3. Purohit, H. J., Raje, D. V., Kapley, A., Padmanabhan, P., & Singh, R. N. (2003). Environmental Science and Technology, 37(19), 356A–363A.

    Article  Google Scholar 

  4. Humbert, J. F., Dorigo, U., Cecchi, P., Le Berre, B., Debroas, D., & Bouvy, M. (2009). Environmental Microbiology, 11(9), 2339–2350.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  6. Kao, C. M., Chien, H. Y., Surampalli, R. Y., Chien, C. C., & Chen, C. Y. (2010). Journal of Environmental Engineering, 136, 54.

    Article  CAS  Google Scholar 

  7. Megharaj, M., Ramakrishnan, B., Venkateswarlu, K., Sethunathan, N., & Naidu, R. (2011). Environment International, 37(8), 1362–1375.

    Article  CAS  Google Scholar 

  8. Zeigler, D. (2007), in Understanding biodiversity, chapter 7: diversity of ecosystem and ecological interactions, 63-70.

  9. Tyson, G. W., & Banfield, J. F. (2005). Trends in Microbiology, 13(9), 411–415.

    Article  CAS  Google Scholar 

  10. Brennerova, M., Josefiova, J., Brenner, V., Pieper, D. H., & Junca, H. (2009). Environmental Microbiology, 11(9), 2216–2227.

    Article  CAS  Google Scholar 

  11. Kapley, A., De Baere, T., & Purohit, H. J. (2007). Research in Microbiology, 158(6), 494–500.

    Article  CAS  Google Scholar 

  12. Rani, A., Porwal, S., Sharma, R., Kapley, A., Purohit, H. J., & Kalia, V. C. (2008). Bioresource Technology, 99(15), 7098–7107.

    Article  CAS  Google Scholar 

  13. Kapley, A., Prasad, S., & Purohit, H. J. (2006). Bioresource Technology, 98(13), 2479–2484.

    Article  CAS  Google Scholar 

  14. Ciric, L., Griffiths, R. I., Philp, J. C., & Whiteley, A. S. (2010). Bioresource Technology, 101, 5235–5241.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  16. Xie, Q., Lin, J., Qin, Y., Zhou, J., & Bu, W. (2011). Protein & Cell, 2(2), 161–170.

    Article  CAS  Google Scholar 

  17. Roeselers, G., Zippel, B., Staal, M., van Loosdrecht, M., & Muyzer, G. (2006). FEMS Microbiology Ecology, 58(2), 169–178.

    Article  CAS  Google Scholar 

  18. Reid, N. M., Bowers, T. H., & Lloyd-Jones, G. (2008). Applied Microbiology and Biotechnology, 79, 285–292.

    Article  CAS  Google Scholar 

  19. Hazen, T. C., et al. (2009). Archives of Microbiology, 191, 221–232.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  21. Uhlík, O., Jecna, K., Leigh, M. B., Mackova, M., & Macek, T. (2009). The Science of the Total Environment, 407, 3611–3619.

    Article  CAS  Google Scholar 

  22. Vishnevetsky, S., & Steinberger, Y. (1997). Journal of Arid Environments, 37, 83–90.

    Article  Google Scholar 

  23. Kapley, A., & Purohit, H. J. (2009). Indian Journal of Microbiology, 49, 108–113.

    Article  CAS  Google Scholar 

  24. El Azhari, N., Devers-Lamrani, M., Chatagnier, G., Rouard, N., & Martin-Laurent, F. (2010). Journal of Hazardous Materials, 177, 593–601.

    Article  CAS  Google Scholar 

  25. Moharikar, A., Kapley, A., & Purohit, H. J. (2003). Environmental Science and Pollution Research International, 10(6), 373–378.

    Article  CAS  Google Scholar 

  26. Ward, B. B., & Bouskill, N. J. (2011). Methods in Enzymology, 496, 373–396.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  28. Chauhan, N. S., Ranjan, R., Purohit, H. J., Kalia, V. C., & Sharma, R. (2009). FEMS Microbiology Ecology, 67(1), 130–139.

    Article  CAS  Google Scholar 

  29. Selvakumaran, S., Kapley, A., Kalia, V. C., & Purohit, H. J. (2008). Bioresource Technology, 99, 1189–1195.

    Article  CAS  Google Scholar 

  30. Purohit, H. J., Raje, D. V., & Kapley, A. (2003). BMC Bioinformatics, 4, 19.

    Article  CAS  Google Scholar 

  31. Raje, D. V., Purohit, H. J., Badhe, Y. P., Tambe, S. S., & Kulkarni, B. D. (2010). Journal of Biosciences, 35(4), 617–627.

