Characterization of the community structure of a dechlorinating mixed culture and comparisons of gene expression in planktonic and biofloc-associated "Dehalococcoides" and Methanospirillum species

Applied and Environmental Microbiology

Volumn 74, Issue 21, 2008, Pages 6709-6719

  Rowe, Annette R ^a   Lazar, Brendan J ^b,c   Morris, Robert M ^b,d   Richardson, Ruth E ^a,b  

^a Department of Molecular Biology and Genetics   (United States)

^b School of Chemical and Molecular Engineering   (United States)

^c TRC Environmental Corporation   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABS RESINS; BIOACTIVITY; BIOMASS; BLAST ENRICHMENT; CLONING; COLLOIDS; ELECTROPHORESIS; FLUORESCENCE MICROSCOPY; GELATION; GENE EXPRESSION; HYDROGEN; MICROSCOPIC EXAMINATION; NUCLEIC ACIDS; POPULATION STATISTICS; RENEWABLE ENERGY RESOURCES; RNA;

16S RRNA; 16S RRNA GENES; ARCHAEA; ARCHAEAL POPULATIONS; BACTERIAL; BIOFLOCS; COMMUNITY STRUCTURES; DEHALOCOCCOIDES; DEHALOCOCCOIDES ETHENOGENES; ENRICHMENT CULTURES; EXPRESSED GENES; EXPRESSION PATTERNS; FLUORESCENCE IN SITU HYBRIDIZATIONS; GENE EXPRESSION PROFILES; GRADIENT GEL ELECTROPHORESIS; HOUSEKEEPING GENES; HYDROGENASE; METHANOGENESIS; MICROBIAL COMMUNITIES; MIXED CULTURES; OXIDOREDUCTASE; PERCHLOROETHENE; PHYLOGENETIC CHARACTERIZATIONS; POPULATION DISTRIBUTIONS; RNA POLYMERASES; STATISTICAL DIFFERENCES; SUBUNIT GENES; TIME POINTS;

CELL CULTURE;

HYDROGENASE; OXIDOREDUCTASE; RNA 16S;

BACTERIUM; COMMUNITY STRUCTURE; COMPARATIVE STUDY; DECHLORINATION; ELECTROKINESIS; FLUORESCENCE; GEL; GENE EXPRESSION; HYDROGEN; MICROBIAL COMMUNITY; PHYLOGENETICS; RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM; CELL SEPARATION; CONTROLLED STUDY; DEHALOCOCCOIDES ETHENOGENES; FLUORESCENCE IN SITU HYBRIDIZATION; GEL ELECTROPHORESIS; GENE EXPRESSION; GENE LIBRARY; GENETIC TRANSCRIPTION; HUPL GENE; METHANOGENESIS; METHANOSPIRILLUM HUNGATEI; MICROBIAL COMMUNITY; MVRD GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANKTON;

BIODIVERSITY; BUTYRATES; CHLORINE; CHLOROFLEXI; DNA FINGERPRINTING; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; ETHANE; GENE EXPRESSION PROFILING; GENES, RRNA; HYDROCARBONS, CHLORINATED; IN SITU HYBRIDIZATION, FLUORESCENCE; METHANOSPIRILLUM; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ARCHAEA; BACTERIA (MICROORGANISMS); DEHALOCOCCOIDES; DEHALOCOCCOIDES ETHENOGENES; DEHALOCOCCOIDES ETHENOGENES 195; METHANOSPIRILLUM; METHANOSPIRILLUM HUNGATEI;

EID: 55049091180     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00445-08     Document Type: Article

References (65)

