Capture by hybridization for full‐length barcode‐based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems

Type Article
Date 2022-02
Language English
Author(s) Günther BabettORCID4, Marre Sophie2, Defois Clémence2, Merzi Thomas3, Blanc Philippe3, Peyret Pierre2, Arnaud-Haond SophieORCID1
Affiliation(s) 1 : MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
2 : Université Clermont Auvergne Microbiology, Digestive Environment and Health (MEDIS), INRAE, UMR 0454 MEDIS 63000 Clermont‐Ferrand, France
3 : Total SE, Centre Scientifique et Technique Jean Feger 64000 Pau, France
4 : MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
Source Molecular Ecology Resources (1755-098X) (Wiley), 2022-02 , Vol. 22 , N. 2 , P. 623-637
DOI 10.1111/1755-0998.13500
WOS© Times Cited 4
Keyword(s) 16S, 18S, environmental DNA, metabarcoding, metazoan
Abstract

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.

Full Text
File Pages Size Access
Publisher's official version 43 1 MB Open access
Supplementary Material 89 KB Open access
Top of the page

How to cite 

Günther Babett, Marre Sophie, Defois Clémence, Merzi Thomas, Blanc Philippe, Peyret Pierre, Arnaud-Haond Sophie (2022). Capture by hybridization for full‐length barcode‐based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems. Molecular Ecology Resources, 22(2), 623-637. Publisher's official version : https://doi.org/10.1111/1755-0998.13500 , Open Access version : https://archimer.ifremer.fr/doc/00720/83221/