title: A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types.
abstract: A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals.
authors.affiliation: Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Lever
authors.affiliation: Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark.
authors.forename: Andrea
authors.initials: A
authors.lastname: Torti
authors.affiliation: Department of Chemistry, University of Duisburg-Essen Essen, Germany.
authors.forename: Philip
authors.initials: P
authors.lastname: Eickenbusch
authors.affiliation: Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA.
authors.forename: Alexander B
authors.initials: AB
authors.lastname: Michaud
authors.affiliation: Microbiology Section, Department of Bioscience, Aarhus University Aarhus, Denmark ; Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University Aarhus, Denmark.
authors.forename: Tina
authors.initials: T
authors.lastname: Šantl-Temkiv
authors.affiliation: Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark.
authors.forename: Bo Barker
authors.initials: BB
authors.lastname: Jørgensen
keywords: DNA; RNA; environmental sample; extracellular; extraction; intracellular; low biomass; modular