FN Archimer Export Format
PT J
TI Influence of DNA Extraction Method, 16S rRNA Targeted Hypervariable Regions, and Sample Origin on Microbial Diversity Detected by 454 Pyrosequencing in Marine Chemosynthetic Ecosystems
BT 
AF CRUAUD, Perrine
   VIGNERON, Adrien
   LUCCHETTI-MIGANEH, Celine
   CIRON, Pierre Emmanuel
   GODFROY, Anne
   CAMBON-BONAVITA, Marie-Anne
AS 1:1,2,3;2:1,2,3;3:4;4:4;5:1,2,3;6:1,2,3;
FF 1:;2:PDG-REM-EEP-LMEE;3:;4:;5:PDG-REM-EEP-LMEE;6:PDG-REM-EEP-LMEE;
C1 IFREMER, Technopole Brest Iroise, Lab Microbiol Environm Extremes, UMR6197, Plouzane, France.
   Univ Bretagne Occidentale, Lab Microbiol Environm Extremes, UMR6197, Plouzane, France.
   Technopole Brest Iroise, CNRS, Lab Microbiol Environm Extremes, UMR6197, Plouzane, France.
   Genostar, Montbonnot St Martin, France.
C2 IFREMER, FRANCE
   UBO, FRANCE
   CNRS, FRANCE
   GENOSTAR, FRANCE
SI BREST
SE PDG-REM-EEP-LMEE
IN WOS Ifremer jusqu'en 2018
   copubli-france
   copubli-univ-france
IF 3.668
TC 56
TU Centre national de la recherche scientifique
   Institut français de recherche pour l'exploitation de la mer
   Université de Bretagne Occidentale
UR https://archimer.ifremer.fr/doc/00204/31495/29907.pdf
   https://archimer.ifremer.fr/doc/00204/31495/29908.pdf
LA English
DT Article
CR BIG
BO L'Atalante
AB Next-generation sequencing (NGS) opens up exciting possibilities for improving our knowledge of environmental microbial diversity, allowing rapid and cost-effective identification of both cultivated and uncultivated microorganisms. However, library preparation, sequencing, and analysis of the results can provide inaccurate representations of the studied community compositions. Therefore, all these steps need to be taken into account carefully. Here we evaluated the effects of DNA extraction methods, targeted 16S rRNA hypervariable regions, and sample origins on the diverse microbes detected by 454 pyrosequencing in marine cold seep and hydrothermal vent sediments. To assign the reads with enough taxonomic precision, we built a database with about 2,500 sequences from Archaea and Bacteria from deep-sea marine sediments, affiliated according to reference publications in the field. Thanks to statistical and diversity analyses as well as inference of operational taxonomic unit (OTU) networks, we show that (i) while DNA extraction methods do not seem to affect the results for some samples, they can lead to dramatic changes for others; and (ii) the choice of amplification and sequencing primers also considerably affects the microbial community detected in the samples. Thereby, very different proportions of pyrosequencing reads were obtained for some microbial lineages, such as the archaeal ANME-1, ANME-2c, and MBG-D and deltaproteobacterial subgroups. This work clearly indicates that the results from sequencing-based analyses, such as pyrosequencing, should be interpreted very carefully. Therefore, the combination of NGS with complementary approaches, such as fluorescence in situ hybridization (FISH)/catalyzed reporter deposition (CARD)-FISH or quantitative PCR (Q-PCR), would be desirable to gain a more comprehensive picture of environmental microbial communities.
PY 2014
PD AUG
SO Applied And Environmental Microbiology
SN 0099-2240
PU Amer Soc Microbiology
VL 80
IS 15
UT 000338707800017
BP 4626
EP 4639
DI 10.1128/AEM.00592-14
ID 31495
ER

EF