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Title: Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods
Authors: Pawlowski, J.; Bruce, K.; Panksep, K.; Aguirre, I, F.; Amalfitano, S.; Apotheloz-Perret-Gentil, L.; Baussant, T.; Bouchez, A.; Carugati, L.; Cermakova, K.; Cordier, T.; Corinaldesi, C.; Costa, F. O.; Danovaro, R.; Dell'Anno, A.; Duarte, S.; Eisendle, U.; Ferrari, B. J. D.; Frontalini, F.; Fruehe, L.; Haegerbaeumer, A.; Kisand, V; Krolicka, A.;; Lanzen, Anders; Leese, F.; Lejzerowicz, F.; Lyautey, E.; Macek, I; Sagova-Mareckova, M.; Pearman, J. K.; Pochon, X.; Stoeck, T.; Vivien, R.; Weigand, A.; Fazi, S.
Abstract: Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
Issue Date: 2022
Publisher: ELSEVIER
Type: Review
DOI: 10.1016/j.scitotenv.2021.151783
ISSN: 0048-9697
E-ISSN: 1879-1026
Funder: European Cooperation in Science and Technology (COST) [CA15219]
Ministry of University and Research of Italy (MUR) [2017EKFA98]
Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA)
Swiss National Science Foundation [31003A\_179125]
Early Postdoc. Mobility grant [P2GEP3\_171829]
Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund [CZ.02.1.01/0.0/0.0/16\_019/0000845, LTC 20063]
European Regional Development Fund within National Programme for Addressing Socio-Economic Challenges through RD [L190003VLVI RITA1/02-60-05]
Estonian University of Life Sciences [P190250PKKH]
Slovenian Research Agency (ARRS) [P4-0085]
Portuguese Foundation for Science and Technology (FCT) [CEECIND/00667/2017]
PON AIM [1854833, 407]
Institute of Technology, University of Tartu
Swiss National Science Foundation (SNF) [P2GEP3\_171829] Funding Source: Swiss National Science Foundation (SNF)
Appears in Publication types:Artículos científicos

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