Microbiota associated with the migration and transformation of chlorinated aliphatic hydrocarbons in groundwater

Environmental Geochemistry and Health

Volumn 35, Issue 4, 2013, Pages 535-549

  Guan, Xiangyu ^a,b   Liu, Fei ^a   Xie, Yuxuan ^a   Zhu, Lingling ^a   Han, Bin ^a  

^a CHINA UNIVERSITY OF GEOSCIENCES BEIJING   (China)

^b CHINA UNIVERSITY OF GEOSCIENCES   (China)

Author keywords

16S rRNA; Chlorinated aliphatic hydrocarbons; Degradation; Microbiota; Remediation

Indexed keywords

BACTERIAL RNA; CHLORINATED HYDROCARBON; GROUND WATER; RNA 16S;

ABUNDANCE; ALIPHATIC HYDROCARBON; BIOREMEDIATION; CHLORINATED HYDROCARBON; CONCENTRATION (COMPOSITION); GROUNDWATER; GROUNDWATER POLLUTION; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; POLLUTANT TRANSPORT; POLYMERASE CHAIN REACTION; RNA; SPECIES DIVERSITY;

ARTICLE; BACTERIUM; CHEMISTRY; CHINA; CLASSIFICATION; ENVIRONMENTAL MONITORING; GENETICS; ISOLATION AND PURIFICATION; MASS FRAGMENTOGRAPHY; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; WATER POLLUTANT;

BACTERIA; CHINA; ENVIRONMENTAL MONITORING; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GROUNDWATER; HYDROCARBONS, CHLORINATED; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA; WATER POLLUTANTS, CHEMICAL;

PROTEOBACTERIA;

EID: 84879782728     PISSN: 02694042     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10653-013-9513-3     Document Type: Article

References (70)

