Identification of waterborne bacteria by the analysis of 16S-23S rRNA intergenic spacer region

Journal of Applied Microbiology

Volumn 97, Issue 1, 2004, Pages 191-204

  Perez Luz S ^a   Adela Yanez M ^a   Catalan V ^a,b  

^a SA   (Spain)

^b Labaqua SA   (Spain)

Author keywords

16S 23S; Bacteria; Identification; ITS; rRNA; Waterborne

Indexed keywords

RNA;

ACRYLAMIDES; BISACRYLAMIDE; HIGH RESOLUTION; IDENTIFICATION; INTERGENIC REGIONS; INTERGENIC SPACER REGIONS; ITS; MICROBIOLOGICAL CONTROL; RRNA; WATERBORNE;

BACTERIA;

ACRYLAMIDE; DNA FRAGMENT; N,N' METHYLENEBISACRYLAMIDE; RNA 16S; SPACER DNA;

BACTERIUM; IDENTIFICATION METHOD; PATHOGEN;

ARTICLE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; DNA SEQUENCE; NONHUMAN;

BACTERIA (MICROORGANISMS);

EID: 3042704477     PISSN: 13645072     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2004.02288.x     Document Type: Article

References (36)

1. Acinas, S.G., Anton, J. and Rodriguez-Valera, F. (1999) Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Applied and Environmental Microbiology 65, 514-522.
2. Anton, A.I., Martínez-Murcia, AJ. and Rodriguez-Valera, F. (1998) Sequence diversity in the 16S-23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection. Journal of Molecular Evolution 47, 62-72.
3. Bej, A.K., Steffan, R.J., DiCesari, J., Haff, L. and Atlas, R.M. (1990) Detection of coliform bacteria in water by polymerase chain reaction and gene probes. Applied and Environmental Microbiology 56, 307-314.
4. Borneman, J. and Triplett, E. W. (1997) Molecular microbial diversity in soils from Eastern Amazonia: evidence for unusual microorganisms and population shifts associated with deforestation. Applied and Environmental Microbiology 63, 2647-2653.
5. Brosius, J., Dull, T.J., Sleeter, D.D. and Noller, H.F. (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. Journal of Molecular Biology 148, 107-127.
6. Chen, Y.C., Eisner, J.D., Kattar, M.M., Rassoulian-Barrett, S.L., Lafe, K., Yarfitz, S.L., Limaye, A.P. and Cookson, B.T. (2000) Identification of medically important yeasts using PCR-based detection of DNA sequence polymorphisms in the internal transcribed spacer 2 region of the rRNA genes. Journal of Clinical Microbiology 38, 2302-2310.
7. Dorigo, U., Berard, A. and Humbert, J.F. (2002) Comparison of eukariotic phytobentic community composition in a polluted river by partial 18S rRNA gene cloning and sequencing. Microbiological Ecology 44, 372-380.
8. Edelstein, P.H., Whittaker, R.E., Kreiling, R.L. and Howell, C.L. (1982) Efficacy of ozone in eradication of Legionella pneumophila for hospital plumbing fixtures. Applied and Environmental Microbiology 44, 1330-1333.
9. Fisher, M.M. and Triplett, E.W. (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Applied and Environmental Microbiology 65, 4630-4636.
10. García-Martínez, J., Bescós, I., Rodriguez-Sala, J.J. and Rodriguez-Valera, F. (2001) RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions. Nucleic Acids Research 29, 178-180.
11. Garcia-Martinez, J., Martinez-Murcia, AJ., Anton, A.L, Rodriguez-Valera, F. and Zorraquino, A. (1996) Molecular evidence supporting the existence of two major groups in uropathogenic Escherichia coli. FEMS Immunological and Medical Microbiology 14, 231-244.
12. Gurtler, V. (1999) The role of recombination and mutation in 16S-23S rDNA spacer rearrangements. Gene 238, 241-252.
13. Gurtler, V. and Barrie, H.D. (1995) Typing of Staphylococcus aureus strains by PCR-amplification of variable-length 16S-23S rDNA spacer regions: characterization of spacer sequences. Microbiology 141, 1255-1265.
14. Gurtler, V. and Mayall, B.C. (1999) rDNA spacer rearrangements and concerted evolution. Microbiology 145, 2-3.
15. Gurtler, V. and Stanisich, V.A. (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3-16.
16. Gurtler, V., YuJun, R., Pearson, S.R., Bates, S.M. and Mayall, B.C. (1999) DNA sequence heterogeneity in the three copies of the long 16S-23S rDNA spacer of Enterococcus faecalis isolates. Microbiology 145, 1785-1796.
