Genomic tools in bioremediation

Indian Journal of Microbiology

Volumn 49, Issue 2, 2009, Pages 108-113

  Kapley, Atya ^a   Purohit, Hemant J ^a  

^a NATIONAL ENVIRONMENTAL ENGINEERING RESEARCH INSTITUTE   (India)

Author keywords

Bioremediation; Catabolic potential; Metagenomics; Molecular tools

Indexed keywords

EID: 70349860023     PISSN: 00468991     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12088-009-0012-2     Document Type: Review

References (52)

1. Jorgensen KS (2007) In situ bioremediation. Adv Appl Microbiol 61:285-305.
2. Grommen R, Verstraete W (2002) Environmental biotechnology: the ongoing quest. J Biotechnol 98:113-123.
3. Chandra R, Raj A, Purohit HJ, Kapley A (2007). Characterisation and optimisation of three potential aerobic bacterial strains for kraft lignin degradation from pulp paper waste. Chemosphere 67:839-846.
4. Raj A, Chandra R, Reddy MMK, Purohit, HJ, Kapley A (2007) Biodegradation of kraft lignin by Bacillus from the sludge of a pulp paper mill. Biodegradation 18:783-792.
5. Kutty R, Kapley A, Purohit HJ (2001) Pseudomonas sp. strain RM2: strain with diverse physiology for aniline and chlorophenol utilization. Asian J Microbiol Biotechnol Environ 3:117-121.
6. Kapley A, Thierry B, Purohit HJ (2007b) Eubacterial diversity of activated biomass from a CETP. Res Microbiol 158: 494-500.
7. Keharia H, Madamwar D (2003) Bioremediation concepts for treatment of dye containing wastewater: a review. Ind J Exp Biol 41:1068-1075.
8. Chhatre SA, Purohit HJ, Shanker R, Chakrabarti T, Khanna P (1996) Bacterial consortia for crude oil spill remediation. Water Sci Technol 34:187-193.
9. Kapley A, Purohit HJ, Chhatre S, Shanker R, Chakrabarti T, Khanna P (1999) Osmotolerance and hydrocarbon degradation by genetically engineered bacterial consortium. Bioresour Technol 67:241-245.
10. Mishra S, Jyoti J, Kuhad RC, Lal B (2001) Evaluation of inoculum addition to stimulate in situ bioremediation of oily-sludge-contaminated soil. Appl Environ Microbiol 67: 1675-1681.
11. Srivastava S, Ahmad AH, Thakur IS (2007) Removal of chromium and pentachlorophenol from tannery effluents. Bioresour Technol 98:1128-1132.
12. Banta G, Kahlon R.S. (2007) Dehalogenation of 4-chlorobenzoic acid by Pseudomonas isolates. Ind J Micorbiol 47: 139-143.
13. Kumar SG, Gupta SK, Singh G (2007) Biodegradation of distillery spent wash in anaerobic hybrid reactor. Water Res 41:721-730.
14. Malhotra S, Sharma P, Kumari H, Singh A, Lal R (2007) Localization of HCH catabolic genes (Lin genes) in Sphigobium indicum B90A. Indian J Microbiol 47: 271-275.
15. Narde G, Kapley A, Purohit HJ (2004) Isolation and characterization of Citrobacter strain HPC255 for broad range substrate specificity for chlorophenols. Curr Microbiol 48: 419-423.
16. Prasanna D, Venkata MS, Purushotham RB, Sarma PN (2008) Bioremediation of anthracene contaminated soil in bio-slurry phase reactor operated in periodic discontinuous batch mode. J Hazard Mater 153:244-251.
17. Qureshi A, Purohit HJ (2002) Isolation of bacterial consortium for degradation of p-nitrophenol from agricultural soil. Annals of Appl Biol 140:159-162.
18. Raina V, Suar M, Singh A, Prakash O, Dadhwal M, Gupta SK, Dogra C, Lawlor K, Lal S, vander Meer JR, Holliger C, Lal R (2008) Enhanced biodegradation of hexachlorocyclohexane (HCH) in contaminated soils via inoculation with Sphingobium indicum B90A. Biodegradation 19:27-40.
19. Tripathi P, Srivastava S (2007) Development and characterization of nickel accumulating mutants of Aspergillus nidulans. Indian J Microbiol 47:241-250.
20. Paul D, Singh R, Jain RK (2006) Chemotaxis of Ralstonia sp. SJ98 towards p-nitrophenol in soil. Environ Microbiol 8: 1797-804.
21. Malik S, Beer M, Megharaj M, Naidu R (2008) The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ Int 34:265-276.
22. Rani A, Porwal S, Sharma R, Kapley A, Purohit HJ, Kalia VC (2008) Assessment of microbial diversity in effluent treatment plants by culture dependent and culture independent approaches. Bioresour Technol 99:7098-7107.
