Identification of a novel group of bacteria in sludge from a deteriorated biological phosphorus removal reactor

Applied and Environmental Microbiology

Volumn 65, Issue 3, 1999, Pages 1251-1258

  Nielsen, Alex T ^a   Liu, Wen Tso ^b,c   Filipe, Carlos ^d   Grady Jr , Leslie ^d   Molin, Søren ^a   Stahl, David A ^c  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b NATIONAL CENTRAL UNIVERSITY   (Taiwan)

^c NORTHWESTERN UNIVERSITY   (United States)

^d CLEMSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; NUCLEIC ACID; ORGANIC MATTER; PHOSPHATE; PHOSPHORUS; POLYHYDROXYALKANOIC ACID; RNA 16S;

ACTINOMYCES; ARTICLE; BACTERIUM IDENTIFICATION; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA SEQUENCE; ELECTRON MICROSCOPY; LEGIONELLA; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEOBACTERIA; SLUDGE;

EID: 0032985537     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.3.1251-1258.1999     Document Type: Article

References (67)

1. Alm, E. W., D. B. Oerther, N. Larsen, D. A. Stahl, and L. Raskin. 1996. The oligonucleotide probe database. Appl. Environ. Microbiol. 62:3557-3559.
2. 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.
3. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
4. American Public Health Association. 1989. Standard methods for the examination of water and wastewater, 17th ed. American Public Health Association, Washington, D.C.
5. Barnard, J. L., G. M. Stevens, and P. J. Leslie. 1985. Design strategies for nutrient removal plants. Water Sci. Technol. 17:233-242.
6. Blackall, L. L., S. Rossetti, C. Christensson, M. Cunningham, P. Hartman, P. Hugenholtz, and V. Tandoi. 1997. The characterization and description of representatives of 'G' bacteria from activated sludge plants. Lett. Appl. Microbiol. 25:63-69.
7. Bond, P. L., P. Hugenholtz, J. Keller, and L. L. Blackall. 1995. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludge from sequencing batch reactors. Appl. Environ. Microbiol. 61:1910-1916.
8. Brodisch, K. E. U. 1985. Interaction of different groups of micro-organisms in biological phosphate removal. Water Sci. Technol. 17:89-97.
9. Cech, J. S., and P. Hartman. 1993. Competition between polyphosphate and polysaccharide accumulating bacteria in enhanced biological phosphate removal systems. Water Res. 27:1219-1225.
10. Comeau, Y., K. J. Hall, R. E. W. Hancock, and W. K. Oldham. 1986. Biochemical model for enhanced biological phosphorus removal. Water Res. 20:1511-1521.
11. Darland, G., and T. D. Brock. 1971. Bacillus acidocaldarius sp. nov., an acidophilic thermophilic spore-forming bacterium. J. Gen. Microbiol. 67:9-15.
12. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for identification of single cells. Science 243: 1360-1362.
13. Farrily, V., F. A. Rainey, and E. Stackebrandlt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:2798-2801.
14. Ferris, M. J., G. Muyzer, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62:340-346.
15. Fuh, G. W., and M. Chen. 1975. Microbiological basis of phosphate removal in the activated sludge process for the treatment of wastewater. Microb. Ecol. 2:119-138.
16. Fukase, T., M. Shibata, and Y. Miyaji. 1985. The role of an anaerobic stage on the biological phosphorus removal. Water Sci. Technol. 17:59-80.
17. Geisbert, T. W., and N. K. Jaax. 1998. Marburg hemorrhagic fever: report of a case studied by immunohistochemistry and electron microscopy. Ultrastruct. Pathol. 22:3-17.
18. Hansen, M. C., T. T. Nielscn, M. Givskov, and S. Molin. 1998. Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol. Ecol. 26:141-149.
19. Jenkins, D., M. G. Richard, and G. T. Diagger. 1986. Manual on the causes and control of activated sludge bulking and foaming. Water Research Commission. Pretoria. Republic of South Africa.
20. Jenkins, D., and V. Tandoi. 1991. The applied microbiology of enhanced biological phosphate removal accomplishments and needs. Water Res. 25: 1471-1478.
21. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. M. Munro (ed.), Mammalian protein metabolism. Academic Press, Inc., New York, N.Y.
22. Kerkhof, L., and B. B. Ward. 1993. Comparison of nucleic acid hybridization and fluorometry for measurement of the relationship between RNA/DNA ratio and growth rate in a marine bacterium. Appl. Environ. Microbiol. 59:1303-1309.
23. Kortstee, G. J. J., K. J. Appeldnorn, C. F. C. Bontning, E. W. J. van Niel, and H. W. van Veen. 1994. Biology of polyphosphate-accumulating bacteria involved in enhanced biological phosphorus removal. FEMS Microbiol. Rev. 15:137-153.
24. Liesack, W., H. Weyland, and E. Stackebrandt. 1991. Potential risk of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol. 21:191-198.
25. Liu, W., T. Mino, K. Nakamura, and T. Matsuo. 1996. Glycogen accumulating population and its anaerobic substrate uptake in anaerobic-aerobic activated sludge without biological phosphorus removal. Water Res. 30:75-82.
26. Liu, W., K. Nakamura, T. Matsuo, and T. Mino. 1997. Internal energy-based competition between polyphosphate-and glycogen-accumulating bacteria in biological phosphorus removal reactors - effect of P/C feeding ratio. Water Res. 31:1430-1438.
27. Liu, W., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphism of 16S ribosomal DNA. Appl. Environ. Microbiol. 63:4516-4522.
28. Liu, W., T. L. Marsh, and L. J. Forney. 1997. Determination of the microbial diversity of anaerobic-aerobic activated sludge by a novel molecular biological technique. Water Sci. Technol. 37:417-422.
29. Lötter, L. H. 1985. The role of bacterial phosphate metabolism in enhanced phosphorus removal from the activated sludge process. Water Sci. Technol. 17:127-138.
30. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1996. The Ribosomal Database Project (RDP). Nucleic Acids Res. 24:82-85.
31. Manz, W., R. I. Amann, W. Ludwig, M. Wagner, and K. H. Schleifer. 1992. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15:593-600.
32. Martinez-Murcia, A. J., S. G. Acinas, and F. Rodriguez-Valera. 1995. Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments. FEMS Microbiol. Ecol. 17:247-256.
33. Maszenan, A. M., R. J. Seviour, B. K. C. Patel, G. N. Rees, and B. M. McDougall. 1997. Amaricoccus gen. nov., a gram-negative coccus occurring in regular packages or tetrads, isolated from activated sludge biomass, and descriptions of Amaricoccus veronensis sp. nov., Amaricoccus tamworthensis sp. nov., Amaricoccus macauensis sp. nov., and Amaricoccus kaplicensis sp. nov. Int. J. Syst. Bacteriol. 47:727-734.
34. Matsuo, Y. 1994. Effect of the anaerobic solids retention time on enhanced biological phosphorus removal. Water Sci. Technol. 30:193-202.
35. Mau, M., and K. N. Timmis. 1998. Use of subtractive hybridization to design habitat-based oligonucleotide probes for investigation of natural bacterial communities. Appl. Environ. Microbiol. 64:185-191.
36. Møller, S., C. S. Kristensin, L. K. Poulsen, J. M. Carstensen, and S. Molin. 1995. Bacterial growth on surfaces: automated image analysis for quantification of growth rate-related parameters. Appl. Environ. Microbiol. 61:741-748.
37. Møller, S., A. R. Pedersen, L. K. Poulsen, E. Arvin, and S. Molin. 1996. Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy. Appl. Environ. Microbiol. 62:4632-4640.
38. Muyzer, G., E. C. De Wall, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
39. Mylvaganam, S., and P. P. Dennis. 1992. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismotui. Genetics 130:399-410.
40. National Institutes of Health. 22 June 1998, posting date. [Online.] NIH Image program. ftp:zippy.nimh.nih.gov. [13 August 1998, date last accessed.]
41. Olsen, G. J., N. Larsen, and C. R. Woese. 1991. The Ribosomal RNA Database Project. Nucleic Acids Res. 19(Suppl.):2017-2021.
42. Pace, N. R., D. A. Stahl, D. J. Lane, and G. J. Olsen. 1986. The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1-55.
