Simple and rapid method for direct extraction of microbial DNA from soil for PCR

Soil Biology and Biochemistry

Volumn 30, Issue 8-9, 1998, Pages 983-993

  Cullen, D W ^a   Hirsch, P R ^a  

^a ROTHAMSTED RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BUFFER; COLUMN CHROMATOGRAPHY; DNA ISOLATION; DNA PURIFICATION; EXTRACTION; LYSIS; OLIGONUCLEOTIDE; POLYMERASE CHAIN REACTION; PRIMER DNA; SOIL;

EXTRACTION TECHNIQUE; MCROBIAL DNA; MICROBIAL DNA; POLYMERASS CHAIN REACTION; SOIL;

RHIZOBIUM LEGUMINOSARUM;

EID: 0032145986     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0038-0717(98)00001-7     Document Type: Article

References (34)

1. Amann R. I., Ludwig W. and Schleifer K. H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59, 143-169.
2. Bruce K. D., Hiorns W. D., Hobman J. L., Osborn A. M., Strike P. and Ritchie D. A. (1992) Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413-3416.
3. Dellaporta S. L., Wood J. and Hicks J. B. (1983) A plant DNA minipreparation: Version II. Plant Molecular Biology Reporter 1, 19-21.
4. Erb R. W. and Wagner-Döbler I. (1993) Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 59, 4065-4073.
5. Flemming C. A., Leung K. T., Lee H., Trevors J. T. and Greer C. W. (1994) Survival of Lux-lac-marked biosurfactant-producing Pseudomonas aeruginosa UG2L in soil monitored by; non-selective plating and PCR. Applied and Environmental Microbiology 60, 1606-1613.
6. Herrick J. B., Madsen E. L., Batt C. A. and Ghiorse W. C. (1993) Polymerase chain reaction amplification of naphthalene catabolic and 16S rRNA gene sequences from indigenous sediment bacteria. Applied and Environmental Microbiology 59, 687-694.
7. Higuchi R. (1992) Simple and rapid preparation of samples for PCR. In PCR Technology, ed. H. A. Erlich, pp. 31-38. W.H. Freeman, New York.
8. Hirsch P. R. and Skinner F. A. (1992) The identification and classification of Rhizobium and Bradyrhizobium. In Identification Methods in Applied and Environmental Microbiology, eds R. G. Board, D. Jones and F. A. Skinner, pp. 45-65. Blackwell Scientific Publications, Oxford.
9. Hirsch P. R. and Spokes J. R. (1994) Survival and dispersal of genetically modified rhizobia in the field and genetic interactions with native strains. FEMS Microbiology Ecology 15, 147-160.
10. Holben W. E., Jansson J. K., Chelm B. K. and Tiedje J. M. (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Applied and Environmental Microbiology 54, 703-711.
11. Knaebel D. B. and Crawford R. L. (1995) Extraction and purification of microbial DNA from petroleum-contaminated soils and detection of low numbers of toluene, octane and pesticide degraders by multiplex polymerase chain reaction and Southern analysis. Molecular Ecology 4, 579-591.
12. Leff L. G., Dana J. R., McArthur J. V. and Shimkets L. J. (1995) Detection of Tn5-like sequences in kanamycin-resistant stream bacteria and environmental DNA. Applied and Environmental Microbiology 59, 417-421.
13. Liesack W., Weyland H. and Stackenbrandt E. (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed culture of strict barophilic bacteria. Microbial Ecology 21, 191-198.
14. McCoy W. F. and Olson B. H. (1985) Fluorimetric determination of the DNA concentration in municipal drinking water. Applied and Environmental Microbiology 49, 811-817.
15. Moran M. A., Torsvik V. L., Torsvik T. and Hodson R. E. (1993) Direct extraction and purification of rRNA for ecological studies. Applied and Environmental Microbiology 59, 915-918.
16. More M. I., Herrick J. B., Silva M. C., Ghiorse W. C. and Madsen E. L. (1994) Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Applied and Environmental Microbiology 60, 1572-1580.
17. Muller-Wegener U. (1988) Interaction of humic substances with biota. In Humic Substances and Their Role in the Environment, eds. F. H. Frimmel and R. F. Christman, pp. 179-192. John Wiley, New York.
18. Ogram A., Sayler G. S. and Barkay T. (1987) The extraction and purification of microbial DNA from sediments. Journal of Microbiological Methods 7, 57-66.
19. Picard C., Ponsonnet C., Paget E., Nesme X. and Simonet P. (1992) Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717-2722.
20. Sambrook J., Fritsch E. F. and Maniatis T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Press, Cold Spring Harbor.
21. Selenska S. and Klingmüller W. (1991) DNA recovery and direct detection of Tn5 sequences from soil. Letters in Applied Microbiology 13, 21-24.
22. Selenska S. and Klingmüller W. (1992) Direct recovery and molecular analysis of DNA and RNA from soil. Microbial Releases 1, 41-46.
23. Smalla K., Cresswell N., Mendonca-Hagler L. C., Wolters A. and van Elsas J. D. (1993) Rapid DNA extraction protocol from soil for polymerase chain reaction mediated amplification. Journal of Applied Bacteriology 74, 78-85.
24. Smith N. C. and Stribley D. P. (1994) A new approach to direct extraction of microorganisms from soil. In Beyond the Biomass, eds. K. Ritz, J. Dighton and K. E. Giller, pp. 49-55. John Wiley, Chichester.
25. Steffan R. J., Goksoyr J., Bej A. K. and Atlas R. M. (1988) Recovery of DNA from soils and sediments. Applied and Environmental Microbiology 54, 2908-2915.
26. Tas E., Saano A., Leinonen P. and Lindström K. (1995) Identification of Rhizobium spp. in peat based inoculants by DNA hybridization and PCR and its application in inoculant quality control. Applied and Environmental Microbiology 61, 1822-1827.
27. Tebbe C. C. and Vahjen W. (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Applied and Environmental Microbiology 59, 2657-2665.
28. Thornhill R. H., Burgess J. G. and Matsunaga T. (1995) PCR for direct detection of indigenous uncultured magnetic cocci in sediment and phylogenetic analysis of amplified 16S ribosomal DNA. Applied Environmental Microbiology 61, 495-500.
29. Torsvik V. L. (1980) Isolation of bacterial DNA from soil. Soil Biology & Biochemistry 12, 15-21.
30. Trevors J. T. (1992) DNA extraction from soil. Microbial Releases 1, 3-9.
31. Tsai Y.-L. and Olson B. H. (1991) Rapid method for direct extraction of DNA from soil and sediments. Applied and Environmental Microbiology 57, 1070-1074.
32. Tsai Y.-L. and Olson B. H. (1992a) Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754-757.
33. Tsai Y.-L. and Olson B. H. (1992b) Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Applied and Environmental Microbiology 58, 2292-2295.
34. Young C. C., Burghoff R. L., Keim L. G., Minak-Berners V., Lute J. R. and Hinton S. M. (1993) Polyvinylpyrrolidone-agarose gel electrophoresis purification of polymerase chain reaction amplifiable DNA from soils. Applied and Environmental Microbiology 59, 1972-1974.