Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods
| Autor(a) principal: | |
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| Data de Publicação: | 2022 |
| Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| Texto Completo: | https://hdl.handle.net/1822/80003 |
Resumo: | Supplementary data to this article can be found online at https://doi. org/10.1016/j.scitotenv.2021.151783 |
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Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methodsAquatic ecosystemsEnvironmental DNAMetabarcodingMonitoringSedimentsScience & TechnologySupplementary data to this article can be found online at https://doi. org/10.1016/j.scitotenv.2021.151783Environmental 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.The work is the result of the DNAqua-Net workshop held in Rome, on June 10–12, 2019, organised by IRSA-CNR and supported by European Cooperation in Science and Technology (COST) grant CA15219 (DNAqua-Net). It largely benefited from the discussions with DNAqua-Net members during this event as well as other DNAqua-Net conferences.This study was carried out within the UNIVPM VIRIDE Project (n. 2017EKFA98) funded by the Ministry of University and Research of Italy (MUR) and the Italian National Project on the use of environmental DNA for the identification of marine non-indigenous species funded by the Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA). JP, TC, and LAPG were supported by the Swiss National Science Foundation (grant 31003A_179125) as well as FL with an Early Postdoc.Mobility grant (P2GEP3_171829). MS-M was supported by the Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund-Project CZ.02.1.01/0.0/0.0/16_019/0000845 and LTC 20063. KP was supported by the European Regional Development Fund within National Programme for Addressing Socio-Economic Challenges through R&D (L190003VLVI RITA1/02-60-05) and base financed project P190250PKKH of Estonian University of Life Sciences, IM was supported by the Slovenian Research Agency (ARRS) programme P4-0085. SD was supported by the Portuguese Foundation for Science and Technology (FCT) (CEECIND/00667/2017). LC was supported by the PON AIM 1854833 – PON Ricerca e Innovazione 2014–2020 – Azione I.2 – D.D. n. 407, 27/02/2018 – Attraction and International Mobility.VK was supported by grants PUT1389 (ETAg) and Institute of Technology, University of Tartu basic funding grant.Elsevier 1Universidade do MinhoPawlowski, J.Bruce, K.Panksep, K.Aguirre, F. I.Amalfitano, S.Apothéloz-Perret-Gentil, L.Baussant, T.Bouchez, A.Carugati, L.Cermakova, K.Cordier, T.Corinaldesi, C.Costa, Filipe O.Danovaro, R.Dell'Anno, A.Duarte, Sofia Alexandra FerreiraEisendle, U.Ferrari, B. J.D.Frontalini, F.Frühe, L.Haegerbaeumer, A.Kisand, V.Krolicka, A.Lanzén, A.Leese, F.Lejzerowicz, F.Lyautey, E.Maček, I.Sagova-Marečková, M.Pearman, J. K.Pochon, X.Stoeck, T.Vivien, R.Weigand, A.Fazi, S.2022-04-202022-04-20T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/1822/80003engPawlowski, J., Bruce, K., Panksep, K., Aguirre, F. I., Amalfitano, S., Apothéloz-Perret-Gentil, L., . . . Fazi, S. (2022). Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. Science of the Total Environment, 818, 151783. doi: https://doi.org/10.1016/j.scitotenv.2021.1517830048-96971879-102610.1016/j.scitotenv.2021.1517833480150434801504https://www.sciencedirect.com/science/article/pii/S0048969721068595info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-11-16T01:28:01Zoai:repositorium.sdum.uminho.pt:1822/80003Portal AgregadorONGhttps://www.rcaap.pt/oai/openairemluisa.alvim@gmail.comopendoar:71602024-11-16T01:28:01Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
| dc.title.none.fl_str_mv |
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods |
| title |
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods |
| spellingShingle |
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods Pawlowski, J. Aquatic ecosystems Environmental DNA Metabarcoding Monitoring Sediments Science & Technology |
| title_short |
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods |
| title_full |
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods |
| title_fullStr |
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods |
| title_full_unstemmed |
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods |
| title_sort |
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods |
| author |
Pawlowski, J. |
| author_facet |
Pawlowski, J. Bruce, K. Panksep, K. Aguirre, F. I. Amalfitano, S. Apothéloz-Perret-Gentil, L. Baussant, T. Bouchez, A. Carugati, L. Cermakova, K. Cordier, T. Corinaldesi, C. Costa, Filipe O. Danovaro, R. Dell'Anno, A. Duarte, Sofia Alexandra Ferreira Eisendle, U. Ferrari, B. J.D. Frontalini, F. Frühe, L. Haegerbaeumer, A. Kisand, V. Krolicka, A. Lanzén, A. Leese, F. Lejzerowicz, F. Lyautey, E. Maček, I. Sagova-Marečková, M. Pearman, J. K. Pochon, X. Stoeck, T. Vivien, R. Weigand, A. Fazi, S. |
| author_role |
author |
| author2 |
Bruce, K. Panksep, K. Aguirre, F. I. Amalfitano, S. Apothéloz-Perret-Gentil, L. Baussant, T. Bouchez, A. Carugati, L. Cermakova, K. Cordier, T. Corinaldesi, C. Costa, Filipe O. Danovaro, R. Dell'Anno, A. Duarte, Sofia Alexandra Ferreira Eisendle, U. Ferrari, B. J.D. Frontalini, F. Frühe, L. Haegerbaeumer, A. Kisand, V. Krolicka, A. Lanzén, A. Leese, F. Lejzerowicz, F. Lyautey, E. Maček, I. Sagova-Marečková, M. Pearman, J. K. Pochon, X. Stoeck, T. Vivien, R. Weigand, A. Fazi, S. |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Universidade do Minho |
| dc.contributor.author.fl_str_mv |
Pawlowski, J. Bruce, K. Panksep, K. Aguirre, F. I. Amalfitano, S. Apothéloz-Perret-Gentil, L. Baussant, T. Bouchez, A. Carugati, L. Cermakova, K. Cordier, T. Corinaldesi, C. Costa, Filipe O. Danovaro, R. Dell'Anno, A. Duarte, Sofia Alexandra Ferreira Eisendle, U. Ferrari, B. J.D. Frontalini, F. Frühe, L. Haegerbaeumer, A. Kisand, V. Krolicka, A. Lanzén, A. Leese, F. Lejzerowicz, F. Lyautey, E. Maček, I. Sagova-Marečková, M. Pearman, J. K. Pochon, X. Stoeck, T. Vivien, R. Weigand, A. Fazi, S. |
| dc.subject.por.fl_str_mv |
Aquatic ecosystems Environmental DNA Metabarcoding Monitoring Sediments Science & Technology |
| topic |
Aquatic ecosystems Environmental DNA Metabarcoding Monitoring Sediments Science & Technology |
| description |
Supplementary data to this article can be found online at https://doi. org/10.1016/j.scitotenv.2021.151783 |
| publishDate |
2022 |
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2022-04-20 2022-04-20T00:00:00Z |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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https://hdl.handle.net/1822/80003 |
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eng |
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eng |
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Pawlowski, J., Bruce, K., Panksep, K., Aguirre, F. I., Amalfitano, S., Apothéloz-Perret-Gentil, L., . . . Fazi, S. (2022). Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. Science of the Total Environment, 818, 151783. doi: https://doi.org/10.1016/j.scitotenv.2021.151783 0048-9697 1879-1026 10.1016/j.scitotenv.2021.151783 34801504 34801504 https://www.sciencedirect.com/science/article/pii/S0048969721068595 |
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openAccess |
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application/pdf |
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Elsevier 1 |
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Elsevier 1 |
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