Pyrosequencing analysis yields comprehensive assessment of microbial communities in pilot-scale two-stage membrane biofilm reactors

Environmental Science and Technology

Volumn 48, Issue 13, 2014, Pages 7511-7518

  Ontiveros Valencia, Aura ^a   Tang, Youneng ^a   Zhao, He Ping ^a   Friese, David ^b   Overstreet, Ryan ^b   Smith, Jennifer ^c   Evans, Patrick ^c   Rittmann, Bruce E ^a   Krajmalnik Brown, Rosa ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

^b APTwater Inc   (United States)

^c CDM SMITH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIOFILMS; BIOREACTORS; DENITRIFICATION; GROUNDWATER; INORGANIC COMPOUNDS;

COMPREHENSIVE ASSESSMENT; CONTAMINATED GROUNDWATER; COOPERATIVE RELATIONSHIPS; MEMBRANE BIOFILM REACTOR; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY STRUCTURES; PRINCIPAL COORDINATE ANALYSIS; SULFATE REDUCING BACTERIA;

LOADING;

GROUND WATER; NITRATE; OXYGEN; PERCHLORATE; SULFATE;

BACTERIUM; BIOFILM; BIOREACTOR; COMMUNITY STRUCTURE; GROUNDWATER POLLUTION; MEMBRANE; MICROBIAL COMMUNITY; PHYLOGENETICS; POLLUTANT REMOVAL;

ARTICLE; BIOFILM; DENITRIFYING BACTERIUM; DESULFOVIBRIONALES; ELECTRON; MEMBRANE FILM REACTOR; MICROBIAL COMMUNITY; NONHUMAN; PERCHLORATE REDUCING BACTERIA; PROKARYOTES BY METABOLISM; PROTEOBACTERIA; PYROSEQUENCING; REACTOR; RHODOBACTERALES; SULFATE REDUCING BACTERIUM; THIOTHRICHALES; XANTHOMONADALES;

BACTERIA; BIOFILMS; BIOREACTORS; DENITRIFICATION; ELECTRONS; HYDROGEN; MEMBRANES, ARTIFICIAL; NITRATES; OXIDATION-REDUCTION; PERCHLORATES; PHYLOGENY; PILOT PROJECTS; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA; SULFATES; TIME FACTORS;

EID: 84903738932     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/es5012466     Document Type: Article

References (54)

