DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols

Type Article
Date 2011-12
Language English
Author(s) Alain Karine1, Callac Nolwenn2, Ciobanu Maria Cristina3, Reynaud Yann1, Duthoit Frederique1, Jebbar Mohamed1
Affiliation(s) 1 : Univ Bretagne Occidentale UBO UEB, IUEM, LMEE, UMR 6197, F-29280 Plouzane, France.
2 : Ifremer, LMEE, UMR6197, F-29280 Plouzane, France.
3 : Inst Univ Europeen Mer, Lab Microbiol Environnements Extremes, CNRS, UMR 6197, F-29280 Plouzane, France.
Source Journal Of Microbiological Methods (0167-7012) (Elsevier Science Bv), 2011-12 , Vol. 87 , N. 3 , P. 355-362
DOI 10.1016/j.mimet.2011.09.015
WOS© Times Cited 22
Keyword(s) Sediment, DNA extraction, Deep subsurface biosphere
Abstract Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low bio-masses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recently obtained by use of a cryogenic mill (Lipp et al., 2008). These findings encouraged us to devise a DNA extraction protocol using this tool. Thirteen procedures involving a combination of grinding in liquid nitrogen (for various durations and beating rates) with different chemical solutions (phenol, chloroform, SDS, sarkosyl, proteinase, GTC), or with use of DNA recovery kits (MagExtractor (R)) were compared. Effective DNA extraction was evaluated in terms of cell lysis efficiency, DNA extraction efficiency, DNA yield and determination of prokaryotic diversity. Results were compared to those obtained by standard protocols: the FastDNA (R) SPIN kit for soil and the Zhou protocol. For most sediment types grinding in a cryogenic mill at a low beating rate in combination with direct phenol-chloroform extraction resulted in much higher DNA yields than those obtained using classical procedures. In general (except for clay-rich sediments), this procedure provided high-quality crude extracts for direct downstream nested-PCR, from cell numbers as low as 1.1 x 10(6) cells/cm(3). This procedure is simple, rapid, low-cost, and could be used with minor modifications for large-scale DNA extractions for a variety of experimental goals. (C) 2011 Elsevier B.V. All rights reserved.
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Alain Karine, Callac Nolwenn, Ciobanu Maria Cristina, Reynaud Yann, Duthoit Frederique, Jebbar Mohamed (2011). DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols. Journal Of Microbiological Methods, 87(3), 355-362. Publisher's official version : https://doi.org/10.1016/j.mimet.2011.09.015 , Open Access version : https://archimer.ifremer.fr/doc/00056/16691/