An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities

Type Article
Date 2020-05
Language English
Author(s) Brandt Miriam1, Trouche Blandine2, Henry Nicolas3, 4, Liautard-Haag Cathy1, Maignien Lois2, De Vargas Colomban3, 4, Wincker Patrick4, 5, Poulain Julie4, 5, Zeppilli DanielaORCID6, Arnaud-Haond SophieORCID1
Affiliation(s) 1 : MARBEC, Univ Montpellier, Ifremer, IRD, CNRS, Sète, France
2 : Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Univ Brest, CNRS, Ifremer, Plouzané, France
3 : Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Roscoff, France
4 : Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
5 : Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
6 : Ifremer, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, Plouzané, France
Source Frontiers In Marine Science (2296-7745) (Frontiers Media SA), 2020-05 , Vol. 7 , P. 234 (12p.)
DOI 10.3389/fmars.2020.00234
WOS© Times Cited 2
Keyword(s) environmental metabarcoding, RNA versus DNA, extracellular DNA, deep-sea biodiversity, benthic ecology, biomonitoring, method testing
Abstract

The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removing short DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from ∼2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (≥10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNA for logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (≥10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.

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Publisher's official version 12 1 MB Open access
DATA SHEET S1 | Supplementary material tables (S1 to S7) and figures (S1 to S6). 16 1 MB Open access
DATA SHEET S2 | Sample metadata. 110 KB Open access
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How to cite 

Brandt Miriam, Trouche Blandine, Henry Nicolas, Liautard-Haag Cathy, Maignien Lois, De Vargas Colomban, Wincker Patrick, Poulain Julie, Zeppilli Daniela, Arnaud-Haond Sophie (2020). An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities. Frontiers In Marine Science, 7, 234 (12p.). Publisher's official version : https://doi.org/10.3389/fmars.2020.00234 , Open Access version : https://archimer.ifremer.fr/doc/00630/74165/