1. Knobeloch, L.; Salna, B.; Hogan, A.; Postle, J.; Anderson, H. Blue babies and nitrate-contaminated well water Environ. Health Perspect. 2000, 108 (7) 675
2. Camargo, J. A.; Alonso, á. Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems: a global assessment Environ. Int. 2006, 32 (6) 831-849 (Pubitemid 44172988)
3. US EPA. Basic Information about Nitrate in Drinking Water. http://water.epa.gov/drink/contaminants/basicinformation/nitrate.cfm (accessed February 17, 2014).
4. Perchlorate treatment technology update, EPA 542-R-05-015; US EPA: Washington, DC, 2005.
5. US EPA. Perchlorate. http://water.epa.gov/drink/contaminants/unregulated/ perchlorate.cfm (accessed February 17, 2014).
6. US EPA. Potential SBAR Panel: Drinking water regulatory actions for perchlorate. http://www.epa.gov/rfa/perchlorate.html (accessed January 30, 2014).
7. Kim, K.; Logan, B. E. Fixed-bed bioreactor treating perchlorate- contaminated waters Environ. Eng. Sci. 2000, 17 (5) 257-265
8. Lee, K. C.; Rittmann, B. E. Applying a novel autohydrogenotrophic hollow-fiber membrane biofilm reactor for denitrification of drinking water Water Res. 2002, 36, 2040-2052 (Pubitemid 34464128)
9. Zhang, H.; Bruns, M. A.; Logan, B. E. Perchlorate reduction by a novel chemolithoautotrophic, hydrogen-oxidizing bacterium Environ. Microbiol. 2002, 4 (10) 570-576 (Pubitemid 35211940)
10. Hatzinger, P. B. Perchlorate biodegradation for water treatment Environ. Sci. Technol. 2005, 39 (11) 239A-247A (Pubitemid 40770213)
11. Herman, D. C.; Frankenberger, W. T. Microbial-mediated reduction of perchlorate in groundwater J. Environ. Qual. 1998, 27 (4) 750-754 (Pubitemid 28341403)
12. Herman, D. C.; Frankenberger, W. T. Bacterial reduction of perchlorate and nitrate in water J. Environ. Qual. 1999, 28 (3) 1018-1024 (Pubitemid 29237050)
13. Chaudhuri, S. K.; OConnor, S. M.; Gustavson, R. L.; Achenbach, L. A.; Coates, J. D. Environmental factors that control microbial perchlorate reduction Appl. Environ. Microbiol. 2002, 68 (9) 4425-4430 (Pubitemid 34988125)
14. Coates, J. D.; Achenbach, L. A. Microbial perchlorate reduction: rocket fuelled metabolism Nat. Rev. Microbiol 2004, 2 (7) 569-580 (Pubitemid 39200031)
15. Tang, Y.; Zhao, H.-P.; Marcus, A. K.; Krajmalnik-Brown, R.; Rittmann, B. E. A steady-state biofilm model for simultaneous reduction of nitrate and perchlorate. Part 2: Parameter optimization and results and discussion Environ. Sci. Technol. 2012, 46 (3) 1608-1615
16. Romanenko, V. I.; Korenkov, V. N.; Kuznetsov, S. I. Bacterial decomposition of ammonium perchlorate Mikrobiologiia 1976, 45 (2) 204
17. Hochstein, L. I.; Tomlinson, G. A. The enzymes associated with denitrification Annu. Rev. Microbiol. 1988, 42, 231-261
18. Kengen, S. W. M.; Rikken, G. B.; Hagen, W. R.; van Ginkel, C. G.; Stams, A. J. M. Purification and characterization of (per)-chlorate reductase from the chlorate-respiring strain GR-1 J. Bacteriol. 1999, 181, 6706-6711 (Pubitemid 29517985)
19. Logan, B. E.; Wu, J.; Unz, R. F. Biological perchlorate reduction in high-salinity solutions Water Res. 2001, 35 (12) 3034-3038 (Pubitemid 32611749)
20. Min, B.; Evans, P. J.; Chu, A. K.; Logan, B. E. Perchlorate removal in sand and plastic media bioreactors Water Res. 2004, 38 (1) 47-60 (Pubitemid 37443394)
21. Evans, P.; Smith, J.; Singh, T.; Hyung, H.; Arucan, C.; Berokoff, D.; Friese, D.; Overstreet, R.; Vigo, R.; Rittmann, B. E.; Ontiveros-Valencia, A.; Zhao, H.-P.; Tang, Y.; Kim, B.-O.; van Ginkel, S.; Krajmalnik-Brown, R. Final Report: Nitrate and Perchlorate Destruction and Potable Water Production Using Membrane Biofilm Reduction. ESTCP Project ER-200541 2013.
22. Rittmann, B. E. The membrane biofilm reactor is a versatile platform for water and wastewater treatment Environ. Eng. Res. 2007, 12 (4) 157-175
23. Zhao, H.-P.; Ontiveros-Valencia, A.; Tang, Y.; Kim, B.-O.; van Ginkel, S.; Friese, D.; Overstreet, R.; Smith, J.; Evans, P.; Krajmalnik-Brown, R.; Rittmann, B. E. Removal of multiple electron acceptors by pilot-scale, two-stage membrane biofilm reactors Water Res. 2014, 54, 115-122
24. Ontiveros-Valencia, A.; Tang, Y.; Krajmalnik-Brown, R.; Rittmann, B. E. Perchlorate reduction from a highly contaminated groundwater in the presence of sulfate-reducing bacteria in a hydrogen-fed biofilm Biotechnol. Bioeng. 2013, 110 (12) 3139-3147
25. Ontiveros-Valencia, A.; Tang, Y.; Krajmalnik-Brown, R.; Rittmann, B. E. Managing the interactions between sulfate- and perchlorate-reducing bacteria when using hydrogen-fed biofilms to treat a groundwater with a high perchlorate concentration Water Res. 2014, 55, 215-224
26. Waller, S. Bioremediation of perchlorate-contaminated groundwater. Masters thesis, University of Toronto, 2002.
27. Attaway, H.; Smith, M. Reduction of perchlorate by an anaerobic enrichment culture J. Ind. Microbiol 1993, 12 (6) 408-412 (Pubitemid 24071710)
28. Bardiya, N.; Bae, J. H. Bioremediation potential of a perchlorate-enriched sewage sludge consortium Chemosphere 2005, 58 (1) 83-90 (Pubitemid 39441106)
