Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지

Microbial Community Profiling in cis- and trans-Dichloroethene Enrichment Systems Using Denaturing Gradient Gel Electrophoresis

  • Olaniran, Ademola O. (Discipline of Microbiology, Faculty of Science and Agriculture, University of KwaZulu-Natal(Westville Campus)) ;
  • Stafford, William H.L. (Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape) ;
  • Cowan, Don A. (Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape) ;
  • Pillay, Dorsamy (Discipline of Microbiology, Faculty of Science and Agriculture, University of KwaZulu-Natal(Westville Campus)) ;
  • Pillay, Balakrishna (Discipline of Microbiology, Faculty of Science and Agriculture, University of KwaZulu-Natal(Westville Campus))
  • Published : 2007.04.30
Download PDF
⟨ Previous Next ⟩

Abstract

The effective and accurate assessment of the total microbial community diversity is one of the primary challenges in modem microbial ecology, especially for the detection and characterization of unculturable populations and populations with a low abundance. Accordingly, this study was undertaken to investigate the diversity of the microbial community during the biodegradation of cis- and trans-dichloroethenes in soil and wastewater enrichment cultures. Community profiling using PCR targeting the l6S rRNA gene and denaturing gradient gel electrophoresis (PCR-DGGE) revealed an alteration in the bacterial community profiles with time. Exposure to cis- and trans-dichloroethenes led to the disappearance of certain genospecies that were initially observed in the untreated samples. A cluster analysis of the bacterial DGGE community profiles at various sampling times during the degradation process indicated that the community profile became stable after day 10 of the enrichment. DNA sequencing and phylogenetic analysis of selected DGGE bands revealed that the genera Acinetobacter, Pseudomonas, Bacillus, Comamonas, and Arthrobacter, plus several other important uncultured bacterial phylotypes, dominated the enrichment cultures. Thus, the identified dominant phylotypes may play an important role in the degradation of cis- and trans-dichloroethenes.