17. Hall, L.M. (1994) Are point mutations or DNA rearrangements responsible for the restriction fragment length polymorphisms that are used to type bacteria? Microbiology: 140, 197-204.
18. Hussong, D., Colwell, R.R., O'Brien, M., Weiss, E., Pearson, A.D., Weiner, R.M. and Burge, W.D. (1987) Viable Legionella pneumophila not detected by culture on agar media. Biotechnology 5, 947-950.
19. Jensen, M.A., Webster, J.A. and Straus, N. (1993) Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Applied and Environmental Microbiology 59, 945-952.
20. Klappenbach, J.A., Saxman, P.R., Cole, J.R. and Schmidt, T.M. (2001) rrndb: The ribosomal RNA operon copy number database. Nucleic Acids Research 29, 181-184.
21. Kur, J., Burkiewicz, A., Zablocka, A. and Gospodarek, E. (1995) Identification of Pseudomonas aeruginosa on the bases of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Acta Microbiologica Polonica 44, 111-117.
22. Luz, S.P., Rodriguez-Valera, F., Lan, R. and Reeves, P.R. (1998) Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies. Journal of Bacteriology 180, 2144-2151.
23. Maniatis, T., Fritsch, E.F. and Sandbook, J. (1982). Molecular Cloning. A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
24. Martinez-Murcia, A.J., Anton, A.I. and Rodriguez-Valera, F. (1999) Patterns of sequence variation in two regions of the 16S rRNA multigene family of Escherichia coli. International Journal of Systematic Bacteriology 49, 601-610.
25. Mendoza, M., Meugnier, H., le Bes, M., Etienne, J. and Freney, J. (1998) Identification of Staphylococcus species by 16S-23S rDNA intergenic spacer PCR analysis. International Journal of Systematic Bacteriology 48, 1049-1055.
26. Min, J. and Baeumner, A.J. (2002) Highly sensitive and specific detection of viable Escherichia coli in drinking water. Analytical Biochemistry 303, 186-193.
27. Normand, P., Ponsonnet, C., Nesme, X., Neyra, M. and Simonet, P. (1996) ITS analysis of prokariotes. In Molecular Microbial Ecology Manual, Vol. 3.4.5. ed. Akkermans, D.L., van Elsas, J.D. and Bruijn, F.J. pp. 1-12. Dordrecht: Kluwer Academic Publishers.
28. Ochman, H. and Selander, R.K. (1984) Standard reference strains of Escherichia coli from natural populations. Journal of Bacteriology 157, 690-693.
29. Pérez-Luz, S., Fernandez, J., Rodriguez-Valera, F., Pascual, L., Moreno, C., Amo, A., Apraiz, D. and Catalan, V. (2002) Sequence diversity of the internal transcribed spacer (ITS) region of the rRNA operons among different serogroups of Legionella pneumophila isolates. Systematic and Applied Microbiology 25, 212-219.
30. Ranjard, L., Poly, F., Lata, J.-C., Mougel, C., Thioulouse, J. and Nazaret, S. (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Applied and Environmental Microbiology 67, 4479-4487.
31. Robleto, E.A., Borneman, J. and Triplett, E.W. (1998) Effects of bacterial antibiotic production of rhizosphere microbial communities from a culture-independent perspective. Applied and Environmental Microbiology 64, 5020-5022.
32. Rompre, A., Servais, P., Baudart, J., De-Roubin, M.R. and Laurent, P. (2002) Detection and enumeration of coliforms in drinking water: current methods and emerging approaches. Journal of Microbiology Methods 49, 31-54.
33. Sasaki, Y., Yamamoto, K., Kojima, A., Norimatsu, M. and Tamura, Y. (2000) Rapid identification and differentiation of pathogenic clostridia in gas gangrene by polymerase chain reaction based on the 16S-23S rDNA spacer region. Research in Veterinary Science 69, 289-294.
34. Shirai, H., Nishibuchi, M., Ramamurthy, T., Bhattacharya, S.K., Pal, S.C. and Takeda, Y. (1991) Polymerase chain reaction for detection of cholera enterotoxin operon of Vibrio cholerae. Journal of Clinical Microbiology 29, 2517-2521.
35. Turenne, C.Y., Sanche, S.E., Hoban, D.J., Karlowsky, J.A. and Kabani, A.M. (1999) Rapid identification of fungi by using ITS2 genetic region and automated fluorescent capillary electrophoresis system. Journal of Clinical Microbiology 37, 1846-1851.
36. Whiley, R.A., Duke, B., Hardie, J.M. and Hall, L.M. (1995) Heterogeneity among 16S-23S rRNA intergenic spacers of species within the 'Streptococcus milleri group'. Microbiology 141, 1461-1467.