DNA extraction method affects microbial community profiles from soils and sediment
| Autor: | Olivia Rice, Siobhán Kavanagh, Vincent O'Flaherty, Gavin Collins, Cora Carrigg |
|---|---|
| Rok vydání: | 2007 |
| Předmět: |
DNA
Bacterial Geologic Sediments Lysis Biology Nucleic Acid Denaturation Applied Microbiology and Biotechnology DNA Ribosomal law.invention chemistry.chemical_compound law RNA Ribosomal 16S Environmental Microbiology Polymerase chain reaction Soil Microbiology Chromatography Bacteria Sediment General Medicine DNA Ribosomal RNA Molecular biology DNA extraction chemistry Electrophoresis Polyacrylamide Gel Soil microbiology Temperature gradient gel electrophoresis Biotechnology |
| Zdroj: | Applied microbiology and biotechnology. 77(4) |
| ISSN: | 0175-7598 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|