Keywords

References

  1. Ahn, J., M. C. Kim, H. C. Shin, M. K. Choi, S. S. Yoon, T. Kim, H. G. Song, G. H. Lee, and J. O. Ka. 2006. Analysis of bacterial diversity and community structure in forest soils contaminated with fuel hydrocarbon. J. Microbiol. Biotechnol. 16: 704-715
  2. Amann, R. L., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169
  3. Abd-El-Haleem, D., H. Moawad, E. A. Zaki, and S. Zaki. 2002. Molecular characterization of phenol-degrading bacteria isolated from different Egyptian ecosystems. Microb. Ecol. 43: 217-224 https://doi.org/10.1007/s00248-002-2003-2
  4. Atlas, R. M. and R. Bartha. 1987. Microbial Ecology, 2nd Ed. The Benjamin Cummings Publishing Co., Inc., Reading, Mass
  5. Benson, D. A., M. S. Boguski, D. J. Lipman, and J. Ostell. 1997. GeneBank. Nucleic Acid Res. 25: 1-6 https://doi.org/10.1093/nar/25.1.1
  6. Boon, N., J. Goris, P. De Vos, W. Verstraete, and E. M. Top. 2000. Bioaugmentation of activated sludge by an indigenous 3-chloroaniline degrading Comamonas testosteroni strain, 12gfp. Appl. Environ. Microbiol. 66: 2906-2913 https://doi.org/10.1128/AEM.66.7.2906-2913.2000
  7. Bradley, P. M. and F. H. Chapelle. 1998. Effect of contaminant concentration on aerobic microbial mineralization of DCE and VC in stream-bed sediments. Environ. Sci. Technol. 32: 553-557 https://doi.org/10.1021/es970498d
  8. Bradley, P. M., F. H. Chapelle, and D. R. Lovley. 1998. Humic acids as electron acceptors for anaerobic microbial oxidation of vinyl chloride and dichloroethene. Appl. Environ. Microbiol. 64: 3102-3105
  9. Casamayor, E. O., H. Schafer, and G. Muyzer. 2000. Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: Comparison by microscopy and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 66: 499-508 https://doi.org/10.1128/AEM.66.2.499-508.2000
  10. Casamayor, E. O., C. Pedros-Alio, G. Muyzer, and R. Amann. 2002. Microheterogeneity in 16S ribosomal DNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations. Appl. Environ. Microbiol. 68: 1706-1714 https://doi.org/10.1128/AEM.68.4.1706-1714.2002
  11. Chang, Y.-J., J. R. Stephen, A. P. Richter, A. D. Venosa, J. Bruggemann, S. J. Macnaughton, G. A. Kowalchuk, and J. R. Haines. 2000. Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: Effect of profiling method. J. Microbiol. Methods 40: 19-31 https://doi.org/10.1016/S0167-7012(99)00134-7
  12. Choo, Y. F., J. Lee, I. S. Chang, and B. Y. Kim. 2006. Bacterial communities in microbial fuel cells enriched with high concentrations of glucose and glutamate. J. Microbiol. Biotechnol. 16: 1481-1484
  13. Coleman, N. V., T. E. Mattes, J. M. Gossett, and J. C. Spain. 2002. Biodegradation of cis-dichloroethene as the sole carbon source by a $\beta$-proteobacterium. Appl. Environ. Microbiol. 68: 2726-2730 https://doi.org/10.1128/AEM.68.6.2726-2730.2002
  14. El Fantroussi, S., L. Verschuere, W. Verstraete, and E. M. Top. 1999. Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl. Environ. Microbiol. 65: 982-988
  15. Fisher, S. G. and L. S. Lerman. 1979. Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell 16: 191-200 https://doi.org/10.1016/0092-8674(79)90200-9
  16. Fromin, N., J. Hamelin, S. Tamawski, D. Roesti, K. Jourdain-Miserez, N. Forestier, S. Teyssier-Cuvelle, F. Gillet, M. Arangno, and P. Rossi. 2002. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ. Microbiol. 4: 634-643 https://doi.org/10.1046/j.1462-2920.2002.00358.x
  17. Gelsomino, A., A. C. Keijzer-Wolters, G. Cacco, and J. D. van Elsas. 1999. Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. J. Microbiol. Methods 38: 1-15 https://doi.org/10.1016/S0167-7012(99)00054-8
  18. Gerhardt, P., R. Murray, R. Costilow, E. Nester, W. Wood, N. Krieg, and G. B. Phillips. 1991. Manual of Methods for General Bacteriology. American Society for Microbiology, Washington, D.C
  19. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60-63 https://doi.org/10.1038/345060a0
