Simultaneous Recovery of RNA and DNA from Soils and Sediments

Applied and Environmental Microbiology

Volumn 67, Issue 10, 2001, Pages 4495-4503

  Hurt, Richard A ^a   Qiu, Xiaoyun ^a   Wu, Liyou ^a,b   Roh, Yul ^a   Palumbo, A V ^a   Tiedje, J M ^b   Zhou, Jizhong ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; FUNGAL DNA; FUNGAL RNA; MESSENGER RNA;

ARTICLE; CHEMISTRY; DNA MICROARRAY; EVALUATION; ISOLATION AND PURIFICATION; MICROBIOLOGY; POLYMERASE CHAIN REACTION; SEDIMENT; SOIL;

DNA, BACTERIAL; DNA, FUNGAL; GEOLOGIC SEDIMENTS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, FUNGAL; RNA, MESSENGER; SOIL; SOIL MICROBIOLOGY;

EID: 0035487188     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.10.4495-4503.2001     Document Type: Article

References (49)

1. Alm, E. W., and D. A. Stahl. 2000. Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in fresh-water sediments. J. Microbiol. Methods 40:153-162.
2. Amann, R. I., W. Ludwig, and K. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
3. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1995. Current protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y.
4. Borneman, J., and E. W. Triplett. 1997. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63:2647-2653.
5. Borneman, J., and E. W. Triplett. 1997. Rapid and direct method for extraction of RNA from soil. Soil Biol. Biochem. 29:1621-1624.
6. Braker, G., J.-Z. Zhou, L.-Y. Wu, A. H. Devol, and J. M. Tiedje. 2000. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in marine sediment communities. Appl. Environ. Microbiol. 66:2096-2104.
7. Chomczynski, P., and N. Sacchi. 1987. Single-step method of RNA isolation by acid guanidinium isothiocyanate-phenol-chloroform extraction. Anal. Biochem. 162:156-159.
8. Dell' Anno, A., M. Fabiano, G. C. A. Duineveld, A. Kok, and R. Danovaro. 1998. Nucleic acid (DNA, RNA) quantification and RNA/DNA ratio determination in marine sediments: comparison of spectrophotometric, fluorometric, and high-performance liquid chromotography methods and estimation of detrietal DNA. Appl. Environ. Microbiol. 64:3238-3245.
9. Duarte, G. F., A. S. Rosado, L. Seldin, A. C. Keijzer-Wolters, and J. D. van Elsas. 1998. Extraction of ribosomal RNA and genomic DNA from soil for studying the diversity of the indigenous bacterial community. J. Microbiol. Methods 32:21-29.
10. Fabiano, M., R. Donavaro, E. Crisafi, R. La Feria, P. Povero, and L. Acosta Pomar. 1995. Particulate matter composition and bacterial distribution in Terra Nova Bay (Antarctica) during summer 1989-1990. Polar Biol. 15:393-400.
11. Fleming, J. T., J. Sanseverino, and G. S. Sayler. 1993. Quantitative relationship between naphthalene catabolic gene frequency and expression in predicting PAH degradation in soils at town gas manufacturing sites. Environ. Sci. Technol. 27:1068-1074.
12. Fries, M. R., J.-Z. Zhou, J. C. Chee-Sanford, and J. M. Tiedje. 1994. Isolation, characterization and distribution of denitrifying toluene degraders from a variety of habitats. Appl. Environ. Microbiol. 60:2802-2810.
13. Frostegard, A., S. Courtois, V. Ramisse, S. Clerc, D. Bernillon, F. Le Gall, P. Jeannin, X. Nesme, and P. Simonet. 1999. Quantification bias related to the extraction of DNA directly from soils. Appl. Environ. Microbiol. 65:5409-5420.
14. Gee, G. W., and J. W. Bauder. 1986. Particle size analysis. Agron. Monogr. 9:383-411.
15. Greaves, M. P., and M. J. Wilson. 1969. The adsorption of nucleic acids by montmorillonite. Soil Biol. Biochem. 1:317-323.
16. Holben, W. H., 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.
17. 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.
18. Jeffrey, W. H., S. Nazaret, and R. Von Haven. 1994. Improved method for recovery of mRNA from aquatic samples and its application to detection of mer expression. Appl. Environ. Microbiol. 60:1814-1821.
19. Jeffrey, W. H., R. Von Haven, M. P. Hoch, and R. B. Coffin. 1996. Bacterioplankton RNA, DNA, protein content and relationships to rates of thymidine and leucine incorporation. Aquat. Microb. Ecol. 10:87-95.