1. Adrian, L., and H. Goerisch. 2002. Microbial transformation of chlorinated benzenes under anaerobic conditions. Res. Microbiol. 153:131-137.
2. Adrian, L., S. K. Hansen, J. M. Fung, H. Gorisch, and S. H. Zinder. 2007. Growth of Dehalococcoides strains with chlorophenols as electron acceptors. Environ. Sci. Technol. 41:2318-2323.
3. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative phylogenetic and environmental studies in microbiology. J. Bacteriol. 172:762-770.
4. Becker, J. G., G. Berardesco, B. E. Rittmann, and D. A. Stahl. 2005. The role of syntrophic associations in sustaining anaerobic mineralization of chlorinated organic compounds. Environ. Health Perspect. 113:310-316.
5. Becker, P., W. Hufnagle, G. Peters, and M. Herrmann. 2001. Detection of differential gene expression in biofilm-forming versus planktonic populations of Staphylococcus aureus using microrepresentational- difference analysis. Appl. Environ. Microbiol. 67:2958-2965.
6. Bedard, D. L., K. A. Ritalahti, and F. E. Loffler. 2007. The Dehalococcoides population in sediment-free mixed cultures metabolically dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260. Appl. Environ. Microbiol. 73:2513-2521.
7. Boone, D. R., R. W. Castenholz, and G. M. Garrity (ed.). 2001. Bergey's manual of systematic bacteriology. Springer, New York, NY.
8. Bowman, K. S., W. M. Moe, B. A. Rash, H. S. Bae, and F. A. Rainey. 2006. Bacterial diversity of an acidic Louisiana groundwater contaminated by dense nonaqueous-phase liquid containing chloroethanes and other solvents. FEMS Microbiol. Ecol. 58:120-133.
9. 2-dependent heterodisulfide reduction in Methanococcus voltae. Arch. Microbiol. 171:115-121.
10. Busch, P. L., and W. Stumm. 1968. Chemical interactions in the aggregation of bacteria bioflocculation in waste treatment. Environ. Sci. Technol. 2:49-53.
11. Chen, G. 2004. Reductive dehalogenation of tetrachloroethylene by microorganisms: current knowledge and application strategies. Appl. Microbiol. Biotechnol. 63:373-377.
12. Dennis, P. C., B. E. Sleep, R. R. Fulthorpe, and S. N. Liss. 2003. Phylogenetic analysis of bacterial populations in an anaerobic microbial consortium capable of degrading saturation concentrations of tetrachloroethylene. Can. J. Microbiol. 49:15-27.
13. DiStefano, T. D., J. M. Gossett, and S. H. Zinder. 1992. Hydrogen as an electron donor for dechlorination of tetrachloroethene by an anaerobic mixed culture. Appl. Environ. Microbiol. 58:3622-3629.
14. DiStefano, T. D., J. M. Gossett, and S. H. Zinder. 1991. Reductive dechlorination of high concentrations of tetrachloroethene to ethene by an anaerobic enrichment culture in the absence of methanogenesis. Appl. Environ. Microbiol. 57:2287-2292.
15. Dojka, M. A., P. Hugenholtz, S. K. Haack, and N. R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-3877.
16. Duhamel, M., and E. A. Edwards. 2007. Growth and yields of dechlorinators, acetogens, and methanogens during reductive dechlorination of chlorinated ethenes and dihaloelimination of 1,2-dichloroethane. Environ. Sci. Technol. 41:2303-2310.
17. Duhamel, M., and E. A. Edwards. 2006. Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides. FEMS Microbiol. Ecol. 58:538-549.
18. Duhamel, M., K. Mo, and E. A. Edwards. 2004. Characterization of a highly enriched Dehalococcoides-containing culture that grows on vinyl chloride and trichloroethene. Appl. Environ. Microbiol. 70:5538-5545.
19. Fennell, D. E., and J. M. Gossett. 1998. Modeling the production of and competition for hydrogen in a dechlorinating culture. Environ. Sci. Technol. 32:2450-2460.
20. Fennell, D. E., J. M. Gossett, and S. H. Zinder. 1997. Comparison of butyric acid, ethanol, lactic acid, and propionic acid as hydrogen donors for the reductive dechlorination of tetrachloroethene. Environ. Sci. Technol. 31:918-926.
21. Flynn, S. J., F. E. Loffler, and J. M. Tiedje. 2000. Microbial community changes associated with a shift from reductive dechlorination of PCE to reductive dechlorination of cis-DCE and VC. Environ. Sci. Technol. 34:1056-1061.
22. Freeborn, R. A., K. A. West, V. K. Bhupathiraju, S. Chauhan, B. G. Rahm, R. E. Richardson, and L. Alvarez-Cohen. 2005. Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors. Environ. Sci. Technol. 39:8358-8368.