23. Kapley A, Prasad S, Purohit HJ (2007a) Changes in microbial diversity in fed-batch reactor operation with wastewater containing nitroaromatic residues. Bioresour Technol 98: 2479-2484.
24. Rossello-Mora R, Amann R. (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39-67.
25. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169.
26. Zelles L, Bai QY, Beck T, Beese F (1992) Signature fatty acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol Biochem 24:317-323.
27. Graham JH, Hodge NC, Morton JB (1995) Fatty acid methyl ester profi les for characterization of glomalean fungi and their endomycorrhizae. Appl Environ Microbiol 61:58-64.
28. Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Methods 58:169-88.
29. Purohit HJ (2003) Biosensors as molecular tools for use in bioremediation. J Cleaner Production 11:293-301.
30. Jansson JK, Bjorklofb K, Elvanga AM, Jorgensen KS (2000) Biomarkers for monitoring efficacy of bioremediation by microbial inoculants. Environ Pollut 107:217-223.
31. Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2: 317-322.
32. Pandey J, Sood SS, Jain RK (2007) Terminal restriction fragment length polymorphism (T-RFLP) analysis: Characterizing the unseen. Indian J Microbiol 47:90-91.
33. Singh R, Paul D, Jain RK (2006) Biofilms: implications in bioremediation. Trends Microbiol 14:389-397.
34. Kumar M, Chaudhary P, Dwivedi M, Kumar R, Paul D, Jain RK, Garg SK, Kumar A (2005) Enhanced biodegradation of beta and delta-hexachlorocyclohexane in the presence of alpha and gamma-isomers in contaminated soils. Environ Sci Technol 39:4005-4011.
35. DeLong E.F, Pace NR (2001) Environmental diversity of bacteria and archaea. Syst Biol 50:470-478.
36. Kapley A, Purohit HJ (2000) Tracking of phenol degrading genotype. Env Sci Pollut Res 16:89-90.
37. Moharikar A, Kapley A, Purohit HJ (2003) Detection of Dioxygenase genes present in various activated sludge. Env Sci Pollut Res 10:373-378.
38. Sutherland TD, Horne I, Lacey MJ, Harcourt RL, Russell RJ, Oakeshott JG (2000) Enrichment of an endosulfan-degrading mixed bacterial culture. Appl Environ Microbiol 66: 2822-2828.
39. Siddique T, Benedict C, Arshad OM, Frankenberger WT (2003) Enrichment and isolation of endosulfan-degrading microorganisms. J Environ Qual 32:47-54.
40. Prakash O, Lal R (2006) 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 56:2147-2152.
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 MJ (2008) Application of fluorescence in situ hybridization technique to detect simazine-degrading bacteria in soil samples. Chemosphere 71:703-710.
43. Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646-649.
44. Kutty R, Purohit HJ, Khanna P (2000) Isolation and characterization of Pseudomonas species strain PH1 utilizing meta-aminophenol. Can J Microbiol 46:211-217.
45. Qureshi A, Prabu SK, Purohit HJ (2001) Isolation and characterization of Pseudomonas strain for utilization of 4-nitrophenol. Microbes and Environ 16:49-52.
46. Khardenavis AA, Kapley A, Purohit HJ (2007) Simultaneous nitrification and denitrification by Diaphorobacter sp. Appl Microbiol Biotechnol 77:403-409.
47. Qureshi A, Verma V, Kapley A, Purohit HJ (2007) Degradation of 4-nitroaniline by Stenotrophomonas strain HPC135. Int Biodeterio Biodeg 60:215-218.
48. Villas-Boas SG, Bruheim P (2007) The potential of metabolomics tools in bioremediation studies. OMICS 11: 305-313.
49. Ahuja SK, Ferreira GM, Moreira AR (2004) Utilization of enzymes for environmental applications. Critical Rev in Biotechnol 24:125-154.
50. Chen WC, Chang N-B, Chen J-C (2003) Rough set-based hybrid fuzzy-neural controller design for industrial wastewater treatment. Water Research 37:95-107.
51. Cadet C, Beteau JF, Hernandez SC (2004) Multi-criteria control strategy for cost/quality compromise in wastewater treatment plants. Control Eng Practice 12: 335-347.
52. Purohit HJ, Raje DV, Kapley A, Padmanabhan P, Singh RN (2003) Genomics tools in environmental impact assessment. Environ Sci Technol 37:356-363.