  20. Gremion, F., A. Chatzinotas, and H. Harms. 2003. Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. Environ. Microbiol. 5: 896-907 https://doi.org/10.1046/j.1462-2920.2003.00484.x
  21. Hartmans, S., A. Kaptein, J. Tramper, and J. A. M. de Bont. 1992. Characterization of a Mycobacterium sp. and a Xanthobacter sp. for the removal of vinyl chloride and 1,2-dichloroethane from waste gases. Appl. Microbiol. Biotechnol. 37: 796-801 https://doi.org/10.1007/BF00174848
  22. Hristova, K., B. Gebreyesus, D. Mackay, and K. M. Scow. 2003. Naturally occurring bacteria similar to the methyl tert-butyl ether (MTBE)-degrading strain PM1 are present in MTBE-contaminated groundwater. Appl. Environ. Microbiol. 69: 2616-2623
  23. Izu, K., F. Nakajima, K. Yamamoto, and F. Kurisu. 2001. Aeration conditions affecting growth of purple nonsulfur bacteria in an organic wastewater treatment process. Syst. Appl. Microbiol. 24: 294-302 https://doi.org/10.1078/0723-2020-00027
  24. Jensen, S., L. Ovreas, F. L. Daae, and V. Torsvik. 1998. Diversity in methane enrichments from an agricultural soil revealed by DGGE separation of PCR amplified 16S rDNA fragments. FEMS Microbiol. Ecol. 26: 17-26 https://doi.org/10.1111/j.1574-6941.1998.tb01557.x
  25. Kaewpipat, K. and C. P. L. Grady Jr. 2002. Microbial population dynamics in laboratory-scale activated sludge reactors. Water Sci. Technol. 46: 19-27
  26. Kaplan, C. W. and C. L. Kitts. 2004. Bacterial succession in a petroleum land treatment unit. Appl. Environ. Microbiol. 70: 1777-1786 https://doi.org/10.1128/AEM.70.3.1777-1786.2004
  27. Klier, N. J., R. J. West, and P. A. Donberg. 1999. Aerobic biodegradation of dichloroethylenes in surface and subsurface soils. Chemosphere 38: 1175-1188 https://doi.org/10.1016/S0045-6535(98)00485-8
  28. LaGrega, M. D., P. L. Buckingham, and J. C. Evans. 1994. Growth kinetics, pp. 581. In Clark, B. J. and Morris, J. M. (eds.), Hazardous Waste Management. McGraw-Hili Inc. Publishers
  29. LaPara, T. M., C. H. Nakatsu, L. M. Pantea, and J. E. Alleman. 2000. Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. Appl. Environ. Microbiol. 66: 3951-3959 https://doi.org/10.1128/AEM.66.9.3951-3959.2000
  30. Li, C. and W. M. Moe. 2004. Assessment of microbial populations in methyl ethyl ketone degrading biofilters by denaturing gradient gel electrophoresis. Appl. Microbiol. Biotechnol. 64: 568-575 https://doi.org/10.1007/s00253-003-1518-x
  31. Liu, W., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63: 4517 -4522
  32. McCaig, A. E., L. A. Glover, and J. I. Prosser. 2001. Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl. Environ. Microbiol. 67: 4554-4559 https://doi.org/10.1128/AEM.67.10.4554-4559.2001
  33. Medlin, L., H. J. Elwood, S. Stickel, and M. L. Sogin. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA coding regions. Gene 71: 491-499 https://doi.org/10.1016/0378-1119(88)90066-2
  34. Murray, A. E., J. T. Hollibaugh, and C. Orrego. 1996. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 62: 2676-2680
  35. Muyzer, G., E. C. de Waal, and A. Uitterlinden. 1993. Profiling of complex microbial populations using denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695-700
  36. Muyzer, G. and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73: 127-141 https://doi.org/10.1023/A:1000669317571
  37. Muyzer, G. 1999. DGGE/TGGE: A method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2: 317-322 https://doi.org/10.1016/S1369-5274(99)80055-1
  38. Nakatsu, C. H., M. Providenti, and R. C. Wyndham. 1997. The cis-diol dehydrogenase cbaC gene of Tn5271 is required for growth on 3-chlorobenzoate. Gene 196: 209-218 https://doi.org/10.1016/S0378-1119(97)00229-1
  39. Nogales, B., E. R. B. Moore, E. Llobet-Brossa, R. Rossello-Mora, R. Amann, and K. N. Timmis. 2001. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl. Environ. Microbiol. 67: 1874-1884 https://doi.org/10.1128/AEM.67.4.1874-1884.2001