23. Reference deleted.
24. Freedman, D. L., and J. M. Gossett. 1989. Biological reductive dechlorination of tetrachloroethylene and trichloroethylene to ethylene under methanogenic conditions. Appl. Environ. Microbiol. 55:2144-2151.
25. Fung, J. M., R. M. Morris, L. Adrian, and S. H. Zinder. 2007. Expression of reductive dehalogenase genes in Dehalococcoides ethenogenes strain 195 growing on tetrachloroethene, trichloroethene, or 2,3-dichlorophenol. Appl. Environ. Microbiol. 73:4439-4445.
26. Futamata, H., N. Yoshida, T. Kurogi, S. Kaiya, and A. Hiraishi. 2007. Reductive dechlorination of chloroethenes by Dehalococcoides-containing cultures enriched from a polychlorinated-dioxin-contaminated microcosm. Isme J. 1:471-479.
27. Gloeckner, F. O., R. Amann, A. Alfreider, J. Pernthaler, R. Psenner, K. Trebesius, and K. H. Schleifer. 1996. An in situ hybridization protocol for detection and identification of planktonic bacteria. Syst. Appl. Microbiol. 19:403-406.
28. Gu, A. Z., B. P. Hedlund, J. T. Staley, S. E. Strand, and H. D. Stensel. 2004. Analysis and comparison of the microbial community structures of two enrichment cultures capable of reductively dechlorinating TCE and cis-DCE. Environ. Microbiol. 6:45-54.
29. Hales, B. A., C. Edwards, D. A. Ritchie, G. Hall, R. W. Pickup, and J. R. Saunders. 1996. Isolation and identification of methanogen-specific DNA from blanket bog feat by PCR amplification and sequence analysis. Appl. Environ. Microbiol. 62:668-675.
30. Harkness, M. R., A. A. Bracco, M. J. Brennan, K. A. Deweerd, and J. L. Spivack. 1999. Use of bioaugmentation to stimulate complete reductive dechlorination of trichloroethene in dover soil columns. Environ. Sci. Technol. 33:1100-1109.
31. He, J. Z., V. F. Holmes, P. K. H. Lee, and L. Alvarez-Cohen. 2007. Influence of vitamin B-12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Appl. Environ. Microbiol. 73:2847-2853.
32. Hoelscher, T., H. Goerisch, and L. Adrian. 2003. Reductive dehalogenation of chlorobenzene congeners in cell extracts of Dehalococcoides sp. strain CBDB1. Appl. Environ. Microbiol. 69:2999-3001.
33. Hohnstock-Ashe, A. M., S. M. Plummer, R. M. Yager, P. Baveye, and E. L. Madsen. 2001. Further biogeochemical characterization of a trichloroethene-contaminated fractured dolomite aquifer: electron source and microbial communities involved in reductive dechlorination. Environ. Sci. Technol. 35:4449-4456.
34. Holmes, V. F., J. Z. He, P. K. H. Lee, and L. Alvarez-Cohen. 2006. Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl. Environ. Microbiol. 72:5877-5883.
35. Holoman, T. R. P., M. A. Elberson, L. A. Cutter, H. D. May, and K. R. Sowers. 1998. Characterization of a defined 2,3,5,6-tetrachlorobiphenyl- ortho-dechlorinating microbial community by comparative sequence analysis of genes coding for 16S rRNA. Appl. Environ. Microbiol. 64:3359-3367.
36. Johnson, D. R., P. K. H. Lee, V. F. Holmes, and L. Alvarez-Cohen. 2005. An internal reference technique for accurately quantifying specific mRNAs by real-time PCR with a application to the tceA reductive dehalogenase gene. Appl. Environ. Microbiol. 71:3866-3871.
37. Johnson, D. R., P. K. H. Lee, V. F. Holmes, A. C. Fortin, and L. Alvarez-Cohen. 2005. Transcriptional expression of the tceA gene in a Dehalococcoides-containing microbial enrichment. Appl. Environ. Microbiol. 71:7145-7151.
38. Kassenga, G., J. H. Pardue, W. M. Moe, and K. S. Bowman. 2004. Hydrogen thresholds as indicators of dehalorespiration in constructed treatment wetlands. Environ. Sci. Technol. 38:1024-1030.
39. Krajmalnik-Brown, R., Y. Sung, K. M. Ritalahti, F. M. Saunders, and F. E. Loffler. 2007. Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides. FEMS Microbiol. Ecol. 59:206-214.
40. Lee, P. K. H., D. R. Johnson, V. F. Holmes, J. Z. He, and L. Alvarez-Cohen. 2006. Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp. Appl. Environ. Microbiol. 72:6161-6168.
41. Logan, B. E., and J. R. Hunt. 1987. Advantages to microbes of growth in permeable aggregates in marine systems. Limnol. Oceanogr. 32:1034-1048.
42. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K. H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
