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.
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Acknowledgements
The authors wish to thank Dr. Fabio Chinalia for assistance with statistical analysis. This research was financially supported by the Irish Environmental Protection Agency Environmental Research Training and Development Program (2000–2006) project “Towards a National Soil Database (2001-CD/S2-M2).”
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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. M1–M4 represent methods 1–4. Identical profiles overlap (asterisk represents a profile generated using a separate extract) (JPG 47 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. M1–M4 represent methods 1–4 (asterisk represents a profile generated using a separate extract) (JPG 55 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)
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)
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)
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)
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Carrigg, C., Rice, O., Kavanagh, S. et al. DNA extraction method affects microbial community profiles from soils and sediment. Appl Microbiol Biotechnol 77, 955–964 (2007). https://doi.org/10.1007/s00253-007-1219-y
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DOI: https://doi.org/10.1007/s00253-007-1219-y