FN Archimer Export Format
PT J
TI How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?
BT 
AF Stauffer, Salomé
   Jucker, Meret
   Keggin, Thomas
   Marques, Virginie
   Andrello, Marco
   Bessudo, Sandra
   Cheutin, Marie-Charlotte
   Borrero-Perez, Giomar Helena
   Richards, Eilish
   Dejean, Tony
   Hocdé, Régis
   JUHEL, Jean-Baptiste
   Ladino, Felipe
   Letessier, Tom b
   LOISEAU, Nicolas
   Maire, Eva
   Mouillot, David
   Mutis Martinezguerra, Maria
   Manel, Stéphanie
   Polanco Fernandez, Andrea
   Valentini, Alice
   Velez, Laure
   ALBOUY, Camille
   Pellissier, Loic
   Waldock, Conor
AS 1:1;2:1;3:1,2;4:3,4;5:5;6:6;7:3;8:7;9:1;10:8;11:14;12:3;13:6;14:9,10;15:3;16:11;17:13;18:7;19:4;20:7;21:8;22:3;23:12;24:1,2;25:1,2;
FF 1:;2:;3:;4:;5:;6:;7:;8:;9:;10:;11:;12:;13:;14:;15:;16:;17:;18:;19:;20:;21:;22:;23:PDG-RBE-EMH;24:;25:;
C1 Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
   Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
   MARBEC, Univ. Montpellier, CNRS, IFREMER, IRD, Montpellier, France
   CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ. Paul Valéry Montpellier 3, Montpellier, France
   Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment, National Research Council, Rome, Italy
   Fundación Malpelo y otros ecosistemas marinos, Bogotá, Colombia
   Instituto de Investigaciones Marinas y Costeras-INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC), Santa Marta, Colombia
   SPYGEN, Le Bourget-du- Lac, France
   Institute of Zoology, Zoological Society of London, London, UK
   Marine Futures Lab, University of Western Australia, Crawley, WA, Australia
   Lancaster Environment Centre, Lancaster University, Lancaster, UK
   IFREMER, unité Écologie et Modèles pour l’Halieutique, Nantes, France
   MARBEC, Univ. Montpellier, CNRS, IFREMER, IRD, Montpellier, France
   MARBEC, Univ. Montpellier, CNRS, IFREMER, IRD, Montpellier, France
C2 ETH ZURICH, SWITZERLAND
   SWISS FED RES INST WSL, SWITZERLAND
   UNIV MONTPELLIER, FRANCE
   UNIV MONTPELLIER, FRANCE
   CNR IAS, ITALY
   FUNDACION MALPELO, COLOMBIA
   INVEMAR, COLOMBIA
   SPYGEN, FRANCE
   ZOOL SOC LONDON, UK
   UNIV WESTERN AUSTRALIA, AUSTRALIA
   UNIV LANCASTER, UK
   IFREMER, FRANCE
   CNRS, FRANCE
   IRD, FRANCE
SI NANTES
SE PDG-RBE-EMH
UM MARBEC
IN WOS Ifremer UPR
   WOS Cotutelle UMR
   DOAJ
   copubli-france
   copubli-p187
   copubli-europe
   copubli-univ-france
   copubli-int-hors-europe
   copubli-sud
IF 3.167
TC 21
UR https://archimer.ifremer.fr/doc/00727/83936/88857.pdf
   https://archimer.ifremer.fr/doc/00727/83936/88858.docx
LA English
DT Article
DE ;biomonitoring;coral reef diversity;environmental DNA;MOTU;sampling variability;tropical marine ecosystems
AB Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one another. As a result, non-saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false-negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA. 
PY 2021
PD NOV
SO Ecology And Evolution
SN 2045-7758
PU Wiley Open Access
VL 11
IS 21
UT 000703915900001
BP 14630
EP 14643
DI 10.1002/ece3.8150
ID 83936
ER

EF