Metagenomic analysis of a stable trichloroethene-degrading microbial community

ISME Journal

Volumn 6, Issue 9, 2012, Pages 1702-1714

  Brisson, Vanessa L ^a   West, Kimberlee A ^a   Lee, Patrick K H ^a,b   Tringe, Susannah G ^c   Brodie, Eoin L ^d   Alvarez Cohen, Lisa ^a,d  

^a 109 McLaughlin Hall   (United States)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

bioremediation; cobalamin; Dehalococcoides; metagenomics; reductive dehalogenation; trichloroethene

Indexed keywords

CYANOCOBALAMIN; HYDROGEN; TRICHLOROETHYLENE;

BACTERIUM; BIODEGRADATION; DECHLORINATION; ETHYLENE; GENOME; GENOMICS; METABOLISM; MICROBIAL COMMUNITY; PHYLOGENETICS; STABILIZATION; TAXONOMY;

ARTICLE; BACTERIAL GENE; BIODIVERSITY; CHLOROFLEXI; CLASSIFICATION; GENETICS; METABOLISM; METAGENOMICS; PHYLOGENY;

BIODIVERSITY; CHLOROFLEXI; GENES, BACTERIAL; HYDROGEN; METAGENOMICS; PHYLOGENY; TRICHLOROETHYLENE; VITAMIN B 12;

BACTERIA (MICROORGANISMS); CLOSTRIDIACEAE; DEHALOCOCCOIDES; DELTAPROTEOBACTERIA; DESULFOVIBRIO; METHANOBACTERIUM; METHANOSPIRILLUM; SPIROCHAETALES;

EID: 84865338068     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2012.15     Document Type: Article

References (65)

