DNA extraction method affects microbial community profiles from soils and sediment
DNA extraction method affects microbial community profiles from soils and sediment
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DOI：
10.1007/s00253-007-1219-y
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发表时间：
2007-12-01
影响因子：
5
通讯作者：
O'Flaherty, Vincent
中科院分区：
文献类型：
--
作者：
Carrigg, Cora;Rice, Olivia;O'Flaherty, Vincent
为了评估不同的脱氧核糖核酸（DNA）提取方法是否会影响细菌群落组成的估计，基于16S核糖体核糖核酸基因变性梯度凝胶电泳（DGGE）图谱，我们比较了三种土壤和一种海洋沉积物的四种原位裂解方法。对纯化的DNA提取物进行聚合酶链反应生成的DGGE图谱进行分析，结果表明DNA提取方法的选择对生成的细菌群落图谱有显著影响。这既反映在从每个样品中检测到的条带或核糖型的数量上，也反映在随后的原理坐标分析和使用算术平均分析的未加权对群法中。这些方法在稳健性上也有显著差异，即在多个分析中的再现性。两种方法，都是基于打珠，被证明是适用于比较研究的范围内的土壤和沉积物类型。
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.