1. Aji, K., Tang, C., Song, X., Kondoh, A., Sakura, Y., Yu, J., et al. (2008). Characteristics of chemistry and stable isotopes in groundwater of Chaobai and Yongding River basin, North China Plain. Hydrological Processes, 22, 63-73.
2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402.
3. APHA. (1998). Standard methods for the examination of water and wastewater (20th ed.). Washington, DC: American Public Health Association.
4. Arciero, D., Vannelli, T., Logan, M., & Hooper, A. B. (1989). Degradation of trichloroethylene by the ammonia-oxidizing bacterium Nitrosomonas europaea. Biochemical and Biophysical Research Communications, 159(2), 640-643.
5. Aulenta, F., Maio, V. D., Ferri, T., & Majone, M. (2010). The humic acid analogue antraquinone-2, 6-disulfonate (AQDS) serves as an electron shuttle in the electricity-driven microbial dechlorination of trichloroethene to cis-dichloroethene. Bioresource Technology, 101(24), 9728-9733.
6. Bae, H. S., Rash, B. A., Rainey, F. A., Nobre, M. F., Tiago, I., da Costa, M. S., et al. (2007). Description of Azospira restricta sp. nov., a nitrogen-fixing bacterium isolated from groundwater. International Journal of Systematic and Evolutionary Microbiology, 57, 1521-1526.
7. Barnes, R. J., Riba, O., Gardner, M. N., Singer, A. C., Jackman, S. A., & Thompson, I. P. (2010). Inhibition of biological TCE and sulphate reduction in the presence of iron nanoparticles. Chemosphere, 80(5), 554-562.
8. Bhatt, P., Kumar, M. S., Mudliar, S., & Chakrabarti, T. (2007). Biodegradation of chlorinated compounds-A review. Critical Reviews in Environmental Science and Technology, 37(2), 165-198.
9. Braker, G., Ayala-del-Rio, H. L., Devol, A. H., Fesefeldt, A., & Tiedje, J. M. (2001). Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Applied and Environment Microbiology, 67(4), 1893-1901.
10. Carreón-Diazconti, C., Santamaria, J., Berkompas, J., Field, J. A., & Brusseau, M. L. (2009). Assessment of in situ reductive dechlorination using compound-specific stable isotopes, functional gene PCR, and geochemical data. Environmental Science & Technology, 43(12), 4301-4307.
11. Carvalho, M. F., Ferreira, M. I., Moreira, I. S., Castro, P. M., & Janssen, D. B. (2006). Degradation of fluorobenzene by Rhizobiales strain F11 via ortho cleavage of 4-fluorocatechol and catechol. Applied and Environment Microbiology, 72(11), 7413-7417.
12. Cheng, D., Chow, W. L., & He, J. Z. (2010). A Dehalococcoides-containing co-culture that dechlorinates tetrachloroethene to trans-1, 2-dichloroethene. ISME Journal, 4(1), 88-97.
13. Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., et al. (2009). The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Research, 37, D141-D145. doi: 10. 1093/Nar/Gkn879.
14. Colwell, R. K. (2005). EstimateS: Statistical estimation of species richness and shared species from samples, Version 7. 5. http://viceroy. eeb. uconn. edu/EstimateS.
15. Doherty, J. (2005). PEST model-independent parameter estimation, user manual (5th ed.). Australia: Watermark Numerical Computing.
16. Ellis, D. E., Lutz, E. J., Odom, J. M., Buchanan, R. J., Bartlett, C. L., Lee, M. D., et al. (2000). Bioaugmentation for accelerated in situ anaerobic bioremediation. Environmental Science and Technology, 34(11), 2254-2260.
17. Ferrey, M. L., Wilkin, R. T., Ford, R. G., & Wilson, J. T. (2004). Nonbiological removal of cis-dichloroethylene and 1, 1-dichloroethylene in aquifer sediment containing magnetite. Environmental Science and Technology, 38(6), 1746-1752.
18. Griffin, B. M., Tiedje, J. M., & Loffler, F. E. (2004). Anaerobic microbial reductive dechlorination of tetrachloroethene to predominately trans-1, 2-dichloroethene. Environmental Science and Technology, 38(16), 4300-4303.
19. Hallin, S., Jones, C. M., Schloter, M., & Philippot, L. (2009). Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME Journal, 3(5), 597-605.
20. He, J. T., Li, Y., Liu, S., & Chen, H. H. (2005). Chlorinate solvents natural biodegradation in shallow groundwater. Environmental Science, 26, 121-125.
21. He, J. Z., Ritalahti, K. M., Yang, K. L., Koenigsberg, S. S., & Loffler, F. E. (2003). Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium. Nature, 424(6944), 62-65.
22. Hendrickson, E. R., Payne, J. A., Young, R. M., Starr, M. G., Perry, M. P., Fahnestock, S., et al. (2002). Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Applied and Environmental Microbiology, 68(2), 485-495.
23. Huson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007). MEGAN analysis of metagenomic data. Genome Research, 17(3), 377-386.
24. Johnson, D. R., Nemir, A., Andersen, G. L., Zinder, S. H., & Alvarez-Cohen, L. (2009). Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides ethenogenes strain 195. FEMS Microbiology Letters, 294(2), 198-206.
25. Kao, C. M., Chen, S. C., & Su, M. C. (2001). Laboratory column studies for evaluating a barrier system for providing oxygen and substrate for TCE biodegradation. Chemosphere, 44(5), 925-934.