    Article  CAS  Google Scholar 

  32. Pandey, J., Chauhan, A., & Jain, R. K. (2009). FEMS Microbiology Reviews, 33, 324–375.

    Article  CAS  Google Scholar 

  33. Tyagi, M., da Fonseca, M. M., & de Carvalho, C. C. (2011). Biodegradation, 22, 231–241.

    Article  CAS  Google Scholar 

  34. Mills, S. A., & Frankenberger, W. T., Jr. (1994). Bulletin of Environmental Contamination and Toxicology, 53(2), 280–284.

    Article  CAS  Google Scholar 

  35. Yang, J., Kloepper, J. W., & Ryu, C. M. (2009). Trends in Plant Science, 14(1), 1–4.

    Article  CAS  Google Scholar 

  36. Keasling, J. D., Van Dien, S. J., Trelstad, P., Renninger, N., & McMahon, K. (2000). Biochemistry (Moscow), 65(3), 324–331.

    CAS  Google Scholar 

  37. Basu, A., Das, D., Bapat, P., Wangikar, P. P., & Phale, P. S. (2009). Microbiology Research, 164(4), 429–437.

    Article  CAS  Google Scholar 

  38. Samanta, S. K., Bhushan, B., & Jain, R. K. (2001). Applied Microbiology and Biotechnology, 55(5), 627–631.

    Article  CAS  Google Scholar 

  39. Ostberga, T. L., Jonsson, A. P., Bylund, D., & Lundstrom, U. S. (2007). International Biodeterioration & Biodegradation, 60, 334–341.

    Article  CAS  Google Scholar 

  40. Blagodatskaya, E., & Kuzyakov, Y. (2008). Biology and Fertility of Soils, 45, 115–131.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  42. Kwapisz, E., Wszelaka, J., Marchut, O., & Bielecki, S. (2008). International Biodeterioration & Biodegradation, 61, 214–222.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  44. K. N. Timmis (ed.), Handbook of hydrocarbon and lipid microbiology, DOI 10.1007/978-3-540-77587-4_355,

  45. Vinas, M., Sabate, J., Espuny, M. J., & Solanas, A. M. (2005). Applied and Environmental Microbiology, 71, 7008–7018.

    Article  CAS  Google Scholar 

  46. Chaineau, C. H., Yepremian, C., Vidalie, J. F., Ducreux, J., & Ballerini, D. (2003). Water, Air, and Soil Pollution, 144, 419–440.

    Article  CAS  Google Scholar 

  47. Vidali, M. (2001). Pure and Applied Chemistry, 73(7), 1163–1172.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  49. Janssen, P. H. (2006). Applied and Environmental Microbiology, 72(3), 1719–1728.

    Article  CAS  Google Scholar 

  50. Purohit, H. J. (2003). Journal of Cleaner Production, 11, 293–301.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  52. Ono, A., Miyazaki, R., Sota, M., Ohtsubo, Y., Nagata, Y., & Tsuda, M. (2007). Applied Microbiology and Biotechnology, 74(2), 501–510.

    Article  CAS  Google Scholar 

  53. Khardenavis, A. A., Kapley, A., & Purohit, H. J. (2010). Applied Biochemistry and Biotechnology, 160, 704–718.

    Article  CAS  Google Scholar 

  54. Schweigert, N., Hunziker, R. W., Escher, B. I., & Eggen, R. I. (2001). Environmental Toxicology and Chemistry, 20(2), 239–247.

    CAS  Google Scholar 

  55. Guerin, T. F. (2008). Journal of Hazardous Materials, 154, 9–20.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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. Burgess, J. E., Quarmby, J., & Stephenson, T. (1999). Biotechnology Advances, 17(1), 49–70.

    Article  CAS  Google Scholar 

  59. Liebeg, E. W., & Cutright, T. J. (1999). International Biodeterioration & Biodegradation, 44, 55–64.

    Article  CAS  Google Scholar 

  60. Jean, J. S., Lee, M. K., Wang, S. M., Chattopadhyay, P., & Maity, J. P. (2008). Bioresource Technology, 99(16), 7807–7815.

