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. 2009 Mar 14;49(2):108–113. doi: 10.1007/s12088-009-0012-2

Genomic tools in bioremediation

Atya Kapley 1, Hemant J Purohit 1,✉
PMCID: PMC3450142  PMID: 23100758

Abstract

Bioremediation is a process that uses microorganisms or their enzymes to remove pollutants from the environment. Generally, bioremediation technologies can be classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site while ex situ involves the removal of the contaminated material to be treated elsewhere. Like so much else in biology, the ease and availability of genomic data has created a new level of understanding this system. Bioremediation capabilities of the microbial population can be analyzed; not only by physiological parameters, but also by the use of genomic tools, and efficient remediation strategies can be planned. PCR and DNA- or oligonucleotide-based microarray technology is a powerful functional genomics tool that allows researchers to view the physiology of a living cell from a comprehensive and dynamic molecular perspective. This paper explores the use of such tools in bioremediation process.

Keywords: Bioremediation, Catabolic potential, Molecular tools, Metagenomics

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References

  • 1.Jorgensen K.S. In situ bioremediation. Adv Appl Microbiol. 2007;61:285–305. doi: 10.1016/S0065-2164(06)61008-3. [DOI] [PubMed] [Google Scholar]
  • 2.Grommen R., Verstraete W. Environmental biotechnology: the ongoing quest. J Biotechnol. 2002;98:113–123. doi: 10.1016/S0168-1656(02)00090-1. [DOI] [PubMed] [Google Scholar]
  • 3.Chandra R., Raj A., Purohit H.J., Kapley A. Characterisation and optimisation of three potential aerobic bacterial strains for kraft lignin degradation from pulp paper waste. Chemosphere. 2007;67:839–846. doi: 10.1016/j.chemosphere.2006.10.011. [DOI] [PubMed] [Google Scholar]
  • 4.Raj A., Chandra R., Reddy M.M.K., Purohit H.J., Kapley A. Biodegradation of kraft lignin by Bacillus from the sludge of a pulp paper mill. Biodegradation. 2007;18:783–792. doi: 10.1007/s10532-007-9107-9. [DOI] [PubMed] [Google Scholar]
  • 5.Kutty R., Kapley A., Purohit H.J. Pseudomonas sp. strain RM2: strain with diverse physiology for aniline and chlorophenol utilization. Asian J Microbiol Biotechnol Environ. 2001;3:117–121. [Google Scholar]
  • 6.Kapley A., Thierry B., Purohit H.J. Eubacterial diversity of activated biomass from a CETP. Res Microbiol. 2007;158:494–500. doi: 10.1016/j.resmic.2007.04.004. [DOI] [PubMed] [Google Scholar]
  • 7.Keharia H., Madamwar D. Bioremediation concepts for treatment of dye containing wastewater: a review. Ind J Exp Biol. 2003;41:1068–1075. [PubMed] [Google Scholar]
  • 8.Chhatre S.A., Purohit H.J., Shanker R., Chakrabarti T., Khanna P. Bacterial consortia for crude oil spill remediation. Water Sci Technol. 1996;34:187–193. [Google Scholar]
  • 9.Kapley A., Purohit H.J., Chhatre S., Shanker R., Chakrabarti T., Khanna P. Osmotolerance and hydrocarbon degradation by genetically engineered bacterial consortium. Bioresour Technol. 1999;67:241–245. doi: 10.1016/S0960-8524(98)00121-7. [DOI] [Google Scholar]
  • 10.Mishra S., Jyoti J., Kuhad R.C., Lal B. Evaluation of inoculum addition to stimulate in situ bioremediation of oily-sludge-contaminated soil. Appl Environ Microbiol. 2001;67:1675–1681. doi: 10.1128/AEM.67.4.1675-1681.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Srivastava S., Ahmad A.H., Thakur I.S. Removal of chromium and pentachlorophenol from tannery effluents. Bioresour Technol. 2007;98:1128–1132. doi: 10.1016/j.biortech.2006.04.011. [DOI] [PubMed] [Google Scholar]
  • 12.Banta G., Kahlon R.S. Dehalogenation of 4-chlorobenzoic acid by Pseudomonas isolates. Ind J Micorbiol. 2007;47:139–143. doi: 10.1007/s12088-007-0027-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Kumar S.G., Gupta S.K., Singh G. Biodegradation of distillery spent wash in anaerobic hybrid reactor. Water Res. 2007;41:721–730. doi: 10.1016/j.watres.2006.11.039. [DOI] [PubMed] [Google Scholar]
  • 14.Malhotra S., Sharma P., Kumari H., Singh A., Lal R. Localization of HCH catabolic genes (Lin genes) in Sphigobium indicum B90A. Indian J Microbiol. 2007;47:271–275. doi: 10.1007/s12088-007-0050-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Narde G., Kapley A., Purohit H.J. Isolation and characterization of Citrobacter strain HPC255 for broad range substrate specificity for chlorophenols. Curr Microbiol. 2004;48:419–423. doi: 10.1007/s00284-003-4230-2. [DOI] [PubMed] [Google Scholar]