43. Picard, C., C. Ponsonnet, E. Paget, X. Nesme, and P. Simonet. 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 58:2717-2722.
44. Pitman, A. K., B. C. Trim, and L. van Dalsen. 1988. Operating experience with biological nutrient removal at the Johannesburg Bushkoppie works. Water Sci. Technol. 20:51-61.
45. Poulsen, L. K., G. liallard, and D. A. Stahl. 1993. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol. 59:1354-1360.
46. Rainey, F. A., N. Ward, L. I. Sly, and E. Stackebrandt. 1994. Dependence on the taxon composition of clone libraries for PCR amplified, naturally occurring 16S rDNA, on the primer pair and the cloning system used. Experientia 50:796-797.
47. Raskin, L., L. K. Poulsen, D. R. Noguera, B. E. Rittmann, and D. A. Stahl. 1994. Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 60: 1241-1248.
48. Reysenbach, A., L. J. Giver, G. S. Wickham, and N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58:3417-3418.
49. Rölleke, S., G. Muyzer, C. Wawer, G. Wanner, and W. Lubitz. 1996. Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 62:2059-2065.
50. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
51. Satoh, H., T. Mino, and T. Matsuo. 1992. Uptake of organic substrates and accumulation of polyhydroxyalkanoates linked with glycolysis of intracellular carbohydrates under anaerobic conditions in the biological excess phosphate removal process. Water Sci. Technol. 26:933-942.
52. Satoh, H., T. Mino, and T. Matsuo. 1994. Deterioration of enhanced biological phosphorus removal by the domination of microorganisms without polyphosphate accumulation. Water Sci. Technol. 30:203-211.
53. Schmidt, T. M., E. F. DeLong, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.
54. Schuppler, M., F. Mertens, G. Schön, and U. B. Göbel. 1995. Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis. Microbiology 141:513-521.
55. Smalla, K., U. Wachtendorf, H. Heuer, W.-T. Liu, and L. J. Forney. 1998. Analysis of Biolog-GN substrate utilization patterns by microbial communities. Appl. Environ. Microbiol. 64:1220-1225.
56. Smolders, G. J. F., J. van der Meij, M. C. M. van Loosdrecht, and J. J. Heijnen. 1994. Model of the anaerobic metabolism of the biological phosphorus removal process: stoichiometry and pH influence. Biotechnol. Bioeng. 43:461-470.
57. Stahl, D. A., B. Flesher, H. R. Mansfield, and L. Montgomery. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1079-1084.
58. Stahl, D. A., and R. I. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Inc., New York, N.Y.
59. Tebbe, C. C., and W. Vahjen. 1993. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl. Environ. Microbiol. 59:2657-2665.
60. Teske, A., C. Wawer, G. Muyzer, and N. B. Ramsing. 1996. Distribution of sulfate-reducing bacteria in a stratified fjord (Manager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62:1405-1415.
61. Van Loosdrecht, M. C. M., G. J. Smolders, T. Kuba, and J. J. Heijnen. 1997. Metabolism of micro-organisms responsible for enhanced biological phosphorus removal from wastewater. Antonie Leeuwenhoek 71:109-116.
62. Wagner, M., R. Amann, H. Lemmer, and K. H. Schleifer. 1993. Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59:1520-1525.
63. Wagner, M., K. Erhart, W. Manz, R. I. Amann, H. Lemmer, D. Wedi, and K. H. Schleifer. 1994. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60:792-800.
64. Wallner, G., R. Erhart, and R. I. Amann. 1995. Flow cytometric analysis of activated sludge with rRNA-targeted probes. Appl. Environ. Microbiol. 61: 1859-1866.
65. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65.
66. Wentzel, M. C., R. E. Loewenthal, G. A. Ekama, and G. V. R. Marais. 1988. Enhanced polyphosphate organism cultures in activated sludge systems. Part 1. Enhanced culture development. Water SA 14:81-92.
67. Wilson, I. G. 1997. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63:3741-3751.