Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16s rRNA genes

Applied and Environmental Microbiology

Volumn 62, Issue 3, 1996, Pages 766-771

  Weidner, Stefan ^a   Arnold, Walter ^a   Pühler, Alfred ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; OLIGONUCLEOTIDE; RIBOSOME DNA; RIBOSOME RNA;

ARTICLE; BACTERIUM IDENTIFICATION; DNA SEQUENCE; GENE AMPLIFICATION; GRASS; MICROORGANISM; NONHUMAN; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

MICROORGANISM; MICROORGANISMS; PCR AMPLIFICATION; SEAGRASS; SPECIES DIVERSITY;

ISRAEL, GULF OF ELAT;

HALOPHILA STIPULACEA;

EID: 0029668450     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.62.3.766-771.1996     Document Type: Article

References (32)

1. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Bassani, B. J., G. Caetano-Anollés, and P. M. Gresshoff. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196:80-81.
3. Britschgi, T. B., and S. J. Giovannoni. 1991. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing Appl. Environ. Microbiol. 57:1707-1713
4. Brosius, J., M. L. Palmer, P. J. Kennedy, and H. F. Noller. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl Acad. Sci. USA 75:4801-4805.
5. Bullock, J. C., J. M. Fernandez, and J. M. Short. 1987. XL1Blue: a high efficiency plasmid transforming recA Escherichia coli strain with beta-galactosidase selection. BioTechniques 5:376-379.
6. Clark, J. M. 1988 Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases. Nucleic Acids Res 16:9677-9686.
7. DeLong, E. F., D. G. Franks, and A. L. Alldredge. 1993. Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr. 38:924-934.
8. Ferguson, R. L., E. N. Buckley, and A. V. Palumbo. 1984. Response of marine bacterioplankton to differential filtration and confinement. Appl Environ Microbiol. 47:49-55.
9. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from Atlantic and Pacific oceans Appl Environ. Microbiol. 59:1294-1302
10. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature (London) 345: 60-63
11. Grimont, F., and P. A. D. Grimont. 1986 Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Ann. Microbiol. (Inst. Pasteur) 137:165-175.
12. Gurtler, V., V. A. Wilson, and B. C. Mayall. 1991. Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J. Gen. Microbiol 137:2673-2679.
13. Jackson, D. A., K. M. Somers, and H. H. Harvey. 1989. Similarity coefficients: measures of co-occurrence and association or simply measures of occurrence. Am Nat. 133:436-453.
14. Lane, D. J. 1991 16S/23S rRNA sequencing, p 115-165. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons. Chichester, England.
15. Lane, D. J., B. Pace, G. J. Olsen, D. A. Stahl, and M. L. Sogin. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analysis. Proc. Natl. Acad Sci. USA 82:6955-6959.
16. Larsen, N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeck, T. J. Macke, and C. R. Woese. 1993 The ribosomal database project Nucleic Acids Res. 21(Suppl.):3021-3023
17. Liesack, W., and E. Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol 174:5072-5078.
18. Lipkin, Y. 1979. Quantitative aspects of seagrass communities, particularly of those dominated by Halophila stipulacea, in Sinai (northern Red Sea). Aquat. Bot. 7:119-128.
19. Morrison, D. A. 1977. Transformation in Escherichia coli. J Bacteriol. 132: 349-351.
20. 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 microbial mat at an active, hydrothermal vent system. Loihi Seamount, Hawaii. Appl Environ. Microbiol 60:871-879.
21. Nei, M., and W.-H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76:5269-5273.
22. Pereg, L. L., Y. Lipkin, and N. Sar. 1994. Different niches of the Halophila stipulacea seagrass bed harbor distinct populations of nitrogen fixing bacteria. Mar. Biol. 119:327-333.
23. Saiki, R. K., D. H. Gelfand, S. Stoffel, S. J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-191.
24. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
25. Sneath, P. H. A., and R. R. Sokal. 1973. Numerical taxonomy. W. H. Freeman & Co . San Francisco.
26. Stahl, D. A., R. Key, B. Flesher, and J. Smit. 1992. The phylogeny of marine and freshwater caulobacters reflects their habitat. J. Bacteriol. 174:2193-2198.
27. Tichy, V. Unpublished observations.
28. Vaneechoutte, M., R. Rossau, P. De Vos, M. Gillis, D. Janssens, N. Paepe, A. De Rouck, T. Fiers, G. Claeys, and K. Kersters. 1992 Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol. Lett 93:227-234.
29. Wahbeh, M. I., and A. M. Mahasneh. 1984. Heterotrophic bacteria attached to leaves, rhizomes and roots of three seagrass species from Aquaba (Jordan). Aquat. Bot. 20:87-96.
30. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. FEMS Microbiol. Rev 75:105-116.
31. Woese, C. R. 1987 Bacterial evolution. Microbiol. Rev. 51:221-271.
32. Zimmermann, J., H. Voss, C. Schwager, J. Stegemann, H. Erfle, K. Stucky, T. Kristensen, and W. Ansorge. 1990. A simplified protocol for fast plasmid DNA sequencing Nucleic Acids Res. 18:1067.