title: A Modified SDS-Based DNA Extraction Method for High Quality Environmental DNA from Seafloor Environments.
abstract: 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.
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China; State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China.
authors.forename: Vengadesh Perumal
authors.initials: VP
authors.lastname: Natarajan
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University Shantou, China.
authors.forename: Xinxu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology Kochi, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Morono
authors.affiliation: Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology Kochi, Japan.
authors.forename: Fumio
authors.initials: F
authors.lastname: Inagaki
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China; State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China.
authors.forename: Fengping
authors.initials: F
authors.lastname: Wang
keywords: DNA extraction; DNA recovery; PCR; cell lysis efficiency; marine sediments; metagenomics