Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton

Environmental Microbiology

Volumn 6, Issue 6, 2004, Pages 638-645

  Replies, Jörg ^a   Lau, Stanley Chun Kwan ^b   Pernthaler, Jakob ^a   Amann, Rudolf ^a   Glöckner, Frank Oliver ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER DNA; RNA 16S; SEA WATER;

ARTICLE; BACTERIUM; COMPARATIVE STUDY; DNA BASE COMPOSITION; DNA MICROARRAY; ELECTROPHORESIS; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GERMANY; METHODOLOGY; PLANKTON; REPRODUCIBILITY;

BACTERIA; BASE COMPOSITION; DNA PRIMERS; ELECTROPHORESIS; GERMANY; IN SITU HYBRIDIZATION, FLUORESCENCE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANKTON; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 16S; SEAWATER;

BACTERIA (MICROORGANISMS);

EID: 2642525491     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2004.00588.x     Document Type: Article

References (29)

1. Amann, R. (1995) Fluorescently labelled, rRNA-targeted oligonucleotide probes in the study of microbial ecology. Mol Ecol 4: 543-554.
2. Amann, R., Ludwig, W., and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169.
3. Benters, R., Niemeyer, C.M., Drutschmann, D., Blohm, D., and Wöhrle, D. (2002) DNA microarrays with PAMAM dendritic linker systems. Nucleic Acids Res 30: e10.
4. 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. J Mol Biol 148: 107-127.
5. Eilers, H., Pernthaler, J., Glöckner, F.O., and Amann, R. (2000) Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 66: 3044-3051.
6. Eilers, H., Pernthaler, J., Peplies, J., Glöckner, F.O., Gerdts, G., and Amann, R. (2001) Isolation of novel pelagic bacteria from the German Bight and their seasonal contributions to surface picoplankton. Appl Environ Microbiol 67: 5134-5142.
7. El Fantroussi, S., Urakawa, H., Bernhard, A.E., Kelly, J.J., Noble, P.A., Smidt, H., et al. (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 69: 2377-2382.
8. Giuliano, L., De Domenico, M., De Domenico, E., Höfle, M.G., and Yakimov, M.M. (1999) Identification of culturable oligotrophic bacteria within naturally occurring bacterioplankton communities of the Ligurian Sea by 16S rRNA sequencing and probing. Microb Ecol 37: 77-85.
9. Gonzalez, J.M., Whitman, W.B., Hodson, R.E., and Moran, M.A. (1996) Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture. Appl Environ Microbiol 62: 4433-4440.
10. Guschin, D.Y., Mobarry, B.K., Proudnikov, D., Stahl, D.A., Rittmann, B.E., and Mirzabekov,. A.D. (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63: 2397-2402.
11. Koizumi, Y., Kelly, J.J., Nakagawa, T., Urakawa, H., El-Fantroussi, S., Al-Muzaini, S., et al. (2002) Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Appl Environ Microbiol 68: 3215-3225.
12. Lander, E.S. (1999) Array of hope. Nature Genet 21: 3-4.
13. Loy, A., Lehner, A., Lee, N., Adamczyk, J., Meier, H., Ernst, J., et al. (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68: 5064-5081.
14. Manz, W., Amann, R., Ludwig, W., Vancanneyt, M., and Schleifer, K.-H. (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.
15. Marchesi, J.R., Sato, T., Weightman, A.J., Martin, T.A., Fry, J.C., Hiom, S.J., and Wade,. W.G. (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 795-799.
16. Neef, A. (1997) Anwendung der in situ-Einzelzell-Identifizierung von Bakterien zur Populationsanalyse in komplexen mikrobiellen Biozönosen. PhD Thesis. Technical University, Munich, Germany.
17. Oelmüller, U., Krüger, N., Steinbüchel, A., and Cornelius, G. (1990) Isolation of prokaryotic RNA and detection of specific mRNA with biotinylated probes. J Microb Methods 11: 73-84.
18. Olsen, G.J., Lane, D.J., Giovannoni, S.J., Pace, N.R., and Stahl, D.A. (1986) Microbial ecology and evolution: a ribosomal rRNA approach. Annu Rev Microbiol 40: 337-365.
19. Pace, N.R., Stahl, D.A., Lane, D.J., and Olsen, G.J. (1986) The use of rRNA sequences to characterize natural microbial populations. Adv Microb Ecol 9: 1-55.
20. Peplies, J., Glöckner, F.O., and Amann, R. (2003) Optimization strategies for the DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69: 1397-1407.
21. Pernthaler, J., Glöckner, F.O., Schönhuber, W., and Amann, R. (2001) Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Methods Microbiol 30: 207-226.
22. Rudi, K., Skulberg, O.M., Skulberg, R., and Jakobsen, K.S. (2000) Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization. Appl Environ Microbiol 66: 4004-4011.
23. Schmalenberger, A., Schwieger, F., and Tebbe, C.C. (2001) Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl Environ Microbiol 67: 3557-3563.
24. Skrypina, N.A., Timofeeva, A.V., Khaspekov, G.L., Savochkina, L.P., and Beabealashvilli, R.S. (2003) Total RNA suitable for molecular biology analysis. J BioTech 105: 1-9.
25. Small, J., Call, D.R., Brockman, F.J., Straub, T.M., and Chandler, D.P. (2001) Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 67: 4708-4716.
26. Suzuki, M.T., and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
27. Wilson, K.H., Wilson, W.J., Radosevich, J.L., DeSantis, T.Z., Viswanathan, V.S., Kuczmarski,. T.A., and Andersen, G.L. (2002) High-density microarray of small subunit ribosomal. DNA probes. Appl Environ Microbiol 68: 2535-2541.
28. Wintzingerode, F.V., Goebel, U.B., and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
29. Zubkov, M.V., Fuchs, B.M., Archer, S.D., Kiene, R.P., Amann, R., and Burkill, P.H. (2001) Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ Microbiol 3: 304-311.