Sequential extraction and genetic fingerprinting of a forest soil metagenome

Applied Soil Ecology

Volumn 42, Issue 2, 2009, Pages 176-181

  Ascher, J ^a   Ceccherini, M T ^a   Pantani, O L ^a   Agnelli, A ^b   Borgogni, F ^a   Guerri, G ^a   Nannipieri, P ^a   Pietramellara, G ^a  

^a UNIVERSITY OF FLORENCE   (Italy)

^b UNIVERSITY OF PERUGIA   (Italy)

Author keywords

Community level DGGE; Compositional genetic differences; DNA extraction efficiency; DNA fractions; Soil metagenome

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 67349108699     PISSN: 09291393     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.apsoil.2009.03.005     Document Type: Article

References (35)

1. Agnelli A., Ascher J., Corti G., Ceccherini M.T., Nannipieri P., and Pietramellara G. Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA. Soil Biol. Biochem. 36 (2004) 859-868
2. Agnelli A., Ascher J., Corti G., Ceccherini M.T., Pietramellara G., and Nannipieri P. Purification and isotopic signatures (δ13C, δ15N Δ14C) of soil extracellular DNA. Biol. Fertil. Soils 44 (2007) 353-361
3. Bakken L.R., and Frostegård A. Nucleic acid extraction from soil. In: Nannipieri P., and Smalla K. (Eds). Soil Biology, Nucleic Acids and Proteins in Soil 8 (2006), Springer-Verlag, Heidelberg, Germany 49-73
4. Brodie E., Suzanne E., and Clipson N. Soil fungal community structure in a temperate upland grassland soil. FEMS Microbiol. Ecol. 1523 (2003) 1-10
5. Ceccherini M.T., Ascher J., Pietramellara G., Vogel T.M., and Nannipieri P. Vertical advection of extracellular DNA by water capillarity in soil columns. Soil Biol. Biochem. 39 (2007) 158-163
6. Courtois S., Frostegård A., Göransson P., Depret G., Pascale J., and Simonet P. Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ. Microbiol. 3 (2001) 431-439
7. Daniel R. The soil metagenome-a rich resource for the discovery of novel natural products. Curr. Opin. Biotechnol. 15 (2004) 199-204
8. Daniel R. The metagenomics of soil. Nat. Rev. Microbiol. 3 (2005) 470-478
9. Dice L.R. Measures of the amount of ecologic association between species. Ecology 26 (1945) 297-302
10. Finkel S.E., and Kolter R. DNA as a nutrient: novel role for bacterial competence gene homologs. J. Bacteriol. 83 (2001) 6288-6293
11. He J., Xu Z., and Hughes J. Pre-lysis washing improves DNA extraction from a forest soil. Soil Biol. Biochem. 37 (2005) 2337-2341
12. Heuer H., and Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities. In: van Elsas J.D., Wellington E.M.H., and Trevors J.T. (Eds). Modern Soil Microbiology (1997), Marcel-Dekker, Inc., NY 353-373
13. IUSS, Working Group, WRB, 2006. World reference base for soil resources. World Soil Resources Reports, vol. 103. FAO, Rome.
14. Kowalchuk G. Fungal community analysis using denaturing gradient gel electrophoresis (DGGE). In: Akkermans A.D.L., van Elsas J.D., and de Bruijn F.J. (Eds). Molecular Microbial Ecology Manual 3.4.6 (1999), Kluwer Academic Publisher, Dordrecht 1-16
15. Kozdrój J., and van Elsas D.J. Application of polymerase chain reaction-denaturing gradient gel electrophoresis for comparison of direct and indirect extraction methods of soil DNA used for microbial community fingerprinting. Biol. Fertil. Soils 31 (2000) 372-378
16. Lejon D.P.H., Chaussod R., Ranger J., and Ranjard L. Microbial community structure and density under different tree species in an acid forest soil (Morvan, France). Microb. Ecol. 50 (2005) 614-625