  40. Nubel, U., F. Garcia-Pichel, M. Kuhl, and G. Muyzer. 1999. Quantifying microbial diversity: Morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl. Environ. Microbiol. 65: 422-430
  41. Olaniran, A. O., D. Pillay, and B. Pillay. 2004. Aerobic dechlorination of cis- and trans-dichloroethenes by some indigenous bacteria isolated from contaminated sites in Africa. J. Environ. Sci. 16: 968-972
  42. Olaniran, A. O., D. Pillay, and B. Pillay. 2005. Characterization of two bacteria isolated from a wastewater treatment plant in South Africa for aerobic dehalogenation of some aliphatic chlorinated compounds. Int. J. Environ. Stud. 62: 59-68 https://doi.org/10.1080/0020723042000286365
  43. Pepper, I. L., T. J. Gentry, D. T. Newby, T. M. Roane, and K. L. Josephson. 2002. The role of cell bioaugmentation and gene bioaugmentation in the remediation of co-contaminated soils. Environ. Health Perspec. 110: 943-946 https://doi.org/10.1289/ehp.02110s6943
  44. Riemann, L., G. F. Steward, L. B. Fandino, L. Campbell, M. R. Landry, and F. Azam. 1999. Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes. Deep Sea Res. A 46: 1791-1811 https://doi.org/10.1016/S0967-0645(99)00044-2
  45. Roane, T. M., K. L. Josephson, and I. L. Pepper. 2001. Dual-bioaugmentation strategy to enhance remediation of co-contaminated soil. Appl. Environ. Microbiol. 67: 3208-3215 https://doi.org/10.1128/AEM.67.7.3208-3215.2001
  46. Seeley, H. W. and P. J. Vandemark. 1981. Microbes in Action. A Laboratory Manual of Microbiology, 3rd Ed. Freeman WH and Company, U.S.A
  47. Shim, H., D. Ryoo, P. Barbieri, and T. K. Wood. 2001. Aerobic degradation of mixtures of tetrachloroethylene, trichloroethylene, dichloroethylenes and vinyl chloride by toluene-o-xylene monooxygenase of Pseudomonas stutzeri OXI. Appl. Microbiol. Biotechnol. 56: 265-269 https://doi.org/10.1007/s002530100650
  48. Simpson, J. M., V. J. McCracken, H. R. Gaskins, and R. I. Mackie. 2000. Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA amplicons to monitor changes in fecal bacterial populations of weaning pigs after introduction of Lactobacillus reuteri strain MM53. Appl. Environ. Microbiol. 66: 4705-4714 https://doi.org/10.1128/AEM.66.11.4705-4714.2000
  49. Teske, A., C. Wawer, G. Muyzer, and N. B. Ramsing. 1996. Distribution of sulfate-reducing bacteria in a stratified fjcrd (Mariager fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62: 1405-1415
  50. Uroz, S., C. D. Angelo-Picard, A. Carlier, M. Elasri, C. Sicot, A. Petit, P. Oger, D. Faure, and Y. Dessaux. 2003. Novel bacteria degrading N-acylhomoserine lactones and their use as quenchers of quorum-sensing-regulated functions of plant-pathogenic bacteria. Microbiology 149: 1981-1989 https://doi.org/10.1099/mic.0.26375-0
  51. Vallaeys, T., E. Topp, G. Muyzer, V. Macheret, G. Laguerre, A. Rigaud, and G. Soulas. 1997. Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecol. 24: 279-285 https://doi.org/10.1111/j.1574-6941.1997.tb00445.x
  52. Ward, J. H. 1963. Hierarchial grouping to optimize an objective function. J. Am. Stat. Assoc. 58: 236-244 https://doi.org/10.2307/2282967
  53. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured inhabitants in a natural community. Nature 345: 63-65 https://doi.org/10.1038/345063a0
  54. Watanabe, K., M. Teramoto, H. Futamata, and S. Harayama. 1998. Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl. Environ. Microbiol. 64: 4396-4402
  55. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221-271
  56. Wu, J. F., C. W. Sun, C. Y. Jiang, Z. P. Liu, and S. J. Liu. 2005. A novel 2-aminophenol 1,6-dioxygenase involved in the degradation of p-chloronitrobenzene by Comamonas strain CNB-1: Purification, properties, genetic cloning and expression in Escherichia coli. Arch. Microbiol. 183: 1-8 https://doi.org/10.1007/s00203-004-0738-5