A Modified SDS-Based DNA Extraction Method for High Quality Environmental DNA from Seafloor Environments
| Autor: | Xinxu Zhang, Fumio Inagaki, Yuki Morono, Vengadesh Perumal Natarajan, Fengping Wang |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Microbiology (medical) Lysis 030106 microbiology Computational biology Biology Microbiology 03 medical and health sciences chemistry.chemical_compound Environmental DNA DNA extraction Original Research Genetics metagenomics DNA recovery Dna concentration genomic DNA 030104 developmental biology PCR chemistry Microbial population biology Metagenomics cell lysis efficiency marine sediments DNA |
| Zdroj: | Frontiers in Microbiology |
| ISSN: | 1664-302X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|