26. Kao, C. M., Chen, S. C., Wang, J. Y., Chen, Y. L., & Lee, S. Z. (2003). Remediation of PCE-contaminated aquifer by an in situ two-layer biobarrier: Laboratory batch and column studies. Water Research, 37(1), 27-38.
27. Kikuchi, T., Iwasaki, K., Nishihara, H., Takamura, Y., & Yagi, O. (2002). Quantitative and rapid detection of the trichloroethylene-degrading bacterium Methylocystis sp. M in groundwater by real-time PCR. Applied Microbiology and Biotechnology, 59(6), 731-736.
28. Krajmalnik-Brown, R., Holscher, T., Thomson, I. N., Saunders, F. M., Ritalahti, K. M., & Loffler, F. E. (2004). Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp strain BAV1. Applied and Environmental Microbiology, 70(10), 6347-6351. doi: 10. 1128/Aem. 70. 10. 6347-6351. 2004.
29. Leahy, J. G., Byrne, A. M., & Olsen, R. H. (1996). Comparison of factors influencing trichloroethylene degradation by toluene-oxidizing bacteria. Applied and Environment Microbiology, 62(3), 825-833.
30. Li, H. M., Chen, H. H., & Zheng, X. L. (2005). Characteristics of chlorinated aliphatic hydrocarbons transported to shallow groundwater in the industrial area of a city. Earth Science Frontiers, 12(Suppl), 132-138.
31. Li, Y., Li, F., Zhang, X., Qin, S., Zeng, Z., Dang, H., et al. (2008). Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (approximately 13° N). Extremophiles, 12(4), 573-585.
32. Liu, M. Z., Chen, H. H., Hu, L. Q., & Sun, W. (2006). Modeling of transformation and transportation of PCE and TCE by biodegradation in shallow groundwater. Earth Science Frontiers, 13(1), 155-159.
33. Loffler, F. E., & Edwards, E. A. (2006). Harnessing microbial activities for environmental cleanup. Current Opinion in Biotechnology, 17(3), 274-284.
34. Loffler, F. E., Sun, Q., Li, J., & Tiedje, J. M. (2000). 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Applied and Environment Microbiology, 66(4), 1369-1374.
35. Lowe, M., Madsen, E. L., Schindler, K., Smith, C., Emrich, S., Robb, F., et al. (2002). Geochemistry and microbial diversity of a trichloroethene contaminated Superfund site undergoing intrinsic in situ reductive dechlorination. Fems Microbiology Ecology, 40(2), 123-134.
36. Lu, X., Wilson, J. T., & Kampbell, D. H. (2006). Relationship between Dehalococcoides DNA in ground water and rates of reductive dechlorination at field scale. Water Research, 40(16), 3131-3140.
37. Luijten, M. L., de Weert, J., Smidt, H., Boschker, H. T., de Vos, W. M., Schraa, G., et al. (2003). Description of Sulfurospirillum halorespirans sp. nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer of Dehalospirillum multivorans to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov. International Journal of Systematic and Evolutionary Microbiology, 53(3), 787-793.
38. Macbeth, T. W., Cummings, D. E., Spring, S., Petzke, L. M., & Sorenson, K. S., Jr. (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. Applied and Environment Microbiology, 70(12), 7329-7341.
39. Magnuson, J. K., Romine, M. F., Burris, D. R., & Kingsley, M. T. (2000). Trichloroethene reductive dehalogenase from Dehalococcoides ethenogenes: Sequence of tceA and substrate range characterization. Applied and Environment Microbiology, 66(12), 5141-5147.
40. Mattes, T. E., Alexander, A. K., & Coleman, N. V. (2010). Aerobic biodegradation of the chloroethenes: Pathways, enzymes, ecology, and evolution. FEMS Microbiology Reviews, 34(4), 445-475.
41. MaymoGatell, X., Chien, Y. T., Gossett, J. M., & Zinder, S. H. (1997). Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science, 276(5318), 1568-1571.
42. Maymo-Gatell, X., Nijenhuis, I., & Zinder, S. H. (2001). Reductive dechlorination of cis-1, 2-dichloroethene and vinyl chloride by "Dehalococcoides ethenogenes". Environmental Science and Technology, 35(3), 516-521.
43. McCarty, P. L. (1997). Breathing with chlorinated solvents. Science, 276(5318), 1521-1522.
44. Middeldorp, P. J. M., van Aalst, M. A., Rijnaarts, H. H. M., Stams, F. J. M., de Kreuk, H. F., Schraa, G., et al. (1998). Stimulation of reductive dechlorination for in situ bioremediation of a soil contaminated with chlorinated ethenes. Water Science and Technology, 37(8), 105-110.
45. Moran, M. J., Zogorski, J. S., & Squillace, P. J. (2007). Chlorinated solvents in groundwater of the United States. Environmental Science and Technology, 41(1), 74-81.
46. Nijenhuis, I., & Zinder, S. H. (2005). Characterization of hydrogenase and reductive dehalogenase activities of Dehalococcoides ethenogenes strain 195. Applied and Environmental Microbiology, 71(3), 1664-1667.
47. Ohlen, K., Chang, Y. K., Hegemann, W., Yin, C. R., & Lee, S. T. (2005). Enhanced degradation of chlorinated ethylenes in groundwater from a paint contaminated site by two-stage fluidized-bed reactor. Chemosphere, 58(3), 373-377.
