A Modified SDS-Based DNA Extraction Method for High Quality Environmental DNA from Seafloor Environments.
A Modified SDS-Based DNA Extraction Method for High Quality Environmental DNA from Seafloor Environments.
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一种改进的基于 SDS 的海底环境高质量环境 DNA 提取方法
DOI：
10.3389/fmicb.2016.00986
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发表时间：
2016
影响因子：
5.2
通讯作者：
Wang F
中科院分区：
文献类型：
--
作者：
Natarajan VP;Zhang X;Morono Y;Inagaki F;Wang F
从环境样品中提取高质量的基因组DNA是通过分子生态学方法了解微生物群落遗传、代谢和进化特征的关键一步。然而，由于在不使基因组DNA片段化的情况下有效细胞裂解的困难，这通常是具有挑战性的。本工作旨在改进以往基于SDS的高生物量海底样品（如远洋沉积物和金属硫化物烟囱）的DNA提取方法，以获得高质量和高分子量的基因组DNA，用于后续的分子生态学分析。在这方面，我们标准化的改良SDS为基础的DNA提取方法（M-SDS），其性能进行了比较，最近开发的热碱DNA提取方法（HA）和商业DNA提取试剂盒提取。结果表明，M-SDS法比其他两种方法具有更高的DNA产量和裂解效率、更低的DNA剪切和更高的多样性得分，为海底沉积环境微生物群落的DNA组合提供了全面的信息。
Recovering high quality genomic DNA from environmental samples is a crucial primary step to understand the genetic, metabolic, and evolutionary characteristics of microbial communities through molecular ecological approaches. However, it is often challenging because of the difficulty of effective cell lysis without fragmenting the genomic DNA. This work aims to improve the previous SDS-based DNA extraction methods for high-biomass seafloor samples, such as pelagic sediments and metal sulfide chimney, to obtain high quality and high molecular weight of the genomic DNA applicable for the subsequent molecular ecological analyses. In this regard, we standardized a modified SDS-based DNA extraction method (M-SDS), and its performance was then compared to those extracted by a recently developed hot-alkaline DNA extraction method (HA) and a commercial DNA extraction kit. Consequently, the M-SDS method resulted in higher DNA yield and cell lysis efficiency, lower DNA shearing, and higher diversity scores than other two methods, providing a comprehensive DNA assemblage of the microbial community on the seafloor depositional environment.