Phylogenetic analysis and in situ identification of bacteria in activated sludge

Applied and Environmental Microbiology

Volumn 63, Issue 7, 1997, Pages 2884-2896

  Snaidr, Jiri ^a,b   Amann, Rudolf ^a,b   Huber, Ingrid ^a   Ludwig, Wolfgang ^a   Schleifer, Karl Heinz ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA;

ACTIVATED SLUDGE; ARTICLE; BACTERIUM IDENTIFICATION; GENE TARGETING; MOLECULAR CLONING; PHYLOGENY; RNA ANALYSIS; WASTE WATER MANAGEMENT;

ARCOBACTER; BACTERIA (MICROORGANISMS); CHLAMYDIAE; PLANCTOMYCES; POSIBACTERIA; PROTEOBACTERIA;

EID: 0030741576     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.7.2884-2896.1997     Document Type: Article

References (67)

1. Amann, R., J. Snaidr, M. Wagner, W. Ludwig, and K.-H. Schleifer. 1996. In situ visualization of high genetic diversity in a natural bacterial community. J. Bacteriol. 178:3496-3500.
2. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
3. 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.
4. 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.
5. Auling, G., F. Pilz, H.-J. Busse, S. Karrasch, M. Streichan, and G. Schön. 1991. Analysis of the polyphosphate-accumulating microflora in phosphorus-eliminating, anaerobic-aerobic activated sludge systems by using diaminopropane as a biomarker for rapid estimation of Acinetobacter spp. Appl. Environ. Microbiol. 57:3585-3592.
6. Barns, S. M., R. E. Fundyga, M. W. Jeffries, and N. R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91:1609-1613.
7. Benedict, R. G., and D. A. Carlson. 1971. Aerobic heterotrophic bacteria in activated sludge. Water Res. 5:1023-1030.
8. Bond, P. L., P. Hugenholtz, J. Keller, and L. L. Blackall. 1995. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl. Environ. Microbiol. 61:1910-1916.
9. Brigmon, R. L., G. Bitton, S. G. Zam, and B. O'Brien. 1995. Development and application of a monoclonal antibody against Thiothrix spp. Appl. Environ. Microbiol. 61:13-20.
10. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
11. Cariello, N. F., W. G. Thilly, J. A. Swenberg, and T. R. Skopek. 1991. Deletion mutagenesis during polymerase chain reaction: dependence on DNA polymerase. Gene 99:105-108.
12. Chen, E. Y., and P. H. Seeburg. 1985. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA 4:165-170.
13. Cloete, T. E., and P. L. Steyn. 1988. A combined membrane filter-immunofluorescent technique for the in situ identification and enumeration of Acinetobacter in activated sludge. Water Res. 22:961-969.
14. Cole, S. T., and I. S. Girons. 1994. Bacterial genomics. FEMS Microbiol. Rev. 14:139-160.
15. Collins, C. I., I. V. Wesley, and E. A. Murano. 1996. Detection of Arcobacter spp. in ground pork by modified plating methods. J. Food Prot. 59:448-452.
16. Collins, M. D., P. A. Lawson, A. Willems, J. J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow. 1994. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44:812-826.
17. Dias, F. F., and J. V. Bhat. 1964. Microbial ecology of activated sludge. Appl. Environ. Microbiol. 12:412-417.
18. Dutton, C. M., C. Paynton, and S. Sommer. 1993. General method for amplifying regions of very high G+C content. Nucleic Acids Res. 21:2953-2954.
19. Farrely, V., F. A. Rainey, and E. Stackebrandt. 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.
20. Fredrickson, J. K., D. L. Balkwill, G. R. Drake, M. F. Romine, D. B. Ringelberg, and D. C. White. 1995. Aromatic-degrading Sphingomonas isolates from the deep subsurface. Appl. Environ. Microbiol. 61:1917-1922.
21. Hernandez, M., D. Jenkins, and B. L. Beaman. 1994. Mass and viability estimations of Nocardia in activated sludge and anaerobic digesters using conventional stains and immunofluorescent methods. Water Sci. Technol. 29:249-259.
22. Hiraishi, A. 1988. Respiratory quinone profiles as tools for identifying different bacterial populations in activated sludge. J. Gen. Appl. Microbiol. 34:39-56.
