Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, PR China.
J Biosci Bioeng. 2011 Feb;111(2):153-7. doi: 10.1016/j.jbiosc.2010.10.006. Epub 2010 Nov 16.
Sufficient lysis of soil or sediment microbes is a critical step for analyzing microbial community structures and for preparing metagenomic DNA libraries. The present study compared lysis methods for recovering archaeal, bacterial, actinomycete, and fungal DNAs from a mangrove sediment sample. PCR results showed that individual procedures using SDS, lysozyme, sonication, freeze-thaw, microwave, and vigorous shaking could extract archaeal or bacterial DNA but failed for actinomycetes or fungi cells. In comparison, an integrated lysis procedure using SDS, lysozyme, and vigorous shaking successfully obtained fungal DNA, and a combination of SDS, lysozyme, vigorous shaking, and microwave treatments recovered DNA from actinomycetes. Denaturing gradient gel electrophoresis (DGGE) results showed that although single lysis procedures can lyse bacterial DNA, all of them assessed the indigenous bacterial community structure with significant biases. The integrated lysis protocols described in the present study could be useful for extracting DNA from various types of sediments.
充分裂解土壤或沉积物中的微生物是分析微生物群落结构和制备宏基因组 DNA 文库的关键步骤。本研究比较了从红树林沉积物样品中提取古菌、细菌、放线菌和真菌 DNA 的裂解方法。PCR 结果表明，单独使用 SDS、溶菌酶、超声、冻融、微波和剧烈振荡的方法可以提取古菌或细菌 DNA，但不能提取放线菌或真菌细胞。相比之下，使用 SDS、溶菌酶和剧烈振荡的综合裂解程序成功获得了真菌 DNA，而 SDS、溶菌酶、剧烈振荡和微波处理的组合则从放线菌中回收了 DNA。变性梯度凝胶电泳 (DGGE) 结果表明，尽管单一的裂解程序可以裂解细菌 DNA，但它们都对土著细菌群落结构产生了显著的偏差。本研究中描述的综合裂解方案可用于从各种类型的沉积物中提取 DNA。
