Strategy for extracting DNA from clay soil and detecting a specific target sequence via selective enrichment and real-time (quantitative) PCR amplification

Applied and Environmental Microbiology

Volumn 75, Issue 18, 2009, Pages 6017-6021

  Yankson, Kweku K ^a,b   Steck, Todd R ^a  

^a UNIVERSITY OF NORTH CAROLINA AT CHARLOTTE   (United States)

^b Two Radnor Corporate Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLAY SOIL; MAGNETIC CAPTURE; PCR AMPLIFICATION; PURE KAOLINITE; REAL-TIME PCR; SELECTIVE ENRICHMENT; TARGET SEQUENCES;

AMPLIFICATION; DESORPTION; DNA; EXTRACTION; GENES; KAOLINITE; NUCLEIC ACIDS;

CLAY;

ALUMINUM SILICATE;

CLAY SOIL; DNA; KAOLINITE; POLYMERASE CHAIN REACTION; REAL TIME;

ARTICLE; CLAY; DESORPTION; DNA BINDING; DNA EXTRACTION; GENE TARGETING; HYBRIDIZATION; MAGNETIC CAPTURE HYBRIDIZATION; REAL TIME POLYMERASE CHAIN REACTION;

ALUMINUM SILICATES; BACTERIOLOGICAL TECHNIQUES; DNA; MOLECULAR BIOLOGY; POLYMERASE CHAIN REACTION; SOIL MICROBIOLOGY;

EID: 70149105502     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00211-09     Document Type: Article

References (40)

