Diversity of nitrite reductase genes in "Candidatus accumulibacter phosphatis"-dominated cultures enriched by flow-cytometric sorting

Applied and Environmental Microbiology

Volumn 73, Issue 16, 2007, Pages 5331-5337

  Miyauchi, Ryuki ^a   Oki, Kazuma ^a   Aoi, Yoshiteru ^a   Tsuneda, Satoshi ^a  

^a WASEDA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; CELLS; DENITRIFICATION; ENZYMES; FLOW CYTOMETRY;

CYTOMETRIC SORTING; FLUORESCENCE IN SITU HYBRIDIZATION (FISH); NITRITE REDUCTASE GENES;

GENES;

NITRATE REDUCTASE; POLYPHOSPHATE;

BACTERIUM; DENITRIFICATION; ENZYME; FLOW CYTOMETRY; GENETIC VARIATION; HYBRIDIZATION; NITRITE;

ARTICLE; CANDIDATUS ACCUMULIBACTER PHOSPHATIS; DENITRIFICATION; ENRICHMENT CULTURE; ENZYME ANALYSIS; FLOW CYTOMETRY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE; GENE AMPLIFICATION; ISOLATION PROCEDURE; MICROORGANISM; MOLECULAR CLONING; NIRK GENE; NIRS GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOSPHATE METABOLISM; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

BACTERIA; BACTERIAL PROTEINS; BIOREACTORS; DNA, BACTERIAL; FLOW CYTOMETRY; IN SITU HYBRIDIZATION, FLUORESCENCE; MOLECULAR SEQUENCE DATA; NITRITE REDUCTASES; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEQUENCE ANALYSIS, DNA;

ACCUMULIBACTER PHOSPHATIS;

EID: 34548246447     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00175-07     Document Type: Article

References (32)

