Direct ribosome isolation from soil to extract bacterial rRNA for community analysis

Applied and Environmental Microbiology

Volumn 62, Issue 11, 1996, Pages 4162-4167

  Felske, Andreas ^a,b   Engelen, Bert ^a   Nübel, Ulrich ^a,c   Backhaus, Horst ^a  

^a INSTITUTE FOR EPIDEMIOLOGY AND PATHOGEN DIAGNOSTICS   (Germany)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; BOVINE SERUM ALBUMIN; POVIDONE; RIBOSOME RNA; RNA 16S;

ARTICLE; BACTERIUM CULTURE; CENTRIFUGATION; CONTROLLED STUDY; EXTRACTION; NONHUMAN; OLIGONUCLEOTIDE PROBE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIBOSOME; RNA ANALYSIS; RNA HYBRIDIZATION; SAMPLE; SOIL;

BACTERIA (MICROORGANISMS); BOVINAE;

EID: 0029805854     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.62.11.4162-4167.1996     Document Type: Article

References (24)

1. 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.
2. Brosius, J., T. L. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organisation and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
3. Cairns, M. J., and V. Murray. 1994. Rapid silver staining and recovery of PCR products separate on polyacrylamide gels. BioTechniques 17:915-919.
4. Engelen, B., H. Heuer, A. Felske, U. Nübel, and H. Backhaus. 1995. Monitoring stress factors on microbial communities by fingerprinting of function and structure, abstr. KV161, p. 50. Biospektrum (Special edition for the spring meeting of the Society for Applied and General Microbiology.)
5. Engelen, B., H. Heuer, A. Felske, U. Nübel, K. Smalla, and H. Backhaus. 1995. Protocols for the TGGE. In Abstracts for the Workshop on Application of DGGE and TGGE in Microbial Ecology 1995. Biologische Bundesanstalt für Land- und Forstwirtschaft, Braunschweig, Germany.
6. Hahn, D., R. Kester, M. J. C. Starrenburg, and A. D. L. Akkermans. 1990. Extraction of ribosomal RNA from soil for detection of Frankia with oligonucleotide probes. Arch. Microbiol. 154:329-335.
7. Herron, P. R., and E. M. H. Wellington. 1990. New method for extraction of streptomycete spores from soil and application to the study of lysogeny in sterile amended and nonsterile soil. Appl. Environ. Microbiol. 56:1406-1412.
8. Lorenz, M. G., and W. Wackernagel. 1987. Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl. Environ. Microbiol. 53:2948-2952.
9. Malkomes, H.-P. 1993. Effect of pesticides used for seed treatment of potatoes on microbial activities in soil. Zentralbl. Mikrobiol. 148:497-504.
10. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
11. Manz, W., R. Amann, W. Ludwig, M. Wagner, and K.-H. Schleifer. 1992. Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15:593-600.
12. Moran, M. A., V. L. Torsvik, T. Torsvik, and R. E. Hodson. 1993. Direct extraction and purification of rRNA for ecological studies. Appl. Environ. Microbiol. 59:915-918.
13. Muyzer, G., E. C. De Waal, 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.
14. Ogram, A. V., M. L. Mathot, J. B. Harsh, J. Boyle, and C. A. Pettigrew, Jr. 1994. Effects of DNA polymer length on its adsorption to soils. Appl. Environ. Microbiol. 61:393-396.
15. Pace, N. A., D. A. Stahl, D. J. Lane, and G. Olsen. 1986. The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1-55.
16. Rosenbaum, V., and D. Riesner. 1987. Temperature-gradient gel electrophoresis - thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys. Chem. 26:235-246.
17. Selenska, S., and W. Klingmüller. 1992. Direct recovery and molecular analysis of DNA and RNA from soil. Microb. Releases 1:41-46.
18. Srivastava, A. K., and D. Schlessinger. 1990. Mechanism and regulation of bacterial ribosomal RNA processing. Annu. Rev. Microbiol. 44:105-129.
19. 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-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62:1405-1415.
20. Tissiéres, A., J. D. Watson, D. Schlessinger, and B. R. Hollingworth. 1959. Ribonucleoprotein particles from Escherichia coli. J. Mol. Biol. 1:221-233.
21. Tsai, Y.-L., M. J. Park, and B. H. Olson. 1991. Rapid method for direct extraction of mRNA from seeded soils. Appl. Environ. Microbiol. 57:765-768.
22. Wagner, M., R. Erhart, W. Manz, R. Amann, H. Lemmer, D. Wede, and K.-H. Schleifer. 1994. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60:792-800.
23. Weller, R., J. W. Weller, and D. M. Ward. 1991. 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA. Appl. Environ. Microbiol. 57:1146-1151.
24. Young, C. C., R. L. Burghoff, L. G. Keim, V. Minak-Bernero, J. R. Lute, and S. M. Hinton. 1993. Polyvinylpyrrolidone-agarose gel electrophoresis purification of polymerase chain reaction-amplifiable DNA from soils. Appl. Environ. Microbiol. 60:1972-1974.