FN Archimer Export Format
PT J
TI Capture by hybridization for full‐length barcode‐based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems
BT 
AF Günther, Babett
   Marre, Sophie
   Defois, Clémence
   Merzi, Thomas
   Blanc, Philippe
   Peyret, Pierre
   ARNAUD-HAOND, Sophie
AS 1:4;2:2;3:2;4:3;5:3;6:2;7:1;
FF 1:;2:;3:;4:;5:;6:;7:PDG-RBE-MARBEC-LHM;
C1 MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
   Université Clermont Auvergne Microbiology, Digestive Environment and Health (MEDIS), INRAE, UMR 0454 MEDIS 63000 Clermont‐Ferrand, France
   Total SE, Centre Scientifique et Technique Jean Feger 64000 Pau, France
   MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
C2 IFREMER, FRANCE
   UNIV CLERMONT AUVERGNE, FRANCE
   TOTAL CSTJF, FRANCE
   CNRS, FRANCE
SI SETE
SE PDG-RBE-MARBEC-LHM
UM MARBEC
IN WOS Ifremer UMR
   WOS Cotutelle UMR
   copubli-france
   copubli-univ-france
IF 7.7
TC 4
UR https://archimer.ifremer.fr/doc/00720/83221/88214.pdf
   https://archimer.ifremer.fr/doc/00720/83221/88215.docx
LA English
DT Article
CR AMIGO
   MARMINE
DE ;16S;18S;environmental DNA;metabarcoding;metazoan
AB Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea. 
PY 2022
PD FEB
SO Molecular Ecology Resources
SN 1755-098X
PU Wiley
VL 22
IS 2
UT 000697252900001
BP 623
EP 637
DI 10.1111/1755-0998.13500
ID 83221
ER

EF