Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis

Applied and Environmental Microbiology

Volumn 65, Issue 8, 1999, Pages 3518-3525

  Moeseneder, Markus M ^a   Arrieta, Jesús M ^a   Muyzer, Gerard ^a   Winter, Christian ^a   Herndl, Gerhard J ^a  

^a ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM IDENTIFICATION; DENATURING GRADIENT GEL ELECTROPHORESIS; DIAGNOSTIC ACCURACY; DNA FINGERPRINTING; INTERMETHOD COMPARISON; NONHUMAN; PHYTOPLANKTON; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; TAXONOMY;

EID: 0032812081     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.8.3518-3525.1999     Document Type: Article

References (26)

1. Acinas, S., F. Rodriguez-Valera, and C. Pedros-Alio. 1997. Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microbiol. Ecol. 24:27-40.
2. Avaniss-Aghajani, E., K. Jones, D. Chapman, and C. Brunk. 1994. A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. BioTechniques 17:144-146, 148-149.
3. Baba, Y., N. Ishimaru, K. Samata, and M. Tushako. 1993. High-resolution separation of DNA restriction fragments by capillary electrophoresis in cellulose derivate solutions. J. Chromatogr. A 653:329-335.
4. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363.
5. Glovannoni, S. 1991. The polymerase chain reaction, p. 177-204. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Inc., New York, N.Y.
6. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-176. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Inc., New York, N.Y.
7. Lee, S. H., and P. F. Kemp. 1994. Single-cell RNA content of natural marine planktonic bacteria measured by hybridization with multiple 16S rRNA-targeted fluorescent probes. Limnol. Oceanogr. 39:869-879.
8. 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.
9. Liu, W.-T., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA Appl. Environ. Microbiol. 63:4516-4522.
10. Marsh, T. L., W.-T. Liu, L. J. Forney, and H. Cheng. 1998. Beginning a molecular analysis of eukaryal community in activated sludge. Water Sci. Technol. 37:455-460.
11. Martinez, J., D. C. Smith, G. F. Steward, and F. Azam. 1996. Variability in ectohydrolytic enzyme activities of pelagic marine bacteria and its significance for substrate processing in the sea. Aquat. Microb. Ecol. 10:223-230.
12. Moyer, C. L., F. C. Dobbs, and D. M. Karl. 1994. Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 60:871-879.
13. Moyer, C. L., J. M. Tiedge, F. C. Dobbs, and D. M. Karl. 1996. A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl. Environ. Microbiol. 62:2501-2507.
14. Müller-Niklas, G., S. Schuster, E. Kaltenböck, and G. J. Herndl. 1994. Organic content and bacterial metabolism in amorphous aggregations of the northern Adriatic Sea. Limnol. Oceanogr. 39:53-68.
15. 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.
16. 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.
17. Muyzer, G., A. Teske, C. O. Wirsen, and H. W. Jannasch. 1995. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164:165-172.
18. Nei, M., and W.-H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 74:5269-5273.
19. Poulsen, L. K., G. Ballard, and D. A. Stahl. 1993. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol. 59:1354-1360.
20. Schmidt, T. M. 1997. Multiplicity of ribosomal RNA operons in prokaryotic genomes, p. 221-229. In F. J. De Bruijn, J. R. Lupski, and G. M. Weinstock (ed.), Bacterial genomes: physical structure and analysis. Chapman & Hall, New York, N.Y.
21. 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.
22. Teske, A., C. Wawer, G. Muyzer, and N. B. Ramsing. 1996. Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62:1405-1415.
23. van der Maarel, M. J. E. C., R. R. E. Artz, R. Haanstra, and L. J. Forney. 1998. Association of marine archaea with the digestive tracts of two marine fish species. Appl. Environ. Microbiol. 64:2894-2898.
24. Vaneechoutte, M., and R. Rossau. 1992. Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol. Lett. 93:227-234.
25. 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.
26. Zervakis, V., D. Georgopoulos, E. Papageorgiou, and V. Papadopoulos. Hydrological characteristics and circulation in the North Aegean throughout 1997-1998. Submitted for publication.