1. Abulencia, C. B., D. L. Wyborski, J. A. Garcia, M. Podar, W. Chen, S. H. Chang, H. W. Chang, D. Watson, E. L. Brodie, T. C. Hazen, and M. Keller. 2006. Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl. Environ. Microbiol. 72:3291-3301.
2. Ahn, J., T. Daidou, S. Tsuneda, and A. Hirata. 2002. Characterization of denitrifying phosphate-accumulating organisms cultivated under different electron acceptor conditions using polymerase chain reaction-denaturing gradient gel electrophoresis assay. Water Res. 36:403-412.
3. Biegala, I. C., F. Not, D. Vaulot, and N. Simon. 2003. Quantitative assessment of picoeukaryotes in the natural environment by using taxon-specific oligonucleotide probes in association with tyramide signal amplification-fluorescence in situ hybridization and flow cytometry. Appl. Environ. Microbiol. 69:5519-5529.
4. Braker, G., A. Fesefeldt, and K. Witzel. 1998. Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl. Environ. Microbiol. 64:3769-3775.
5. Crocetti, G. R., P. Hugenholtz, P. L. Bond, A. Schuler, J. Keller, D. Jenkins, and L. L. Blackall. 2000. Identification of polyphosphate- accumulating organisms and design of 16S rRNA-directed probes for their detection and quantitation. Appl. Environ. Microbiol. 66:1175-1182.
6. Hallin, S., and P. E. Lindgren. 1999. PCR detection of genes encoding nitrite reductase in denitrifying bacteria. Appl. Environ. Microbiol. 65:1652-1657.
7. Hesselmann, R. P. X., C. Werlen, D. Hahn, J. R. van der Meer, and A. J. B. Zehender. 1999. Enrichment, phylogenetic analysis and detection of a bacterium that performs enhanced biological phosphate removal in activated sludge. Syst. Appl. Microbiol. 22:454-465.
8. Hung, C. H., J. Peccia, J. L. Zilles, and D. R. Noguera. 2002. Physical enrichment of polyphosphate-accumulating organisms in activated sludge. Water Environ. Res. 74:354-361.
9. Kanagawa, T. 2003. Bias and artifacts in multitemplate polymerase chain reaction (PCR). J. Biosci. Bioeng. 96:317-323.
10. Kerrn-Jespersen, J. P., and M. Henze. 1993. Biological phosphorus uptake under anoxic and aerobic conditions. Water Res. 27:617-624.
11. Kong, Y. H., M. Beer, G. N. Rees, and R. J. Seviour. 2002. Functional analysis of microbial communities in aerobic-anaerobic sequencing batch reactors fed with different phosphorus/carbon (P/C) ratios. Microbiology 148:2299-2307.
12. Kong, Y. H., J. L. Nielsen, and P. H. Nielsen. 2004. Microautoradiographic study of Rhodocyclus-related polyphosphate- accumulating bacteria in full-scale enhanced biological phosphorus removal plants. Appl. Environ. Microbiol. 70:5383-5390.
13. Kuba, T., M. C. M. van Loosdrecht, F. A. Brandse, and J. J. Heijnen. 1997. Occurrence of denitrifying phosphorus removing bacteria in modified UCT-type wastewater treatment plants. Water Res. 31:777-786.
14. Kuba, T., M. C. M. van Loosdrecht, and J. J. Heijnen. 1996. Phosphorus and nitrogen removal with minimal COD requirement by integration of denitrification in a two-sludge system. Water Res. 30:1702-1710.
15. Liu, W. T., A. T. Nielsen, J. H. Wu, C. S. Tsai, Y. Matsuo, and S. Molin. 2001. In situ identification of polyphosphate- and polyhydroxyalkanoate-accumulating traits for microbial populations in a biological phosphorus removal process. Environ. Microbiol. 3:110-122.
16. Martin, H. G., N. Ivanova, V. Kunin, F. Warnecke, K. W. Barry, A. C. McHardy, C. Yeates, S. He, A. A. Salamov, E. Szeto, E. Dalin, N. H. Putnam, H. J. Shapiro, J. L. Pangilinan, I. Rigoutsos, N. C. Kyrpides, L. L. Blackall, K. D. McMahon, and P. Hugenholtz. 2006. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol. 24:1263-1269.
17. Onuki, M., H. Satoh, and T. Mino. 2002. Analysis of microbial community that performs enhanced biological phosphorus removal in activated sludge fed with acetate. Water Sci. Technol. 46:145-154.
18. Reference deleted.
19. Raghunathan, A., H. R. Ferguson, Jr., C. J. Bornarth, W. Song, M. Driscoll, and R. S. Lasken. 2005. Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol. 71:3342-3347.
20. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
21. Scala, D., and L. J. Kerkhof. 1998. Nitrous oxide reductase (nosZ) genes in continental shelf sediments. FEMS Microbiol. Lett. 162:61-68.
22. Schonhuber, W., B. Fuchs, S. Juretschko, and R. Amann. 1997. Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Appl. Environ. Microbiol. 63:3268-3273.
23. Schuler, A. J., M. Onuki, H. Satoh, and T. Mino. 2002. Density separation and molecular methods to characterize enhanced biological phosphorus removal system populations. Water Sci. Technol. 46:195-198.
24. Sekar, R., B. M. Fuchs, R. Amann, and J. Pernthaler. 2004. Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 70:6210-6219.
25. Seviour, R. J., T. Mino, and M. Onuki. 2003. The microbiology of biological phosphorus removal in activated sludge systems. FEMS Microbiol. Rev. 27:99-127.
26. Smolders, G. J. F., J. van der Meij, M. C. M. van Loosdrecht, and J. J. Heijnen. 1994. Stoichiometric model of the aerobic metabolism of the biological phosphorus removal process. Biotechnol. Bioeng. 44:837-848.
27. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
28. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
29. Tsuneda, S., R. Miyauchi, T. Ohno, and A. Hirata. 2005. Characterization of denitrifying polyphosphate-accumulating organisms in activated sludge based on nitrite reductase gene. J. Biosci. Bioeng. 99:403-407.
30. Wallner, G., B. Fuchs, S. Spring, W. Beisker, and R. Amann. 1997. Flow sorting of microorganisms for molecular analysis. Appl. Environ. Microbiol. 63:4223-4231.
31. Zeng, R. J., A. M. Saunders, Z. G. Yuan, L. L. Blackall, and J. Keller. 2003. Identification and comparison of aerobic and denitrifying polyphosphate-accumulating organisms. Biotechnol. Bioeng. 83:140-148.
32. Zilles, J. L., C. H. Hung, and D. R. Noguera. 2002. Presence of Rhodocyclus in a full-scale wastewater treatment plant and their participation in enhanced biological phosphorus removal. Water Sci. Technol. 46:123-128.