Distribution of bacterioplankton in meromictic lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA

Applied and Environmental Microbiology

Volumn 63, Issue 9, 1997, Pages 3367-3373

  Øvreås, Lise ^a   Forney, Larry ^b   Daae, Frida Lise ^a   Torsvik, Vigdis ^a  

^a UNIVERSITY OF BERGEN   (Norway)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARCHAEA; BACTERIOPLANKTON; METHANOGENIC BACTERIA; MICROBIAL COMMUNITY; SULPHATE-REDUCING BACTERIA;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BACTERIUM IDENTIFICATION; CHLOROBIUM; GEL ELECTROPHORESIS; GENE AMPLIFICATION; LAKE; NONHUMAN; PLANKTON; POLYMERASE CHAIN REACTION;

LAKE SAELENVANNET; NORWAY;

ALGAE; ARCHAEA; BACTERIA (MICROORGANISMS); CHLOROBIUM; CHLOROBIUM PHAEOVIBRIODES; CHLOROBIUM PHAEOVIBRIOIDES; EUKARYOTA; UNIDENTIFIED ARCHAEON;

EID: 0030805150     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.9.3367-3373.1997     Document Type: Article

References (40)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
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., J. Stromley, R. Devereux, R. Key, and D. A. Stahl. 1992. Molecular and microscopic identification of sulfate-reducing bacteria on multispecies biofilms. Appl. Environ. Microbiol. 58:614-623.
4. Brock, T. D., and M. T. Madigan. 1988. Biology of microorganisms, 5th ed. Prentice Hall International Inc., London, United Kingdom.
5. DeLong, E. F. 1992. Archaea in costal marine environments. Proc. Natl. Acad. Sci. 89:5685-5689.
6. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1362.
7. DeLong, E. F., K. Y. Wu, B. B. Prezelin, and R. V. M. Jovine. 1994. High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-697.
8. Ferris, M., G. Muyzer, and D. 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.
9. Fuhrman, J. A., K. McCallum, and A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59:1294-1302.
10. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1992. Novel major archaebacterial group from marine plankton. Nature 345:60-63.
11. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-62.
12. Grasshoff, K., M. Ehrhardt, and K. Kremling. 1983. Methods of seawater analysis, 2nd ed. Verlag Chemie, Weinheim, Germany.
13. Höfle, M. G., and I. Brettar. 1995. Taxonomic diversity and the metabolic activity of microbial communities in the watercolumn. Limnol. Oceanogr. 40:868-874.
14. Indrebø, G., B. Pengerud, and I. Dundas. 1979. Microbial activities in a permanently stratified estuary. I. Primary production and sulphate reduction. Mar. Biol. 51:295-304.
15. Indrebø, G., B. Pengerud, and I. Dundas. 1979. Microbial activities in a permanently stratified estuary. II. Microbial activities at the oxic-anoxic interface. Mar. Biol. 51:305-309.
16. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons Ltd., West Sussex, United Kingdom.
17. Liesack,W., H. Weyland, and E. Stackebrandt. 1991. Potential risks of gene amplification by PCR as determined by 16S rRNA analysis of a mixed culture of strict barophilic bacteria. Microb. Ecol. 21:191-198.
18. Ludwig, W., S. Dorin, N. Springer, G. Kirchhof, and K.-H. Schleifer. 1994. PCR-based preparation of 23S rRNA-targeted group-specific polynucleotide probes. Appl. Environ. Microbiol. 60:3236-3244.
19. Murray, A. E., J. T. Hollibaugh, and C. Orrego. 1996. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 62:2676-2680.
20. Muyzer, G., E. C. Dewaal, 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.
21. Muyzer, G., and N. B. Ramsing. 1995. Molecular methods to study the organization of microbial communities. Water Sci. Technol. 32:1-9.
22. Myers, R. M., T. Maniatis, and L. S. Lerman. 1987. Detection and localization of single base changes by denaturant gradient gel electrophoresis. Methods Enzymol. 155:501-527.
23. Porter, K. C., and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25:943-948.
24. Ramsing, N. B., H. Fossing, T. G. Ferdelmann, F. Andersen, and B. Thamdrup. 1996. Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Appl. Environ. Microbiol. 62:1391-1404.
25. Raskin, L., R. I. Amann, L. K. Poulsen, B. E. Rittmann, and D. A. Stahl. 1995. Use of ribosomal RNA based molecular probes for characterization of complex microbial communities in anaerobic biofilms. Water Sci. Technol. 31:261-272.
26. Rehnstam, A.-S., S. Backman, D. C. Smith, F. Azam, and Å. Hagstrom. 1993. Blooms of sequence specific culturable bacteria in the sea. FEMS Microbiol. Ecol. 102:161-166.
27. Reysenbach, A.-L., 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.
28. 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.
29. Schlegel, H. G. 1986. General microbiology. Cambridge University Press, Cambridge, United Kingdom.
30. Stahl, D. A., and R. 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 Ltd., West Sussex, United Kingdom.
31. Suzuki, T. M., 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.
32. 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-numher counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62:1405-1415.
33. Torsvik, T., V. Torsvik, J. Keswani, and W. B. Whitman. 1993. Oligonucleotide probes to 16S rRNA of methanogenic bacteria, abstr. N-19, p. 300. In Abstracts of the 93rd General Meeting of the American Society for Microbiology 1993. American Society for Microbiology, Washington, D.C.
34. Torsvik, T., V. Torsvik, J. Keswani, and W. B. Whitman. Unpublished results.
35. Tuomi, P., T. Torsvik, M. Heldal, and G. Bratbak. 1997. Bacterial population dynamics in a meromictic lake. Appl. Environ. Microbiol. 63:2181-2188.
36. 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.
37. Wawer, C., H. Ruggeberg, G. Meyer, and G. Muyzer. 1995. A simple and rapid electrophoresis method to detect sequence variation in PCR-amplified DNA fragments. Nucleic Acids Res. 23:4928-4929.
38. Weidner, S., W. Arnold, and A. Puhler. 1996. Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbiol. 62:766-771.
39. Wetzel, R. G. 1983. Limnology. Saunders College Publishing, Philadelphia, Pa.
40. Whitman, W. B., T. L. Bowen, and D. R. Boone. 1992. The methanogenic bacteria, p. 719-767. In A. Balows, H. G. Truper, M. Dworkin, W. Harder, and K. H. Schleifer (ed.), The procaryotes. Springer-Verlag, Berlin, Germany.