FN Archimer Export Format
PT J
TI DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols
BT 
AF ALAIN, Karine
   CALLAC, Nolwenn
   CIOBANU, Maria Cristina
   REYNAUD, Yann
   DUTHOIT, Frederique
   JEBBAR, Mohamed
AS 1:1;2:2;3:3;4:1;5:1;6:1;
FF 1:;2:PDG-REM-EEP-LMEE;3:;4:;5:;6:;
C1 Univ Bretagne Occidentale UBO UEB, IUEM, LMEE, UMR 6197, F-29280 Plouzane, France.
   Ifremer, LMEE, UMR6197, F-29280 Plouzane, France.
   Inst Univ Europeen Mer, Lab Microbiol Environnements Extremes, CNRS, UMR 6197, F-29280 Plouzane, France.
C2 UBO, FRANCE
   IFREMER, FRANCE
   UBO, FRANCE
SI BREST
   ANTES
SE PDG-REM-EEP-LMEE
IN WOS Ifremer jusqu'en 2018
   copubli-france
   copubli-univ-france
IF 2.086
TC 25
UR https://archimer.ifremer.fr/doc/00056/16691/14364.pdf
LA English
DT Article
CR ESSCAR-9
   MD 153 / AUSFAIR
   RHOSOS
BO Le Suroît
   Marion Dufresne
DE ;Sediment;DNA extraction;Deep subsurface biosphere
AB 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.
PY 2011
PD DEC
SO Journal Of Microbiological Methods
SN 0167-7012
PU Elsevier Science Bv
VL 87
IS 3
UT 000297892200016
BP 355
EP 362
DI 10.1016/j.mimet.2011.09.015
ID 16691
ER

EF