Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples

Applied and Environmental Microbiology

Volumn 65, Issue 11, 1999, Pages 4715-4724

  Miller, D N ^a,b   Bryant, J E ^a,c   Madsen, E L ^a   Ghiorse, W C ^a  

^a Department of Obstetrics Gynecology   (United States)

^b U S MEAT ANIMAL RESEARCH CENTER   (United States)

^c NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIUM ACETATE; BUFFER; CHLOROFORM; DNA; DODECYL SULFATE SODIUM; GUANIDINE DERIVATIVE; LYSOZYME; ORGANIC MATTER; PHENOL; RESIN; SEPHADEX; SODIUM CHLORIDE; TROMETAMOL;

DNA; EXTRACTION METHOD; SEDIMENT; SOIL;

AGAR GEL ELECTROPHORESIS; ARTICLE; DNA BINDING; DNA DEGRADATION; DNA DETERMINATION; DNA PURIFICATION; GEL FILTRATION; MOLECULAR SIZE; POLYMERASE CHAIN REACTION; PRECIPITATION; SEDIMENT; SOIL;

EID: 0032703237     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.11.4715-4724.1999     Document Type: Article

References (45)

1. Ausubel, F., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1997. Short protocols in molecular biology. John Wiley and Sons, Inc., New York, N.Y.
2. Beloin, R. M., J. L. Sinclair, and W. C. Ghiorse. 1988. Distribution and activity of microorganisms in subsurface sediments of a pristine study site in Oklahoma. Microb. Ecol. 16:85-97.
3. Boccuzzi, V. M., W. L. Straube, J. Ravel, R. R. Colwell, and R. T. Hill. 1995. Removal of contaminating substances from environmental samples prior to PCR by Sephadex G-200 Spun columns, abstr. N-168, p. 361. In Abstracts of the 95th General Meeting of the American Society for Microbiology 1995. American Society for Microbiology, Washington, D.C.
4. Bruce, K. D., W. D. Horns, J. L. Hobman, A. M. Osborn, P. Strike, and D. A. Ritchie. 1992. Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl. Environ. Microbiol. 58:3413-3416.
5. Brusseau, G. A., E. S. Bulygina, and R. S. Hanson. 1994. Phylogenetic analysis and development of probes for differentiating methylotrophic bacteria. Appl. Environ. Microbiol. 60:626-636.
6. Bryant, J. E. 1995. Detection of Cryptosporidium parvum oocysts in soil using the polymerase chain reaction. M.S. thesis. Cornell University, Ithaca, N.Y.
7. DeGrange, V., and R. Bardin. 1995. Detection and counting of Nitrobacter populations in soil by PCR. Appl. Environ. Microbiol. 61:2093-2098.
8. Erb, R. W., and I. Wagner-Döbler. 1993. Detection of polychlorinated biphenyl genes in polluted sediments by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 59:4065-4073.
9. Fuhrman, J. A., S. H. Lee, Y. Masuchi, A. A. Davis, and R. M. Wilcox. 1994. Characterization of marine prokaryotic communities via DNA and RNA. Microb. Ecol. 28:133-145.
10. Haldeman, D. L., P. S. Amy, D. Ringelberg, D. C. White, R. E. Garen, and W. C. Ghiorse. 1995. Microbial growth and resuscitation alter community structure after perturbation. FEMS Microbiol. Lett. 17:27-38.
11. Herrick, J. B., E. L. Madsen, C. A. Batt, and W. C. Ghiorse. 1993. Polymerase chain reaction amplification of naphthalene catabolic and 16S rRNA gene sequences from indigenous sediment bacteria. Appl. Environ. Microbiol. 59:687-694.
12. Herrick, J. B., D. N. Miller, E. L. Madsen, and W. C. Ghiorse. 1996. Extraction, purification, and amplification of microbial DNA from sediments and soils, p. 130-133. In J. F. Burke (ed.), PCR: essential techniques. John Wiley & Sons, New York, N.Y.
13. Holben, W. E., J. K. Jansson, B. K. Chelm, and J. M. Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:703-711.
14. Holben, W. E. 1994. Isolation and purification of bacterial DNA from soil, p. 727-751. In R. W. Weaver, S. Angle, P. Bottomley, D. Bezdicek, S. Smith, A. Tabatabai, and A. Wollum (ed.), Methods of soil analysis, part 2. Microbiological and biochemical properties. Soil Science Society of America, Inc., Madison, Wis.
15. Holben, W. E. 1997. Isolation and purification of bacterial community DNA from environmental samples, p. 431-436. In C. J. Hurst, G. R. Knudsen, M. J. McInerney, L. D. Stetzenbach, and M. V. Walter (ed.), Manual of methods in environmental microbiology. American Society for Microbiology, Washington, D.C.
16. Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