    Article  CAS  Google Scholar 

  61. Ronen, Z., Visnovsky, S., & Nejidat, A. (2005). Soil Biology and Biochemistry, 37, 1640–1647.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  63. Morel, F. M., (2000). in Opportunities For Environmental Applications Of Marine Biotechnology

  64. Alcalde, M., Ferrer, M., Plou, F. J., & Ballesteros, A. (2006). Trends in Biotechnology, 24(6), 281–287.

    Article  CAS  Google Scholar 

  65. Mancini, G., Lanciotti, E., & Bruno, M. (2010). Chemical Engineering Transactions, 20, 271–278.

    Google Scholar 

  66. Scott, C., et al. (2008). Indian Journal of Microbiology, 48, 65–79.

    Article  CAS  Google Scholar 

  67. Chauhan, A., Fazlurrahman, Oakeshott, J. G., & Jain, R. K. (2008). Indian Journal of Microbiology, 48, 95–113.

    Article  CAS  Google Scholar 

  68. Joo, H., Lin, Z., & Arnold, F. H. (1999). Nature, 399(6737), 670–673.

    Article  CAS  Google Scholar 

  69. Tortella, G. R., Rubilar, O., Gianfreda, L., Valenzuela, E., & Diez, M. C. (2008). World Journal of Microbiology and Biotechnology, 24, 2805–2818.

    Article  CAS  Google Scholar 

  70. Diaz, E., & Prieto, M. A. (2000). Current Opinion in Biotechnology, 11(5), 467–475.

    Article  CAS  Google Scholar 

  71. Cao, B., Nagarajan, K., & Loh, K. C. (2009). Applied Microbiology and Biotechnology, 85, 207–228.

    Article  CAS  Google Scholar 

  72. Govantes, F., Garcia-González, V., Porrua, O., Platero, A. I., Jimenez-Fernandez, A., & Santero, E. (2010). FEMS Microbiology Letters, 310, 1–8.

    Article  CAS  Google Scholar 

  73. Smith, C. J., & Osborn, A. M. (2008). FEMS Microbiology Ecology, 67, 6–20.

    Article  CAS  Google Scholar 

  74. Peng, J. J., Cai, C., Qiao, M., Li, H., & Zhu, Y. G. (2010). Environmental Pollution, 158, 2872–2879.

    Article  CAS  Google Scholar 

  75. Shi, Y., Tyson, G. W., & DeLong, E. F. (2009). Nature, 459(7244), 266–269.

    Article  CAS  Google Scholar 

  76. Ng, W. L., & Bassler, B. L. (2009). Annual Review of Genetics, 43, 197–222.

    Article  CAS  Google Scholar 

  77. Horswill, A. R., Stoodley, P., Stewart, P. S., & Parsek, M. R. (2007). Analytical and Bioanalytical Chemistry, 387(2), 371–380.

    Article  CAS  Google Scholar 

  78. Kalia, V. C., Raju, S. C., & Purohit, H. J. (2010). The Open Microbiology Journal, 4, 1–13.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  80. Kang, Y. S., & Park, W. (2010). Journal of Applied Microbiology, 109(5), 1650–1659.

