RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: A phylogenetic approach

International Journal of Systematic Bacteriology

Volumn 49, Issue 1, 1999, Pages 123-130

  Aakra, Ågot ^a   Utåker, Janne B ^a   Nes, Ingolf F ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

Author keywords

16S 23S rDNA intergenic spacer region; 16S and 23S rDNA ribotyping; Chemoautotrophic ammonia oxidizing bacteria; Copy number of rRNA genes

Indexed keywords

BACTERIAL RNA; RIBOSOME DNA; RNA 16S;

ARTICLE; BACTERIOLOGY; BACTERIUM IDENTIFICATION; GENE SEQUENCE; INTERMETHOD COMPARISON; NITROSOMONAS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; PRIORITY JOURNAL; RIBOTYPING; RNA ANALYSIS; RNA SEQUENCE;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; NITROSOMONADALES; NITROSOMONAS; NITROSOSPIRA; PROTEOBACTERIA;

EID: 0345004957     PISSN: 00207713     EISSN: None     Source Type: Journal    
DOI: 10.1099/00207713-49-1-123     Document Type: Article

References (49)

1. Bairoch, A. (1993). PC/GENE program package, release 6.80. Department of Medical Biochemistry, University of Geneva, Switzerland.
2. Barry, T., Colleran, G., Glennon, M., Dunican, L. K. & Gannon, F. (1991). The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Appl 1, 51-56.
3. Belser, L. W. (1979). Population ecology of nitrifying bacteria. Annu Rev Microbiol 33, 309-333.
4. Bercovier, H., Kafri, O. & Sela, S. (1986). Mycobacteria possess a surprisingly small number of ribosomal RNA genes in relation to the size of their genome. Biochem Biophys Res Commun 136, 1136-1141.
5. Brosch, R., Lefèvre, M., Grimont, F. & Grimont, P. A. D. (1996). Taxonomic diversity of pseudomonads revealed by computer interpretation of ribotyping data. Syst Appl Microbiol 19, 541-555.
6. Brosius, J., Palmer, M. L., Kennedy, P. J. & Noller, H. F. (1978). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75, 4801-4805.
7. Church, G. M. & Gilbert, W. (1984). Genomic sequencing. Proc Nail Acad Sci USA 81, 1991-1995.
8. Donaldson, J. M. & Henderson, G. S. (1989). A dilute medium to determine population size of ammonium oxidizers in soil. Soil Sci Soc Am 53, 1608-1611.
9. Dorsch, M. & Stackebrandt, E. (1992). Some modifications in the procedure of direct sequencing of PCR amplified 16S rDNA. J Microbiol Methods 16, 271-279.
10. Edwards, U., Rogall, T., Blocker, H., Emde, M. & Bottger, E. C. (1989). Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17, 7843-7853.
11. EGCG (1996). Program Manual for the EGCG Package, version 8.1.0, March 1996. Peter Rice, The Sanger Centre, Hinxton Hall, Cambridge CB10 1RQ, UK.
12. Felsenstein, J. (1993). PHYLIP (Phylogeny Inference Package) 3.572c. Department of Genetics, University of Washington, Seattle, USA.
13. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
14. Fox, G. E., Wisotzkey, J. D. & Jurtshuk, P., Jr (1992). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42, 166-170.
15. GCG (1994). Program Manual for the Wisconsin Package, Genetics Computer Group, version 8.1, August 1995. 575 Science Drive, Madison, WI 53711, USA.
16. Graham, T., Golsteyn-Thomas, E. J., Gannon, V. P. J. & Thomas, J. E. (1996). Genus-and species specific detection of Listeria monocytogenes using polymerase chain reaction assays targeting the 16S/23S intergenic spacer region of the rRNA operon. Can J Microbiol 42, 1155-1162.
17. Gürtler, V. & Stanisich, V. A. (1996). New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3-16.
18. Head, I. M., Hiorns, W. D., Embley, T. M., McCarthy, A. J. & Saunders, J. R. (1993). The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences. J Gen Microbiol 139, 1147-1153.
19. Head, I. M., Hiorns, W. D., Embley, T. M., McCarthy, A. J. & Saunders, J. R. (1995). In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 54. Int J Syst Bacteriol 45, 619-620.
20. Jiang, Q. Q. (1996). Nitrosospira from terrestrial environments, its urease activity and nitrous oxide production. Doctor Scientarium thesis 1996:21, Agricultural University of Norway.
21. Koops, H.-P. & Harms, H. (1985). Deoxyribonucleic acid homologies among 96 strains of ammonia oxidizing bacteria. Arch Microbiol 141, 214-218.
22. Koops, H.-P. & Möller, U. C. (1992). The lithotrophic ammonia-oxidizing bacteria. In The Prokaryotes, pp. 2625-2637. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York : Fischer-Verlag.
23. Lane, D. J., Pace, B., Olsen, G. J., Stahl, D. A., Sogin, M. L. & Pace, N. R. (1985). Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82, 6955-6959.