23. Howgrave-Graham, A. R., and P. L. Steyn. 1988. Application of the fluorescent-antibody technique for the detection of Sphaerotilus natans in activated sludge. Appl. Environ. Microbiol. 54:799-802.
24. Kämpfer, P., R. Erhart, C. Beimfohr, J. Böhringer, M. Wagner, and R. Amann. 1996. Characterization of bacterial communities from activated sludge plant: culture-dependent numerical identification versus in situ identification using group- and genus-specific rRNA-targeted oligonucleotide probes. Microb. Ecol. 32:101-121.
25. Kopczinsky, E. D., M. M. Bateson, and D. M. Ward. 1994. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl. Environ. Microbiol. 60:746-748.
26. Kuhm, A. E., A. Stolz, K.-L. Ngai, and H.-J. Knackmuss. 1991. Purification and characterization of a 1,2-dihydroxynaphthalene dioxygenase from a bacterium that degrades naphthalenesulfonic acids. J. Bacteriol. 173:3795-3802.
27. Liesack, W., H. Weyland, and E. Stackebrandt. 1991. Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol. 21:191-198.
28. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1996. The ribosomal database project. Nucleic Acids Res. 24:82-85.
29. Manz, W., R. Amann, W. Ludwig, M. Vancanneyt, and K.-H. Schleifer. 1996. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 142:1097-1106.
30. Manz, W., R. 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.
31. Manz, W., M. Wagner, R. Amann, and K.-H. Schleifer. 1994. In situ characterization of the microbial consortia active in two wastewater treatment plants. Water Res. 28:1715-1723.
32. Meyerhans, A., J. Vartanian, and S. Wain-Hobson. 1990. DNA recombination during PCR. Nucleic Acids Res. 18:1687.
33. Mueller, J. G., P. J. Chapman, B. O. Blattman, and P. H. Pritchard. 1990. Isolation of a fluoranthene-utilizing strain of Pseudomonas paucimobilis. Appl. Environ. Microbiol. 56:1079-1086.
34. Ogram, A. V., G. S. Sayler, and T. T. Barkay. 1988. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7:57-66.
35. Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal rRNA approach. Annu. Rev. Microbiol. 40:337-365.
36. Palmer, C. J., Y.-L. Tsai, C. Paszko-Kolva, C. Mayer, and L. R. Sangermano. 1993. Detection of Legionella species in sewage and ocean water by polymerase chain reaction, direct fluorescent-antibody, and plate culture methods. Appl. Environ. Microbiol. 59:3618-3624.
37. 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.
38. Porter, K. G., and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25:943-948.
39. Prakasam, T. B. S., and N. C. Dondero. 1967. Aerobic heterotrophic populations of sewage and activated sludge. I. Enumeration. Appl. Microbiol. 15:461-467.
40. Pugina, P., G. Benzi, S. Lauwers, R. Van Etterijck, J. P. Butzler, L. Vlaes, and P. Vandamme. 1991. An outbreak of Arcobacter (Campylobacter) butzleri in Italy. Microb. Ecol. Health Dis. Suppl. 4:S94.
41. 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.
42. 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.
43. Riley, M., and S. Krawiec. 1987. Genome organization, p. 967-981. In F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
44. Roller, C., M. Wagner, R. Amann, W. Ludwig, and K.-H. Schleifer. 1994. In situ probing of gram-positive bacteria with high DNA G+C content using 23S rRNA-targeted oligonucleotides. Microbiology 140:2849-2858.
45. Schleifer, K.-H., R. Amann, W. Ludwig, C. Rothemund, N. Springer, and S. Dorn. 1992. Nucleic acid probes for the identification and in situ detection of pseudomonads, p. 127-134. In E. Galli, S. Dilver, and B. Witholt (ed.), Pseudomonas: molecular biology and biotechnology. American Society for Microbiology, Washington, D.C.
46. 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.
47. Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes in bacterial systematics, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons Ltd., Chichester, England.
48. Strunk, O., O. Gross, B. Reichel, M. May, S. Hermann, N. Stuckman, B. Nonhoff, M. Lenke, A. Ginhart, A. Vilbig, T. Ludwig, A. Bode, K.-H. Schleifer, and W. Ludwig. ARB: a software environment for sequence data. Submitted for publication.
49. 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.
50. Taira, K., N. Hayase, N. Arimura, S. Yamashita, T. Miyazaki, and K. Furukawa. 1988. Cloning and nucleotide sequence of the 2,3-dihydroxybiphenyl dioxygenase gene from the PCB-degrading strain of Pseudomonas paucimobilis Q1. Biochemistry 27:3990-3996.
51. Taylor, D. N., J. A. Kiehlbauch, W. Tee, C. Pitarangsi, and P. Echeverria. 1991. Isolation of group 2 aerotolerant Campylobacter species from Thai children with diarrhea. J. Infect. Dis. 163:1062-1067.
52. 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.
53. Teske, A., P. Sigalevich, Y. Cohen, and G. Muyzer. 1996. Molecular identification of bacteria from a coculture by denaturing gradient gel electrophoresis of 16S ribosomal DNA fragments as a tool for isolation in pure cultures. Appl. Environ. Microbiol. 62:4210-4215.
54. Vandamme, P., E. Falsen, R. Rossau, B. Hoste, P. Segers, R. Tytgat, and J. De Ley. 1991. Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov. Int. J. Syst. Bacteriol. 41:88-103.
55. Vandamme, P., M. Vancanneyt, B. Pot, L. Mels, B. Hoste, D. Dewettinck, L. Vlaes, C. Van den Borre, R. Higgins, J. Hommez, K. Kersters, J.-P. Butzler, and H. Goossens. 1992. Polyphasic taxonomic studies of the emended genus Arcobacter with Arcobacter butzleri comb. nov. and Arcobacter skirrowii sp. nov., an aerotolerant bacterium isolated from veterinary specimens. Int. J. Syst. Bacteriol. 42:344-356.
56. Van de Peer, Y., S. Nicolai, P. De Rijk, and R. De Wachter. 1996. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 24: 86-91.
57. Völsch, A., W. F. Nader, H. K. Geiss, G. Nebe, and C. Birr. 1990. Detection and analysis of two serotypes of ammonia-oxidizing bacteria in sewage plants by flow-cytometry. Appl. Environ. Microbiol. 56:2430-2435.
58. Wagner, M., R. Amann, P. Kämpfer, B. Assmus, A. Hartmann, P. Hutzler, N. Springer, and K.-H. Schleifer. 1994. Identification and in situ detection of gram-negative filamentous bacteria in activated sludge. Syst. Appl. Microbiol. 17:405-417.
59. Wagner, M., R. Amann, H. Lemmer, and K. H. Schleifer. 1993. Probing activated sludge with proteobacteria-specific oligonucleotides: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59:1520-1525.
60. Wagner, M., R. Erhart, W. Manz, R. 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.
61. Wallner, G., R. Erhart, and R. Amann. 1995. Flow cytometric analysis of activated sludge with rRNA-targeted probes. Appl. Environ. Microbiol. 61: 1859-1866.
62. Weller, R., J. Walsh Weller, and D. M. Ward. 1991. 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA. Appl. Environ. Microbiol. 57:1146-1151.
63. Wesley, I. V., L. Schroeder-Tucker, A. L. Baetz, F. E. Dewhirst, and B. J. Paster. 1995. Arcobacter-specific and Arcobacter butzleri-specific 16S rRNA-based DNA probes. J. Clin. Microbiol. 33:1691-1698.
64. Wittich, R.-M., H. Wilkes, V. Sinnwell, W. Francke, and P. Fortnagel. 1992. Metabolism of dibenzo-p-dioxin by Sphingomonas sp. strain RW1. Appl. Environ. Microbiol. 58:1005-1010.
65. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
66. Young, M., and S. T. Cole. 1993. Clostridium, p. 35-52. In A. L. Sonenshein, J. A. Hoch, and R. Losick (ed.), Bacillus subtilis and other gram-positive organisms. American Society for Microbiology, Washington, D.C.
67. Zarda, B., R. Amann, G. Wallner, and K.-H. Schleifer. 1991. Identification of single bacterial cells using digoxigenin-labelled, rRNA-targeted oligonucleotides. J. Gen. Microbiol. 137:2823-2830.