Revealing genetic diversity of eukaryotic microorganisms in aquatic environments by denaturing gradient gel electrophoresis

Journal of Phycology

Volumn 34, Issue 2, 1998, Pages 206-213

  Van Hannen, Erik J ^a   Van Agterveld, Miranda P ^a   Gons, Herman J ^a   Laanbroek, Hendrikus J ^a  

^a NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

Author keywords

18S rRNA; Aquatic environments; Community structure; DGGE; Eucarya; Genetic diversity; Nucleotide mismatches; Southern blot hybridization

Indexed keywords

AQUATIC ENVIRONMENT; CLUSTER ANALYSIS; EUKARYOTE; EUKARYOTIC MICROORGANISM; GEL ELECTROPHORESIS; GENETIC DIVERSITY; GENOMIC DNA; MICROORGANISM; MICROORGANISM DETECTION; MICROSPORA; NUCLEOTIDE MISMATCH; POLYMERASE CHAIN REACTION; POPULATION STRUCTURE; SPECIFICITY;

EID: 0031960173     PISSN: 00223646     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1529-8817.1998.340206.x     Document Type: Article

References (41)

1. Amann, R. I., Ludwig, W. & Schleifer, K-H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-69.
2. Appels, R., Gerlach, W. L., Dennis, E. S., Swift, H. & Peacock, W. J. 1980. Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals. Chromosoma 78:293-311.
3. Backeljau, T., Debruyn, L., Dewolf, H., Jordaens, K., Vandongen, S. & Winnepenninckx, B. 1996. Multiple UPGMA and neighbor-joining trees and the performance of some computer packages. Mol. Biol. Evol. 13:309-13.
4. Berger, C. 1987. Habitat en ecologie van Oscillatoria agardhii Gomont. Een limnologische studie van ondiepe hypertrofe meren (Drontermeer, Veluwemeer, Wolderwijd en Eemmeer; IJsselmeer; Lauwersmeer) van 1971-1981. Ph.D. thesis, University of Groningen, The Netherlands, 233 pp.
5. Berger, C. & Sweers, H. E. 1988. The IJsselmeer and its phytoplankton - with special attention to the suitability of the lake as a habitat for Oscillatoria agardhii Gom. J. Plankton Res. 10: 579-99.
6. Demeke, T. & Adams, R. P. 1992. The effects of plant polysaccharides and buffer additives on PCR. BioTechniques 12:332-34.
7. De Rijk, P. & De Wachter, R. 1993. DCSE, an interactive tool for sequence alignment and secondary structure research. Comput. Appl. Biosci. 9:735-40.
8. Farrelly, V., Rainey, F. A. & Stackebrandt, E. 1992. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:2798-801.
9. Felsenstein, J. 1989. PHYLIP - phylogeny inference package. Cladistics 5:164-6.
10. Ferris, M. J., Muyzer, G. & Ward, D. M. 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62:340-6.
11. Ferris, M. J., Nold, S. C., Revsbech, N. P. & Ward, D. M. 1997. Population structure and physiological changes within a hot spring microbial community following disturbance. Appl. Environ. Microbiol. 63:1367-74.
12. Ferris, M. J. & Ward, D. M. 1997. Seasonal distribution of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63:1375-81.
13. Fisher, S. G. & Lerman, L. S. 1979. Length-independent separation of DNA restriction fragments in two dimensional gel electrophoresis. Cell 16:191-200.
14. Giovannoni, S. J., DeLong, E. F., Schmidt, T. M. & Pace, N. R. 1990. Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl. Environ. Microbiol. 56: 2572-5.
15. Hillis, D. M. & Dixon, M. T. 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol. 66:411-53.
16. Johnson, J. L. 1991. Isolation and purification of nucleic acids. In Stackebrandt, E. & Goodfellow, M. [Eds.] Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons Ltd., West-Sussex, United Kingdom, pp. 1-19.
17. Kowalchuk, G .A., Gerards, S. & Woldendorp, J. W. 1997a. Detection and characterisation of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA. Appl. Environ. Microbiol. 63:3858-65.