    CAS  Google Scholar 

  81. Singh, R., Paul, D., & Jain, R. K. (2006). Trends in Microbiology, 14(9), 389–397.

    Article  CAS  Google Scholar 

  82. Ron, E. Z., & Rosenberg, E. (2002). Current Opinion in Biotechnology, 13(3), 249–252.

    Article  CAS  Google Scholar 

  83. Atkinson, S., & Williams, P. (2009). Journal of the Royal Society, Interface, 6(40), 959–978.

    Article  CAS  Google Scholar 

  84. Desai, C., Pathak, H., & Madamwar, D. (2010). Bioresource Technology, 101, 1558–1569.

    Article  CAS  Google Scholar 

  85. Chauhan, A., & Jain, R. K. (2010). Biodegradation, 21, 861–879.

    Article  CAS  Google Scholar 

  86. Trigo, A., Valencia, A., & Cases, I. (2009). FEMS Microbiology Reviews, 33, 98–108.

    Article  CAS  Google Scholar 

  87. Ellis, L. B., Roe, D., & Wackett, L. P. (2006). Nucleic Acids Research, 34, D517–D521.

    Article  CAS  Google Scholar 

  88. Pazos, F., Guijas, D., Valencia, A., & De Lorenzo, V. (2005). Nucleic Acids Research, 33, D588–D592.

    Article  CAS  Google Scholar 

  89. Carbajosa, G., Trigo, A., Valencia, A., & Cases, I. (2009). Nucleic Acids Research, 37, D598–D602.

    Article  CAS  Google Scholar 

  90. Domde, P., Kapley, A., & Purohit, H. J. (2006). Environmental Science and Pollution Research, 5, 1–5.

    Google Scholar 

  91. Byss, M., Elhottova, D., Triska, J., & Baldrian, P. (2008). Chemosphere, 73(9), 1518–1523.

    Article  CAS  Google Scholar 

  92. Dalby, A. P., Kormas, K. A., Christaki, U., & Karayanni, H. (2008). Environmental Microbiology, 10(1), 47–56.

    CAS  Google Scholar 

  93. Behzadian, F., Barjeste, H., Hosseinkhani, S., & Zarei, A. R. (2011). Current Microbiology, 62(2), 690–696.

    Article  CAS  Google Scholar 

  94. Lee, J. H., Mitchell, R. J., Kim, B. C., Cullen, D. C., & Gu, M. B. (2005). Biosensors & Bioelectronics, 21(3), 500–507.

    Article  CAS  Google Scholar 

  95. Liao, V. H., Chien, M. T., Tseng, Y. Y., & Ou, K. L. (2006). Environmental Pollution, 142(1), 17–23.

    Article  CAS  Google Scholar 

  96. Hynninen, A., Tonismann, K., & Virta, M. (2010). Bioengineered Bugs, 1(2), 132–138.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  98. Diplock, E. E., Mardlin, D. P., Killham, K. S., & Paton, G. I. (2009). Environmental Pollution, 15, 1831–1840.

    Article  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  100. Couto, M. N., Monteiro, E., & Vasconcelos, M. T. (2010). Environmental Science and Pollution Research International, 17(7), 1339–1346.

    Article  CAS  Google Scholar 

  101. Jorgensen, K. S., Salminen, J. M., & Bjorklof, K. (2010). Methods in Molecular Biology, 599, 217–233.

    Article  CAS  Google Scholar 

  102. Walter, M., Boyd-Wilson, K., Boul, L., Ford, C., McFadden, D., Chong, B., & Pinfold, J. (2005). International Biodeterioration & Biodegradation, 56, 51–57.

    Article  CAS  Google Scholar 

  103. Hazen, T. C. (2010). Peer Reviewed. Berkeley, California USA: Lawrence Berkeley National Laboratory.

    Google Scholar 

  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. Hansel, C. M., Fendorf, S., Jardine, P. M., & Francis, C. A. (2008). Applied and Environmental Microbiology, 74(5), 1620–1633.

    Article  CAS  Google Scholar 

  106. Diplock, E. E., Alhadrami, H. A., & Paton, G. I. (2009). Advances in Biochemical Engineering/Biotechnology, 118, 189–209.

    Article  CAS  Google Scholar 

  107. Ohtsubo, Y., Shimura, M., Delawary, M., Kimbara, K., Takagi, M., Kudo, T., et al. (2003). Applied and Environmental Microbiology, 69(1), 146–53.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  109. Rojas, L. A., Yanez, C., Gonzalez, M., Lobos, S., Smalla, K., & Seeger, M. (2011). PLoS One, 6(3), 17555.

    Article  CAS  Google Scholar 

  110. Khardenavis, A. A., Kapley, A., & Purohit, H. J. (2008). International Biodeterioration & Biodegradation, 62, 38–45.

    Article  CAS  Google Scholar 

  111. Wu, Z., Dong, H., Zou, L., Lu, D., & Liu, Z. (2011). Applied Biochemistry and Biotechnology. doi:10.1007/s12010-011-9195-1.

  112. Kitano, H. (2002). Science, 295, 1662–1664.

    Article  CAS  Google Scholar 

  113. Raes, J., & Bork, P. (2008). Nature Reviews Microbiology, 6, 693–699.

    Article  CAS  Google Scholar 

  114. Lorenzo, V. (2008). Current Opinion in Biotechnology, 19(6), 579–589.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  116. Loreau, M. (2010). Philosophical Transaction of the Royal Society B, 365, 49–60.

    Article  Google Scholar 

  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. Loreau, M. (2010). in From populations to ecosystems: monographs in population biology- 46.

  119. Vergara, P. M., Pizarro, J., & Castro, S. A. (2011). Ecological Modelling, 222, 1964–1971.

    Article  Google Scholar 

  120. Pascual, M. (2005). PLoS Computational Biology, 1(2), e18.

    Article  CAS  Google Scholar 

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  1. Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR, Nehru Marg, Nagpur, 440020, India

    Vasundhara Paliwal, Sampada Puranik & Hemant J. Purohit

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Paliwal, V., Puranik, S. & Purohit, H.J. Integrated Perspective for Effective Bioremediation. Appl Biochem Biotechnol 166, 903–924 (2012). https://doi.org/10.1007/s12010-011-9479-5

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