17. Levy-Booth D.J., Campbell R.G., Gulden R.H., Hart M.M., Powell J.R., Klironomos J.N., Pauls K.P., Swanton C.J., Trevors J.T., and Dunfield K.E. Cycling of extracellular DNA in the soil environment. Soil Biol. Biochem. 39 (2007) 2977-2991
18. Matsui K., Ishii N., and Kawabata Z. Release of extracellular transformable plasmid DNA from Escherichia coli cocultivated with algae. Appl. Environ. Microbiol. 69 (2003) 2399-2404
19. Murrell P. R graphics. Computer Science & Data Analysis Series (2006), Chapman & Hall/CRC, Boca Raton, FL, USA
20. Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2 (1999) 317-322
21. Nielsen K.M., Calamai L., and Pietramellara G. Stabilization of extracellular DNA and proteins by transient binding to various soil components. In: Nannipieri P., and Smalla K. (Eds). Soil Biology, Nucleic Acids and Proteins in Soil 8 (2006), Springer-Verlag, Heidelberg, Germany 141-153
22. Nielsen K.M., Johnsen P.J., Bensasson D., and Daffonchio D. Release and persistence of extracellular DNA in the environment. Environ. Biosaf. Res. 6 (2007) 37-53
23. Niemeyer J., and Gessler F. Determination of free DNA in soils. J. Plant Nutr. Soil Sci. 165 (2002) 121-124
24. Nübel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R.I., Ludwig W., and Backhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178 (1996) 5636-5643
25. Pietramellara G., Ceccherini M.T., Ascher J., and Nannipieri P. Persistence of transgenic and not transgenic extracellular DNA in soil and bacterial transformation. Biol. Forum 99 (2006) 37-68
26. Pietramellara G., Ascher J., Ceccherini M.T., Nannipieri P., and Wenderoth D. Adsorption of pure and dirty bacterial DNA on clay minerals and their transformation frequency. Biol. Fertil. Soils 43 (2007) 731-739
27. Pinchuk G.E., Ammons C., Culley D.E., Li S.M.L., McLean J.S., Romine M.F., Nealson K.H., Fredrickson J.K., and Beliaev A.S. Utilization of DNA as a sole source of phosphorus, carbon, and energy by Shewanella spp.: ecological and physiological implications for dissimilatory metal reduction. Appl. Environ. Microbiol. 74 (2008) 1198-1208
28. Pinheiro, J.C., Bates, D.M., DebRoy, S., Sarkar, D., 2007. The R Core team, nlme: linear and nonlinear mixed effects models. R Package Version 3.1-86.
29. Pinheiro J.C., and Bates D.M. Mixed-effects Models in S and S-PLUS (2000), Springer-Verlag pp. 1-528
30. Potè J., Ceccherini M.T., van Tran V., Rosselli W., Wildi W., Simonet P., and Vogel T. Fate and transfer of antibiotic resistance genes in saturated soil columns. Eur. J. Soil Biol. 39 (2003) 65-71
31. R Development Core Team, 2007. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-07-0, http://www.R-project.org.
32. Robe P., Nalin R., Capellano C., Vogel T.M., and Simonet P. Extraction of DNA from soil. Eur. J. Soil Biol. 39 (2003) 183-190
33. Rondon M.R., August P.R., Bettermann A.D., Brady S.F., Grossman T.H., Liles M.R., Loiacono K.A., Lynch B.A., Macneil I.A., Minor C., Tiong C.L., Gilman M., Osburne M.S., Clardy J., Handelsman J., and Goodman R.M. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66 (2000) 2541-2547
34. Steinberger R.E., and Holden P.A. Extracellular DNA in single- and multiple-species unsaturated biofilms. Appl. Environ. Microbiol. 71 (2005) 5404-5410
35. Wackernagel W. The various sources and the fate of nucleic acids in soil. In: Nannipieri P., and Smalla K. (Eds). Soil Biology, Nucleic Acids and Proteins in Soil 8 (2006), Springer-Verlag, Heidelberg, Germany 117-134