18. Kowalchuk, G. A., Stephen, J. R., de Boer, W., Prosser, J. I., Embley, T. M. & Woldendorp, J. W. 1997b. Analysis of ammonia-oxidising bacteria of the β subdivision of the class Proteobacteria in sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63:1489-97.
19. Lange, M., Guillou, L., Vaulot, D., Simon, N., Amann, R. I., Ludwig, W. & Medlin, L. K. 1996. Identification of the class Prymnesiophyceae and the genus Phaeocystis with ribosomal RNA-targeted nucleic acid probes detected by flow cytometry. J. Phycol. 32:858-68.
20. Lim, E. L., Amaral, L. A., Caron, D. A. & DeLong, E. F. 1993. Application of rRNA-based probes for observing marine nanoplanktonic protists. Appl. Environ. Microbiol. 59:1647-55.
21. Long, E. O. & Dawid, I. B. 1980. Repeated genes in Eukaryotes. Annu. Rev. Biochem. 49:727-64.
22. Maidak, B. L., Olsen, G. J., Larsen, N., Overbeek, R., McCaughey, M. J. & Woese, C. R. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-11.
23. Manly, B. F. J. 1994. Multivariate Statistical Methods. A Primer, 2nd ed. Chapman & Hall, London, 215 pp.
24. Moed, J. R. & Hallegraeff, G. M. 1978. Some problems in the estimation of chlorophyll-a and phaeopigments from pre-and post-acidification spectrophotometric measurements. Int. Rev. Ges. Hydrobiol. 63:787-800.
25. Muyzer, G. & de Waal, E. C. 1994. Determination of the genetic diversity of microbial communities using DGGE analysis of PCR-amplified 16S rDNA. In Stal, L. J. & Caumette, P. [Eds.] Microbial Mats: Structure, Development and Environmental Significance. Springer-Verlag, Heidelberg, Germany, pp. 207-14.
26. Muyzer, G., de Waal, E. C. & Uitterlinden, A. G. 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.
27. Muyzer, G., Teske, A., Wirsen, C. O. & Jannasch, H. W. 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. 164:165-72.
28. Nei, M. & Li, W. H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76:5269-73.
29. Ogram, A. V., Sayler, G. S. & Barkay, T. T. 1988. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7:57-66.
30. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-40.
31. Page, R. D. M. 1994. Parallel phylogenies: reconstructing the history of host-parasite assemblages. Cladistics. 10:155-73.
32. Reysenbach, A., Giver, L. J., Wickham, G. S. & Pace, N. R. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58:3417-18.
33. Santegoeds, C. M., Nold, S. C. & Ward, D. M. 1996. Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 62:3922-28.
34. Schmidt, T. M., Delong, E. F. & Pace, N. R. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-78.
35. Simon, N., Lebot, N., Marie, D., Partensky, F. & Vaulot, D. 1995. Fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes to identify small phytoplankton by flow cytometry. Appl. Environ. Microbiol. 61:2506-13.
36. Teske, A., Wawer, C., Muyzer, G. & Ramsing, N. B. 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. 62:1405-15.
37. Van de Peer, Y., Jansen, J., De Rijk, P. & De Wachter, R. 1997. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 24:111-16.
38. Van Hannen, E. J. & Gons, H. J. 1997. UV-C induced lysis and detritus production of Oscillatoria limnetica in a two stage continuous flow system. J. Plankton Res. 19:723-33.
39. Wawer, C. & Muyzer, G. 1995. Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel electrophoresis of [nife] hydrogenase gene fragments. Appl. Environ. Microbiol. 61:2203-10.
40. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 15:221-71.
41. Woese, C. R., Kandler, O. & Wheelis, M. L. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-79.