Applied Microbiology and Biotechnology

, Volume 77, Issue 4, pp 955–964

DNA extraction method affects microbial community profiles from soils and sediment

  • Cora Carrigg
  • Olivia Rice
  • Siobhán Kavanagh
  • Gavin Collins
  • Vincent O’Flaherty
Methods

Abstract

To evaluate whether different deoxyribonucleic acid (DNA) extraction procedures can affect estimates of bacterial community composition, based on the 16S ribosomal ribonucleic acid gene denaturing gradient gel electrophoresis (DGGE) profiles, we compared four in situ lysis procedures using three soils and one marine sediment. Analysis of DGGE profiles, generated by polymerase chain reaction of purified DNA extracts, demonstrated that the choice of DNA extraction method significantly influenced the bacterial community profiles generated. This was reflected both in the number of bands or ribotypes detected from each sample and in subsequent principle coordinate analysis and unweighted-pair group method using arithmetic average analyses. The methods also differed significantly in their robustness, i.e. reproducibility across multiple analyses. Two methods, both based on bead beating, were demonstrated to be suitable for comparative studies of a range of soil and sediment types.

Keywords

Soil Sediment DNA extraction DGGE Lysis efficiency Microbial diversity 

Supplementary material

253_2007_1219_Fig1_ESM.jpg (47 kb)
Fig. 1

PCO analysis of the four extraction methods tested on each of the four soils a Corrib soil, b Silvermines soil, c Inverin peat and d PAP marine sediment. M1M4 represent methods 1–4. Identical profiles overlap (asterisk represents a profile generated using a separate extract) (JPG 47 kb)

253_2007_1219_Fig1_ESM.tif (1.1 mb)
High resolution image file (TIFF 1.07 MB)
253_2007_1219_Fig2_ESM.jpg (55 kb)
Fig. 2

UPGMA analysis of the four extraction methods tested on each of the four soils a Corrib soil, b Silvermines soil, c Inverin peat and d PAP marine sediment. M1M4 represent methods 1–4 (asterisk represents a profile generated using a separate extract) (JPG 55 kb)

253_2007_1219_Fig2_ESM.tif (342 kb)
High resolution image file (TIFF 342 kb)
253_2007_1219_Fig3_ESM.jpg (25 kb)
Fig. 3

PCO analysis of the method reproducibility found with each of the four methods tested on Corrib soil a M1, b M2 , c M3 and d M4. Identical profiles overlap (JPG 25 kb)

253_2007_1219_Fig3_ESM.tif (94 kb)
High resolution image file (TIFF 94 kb)
253_2007_1219_Fig4_ESM.jpg (69 kb)
Fig. 4

UPGMA analysis of the method reproducibility found with each of the four methods tested on Corrib soil a M1, b M2, c M3 and d M4 (JPG 69 KB)

253_2007_1219_Fig4_ESM.tif (1.1 mb)
High resolution image file (TIFF 1.11 MB)
253_2007_1219_Fig5_ESM.jpg (25 kb)
Fig. 5

PCO analysis of the method reproducibility found with each of the four methods tested on Silvermines soil a M1, b M2, c M3 and d M4. Identical profiles overlap (JPG 25 kb)

253_2007_1219_Fig5_ESM.tif (115 kb)
High resolution image file (TIFF 115 kb)
253_2007_1219_Fig6_ESM.jpg (71 kb)
Fig. 6

UPGMA analysis of the method reproducibility found with each of the four methods tested on Silvermines soil a M1, b M2, c M3 and d M4 (JPG 71 kb)

253_2007_1219_Fig6_ESM.tif (1.1 mb)
High resolution image file (TIFF 1.11 MB)

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Cora Carrigg
    • 1
  • Olivia Rice
    • 2
  • Siobhán Kavanagh
    • 3
  • Gavin Collins
    • 4
  • Vincent O’Flaherty
    • 1
  1. 1.Microbial Ecology Laboratory, Department of Microbiology and Environmental Change Institute (ECI)National University of IrelandGalwayIreland
  2. 2.Biomerit Research Centre, Department of MicrobiologyUniversity College CorkCorkIreland
  3. 3.DNA Laboratory, National Diagnostics CentreNational University of IrelandGalwayIreland
  4. 4.Nutrient GroupMax Planck Institute for Marine MicrobiologyBremenGermany

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