title: Integrated lysis procedures reduce extraction biases of microbial DNA from mangrove sediment.
abstract: 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.
authors.affiliation: Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, PR China.
authors.forename: Yun-Xia
authors.initials: YX
authors.lastname: Jiang
authors.forename: Ji-Guo
authors.initials: JG
authors.lastname: Wu
authors.forename: Ke-Qiang
authors.initials: KQ
authors.lastname: Yu
authors.forename: Chun-Xiang
authors.initials: CX
authors.lastname: Ai
authors.forename: Fei
authors.initials: F
authors.lastname: Zou
authors.forename: Hong-Wei
authors.initials: HW
authors.lastname: Zhou
mesh_terms: D019641:DNA, Archaeal / Q000302:isolation & purification*; D004269:DNA, Bacterial / Q000302:isolation & purification*; D004271:DNA, Fungal / Q000302:isolation & purification*; D058645:Denaturing Gradient Gel Electrophoresis / Q000379:methods; D019015:Geologic Sediments / Q000382:microbiology*; D016133:Polymerase Chain Reaction; D014871:Water Microbiology
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004271:DNA, Fungal