1. Adrian L, Rahnenführer J, Gobom J, Hölscher T. (2007). Identification of a chlorobenzene reductive dehalo-genase in Dehalococcoides sp. strain CBDB1. Appl Environ Microbiol 73: 7717-7724.
2. Adrian L, Szewzyk U, Wecke J, Görisch H. (2000). Bacterial dehalorespiration with chlorinated benzenes. Nature 408: 580-583.
3. Amend AS, Seifert KA, Bruns TD. (2010). Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol Ecol 19: 5555-5565.
4. Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL et al. (2006). Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72: 6288-6298. (Pubitemid 44414663)
5. Campbell BJ, Cary SC. (2001). Characterization of a novel spirochete associated with the hydrothermal vent polychaete annelid, Alvinella pompejana. Appl Environ Microbiol 67: 110-117. (Pubitemid 32044407)
6. Chow WL, Cheng D, Wang S, He J. (2010). Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species. ISME J 4: 1020-1030.
7. Cole K, Truong V, Barone D, McGall G. (2004). Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes. Nucleic Acids Res 32: e86.
8. DeLong EF. (2005). Microbial community genomics in the ocean. Nat Rev Microbiol 3: 459-469.
9. DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL. (2007). High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53: 371-383. (Pubitemid 46716624)
10. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP et al. (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biol 10: R85.
11. Duhamel M, Edwards EA. (2006). Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides. FEMS Microbiol Ecol 58: 538-549. (Pubitemid 44748161)
12. Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS et al. (2006). Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359. (Pubitemid 43839542)
13. Goldberg SMD, Johnson J, Busam D, Feldblyum T, Ferriera S, Friedman R et al. (2006). A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci USA 103: 11240-11245. (Pubitemid 44156503)
14. Gu AZ, Hedlund BP, Staley JT, Strand SE, Stensel HD. (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. (Pubitemid 38162026)
15. He J, Holmes VF, Lee PKH, Alvarez-Cohen L. (2007). Influence of vitamin B12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Appl Environ Microbiol 73: 2847-2853. (Pubitemid 46718566)
16. He J, Ritalahti KM, Yang KL, Koenigsberg SS, Löffler FE. (2003). Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium. Nature 424: 62-65. (Pubitemid 36834840)
17. Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, Tindall B et al. (1998). Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra-and trichlor-oethene in an anaerobic respiration. Arch Microbiol 169: 313-321. (Pubitemid 28189535)
18. Holmes VF, He J, Lee PKH, Alvarez-Cohen L. (2006). Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl Environ Microbiol 72: 5877-5883. (Pubitemid 44414614)
19. Hongoh Y, Ohkuma M, Kudo T. (2003). Molecular analysis of bacterial microbiota in the gut of the termite Reticulitermes speratus (Isoptera; Rhinotermitidae). FEMS Microbiol Ecol 44: 231-242. (Pubitemid 36423418)
20. Kanehisa M, Goto S. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30. (Pubitemid 30047706)
21. Kielhorn J, Melber C, Wahnschaffe U, Aitio A, Mangelsdorf I. (2000). Vinyl chloride: still a cause for concern. Environ Health Perspect 108: 579-588. (Pubitemid 30657861)
22. Krajmalnik-Brown R, Hölscher T, Thomson IN, Saunders FM, Ritalahti KM, Löffler FE. (2004). Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1. Appl Environ Microbiol 70: 6347-6351. (Pubitemid 39471893)
23. Kube M, Beck A, Zinder SH, Kuhl H, Reinhardt R, Adrian L. (2005). Genome sequence of the chlorinated compound respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol 23: 1269-1273. (Pubitemid 41486854)
24. Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P. (2008). A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev 72: 557-578.
25. 2 by Spirochetes from termite guts. Science 283: 686-689.
26. Lee PKH, Cheng D, Hu P, West KA, Dick GJ, Brodie EL et al. (2011). Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J 5: 1014-1024.
27. Lee PKH, Johnson DR, Holmes VF, He J, Alvarez-Cohen L. (2006). Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococ-coides spp. Appl Environ Microbiol 72: 6161-6168. (Pubitemid 44414649)
28. Löffler FE, Cole JR, Ritalahti KM, Tiedje JM. (2004). Diversity of Dechlorinating Bacteria. In: Häggblom MM, Bossert ID (eds), Dehalogenation: Microbial Processes and Environmental Applications. Kluwer Academic Publishers: New York, pp 53-87.
29. Luijten MLGC, de Weert J, Smidt H, Boschker HTS, de Vos WM, Schraa G et al. (2003). Description of Sulfurospirillum halorespirans sp nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer of Dehalospirillum multivorans to the genus Sulfurospir-illum as Sulfurospirillum multivorans comb. nov. Int J Syst Evol Microbiol 53: 787-793. (Pubitemid 36675475)
30. Macbeth TW, Cummings DE, Spring S, Petzke LM, Sorenson Jr KS. (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. (Pubitemid 39643798)
31. Madigan MT, Martinko JM, Dunlap PV, Clark DP. (2008). Brock Biology of Microorganisms, 12th edn, Benjamin Cummings: Boston.
32. Magnuson JK, Romine MF, Burris DR, Kingsley MT. (2000). Trichloroethene reductive dehalogenase from Dehalococcoides ethenogenes: sequence of tceA and substrate range characterization. Appl Environ Micro-biol 66: 5141-5147. (Pubitemid 32217110)
