Evaluation of Soil DNA from Arable Land in Japan Using a Modified Direct-extraction Method

Microbes and Environments

Volumn 19, Issue 4, 2004, Pages 301-309

  Ikeda, Seishi ^a   Watanabe, Kazuo N ^a   Minamisawa, Kiwamu ^b   Ytow, Nozomi ^a  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b TOHOKU UNIVERSITY   (Japan)

Author keywords

agricultural ecosystem; DEAE cellulose column; DSPD method; potassium acetate precipitation; soil DNA

Indexed keywords

EID: 84975823160     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.19.301     Document Type: Article

References (27)

1. Amann, R.I., W. Ludwig and K.H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143–169.
2. Ball, D.F. 1964. Factors affecting the concentrations of lead in British wheat and barley grain. Environ. Pollut. 131: 461–468.
3. Berthelet, M., L.G. Whyte and C.W. Greer. 1996. Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol. Lett. 138: 17–22.
4. Blackwood, C.B., T. Marsh, S. H. Kim and E.A. Paul. 2003. Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl. Environ. Microbiol. 69: 926–932.
5. Frostegård, Å., S. Courtois, V. Ramisse, S. Clerc, D. Bernillon, F. Le Gall, P. Jeannin, X. Nesme and P. Simonet. 1999. Quantification of bias related to the extraction of DNA directly from soils. Appl. Environ. Microbiol. 65: 5409–5420.
6. Hasegawa, S., K. Kamewada, Y. Yamada, S. Hidaka, Y. Ogawa and M. Nanjo. 1997. Physics, and chemistry of soil, p. 21–265. In the Committee of Analytical Methods of Soil Environment (ed.), Analytical methods of soil environment. Hakuyusha, Tokyo.
7. 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, WI.
8. Kageyama, K., T. Komatsu and H. Suga. 2003. Refined PCR protocol for detection of plant pathogens in soil. J. Gen. Plant Pathol. 69: 153–160.
9. Kresk, 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: 1–16.
10. Kuske, C.R., K.L. Banton, D.L. Adorada, P.C. Stark, K.K. Hill and P.J. Jackson. 1998. Small-scale DNA preparation method for field PCR detection of microbial cells and spores in soil. Appl. Environ. Microbiol. 64: 2463–2472.
11. Liesack, W., H. Weyland and E. Stackbrandt. 1991. Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol. 21: 191–198.
12. Ogram, A., G.S. Sayler and T. Barkay. 1987. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7: 57–66.
13. Ogram, A., G.S. Sayler, D. Gustin and R.J. Lewis. 1988. DNA adsorption to soils and sediments. Environ. Sci. Technol. 22: 982–984.
14. Porteous, L.A. and J.L. Armstrong. 1991. Recovery of bulk DNA from soil by a rapid, small-scale extraction method. Curr. Microbiol. 22: 345–348.
15. Sambrook, J. and D.W. Russel. 2001. Molecular Cloning: A Laboratory Manual, 3rd edn. Vol. 1, 5.26–5.28, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
16. Schneegurt, M.A., S.Y. Dore and C.F. Kulpa Jr. 2003. Direct extraction of DNA from soils for studies in microbial ecology. Curr. Issues Mol. Biol. 5: 1–8.
17. Selenska, S. and W. Klingmuller. 1991. DNA recovery and direct detection of Tn5 sequences from soil. Lett. Appl. Microbiol. 13: 21–24.
18. 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.
19. 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.
20. Steffan, R.J. and R.M. Atlas. 1988. DNA amplification to enhance detection of genetically engineered bacteria in environmental samples. Appl. Environ. Microbiol. 54: 2185–2191.
21. Takada-Hoshino, Y. and N. Matsumoto. 2004. An improved DNA extraction method using skim milk from soils that strongly adsorb DNA. Microbes Environ. 19: 13–19.
22. Torsvik, V.L. and J. Goksoyr. 1978. Determination of bacterial DNA in soil. Soil Biol. Biochem. 10: 7–23.
23. Tsai, Y.L. and B.H. Olson. 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl. Environ. Microbiol. 58: 754–757.
24. Tyson, G., W.J. Chapman, R. Hugenholtz, E.E. Allen, R.J. Ram, P.M. Richardson, V.V. Solovyev, E.M. Rubin, D.S. Rokhsar and J.F. Banfield. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37–43.
25. Tyurin, I.V. 1951. Analytical procedure for a comparative study of soil humus. Trudy poch. Inst. Dokuchaev. 33: 5–21.
26. 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.
27. Zhou, J., M.A. Bruns and J.M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316- 322.