1. Alvarez, A. J., M. Khanna, G. A. Toranzos, and G. Stotzky. 1998. Amplification of DNA bound on clay minerals. Mol. Ecol. 7:775-778.
2. Reference deleted.
3. Andersen, J. B., C. Sternberg, L. K. Poulsen, S. P. Bjorn, M. Givskov, and S. Molin. 1998. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64:2240-2246.
4. Borden, D., and R. F. Giese. 2001. Baseline studies of the clay mineral society source clays: cation exchange capacity measurements by the ammonia-electrode method. Clays Clay Miner. 49:444-445.
5. Braid, M. D., L. M. Daniels, and C. L. Kitts. 2003. Removal of PCR inhibitors from soil DNA by chemical flocculation. J. Microbiol. Methods 52:389-393.
6. Buergmann, H., M. Pesaro, F. Widmer, and J. Zeyer. 2001. A strategy for optimizing quality and quantity of DNA extracted from soil. J. Microbiol. Methods 45:7-20.
7. Cai, P., Q. Huang, X. Zhang, and H. Chen. 2006. Adsorption of DNA on clay minerals and various colloidal particles from an alfisol. Soil Biol. Biochem. 38:471-476.
8. Chipera, S. J., and L. B. David. 2001. Baseline studies of the Clay Mineral Society source slays: powder X-ray diffraction analysis. Clays Clay Miner. 49:398-409.
9. Cormack, B. P., R. H. Valdivia, and S. Falkow. 1996. FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173:33-38. (Pubitemid 26239677)
10. Crecchio, C., and G. Stotzky. 1998. Binding of DNA on humic acids: effect on transformation of Bacillus subtilis and resistance to DNase. Soil Biol. Biochem. 30:1061-1067.
11. Crosby, L. D., and C. S. Criddle. 2007. Gene capture and random amplification for quantitative recovery of homologous genes. Mol. Cell. Probes 21:140-147.
12. de Moraes, R. R., J. E. Maruniak, and J. E. Funderburk. 1999. Methods for detection of Anticarsia gemmatalis nucleopolyhedrovirus DNA in soil. Appl. Environ. Microbiol. 65:2307-2311.
13. Dong, D., A. Yan, H. Liu, X. Zhang, and Y. Xu. 2006. Removal of humic substances from soil DNA using aluminium sulfate. J. Microbiol. Methods 66:217-222.
14. Fire, A., S. W. Harrison, and D. Dixon. 1990. A modular set of lazZ fusion vectors for studying gene expression in Caenorhabditis elegans. Gene 93:189-198.
15. Hengpraprom, S., C. M. Lee, and J. T. Coates. 2006. Sorption of humic acids and α-endosulfan by clay minerals. Environ. Toxicol. Chem. 25:11-17.
16. Hoshino, Y. T., and N. Matsumoto. 2004. An improved DNA extraction method using skim milk from soils that strongly adsorb DNA. Microbes Environ. 19:13-19.
17. Hoshino, Y. T., and N. Matsumoto. 2007. DNA- versus RNA-based denaturing gradient gel electrophoresis profiles of a bacterial community during replacement after soil fumigation. Soil Biol. Biochem. 39:434-444.
18. Jackson, N. E., J. C. Corey, L. R. Frederick, and J. C. Picken, Jr. 1967. Gamma irradiation and the microbial population of soils at two water contents. Soil Sci. Soc. Am. 31:491-494.
19. Jacobsen, C. S. 1995. Microscale detection of specific bacterial DNA in soil with a magnetic capture-hybridization and PCR amplification assay. Appl. Environ. Microbiol. 61:3347-3352.
20. Khanna, M., and G. Stotzky. 1992. Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the transforming ability of bound DNA. Appl. Environ. Microbiol. 58:1930-1939.
21. Krsek, M., and E. M. H. Wellington. 1999. Comparison of different methods for the isolation and purification of total community DNA from soil. J. Microbiol. Methods 39:1-6. (Pubitemid 29502447)
22. LaMontagne, M. G., F. C. Michel, P. A. Holden, and C. A. Reddy. 2002. Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. J. Microbiol. Methods 49:255-264.
23. Mangiapan, G., M. Vokurka, L. Schouls, J. Cadranel, D. Lecossier, J. van Embden, and A. J. Hance. 1996. Sequence capture-PCR improves detection of mycobacterial DNA in clinical samples. J. Clin. Microbiol. 34:1209-1215.
24. Martin-Laurent, F., L. Philippot, S. Hallet, R. Chaussod, J. C. Germon, G. Soulas, and G. Catroux. 2001. DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl. Environ. Microbiol. 67:2354-2359.
25. McNamara, N. P., H. I. J. Black, N. A. Beresford, and N. R. Parekh. 2003. Effects of acute gamma irradiation on chemical, physical and biological properties of soils. Appl. Soil Ecol. 24:117-132.
26. 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.
27. Pietramellara, G., J. Ascher, M. T. Ceccherini, P. Nannipieri, and D. Wenderoth. 2007. Adsorption of pure and dirty bacterial DNA on clay minerals and their transformation frequency. Biol. Fertil. Soils 43:731-739.
28. Ririe, K. M., R. P. Rasmussen, and C. T. Wittwer. 1997. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem. 245:154-160.
29. Rochette, E. A., and W. C. Koskinen. 1996. Supercritical carbon dioxide for determining atrazine sorption by field-moist soils. Soil Sci. Soc. Am. J. 60:453-460.
30. Romanovskaya, V. A., P. V. Rokitko, Y. R. Malashenko, T. P. Krishtab, and N. A. Chernaya. 1999. Sensitivity of soil bacteria isolated from the alienated zone around Chernobyl nuclear power plant to various stress factors. Microbiology 68:465-469.
31. Rozen, S., and H. J. Skaletzky. 2000. Primer3 on the WWW for general users and for biologist programmers, p. 365-386. In S. Krawetz and S. Misener (ed.), Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ.
32. Schneegurt, M. A., S. Y. Dore, and C. F. Kulpa. 2003. Direct extraction of DNA from soils for studies in microbial ecology. Curr. Issues Mol. Biol. 5:1-8.
33. Schulthes, C. P., and D. K. Dey. 1996. Estimation of Langmuir constants using linear and nonlinear least squares regression analysis. Soil Sci. Soc. Am. J. 60:433-442.
34. Smalla, K., N. Cresswell, L. C. Mendoca-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.
35. Stroetmann, I., P. Kaempfer, and W. Dott. 1994. Untersuchungen zur Effizienz von Sterilisationsverfahren an unterschiedlichen Boeden. Zentralbl. Hyg. Umweltmed. 195:111-120.
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. Torsvik, V., J. Goksoyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
38. Tsai, Y. L., J. Y. Le, and B. M. Olson. 2003. Magnetic bead hybridization to detect enterotoxigenic Escherichia coli strains associated with cattle in environmental water samples. Can. J. Microbiol. 49:391-398.
39. Vettori, C., L. Calamai, M. Yoder, G. Stotzky, and E. Gallori. 1999. Adsorption and binding of AmpliTaq DNA polymerase on the clay minerals, montmorillonite and kaolinite. Soil Biol. Biochem. 31:587-593.
40. Wilson, I. G. 1997. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63:3741-3751.