DNA extraction method affects microbial community profiles from soils and sediment

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 soi...

Full description

Saved in:
Bibliographic Details
Published in:Applied microbiology and biotechnology 2007-12, Vol.77 (4), p.955-964
Main Authors: Carrigg, Cora, Rice, Olivia, Kavanagh, Siobhán, Collins, Gavin, O'Flaherty, Vincent
Format: Article
Language:English
Subjects:
Bacteria - genetics
Biological and medical sciences
Biotechnology
Community composition
Comparative studies
Deoxyribonucleic acid
DGGE
DNA
DNA extraction
DNA, Bacterial - genetics
DNA, Bacterial - isolation & purification
DNA, Ribosomal - analysis
Efficiency
Electrophoresis, Polyacrylamide Gel - methods
Environmental Microbiology
Fundamental and applied biological sciences. Psychology
Genes
Geologic Sediments - microbiology
Laboratories
Lysis efficiency
Marine sediments
Methods
Microbial diversity
Microbiology
Microorganisms
Nucleic Acid Denaturation
Polymerase chain reaction
Reproducibility
RNA, Ribosomal, 16S - genetics
Sediments
soil
Soil Microbiology
Soils
Studies
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0175-7598
1432-0614
DOI:10.1007/s00253-007-1219-y