The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems.

Autor: Pawlowski J; Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland. Electronic address: jan.pawlowski@unige.ch., Kelly-Quinn M; School of Biology & Environmental Science, University College Dublin, Ireland., Altermatt F; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland(;) Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland., Apothéloz-Perret-Gentil L; Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland., Beja P; CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal., Boggero A; LifeWatch, Italy and CNR-Institute of Ecosystem Study (CNR-ISE), Largo Tonolli 50, 28922 Verbania Pallanza, Italy., Borja A; AZTI, Marine Research Division, Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain., Bouchez A; INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France., Cordier T; Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland., Domaizon I; INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France., Feio MJ; Marine and Environmental Sciences Centre, Faculty of Sciences and Technology, Department of Life Sciences, University of Coimbra, Portugal., Filipe AF; CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal., Fornaroli R; University of Milano Bicocca, Department of Earth and Environmental Sciences(DISAT), Piazza della Scienza 1,20126 Milano, Italy., Graf W; Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), 1180 Vienna, Austria., Herder J; RAVON, Postbus 1413, Nijmegen 6501 BK, The Netherlands., van der Hoorn B; Naturalis Biodiversity Center, Leiden, The Netherlands., Iwan Jones J; School of Biological and Chemical Sciences, Queen Mary University of London, London, UK., Sagova-Mareckova M; Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovska 507, 16106 Praha 6, Czechia., Moritz C; ARGE Limnologie GesmbH, Hunoldstraße 14, 6020 Innsbruck, Austria., Barquín J; Environmental Hydraulics Institute 'IHCantabria', Universidad de Cantabria, C/ Isabel Torres n°15, Parque Científico y Tecnológico de Cantabria, 39011 Santander, Spain., Piggott JJ; Department of Zoology, School of Natural Sciences, Trinity College Dublin, the University of Dublin, College Green, Dublin 2, Ireland; Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand., Pinna M; Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy., Rimet F; INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France., Rinkevich B; Israel Oceanographic and Limnological Research, Tel- Shikmona, Haifa 31080, Israel., Sousa-Santos C; MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal., Specchia V; Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy., Trobajo R; IRTA, Institute of Agriculture and Food Research and Technology, Marine and Continental Waters Program, Carretera Poble Nou Km 5.5, E-43540 St. Carles de la Ràpita, Catalonia, Spain., Vasselon V; INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France., Vitecek S; Department of Limnology and Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany., Zimmerman J; Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany., Weigand A; University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany; Musée National d'Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg., Leese F; University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany., Kahlert M; Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE - 750 07 Uppsala, Sweden.
Jazyk: angličtina
Zdroj: The Science of the total environment [Sci Total Environ] 2018 Oct 01; Vol. 637-638, pp. 1295-1310. Date of Electronic Publication: 2018 May 22.
DOI: 10.1016/j.scitotenv.2018.05.002
Abstrakt: The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.
(Copyright © 2018 Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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