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Pawlowski J, Bruce K, Panksep K, et al. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. Sci Total Environ. 2021;151783doi: 10.1016/j.scitotenv.2021.151783.
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, F. O., Danovaro, R., Dell'Anno, A., Duarte, S., 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. (2021). Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. The Science of the total environment, 151783. https://doi.org/10.1016/j.scitotenv.2021.151783
Pawlowski, J, et al. "Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods." The Science of the total environment vol. (2021): 151783. doi: https://doi.org/10.1016/j.scitotenv.2021.151783
Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. Sci Total Environ. 2021 Nov 19;151783. doi: 10.1016/j.scitotenv.2021.151783. Epub 2021 Nov 19. PMID: 34801504.
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Sci Total Environ. 2021 Nov 19;151783. doi: 10.1016/j.scitotenv.2021.151783. Epub 2021 Nov 19.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods.

The Science of the total environment

J Pawlowski, K Bruce, K Panksep, F I Aguirre, S Amalfitano, L Apothéloz-Perret-Gentil, T Baussant, A Bouchez, L Carugati, K Cermakova, T Cordier, C Corinaldesi, F O Costa, R Danovaro, A Dell'Anno, S Duarte, U Eisendle, B J D Ferrari, F Frontalini, L Frühe, A Haegerbaeumer, V Kisand, A Krolicka, A Lanzén, F Leese, F Lejzerowicz, E Lyautey, I Maček, M Sagova-Marečková, J K Pearman, X Pochon, T Stoeck, R Vivien, A Weigand, S Fazi

Affiliations

  1. Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland.
  2. NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK.
  3. Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia.
  4. Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
  5. Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland.
  6. Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway.
  7. INRAE, CARRTEL, 74200 Thonon-les-Bains, France.
  8. Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy.
  9. ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland.
  10. Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway.
  11. Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy.
  12. Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
  13. University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria.
  14. Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland.
  15. Department of Pure and Applied Sciences, Urbino University, Urbino, Italy.
  16. Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany.
  17. Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany.
  18. Institute of Technology, University of Tartu, Tartu 50411, Estonia.
  19. AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain.
  20. University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany.
  21. Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
  22. Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France.
  23. Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia.
  24. Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic.
  25. Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand.
  26. Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand.
  27. National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg.
  28. Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy. Electronic address: [email protected].

PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783

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.

Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.

Keywords: Aquatic ecosystems; Environmental DNA; Metabarcoding; Monitoring; Sediments

Conflict of interest statement

Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this pa

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