29. Lozupone, C.; Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities Appl. Environ. Microbiol. 2005, 71, 8228-8235 (Pubitemid 41803949)
30. Lozupone, C.; Hamady, M.; Knight, R. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context BMC Bioinformatics 2006, 7 (1) 371
31. 2-based membrane biofilm reactors J. Membr. Sci. 2012, 407-408, 176-183
32. Sun, Y.; Wolcott, R. D.; Dowd, S. E. Tag-encoded FLX amplicon pyrosequencing for the elucidation of microbial and functional gene diversity in any environment. High-Throughput Next Generation Sequencing Methods Mol. Biol. 2011, 733, 129-141
33. Ontiveros-Valencia, A.; Ilhan, Z. E.; Kang, D.-W.; Rittmann, B. E.; Krajmalnik-Brown, R. Phylogenetic analysis of nitrate- and sulfate-reducing bacteria in a hydrogen-fed biofilm FEMS Microbiol. Ecol. 2013, 85, 158-167
34. Caporaso, J. G.; Kuczynski, J.; Stombaugh, J.; Bittinger, K.; Bushman, F. D.; Costello, E. K.; Fierer, N.; Pena, A. G.; Goodrich, J. K.; Gordon, J. I.; Huttley, G. A.; Kelley, S. T.; Knight, D.; Koenig, J. E.; Ley, R. E.; Lozupone, C. A.; McDonald, D.; Muegge, B. D.; Pirrung, M.; Reeder, J.; Sevinsky, J. R.; Tumbaugh, P. J.; Walters, W. A.; Widmann, J.; Yatsunenko, T.; Zaneveld, J.; Knight, R. Qiime allows analysis of high-throughput community sequencing data Nat. Methods 2010, 7, 335-336
35. Edgar, R. C. Search and clustering orders of magnitude faster than blast Bioinformatics 2010, 26, 2460-2461
36. DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.; Rojas, M.; Brodie, E. L.; Keller, K.; Huber, T.; Dalevi, D.; Hu, P.; Andersen, G. L. Greengenes, a chimera-checked 16s rrna gene database and workbench compatible with arb Appl. Environ. Microbiol. 2006, 72, 5069-5072 (Pubitemid 44078840)
37. Caporaso, J. G.; Bittinger, K.; Bushman, F. D.; DeSantis, T. Z.; Andersen, G. L.; Knight, R. Pynast: A flexible tool for aligning sequences to a template alignment Bioinformatics 2010, 26, 266-267
38. Haas, B. J.; Gevers, D.; Earl, A. M.; Feldgarden, M.; Ward, D. V.; Giannoukos, G.; Ciulla, D.; Tabaa, D.; Highlander, S. K.; Sordergren, E.; Methé, B.; DeSantis, T. Z.; The Human Microbiome Consortium; Petrosino, J. F.; Knight, R.; Birren, B. W. Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons Genome Res. 2011, 21, 494-504
39. Pruesse, E.; Quast, C.; Knittel, K.; Fuchs, B. M.; Ludwig, W.; Peplies, J.; Gloeckner, F. O. Silva. A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Nucleic Acids Res. 2007, 35, 7188-7196
40. Price, M. N.; Dehal, P. S.; Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix Mol. Biol. Evol. 2009, 26, 1641-1650
41. Hughes, J. B.; Hellmann, J. J.; Ricketts, T. H.; Bohannan, B. J. Counting the uncountable: statistical approaches to estimating microbial diversity Appl. Environ. Microbiol. 2001, 67 (10) 4399-4406 (Pubitemid 33646064)
42. Faith, D. P. Conservation evaluation and phylogenetic diversity Biol. Conserv. 1992, 61, 1-10
43. Shannon, C. E. A mathematical theory of communication Bell Syst. Tech. J. 1948, 27, 379-423
44. Simpson, E. H. Measurement of diversity Nature 1949, 163, 688
45. Ontiveros-Valencia, A.; Ziv-El, M.; Zhao, H.-P.; Feng, L.; Rittmann, B. E.; Krajmalnik-Brown, R. Interactions between nitrate-reducing and sulfate-reducing bacteria coexisting in a hydrogen-fed biofilm Environ. Sci. Technol. 2012, 46, 11289-11298
46. Tang, Y.; Ontiveros-Valencia, A.; Liang, F.; Zhou, C.; Krajmalnik-Brown, R.; Rittmann, B. E. A biofilm model to understand the onset of sulfate reduction in denitrifying membrane biofilm reactors Biotechnol. Bioeng. 2012, 110, 763-772
47. Wu, W.-M.; Gu, B.; Fields, M. W.; Gentile, M.; Ku, Y.-K.; Yan, H.; Tiquias, S.; Yan, T.; Nyman, J.; Zhou, J.; Jardine, P. M.; Craig, C. S. Uranium reduction by denitrifying biomass J. Bioremed. 2005, 9 (1) 41-61
48. Adav, S. S.; Lee, D. J.; Lai, J. Y. Microbial community of acetate utilizing denitrifiers in aerobic granules Appl. Microbiol. Biotechnol. 2010, 85 (3) 753-762
49. Madigan, M.; Markinko, J.; Stahl, D.; Clark, D. Brock Biology of Microorganisms, 12 th ed.; Pearson: San Francisco California, 2009.
50. Williams, T. M.; Unz, R. F. Isolation and characterization of filamentous bacteria present in bulking activated sludge Appl. Microbiol. Biotechnol. 1985, 22 (4) 273-282 (Pubitemid 15007759)
51. Williams, T. M.; Unz, R. F.; Doman, J. T. Ultrastructure of Thiothrix spp. and "type 021N" bacteria Appl. Environ. Microbiol. 1987, 53 (7) 1560-1570
52. Zhao, H.-P.; Ilhan, Z. E.; Ontiveros-Valencia, A.; Tang, Y.; Rittmann, B. E.; Krajmalnik-Brown, R. Effects of multiple electron acceptors on microbial interactions in a hydrogen-based biofilm Environ. Sci. Technol. 2013, 47, 7396-7403
53. Martin, K. J.; Picioreanu, C.; Nerenberg, R. Multidimensional modeling of biofilm development and fluid dynamics in a hydrogen-based, membrane biofilm reactor (MBfR) Water Res. 2013, 47 (13) 4739-4751
54. Roldan, M. D. Chlorate and nitrate reduction in phototrophic bacteria Rhodobacter capsulatus and Rhodobacter sphaeroides Curr. Microbiol. 1994, 29, 241-245 (Pubitemid 24271164)