17. Jackson, C. R., J. P. Harper, D. Willoughby, E. E. Rosen, and P. F. Churchill. 1997. A simple, efficient method for separation of humic substances and DNA from environmental samples. Appl. Environ. Microbiol. 63:4993-4995.
18. Jacobsen, C. S., and O. F. Rasmussen. 1992. Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin. Appl. Environ. Microbiol. 58:2458-2462.
19. King, G. M. 1994. Associations of methanotrophs with the roots and rhizomes of aquatic vegetation. Appl. Environ. Microbiol. 60:3220-3227.
20. Kuske, C. R., K. L. Banton, D. L. Adorada, P. C. Stark, K. K. Hill, and P. J. Jackson. 1998. Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl. Environ. Microbiol. 64:2463-2472.
21. Leff, L. G., J. R. Dana, J. V. McArthur, and L. J. Shimkets. 1995. Comparison of methods of DNA extraction from stream sediments. Appl. Environ. Microbiol. 61:1141-1143.
22. 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.
23. Madsen, E. L. 1998. Epistemology of environmental microbiology. Environ. Sci. Technol. 32:429-539.
24. Madsen, E. L. 1996. A critical analysis of methods for determining the composition and biogeochemical activities of soil microbial communities in situ. Soil Biochem. 9:287-370.
25. Malik, M., J. Kain, C. Pettigrew, and A. Ogram. 1994. Purification and molecular analysis of microbial DNA from compost. J. Microbiol. Methods 20:183-196.
26. Miller, D. N. 1996. Biogeochemical, microbiological, and molecular insights into the controls of methane emissions from a forested wetland. Ph.D. thesis. Cornell University, Ithaca, N.Y.
27. Moré, M. I., J. B. Herrick, M. C. Silva, W. C. Ghiorse, and E. L. Madsen. 1994. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60:1572-1580.
28. Ogram, A. 1998. Isolation of nucleic acids from environmental samples, p. 273-288. In R. S. Burlage, R. Atlas, D. Stahl, G. Geesey, and G. Sayler (ed.), Techniques in microbial ecology. Oxford University Press, New York, N.Y.
29. Ogram, A., G. S. Sayler, and T. Barkay. 1987. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7:57-66.
30. Picard, C., C. Ponsonnet, E. Paget, X. Nesme, and P. Simonet. 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 58:2717-2722.
31. Rochelle, P. A., J. C. Fry, R. J. Parkes, and A. J. Weightman. 1992. DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities. FEMS Microbiol. Lett. 100:59-66.
32. 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.
33. Smalla, K., N. Cresswell, L. C. Mendonca-Hagler, A. Wolters, and J. D. van Elsas. 1993. Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J. Appl. Bacteriol. 74:78-85.
34. Smith, G. B., and J. M. Tiedje. 1992. Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria. Appl. Environ. Microbiol. 58:376-384.
35. Steffan, R. J., J. Goksoyr, A. K. Bej, and R. M. Atlas. 1988. Recovery of DNA from soils and sediments. Appl. Environ. Microbiol. 54:2908-2915.
36. Tebbe, C. C., and W. Vahjen. 1993. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl. Environ. Microbiol. 59:2657-2665.
37. Trevors, J. T., H. Lee, and S. Cook. 1992. Direct extraction of DNA from soil. Microb. Releases 1:111-115.
38. Tsai, Y., and B. H. Olson. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1070-1074.
39. Tsai, Y., and B. H. Olson. 1992. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. Environ. Microbiol. 58:2292-2295.
40. Tsai, Y., M. J. Park, and B. H. Olson. 1991. Rapid method for direct extraction of mRNA from seeded soils. Appl. Environ. Microbiol. 57:765-768.
41. U. S. National Institutes of Health. 1999. [Online.] NIH Image program. National Institutes of Health, Washington, D.C. http://rsb.info.nih.gov/nih-image. [7 September 1999, last date accessed.]
42. Volossiouk, T., E. J. Robb, and R. N. Nazar. 1995. Direct DNA extraction for PCR-mediated assays of soil organisms. Appl. Environ. Microbiol. 61:3972-3976.
43. Winans, S. C., and M. J. Rooks. 1993. Sensitive, economic laboratory photodocumentation using standard video camera and thermal printer. Bio-Techniques 14:902.
44. 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 soils. Appl. Environ. Microbiol. 59:1972-1974.
45. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.