43. Macbeth, T. W., D. E. Cummings, S. Spring, L. M. Petzke, and K. S. Sorenson. 2004. Molecular characterization of a dechlorinating community resulting from in situ biostimulation in a trichloroethene-contaminated deep, fractured basalt aquifer and comparison to a derivative laboratory culture. Appl. Environ. Microbiol. 70:7329-7341.
44. Maymo-Gatell, X., Y. T. Chien, J. M. Gossett, and S. H. Zinder. 1997. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276:1568-1571.
45. Maymo-Gatell, X., V. Tandoi, J. M. Gossett, and S. H. Zinder. 1995. Characterization of an H-2-utilizing enrichment culture that reductively dechlorinates tetrachloroethene to vinyl chloride and ethene in the absence of methanogenesis and acetogenesis. Appl. Environ. Microbiol. 61:3928-3933.
46. Morris, R. M., S. Sowell, D. Barofsky, S. Zinder, and R. Richardson. 2006. Transcription and mass-spectroscopic proteomic studies of electron transport oxidoreductases in Dehalococcoides ethenogenes. Environ. Microbiol. 8:1499-1509.
47. Morris, R. M., M. S. Rappe, E. Urbach, S. A. Connon, and S. J. Giovannoni. 2004. Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean. Appl. Environ. Microbiol. 70:2836-2842.
48. Morris, R. M., J. M. Fung, B. G. Rahm, S. Zhang, D. L. Freedman, S. H. Zinder, and R. E. Richardson. 2007. Comparative proteomics of Dehalococcoides spp. reveals strain-specific peptides associated with activity. Appl. Environ. Microbiol. 73:320-326.
49. Nakatsu, C. H., V. Torsvik, and L. Ovreas. 2000. Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products. Soil Sci. Soc. Am. J. 64:1382-1388.
50. Nielson, R. B. 1999. PhD Thesis. University of California, Berkeley, Berkeley, CA.
51. Pernthaler, A., and R. Amann. 2004. Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl. Environ. Microbiol. 70:5526-5533.
52. Rahm, B. G., and R. E. Richardson. 2008. Correlation of respiratory gene expression levels and pseudo-steady-state PCE respiration rates in Dehalococcoides ethenogenes. Environ. Sci. Technol. 42:416-421.
53. Rahm, B. G., R. M. Morris, and R. E. Richardson. 2006. Temporal expression of respiratory genes in an enrichment culture containing Dehalococcoides ethenogenes. Appl. Environ. Microbiol. 72:5486-5491.
54. Richardson, R. E., V. K. Bhupathiraju, D. L. Song, T. A. Goulet, and L. Alvarez-Cohen. 2002. Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques. Environ. Sci. Technol. 36:2652-2662.
55. Rossetti, S., L. L. Blackall, M. Majone, P. Hugenholtz, J. J. Plumb, and V. Tandoi. 2003. Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community. Microbiology 149:459-469.
56. Reference deleted.
57. Smatlak, C. R., J. M. Gossett, and S. H. Zinder. 1996. Comparative kinetics of hydrogen utilization for reductive dechlorination of tetrachloroethene and methanogenesis in an anaerobic enrichment culture. Environ. Sci. Technol. 30:2850-2858.
58. Smidt, H., and W. M. de Vos. 2004. Anaerobic microbial dehalogenation. Annu. Rev. Microbiol. 58:43-73.
59. Stams, A. J. M. 1994. Metabolic interactions between anaerobic-bacteria in methanogenic environments. Antonie van Leeuwenhoek Int. J. Gen. Mol. Microbiol. 66:271-294.
60. Thiele, J. H., M. Chartrain, and J. G. Zeikus. 1988. Control of interspecies electron flow during anaerobic digestion: role of floc formation in syntrophic methanogenesis. Appl. Environ. Microbiol. 54:10-19.
61. Waller, A. S., R. Krajmalnik-Brown, F. E. Loffler, and E. A. Edwards. 2005. Multiple reductive-dehalogenase-homologous genes are simultaneously transcribed during dechlorination by Dehalococcoides-containing cultures. Appl. Environ. Microbiol. 71:8257-8264.
62. Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
63. Yang, Y. R., and J. Zeyer. 2003. Specific detection of Dehalococcoides species by fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 69:2879-2883.
64. Yang, Y. R., M. Pesaro, W. Sigler, and J. Zeyer. 2005. Identification of microorganisms involved in reductive dehalogenation of chlorinated ethenes in an anaerobic microbial community. Water Res. 39:3954-3966.
65. Yilmaz, L. S., and D. R. Noguera. 2004. Mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization. Appl. Environ. Microbiol. 70:7126-7139.