  • 16.Prasanna D., Venkata M.S., Purushotham R.B., Sarma P.N. Bioremediation of anthracene contaminated soil in bio-slurry phase reactor operated in periodic discontinuous batch mode. J Hazard Mater. 2008;153:244–251. doi: 10.1016/j.jhazmat.2007.08.063. [DOI] [PubMed] [Google Scholar]
  • 17.Qureshi A., Purohit H.J. Isolation of bacterial consortium for degradation of p-nitrophenol from agricultural soil. Annals of Appl Biol. 2002;140:159–162. doi: 10.1111/j.1744-7348.2002.tb00168.x. [DOI] [Google Scholar]
  • 18.Raina V., Suar M., Singh A., Prakash O., Dadhwal M., Gupta S.K., Dogra C., Lawlor K., Lal S., Meer J.R., Holliger C., Lal R. Enhanced biodegradation of hexachlorocyclohexane (HCH) in contaminated soils via inoculation with Sphingobium indicum B90A. Biodegradation. 2008;19:27–40. doi: 10.1007/s10532-007-9112-z. [DOI] [PubMed] [Google Scholar]
  • 19.Tripathi P., Srivastava S. Development and characterization of nickel accumulating mutants of Aspergillus nidulans. Indian J Microbiol. 2007;47:241–250. doi: 10.1007/s12088-007-0045-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Paul D., Singh R., Jain R.K. Chemotaxis of Ralstonia sp. SJ98 towards p-nitrophenol in soil. Environ Microbiol. 2006;8:1797–804. doi: 10.1111/j.1462-2920.2006.01064.x. [DOI] [PubMed] [Google Scholar]
  • 21.Malik S., Beer M., Megharaj M., Naidu R. The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ Int. 2008;34:265–276. doi: 10.1016/j.envint.2007.09.001. [DOI] [PubMed] [Google Scholar]
  • 22.Rani A., Porwal S., Sharma R., Kapley A., Purohit H.J., Kalia V.C. Assessment of microbial diversity in effluent treatment plants by culture dependent and culture independent approaches. Bioresour Technol. 2008;99:7098–7107. doi: 10.1016/j.biortech.2008.01.003. [DOI] [PubMed] [Google Scholar]
  • 23.Kapley A., Prasad S., Purohit H.J. Changes in microbial diversity in fed-batch reactor operation with wastewater containing nitroaromatic residues. Bioresour Technol. 2007;98:2479–2484. doi: 10.1016/j.biortech.2006.09.012. [DOI] [PubMed] [Google Scholar]
  • 24.Rossello-Mora R., Amann R. The species concept for prokaryotes. FEMS Microbiol Rev. 2001;25:39–67. doi: 10.1016/S0168-6445(00)00040-1. [DOI] [PubMed] [Google Scholar]
  • 25.Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143–169. doi: 10.1128/mr.59.1.143-169.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Zelles L., Bai Q.Y., Beck T., Beese F. Signature fatty acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol Biochem. 1992;24:317–323. doi: 10.1016/0038-0717(92)90191-Y. [DOI] [Google Scholar]
  • 27.Graham J.H., Hodge N.C., Morton J.B. Fatty acid methyl ester profi les for characterization of glomalean fungi and their endomycorrhizae. Appl Environ Microbiol. 1995;61:58–64. doi: 10.1128/aem.61.1.58-64.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Kirk J.L., Beaudette L.A., Hart M., Moutoglis P., Klironomos J.N., Lee H., Trevors J.T. Methods of studying soil microbial diversity. J Microbiol Methods. 2004;58:169–88. doi: 10.1016/j.mimet.2004.04.006. [DOI] [PubMed] [Google Scholar]
  • 29.Purohit H.J. Biosensors as molecular tools for use in bioremediation. J Cleaner Production. 2003;11:293–301. doi: 10.1016/S0959-6526(02)00072-0. [DOI] [Google Scholar]
  • 30.Jansson J.K., Bjorklofb K., Elvanga A.M., Jorgensen K.S. Biomarkers for monitoring efficacy of bioremediation by microbial inoculants. Environ Pollut. 2000;107:217–223. doi: 10.1016/S0269-7491(99)00140-2. [DOI] [PubMed] [Google Scholar]
  • 31.Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol. 1999;2:317–322. doi: 10.1016/S1369-5274(99)80055-1. [DOI] [PubMed] [Google Scholar]
  • 32.Pandey J., Sood S.S., Jain R.K. Terminal restriction fragment length polymorphism (T-RFLP) analysis: Characterizing the unseen. Indian J Microbiol. 2007;47:90–91. doi: 10.1007/s12088-007-0017-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Singh R., Paul D., Jain R.K. Biofilms: implications in bioremediation. Trends Microbiol. 2006;14:389–397. doi: 10.1016/j.tim.2006.07.001. [DOI] [PubMed] [Google Scholar]