48. Ritalahti, K. M., Amos, B. K., Sung, Y., Wu, Q., Koenigsberg, S. S., & Loffler, F. E. (2006a). Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Applied and Environment Microbiology, 72(4), 2765-2774.
49. Ritalahti, K. M., Amos, B. K., Sung, Y., Wu, Q. Z., Koenigsberg, S. S., & Loffler, F. E. (2006b). Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Applied and Environmental Microbiology, 72(4), 2765-2774.
50. Ryoo, D., Shim, H., Arenghi, F. L., Barbieri, P., & Wood, T. K. (2001). Tetrachloroethylene, trichloroethylene, and chlorinated phenols induce toluene-o-xylene monooxygenase activity in Pseudomonas stutzeri OX1. Applied Microbiology and Biotechnology, 56(3-4), 545-549.
51. Saber, D. L., & Crawford, R. L. (1985). Isolation and characterization of flavobacterium strains that degrade pentachlorophenol. Applied and Environmental Microbiology, 50(6), 1512-1518.
52. Schloss, P. D., & Handelsman, J. (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environment Microbiology, 71(3), 1501-1506.
53. Semprini, L. (1995). In situ bioremediation of chlorinated solvents. Environmental Health Perspectives, 103(Suppl 5), 101-105.
54. Singleton, D. R., Furlong, M. A., Rathbun, S. L., & Whitman, W. B. (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Applied and Environment Microbiology, 67(9), 4374-4376.
55. Smidt, H., & de Vos, W. M. (2004). Anaerobic microbial dehalogenation. Annual Review of Microbiology, 58, 43-73.
56. Soares, A., Guieysse, B., Delgado, O., & Mattiasson, B. (2003). Aerobic biodegradation of nonylphenol by cold-adapted bacteria. Biotechnology Letters, 25(9), 731-738.
57. Song, B. K., Palleroni, N. J., & Haggblom, M. M. (2000). Isolation and characterization of diverse halobenzoate-degrading denitrifying bacteria from soils and sediments. Applied and Environmental Microbiology, 66(8), 3446-3453.
58. Sung, Y., Ritalahti, K. M., Sanford, R. A., Urbance, J. W., Flynn, S. J., Tiedje, J. M., et al. (2003). Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp nov. Applied and Environmental Microbiology, 69(5), 2964-2974.
59. Sung, Y., Ritalahti, K. M., Apkarian, R. P., & Loffler, F. E. (2006). Quantitative PCR confirms purity of strain GT, a novel trichloroethene-to-ethene-respiring Dehalococcoides isolate. Applied and Environment Microbiology, 72(3), 1980-1987.
60. Suyama, A., Iwakiri, R., Kimura, N., Nishi, A., Nakamura, K., & Furukawa, K. (1996). Engineering hybrid pseudomonads capable of utilizing a wide range of aromatic hydrocarbons and of efficient degradation of trichloroethylene. Journal of Bacteriology, 178(14), 4039-4046.
61. Tamura, K., Dudley, J., Nei, M., & Kumar, S. (2007). MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4. 0. Molecular Biology and Evolution, 24(8), 1596-1599.
62. Toraason, M., Clark, J., Dankovic, D., Mathias, P., Skaggs, S., Walker, C., et al. (1999). Oxidative stress acid DNA damage in Fischer rats following acute exposure to trichloroethylene or perchloroethylene. Toxicology, 138(1), 43-53.
63. Utkin, I., Woese, C., & Wiegel, J. (1994). Isolation and characterization of Desulfitobacterium dehalogenans gen. nov., sp. nov., an anaerobic bacterium which reductively dechlorinates chlorophenolic compounds. International Journal of Systematic Bacteriology, 44(4), 612-619.
64. van der Zaan, B., Smidt, H., De Vos, W. M., Rijnaarts, H., & Gerritse, J. (2010). Stability of the total and functional microbial communities in river sediment mesocosms exposed to anthropogenic disturbances. Fems Microbiology Ecology, 74(1), 72-82.
65. Wang, Z., Shi, J. S., Zhang, Z. J., Fei, Y. H., Li, Y. S., Zhang, F., Chen J. S., & Qian Y. (2009). A tentative discussion on the assessment standards of groundwater quality: A case study of the groundwater quality in the North China Plain. Acta Geoscientica Sinica, 30(5), 659-664.
66. Yeh, H. C., & Kastenberg, W. E. (1991). Health risk assessment of biodegradable volatile organic-chemicals: A case-study of PCE, TCE, DCE and VC. Journal of Hazardous Materials, 27(2), 111-126.
67. Zahn, J. A., & DiSpirito, A. A. (1996). Membrane-associated methane monooxygenase from Methylococcus capsulatus (Bath). Journal of Bacteriology, 178(4), 1018-1029.
68. Zhang, C., & Bennett, G. N. (2005). Biodegradation of xenobiotics by anaerobic bacteria. Applied Microbiology and Biotechnology, 67(5), 600-618.
69. Zhang, H., Hanada, S., Shigematsu, T., Shibuya, K., Kamagata, Y., Kanagawa, T., et al. (2000a). Burkholderia kururiensis sp. nov., a trichloroethylene (TCE)-degrading bacterium isolated from an aquifer polluted with TCE. International Journal of Systematic and Evolutionary Microbiology, 50 Pt 2, 743-749.
70. Zhang, H., Hanada, S., Shigematsu, T., Shibuya, K., Kamagata, Y., Kanagawa, T., et al. (2000b). Burkholderia kururiensis sp. nov., a trichloroethylene (TCE)-degrading bacterium isolated from an aquifer polluted with TCE. International Journal of Systematic and Evolutionary Microbiology, 50(2), 743-749.