Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

Type Article
Date 2021-04
Language English
Author(s) Brandt Miriam1, Pradillon FlorenceORCID2, Trouche Blandine6, Henry Nicolas4, Liautard-Haag Cathy7, Cambon-Bonavita Marie-AnneORCID3, Cueff-Gauchard ValerieORCID3, Wincker Patrick5, Belser Caroline5, Poulain Julie5, Arnaud-Haond SophieORCID1, Zeppilli DanielaORCID2
Affiliation(s) 1 : MARBEC, IFREMER, IRD, CNRS, Univ Montpellier, Sète, France
2 : Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), IFREMER, CS10070, 29280, Plouzané, France
3 : IFREMER, CNRS, Laboratoire de Microbiologie Des Environnements Extrêmes (LM2E), Univ Brest, Plouzané, France
4 : CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Sorbonne University, 29680, Roscoff, France
5 : Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057, Evry, France
6 : IFREMER, CNRS, Laboratoire de Microbiologie Des Environnements Extrêmes (LM2E), Univ Brest, Plouzané, France
7 : MARBEC, IFREMER, IRD, CNRS, Univ Montpellier, Sète, France
Source Scientific Reports (2045-2322) (Springer Science and Business Media LLC), 2021-04 , Vol. 11 , N. 1 , P. 7856 (14p.)
DOI 10.1038/s41598-021-86396-8
WOS© Times Cited 2
Abstract

Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1–V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.

Full Text
File Pages Size Access
Publisher's official version 14 1 MB Open access
Supplementary Information 1. 11 1 MB Open access
Supplementary Information 2. 68 KB Open access
Supplementary Information 3. 75 KB Open access
Top of the page

How to cite 

Brandt Miriam, Pradillon Florence, Trouche Blandine, Henry Nicolas, Liautard-Haag Cathy, Cambon-Bonavita Marie-Anne, Cueff-Gauchard Valerie, Wincker Patrick, Belser Caroline, Poulain Julie, Arnaud-Haond Sophie, Zeppilli Daniela (2021). Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA. Scientific Reports, 11(1), 7856 (14p.). Publisher's official version : https://doi.org/10.1038/s41598-021-86396-8 , Open Access version : https://archimer.ifremer.fr/doc/00689/80094/