24. Leblond-Bourget, N., Philippe, H., Mangin, I. & Decaris, B. (1996). 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter-and intraspecific Bifidobacterium phylogeny. Int J Syst Bacteriol 46, 102-111.
25. Li, X. & De Boer, S. H. (1995). Selection of polymerase chain reaction chain reaction primers from an RNA intergenic spacer region for specific detection of Clavibacter michiganensis subsp. sepedonicus. Phytopathology 85, 837-842.
26. Lillehaug, D., Nes, I. F. & Birkeland, N. K. (1997). A highly efficient and stable system for site-specific integration of genes and plasmids into the phage phiLC3 attachment site (attB) of the Lactococcus lactis chromosome. Gene 188, 129-36.
27. McCaig, A. E., Embley, T. M. & Prosser, J. I. (1994). Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiol Lett 120, 363-368.
28. MacDonald, R. M. & Spokes, J. R. (1980). A selective and diagnostic medium for ammonia oxidising bacteria. FEMS Microbiol Lett 8, 143-145.
29. Mobarry, B. K., Wagner, M., Urbain, V., Rittmann, B. E. & Stahl, D. A. (1996). Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl Environ Microbiol 62, 2156-2162.
30. Moreira, D. & Amils, R. (1996). PCR-mediated detection of the chemolithotrophic bacterium Thiobacillus cuprinus using 23S rDNA and 16S/23S rDNA intergenic spacer region-targeted oligonucleotide primers. FEMS Microbiol Lett 142, 289-293.
31. Navarro, E., Fernandez, M. P., Grimont, F., Claysjosserand, A. & Bardin, R. (1992a). Genomic heterogeneity of the genus Nitrobacter. Int J Syst Bacteriol 42, 554-560.
32. Navarro, E., Simonet, P., Normand, P. & Bardin, R. (1992b). Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch Microbiol 157, 107-115.
33. Page, R. D. M. (1996). Tree View: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357-358.
34. Pang, H. & Winkler, H. H. (1993). Copy number of the 16S rRNA gene in Rickettsia prowazekii. J Bacteriol 175, 3893-3896.
35. Pearson, W. R. (1990). Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183, 63-98.
36. Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85, 2444-2448.
37. Pommerening-Röser, A., Rath, G. & Koops, H.-P. (1996). Phylogenetic diversity within the genus Nitrosomonas. Syst Appl Microbiol 19, 344-351.
38. Riedl, K.-H. J. & Britz, T. J. (1996). Justification of the 'classical' Propionibacterium species concept by ribotyping. Syst Appl Microbiol 19, 370-380.
39. Rijpens, N. P., Jannes, G., Van Asbroeck, M., Rossau, R. & Herman, L. M. F. (1996). Direct detection of Brucella spp. in raw milk by PCR and reverse hybridization with 16S-23S rRNA spacer probes. Appl Environ Microbiol 62, 1683-1688.
40. Rudner, R., Studamire, B. & Jarvis, E. D. (1994). Determination of restriction fragment length polymorphism in bacteria using ribosomal RNA genes. Methods Enzymol 235, 184-196.
41. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
42. Schwartz, J. J., Gazumyan, A. & Schwartz, I. (1992). rRNA gene organization in the Lyme disease spirochete, Borrelia burgdorferi. J Bacteriol 174, 3757-3765.
43. Smart, C. D., Schneider, B., Blomquist, C. L, Guerra, L J., Harrison, N. A., Ahrens, U., Lorenz, K. H., Seemuller, E. & Kirkpatrick, B. C. (1996). Phytoplasma-specific PCR primers based on sequences of the 16S-23S rRNA spacer region. Appl Environ Microbiol 62, 2988-2993.
44. Teske, A., Alm, E., Regan, J. M., Toze, S., Rittmann, B. E. & Stahl, D. A. (1994). Evolutionary relationships among ammonia-and nitrite-oxidizing bacteria. J Bacteriol 176, 6623-6630.
45. Utåker, J. B. & Nes, I. F. (1998). A qualitative evaluation of the published oligonucleotides specific for the 16S rDNA gene sequences of the ammonia-oxidizing bacteria. Syst Appl Microbiol 21, 72-88.
46. Utåker, J. B., Bakken, L, Jiang, Q. Q. & Nes, I. F. (1995). Phylogenetic analysis of seven new isolates of ammonia-oxidizing bacteria based on 16S rRNA gene sequences. Syst Appl Microbiol 18, 549-559.
47. Wagner, M., Rath, G., Amann, R., Koops, H.-P. & Schleifer, K. H. (1995). In-situ identification of ammonia-oxidizing bacteria. Syst Appl Microbiol 18, 251-264.
48. Watson, S. W., Bock, E., Harms, H., Koops, H.-P. & Hooper, A. B. (1989). Nitrifying bacteria. In Bergey's Manual of Systematic Bacteriology, pp. 1808-1834. Edited by J. T. Staley, M. P. Bryant, N. Pfenning & J. G. Holt. Baltimore: Williams & Wilkins.
49. Yoon, J.-H., Lee, S. T., Kim, S.-B., Goodfellow, M. & Park, Y.-H. (1997). Inter-and intraspecific genetic analysis of the genus Saccharomonospora with 16S to 23S ribosomal DNA (rDNA) and 23S to 5S rDNA internally transcribed spacer sequences. Int J Syst Bacteriol 47, 661-669.