  • 34.Kumar M., Chaudhary P., Dwivedi M., Kumar R., Paul D., Jain R.K., Garg S.K., Kumar A. Enhanced biodegradation of beta and delta-hexachlorocyclohexane in the presence of alpha and gamma-isomers in contaminated soils. Environ Sci Technol. 2005;39:4005–4011. doi: 10.1021/es048497q. [DOI] [PubMed] [Google Scholar]
  • 35.DeLong E.F., Pace N.R. Environmental diversity of bacteria and archaea. Syst Biol. 2001;50:470–478. doi: 10.1080/106351501750435040. [DOI] [PubMed] [Google Scholar]
  • 36.Kapley A., Purohit H.J. Tracking of phenol degrading genotype. Env Sci Pollut Res. 2000;16:89–90. doi: 10.1007/BF02987299. [DOI] [PubMed] [Google Scholar]
  • 37.Moharikar A., Kapley A., Purohit H.J. Detection of Dioxygenase genes present in various activated sludge. Env Sci Pollut Res. 2003;10:373–378. doi: 10.1065/espr2003.07.164. [DOI] [PubMed] [Google Scholar]
  • 38.Sutherland T.D., Horne I., Lacey M.J., Harcourt R.L., Russell R.J., Oakeshott J.G. Enrichment of an endosulfan-degrading mixed bacterial culture. Appl Environ Microbiol. 2000;66:2822–2828. doi: 10.1128/AEM.66.7.2822-2828.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Siddique T., Benedict C., Arshad O.M., Frankenberger W.T. Enrichment and isolation of endosulfan-degrading microorganisms. J Environ Qual. 2003;32:47–54. doi: 10.2134/jeq2003.0047. [DOI] [PubMed] [Google Scholar]
  • 40.Prakash O., Lal R. Description of Sphingobium fuliginis sp. nov, a phenanthrenedegrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov. Int J Syst Evol Microbiol. 2006;56:2147–2152. doi: 10.1099/ijs.0.64080-0. [DOI] [PubMed] [Google Scholar]
  • 41.Eickhorst T, Tippkotter R. (2008) Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARDFISH). Soil Biol Biochem (in press) doi:10.1016/j.soilbio.2008.03.024
  • 42.Martýn M., Gibello A., Lobo C., Nande M., Garbi C., Fajardo C., Barra-Caracciolo A., Grenni P., Martýnez-Inigo M.J. Application of fluorescence in situ hybridization technique to detect simazine-degrading bacteria in soil samples. Chemosphere. 2008;71:703–710. doi: 10.1016/j.chemosphere.2007.10.071. [DOI] [PubMed] [Google Scholar]
  • 43.Radajewski S., Ineson P., Parekh N.R., Murrell J.C. Stable-isotope probing as a tool in microbial ecology. Nature. 2000;403:646–649. doi: 10.1038/35001054. [DOI] [PubMed] [Google Scholar]
  • 44.Kutty R., Purohit H.J., Khanna P. Isolation and characterization of Pseudomonas species strain PH1 utilizing meta-aminophenol. Can J Microbiol. 2000;46:211–217. doi: 10.1139/cjm-46-3-211. [DOI] [PubMed] [Google Scholar]
  • 45.Qureshi A., Prabu S.K., Purohit H.J. Isolation and characterization of Pseudomonas strain for utilization of 4-nitrophenol. Microbes and Environ. 2001;16:49–52. doi: 10.1264/jsme2.2001.49. [DOI] [Google Scholar]
  • 46.Khardenavis A.A., Kapley A., Purohit H.J. Simultaneous nitrification and denitrification by Diaphorobacter sp. Appl Microbiol Biotechnol. 2007;77:403–409. doi: 10.1007/s00253-007-1176-5. [DOI] [PubMed] [Google Scholar]
  • 47.Qureshi A., Verma V., Kapley A., Purohit H.J. Degradation of 4-nitroaniline by Stenotrophomonas strain HPC135. Int Biodeterio Biodeg. 2007;60:215–218. doi: 10.1016/j.ibiod.2007.03.004. [DOI] [Google Scholar]
  • 48.Villas-Boas S.G., Bruheim P. The potential of metabolomics tools in bioremediation studies. OMICS. 2007;11:305–313. doi: 10.1089/omi.2007.0005. [DOI] [PubMed] [Google Scholar]
  • 49.Ahuja S.K., Ferreira G.M., Moreira A.R. Utilization of enzymes for environmental applications. Critical Rev in Biotechnol. 2004;24:125–154. doi: 10.1080/07388550490493726. [DOI] [PubMed] [Google Scholar]
  • 50.Chen W.C., Chang N.-B., Chen J.-C. Rough set-based hybrid fuzzy-neural controller design for industrial wastewater treatment. Water Research. 2003;37:95–107. doi: 10.1016/S0043-1354(02)00255-5. [DOI] [PubMed] [Google Scholar]
  • 51.Cadet C., Beteau J.F., Hernandez S.C. Multi-criteria control strategy for cost/quality compromise in wastewater treatment plants. Control Eng Practice. 2004;12:335–347. doi: 10.1016/S0967-0661(03)00134-5. [DOI] [Google Scholar]
  • 52.Purohit H.J., Raje D.V., Kapley A., Padmanabhan P., Singh R.N. Genomics tools in environmental impact assessment. Environ Sci Technol. 2003;37:356–363. doi: 10.1021/es032594m. [DOI] [PubMed] [Google Scholar]

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