20. Johnston, W. H., R. Stapelton, and G. S. Sayler. 1996. Direct extraction of microbial DNA from soils and sediments, p. 1-9. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual, vol. 1.3.2. Kluwer Academic Publishers, Dordrecht, The Netherlands.
21. Kerkhof, L., and B. B. Ward. 1993. Comparison of nucleic acid hybridization and flourometry for measurement of the relationship between RNA/DNA ratio and growth rate in a marine bacterium. Appl. Environ. Microbiol. 59:1303-1309.
22. Kilmer, V. J., and L. T. Alexander. 1949. Methods of making mechanical analyses of soils. Soil Sci. 68:15-24.
23. Lovell, C. R., and Y. Piceno. 1994. Purification of DNA from estuarine sediments. J. Microbiol. Methods 20:161-174.
24. 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.
25. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
26. McLean, E. O. 1982. Soil and pH in lime requirement. Agron. Monogr. 9:199-224.
27. 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.
28. Muttray, A. F., and W. W. Mohn. 1999. Quantitation of the population size and metabolic activity of a resin acid degrading bacterium in activated sludge using slot-blot hybridization to measure the rRNA:rDNA ratio. Microb. Ecol. 38:348-357.
29. 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. 60:393-396.
30. Ogram, A., G. S. Sayler, and T. Barkay. 1987. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7:57-66.
31. Ogram, A., G. S. Sayler, D. Gustin, and R. J. Lewis. 1988. DNA adsorption to soils and sediments. Environ. Sci. Technol. 22:982-984.
32. Ogram, A., W. Sun, F. J. Brockman, and J. K. Fredrickson. 1995. Isolation and characterization of RNA from low-biomass deep-subsurface sediments. Appl. Environ. Microbiol. 61:763-768.
33. Picard, C., E. Ponsonnet, E. Padget, 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.
34. Pichard, S. L., and J. H. Paul. 1993. Gene expression per gene dose, a specific measure of gene expression in aquatic microorganisms. Appl. Environ. Microbiol. 59:451-457.
35. Purdy, K. J., T. M. Embley, S. Takaii, and D. B. Nedwell. 1996. Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method. Appl. Environ. Microbiol. 62:3905-3907.
36. Rauhut, R., and G. Klug. 1999. mRNA degradation in bacteria. FEMS Microbiol. Rev. 23:353-370.
37. Romanowski, G., M. G. Lorenz, and W. Wackernagel. 1991. Adsorption of plasmid DNA to mineral surfaces and protection against DNase I. Appl. Environ. Microbiol. 57:1057-1061.
38. Selenska, S., and W. Klingmüller. 1992. Direct recovery and molecular analysis of DNA and RNA from soil. Microb. Releases 1:41-46.
39. Stackebrandt, E., W. Liesack, and B. M. Goebel. 1993. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by SSU rDNA analysis. FASEB J. 7:232-236.
40. 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.
41. 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 yeast. Appl. Environ. Microbiol. 59:2657-2665.
42. Tiedje, J. M., J.-Z. Zhou, K. Nusslein, C. L. Moyer, and R. R. Fulthorpe. 1997. Extent and patterns of soil microbial diversity, p. 35-41. In M. T. Martins et al. (ed.), Progress in microbial ecology. Brazilian Society for Microbiology, Sao Paulo, Brazil.
43. Tsai, Y.-L., and B. H. Olson. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1070-1074.
44. 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.
45. Vesico, P. A., and S. A. Nierzwicki-Bauer. 1995. Extraction and purification of PCR amplifiable DNA from lacustrine subsurface sediments. J. Microbiol. Methods 21:225-233.
46. Wintzingerode, F. V., U. B. Gohel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis FEMS Microbiol. Rev. 21:213-229.
47. Yu, Z., and W. W. Mohn. 1999. Killing two birds with one stone: simultaneous extraction of DNA and RNA from activated sludge biomass. Can. J. Microbiol. 45:269-272.
48. Zhou, J.-Z., M. E. Davey, J. B. Figueras, E. Rivkina, D. Gilichinsky, and J. M. Tiedje. 1997. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:3913-3919.
49. Zhou, J.-Z., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.