33. Magnuson JK, Stern RV, Gossett JM, Zinder SH, Burris DR. (1998). Reductive dechlorination of tetrachloroethene to ethene by two-component enzyme pathway. Appl Environ Microbiol 64: 1270-1275. (Pubitemid 28188382)
34. Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Grechkin Y et al. (2010). The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res 38: D382-D390.
35. Markowitz VM, Ivanova NN, Anderson I, Lykidis A, Mavromatis K, Pati A et al. (2008a). Using IMG-M: Comparative Analysis with the IMG/M System: Addendum to Using IMG. Technical Report LBNL-63614. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory: Berkeley.
36. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D et al. (2008b). IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 36: D534-D538. (Pubitemid 351149780)
37. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC et al. (2007). Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods 4: 495-500. (Pubitemid 46852075)
38. Mavromatis K, Ivanova NN, Chen IMA, Szeto E, Markowitz VM, Kyrpides NC. (2009). The DOE-JGI standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci 1: 63-67.
39. Maymó-Gatell X, Chien YT, Gossett JM, Zinder SH. (1997). Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276: 1568-1571. (Pubitemid 27255322)
40. McCarty PL. (1997). Breathing with chlorinated solvents. Science 276: 1521-1522. (Pubitemid 27255305)
41. McCutcheon JP, McDonald BR, Moran NA. (2009). Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci USA 106: 15394-15399.
42. McMurdie PJ, Behrens SF, Muller JA, Göke J, Ritalahti KM, Wagner R et al. (2009). Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet 5: e1000714.
43. Men Y, Feil H, VerBerkmoes NC, Shah MB, Johnson DR, Lee PKH et al. (2012). Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analysis. ISME J 6: 410-421.
44. Mohn WW, Tiedje JM. (1992). Microbial reductive deha-logenation. Microbiol Rev 56: 482-507.
45. Moran MJ, Zogorski JS, Squillace PJ. (2007). Chlorinated solvents in groundwater of the United States. Environ Sci Technol 41: 74-81. (Pubitemid 46047825)
46. Morgan JL, Darling AE, Eisen JA. (2010). Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One 5: e10209.
47. Müller JA, Rosner BM, von Abendroth G, Meshulam-Simon G, McCarty PL, Spormann AM. (2004). Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp strain VS and its environmental distribution. Appl Environ Microbiol 70: 4880-4888. (Pubitemid 39095517)
48. Richardson RE, Bhupathiraju VK, Song DL, Goulet TA, Alvarez-Cohen L. (2002). Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques. Environ Sci Technol 36: 2652-2662. (Pubitemid 34633486)
49. Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM. (2009). Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. Appl Environ Microbiol 75: 1688-1696.
50. Scholz-Muramatsu H, Neumann A, Meßmer M, Moore E, Diekert G (1995). Isolation and characterization of Dehalospirillum Multivorans gen. nov., sp. nov., a tetrachloroethene-utilizing, strictly anaerobic bacterium. Arch Microbiol 163: 48-56.
51. Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA et al. (2005). Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307: 105-108. (Pubitemid 40093488)
52. Sharma PK, McCarty PL. (1996). Isolation and characterization of a facultatively aerobic bacterium that reductively dehalogenates tetrachloroethene to cis-1, 2-dichloroethene. Appl Environ Microbiol 62: 761-765. (Pubitemid 26071443)
53. Smidt H, de Vos WM. (2004). Anaerobic microbial dehalogenation. Annu Rev Microbiol 58: 43-73. (Pubitemid 39551978)
54. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM et al. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43. (Pubitemid 38332350)
55. US Department of Health and Human Services. (2005). Report on Carcinogens, 11th edition.
56. US Department of Health and Human Services. (2007). 2007 CERCLA Priority List of Hazardous Substances.
57. von Wintzingerode F, Göbel UB, Stackebrandt E. (1997). Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229. (Pubitemid 28018202)
58. Waller AS. (2009). Molecular Investigation of Chloro-ethene Resuctive Dehalogenation by the Mixed Microbial Community KB1. Doctor of Philosophy thesis, University of Toronto, Toronto, 2009.
59. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT et al. (2007). Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560-565. (Pubitemid 350190243)
60. 12). Nat Prod Rep 19: 390-412. (Pubitemid 34877901)
61. West KA, Johnson DR, Hu P, DeSantis TZ, Brodie EL, Lee PKH et al. (2008). Comparative genomics of 'Dehalococcoides ethenogenes' 195 and an enrichment culture containing unsequenced 'Dehalococ-coides' strains. Appl Environ Microbiol 74: 3533-3540. (Pubitemid 351812808)
62. Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H et al. (2009). Assembling the marine metagenome, one cell at a time. PLoS One 4: 55299.
63. Zhang Z, Schwartz S, Wagner L, Miller W. (2000). A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203-214. (Pubitemid 30412170)
64. Zhou J, Kang S, Schadt CW, Garten Jr CT. (2008). Spatial scaling of functional gene diversity across various microbial taxa. Proc Natl Acad Sci USA 105: 7768-7773. (Pubitemid 351872713)
65. Zhou J, Wu L, Deng Y, Zhi X, Jiang YH, Tu Q et al. (2011). Reproducibility and quantitation of amplicon sequencing-based detection. ISME J 5: 1303-1313.