| Text | 388023 2018 10.1016/j.scitotenv.2018.05.002 Scopus 2 s2.0 85047091292 ISI Web of Science WOS WOS 000436605400123 Bioassessment Biomonitoring Environmental DNA Freshwater Marine Metabarcording The future of biotic indices in the ecogenomic era Integrating e DNA metabarcoding in biological assessment of aquatic ecosystems Pawlowski J.; Kelly Quinn M.; Altermatt F.; Apotheloz Perret Gentil L.; Beja P.; Boggero A.; Borja A.; Bouchez A.; Cordier T.; Domaizon I.; Feio M.J.; Filipe A.F.; Fornaroli R.; Graf W.; Herder J.; van der Hoorn B.; Iwan Jones J.; Sagova Mareckova M.; Moritz C.; Barquin J.; Piggott J.J.; Pinna M.; Rimet F.; Rinkevich B.; Sousa Santos C.; Specchia V.; Trobajo R.; Vasselon V.; Vitecek S.; Zimmerman J.; Weigand A.; Leese F.; Kahlert M. Department of Genetics and Evolution, University of Geneva, Geneva, CH 1211, , Switzerland; School of Biology Environmental Science, University College Dublin, , Ireland; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, Dubendorf, CH 8600, , Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, CH 8057, , Switzerland; CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairão, Rua Padre Armando Quintas, Vairão, 4485 601, , , Portugal; CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairão, Rua Padre Armando Quintas, Vairão, 4485 601, , , Portugal; CEABN/InBIO Centro de Estudos Ambientais Prof. Baeta Neves , Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, 1349 017, , , Portugal; CEABN/InBIO Centro de Estudos Ambientais Prof. Baeta Neves , Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, 1349 017, , , Portugal; LifeWatch, Italy and CNR Institute of Ecosystem Study CNR ISE , Largo Tonolli 50, Verbania Pallanza, 28922, , Italy; AZTI, Marine Research Division, Herrera Kaia, Portualdea s/n, Pasaia, 20110, , Spain; INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, Thonon les Bains Cedex, 74203, , France; Marine and Environmental Sciences Centre, Faculty of Sciences and Technology, Department of Life Sciences, University of Coimbra, , Portugal; University of Milano Bicocca, Department of Earth and Environmental Sciences DISAT , Piazza della Scienza 1, Milano, 20126, , Italy; Institute of Hydrobiology and Aquatic Ecosystem Management IHG , Vienna, 1180, , Austria; RAVON, Postbus 1413, Nijmegen, BK, 6501, , Netherlands; Naturalis Biodiversity Center, Leiden, , Netherlands; School of Biological and Chemical Sciences, Queen Mary University of London, London, , , United Kingdom; School of Biological and Chemical Sciences, Queen Mary University of London, London, , , United Kingdom; Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovska 507, Praha 6, 16106, , Czech Republic; ARGE Limnologie GesmbH, Hunoldstraße 14, Innsbruck, 6020, , Austria; Environmental Hydraulics Institute IHCantabria , Universidad de Cantabria, C/ Isabel Torres n°15, Parque Cientifico y Tecnologico de Cantabria, Santander, 39011, , Spain; 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; Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce Monteroni, Lecce, 73100, , Italy; Israel Oceanographic and Limnological Research, Tel Shikmona, Haifa, 31080, , Israel; MARE Marine and Environmental Sciences Centre, ISPA Instituto Universitario, Rua Jardim do Tabaco 34, Lisboa, 1149 041, , , Portugal; MARE Marine and Environmental Sciences Centre, ISPA Instituto Universitario, Rua Jardim do Tabaco 34, Lisboa, 1149 041, , , Portugal; IRTA, Institute of Agriculture and Food Research and Technology, Marine and Continental Waters Program, Carretera Poble Nou Km 5.5, St. Carles de la Rapita, Catalonia, E 43540, , Spain; Department of Limnology and Bio Oceanography, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090, , Austria; Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, Frankfurt am Main, 60325, , Germany; Botanic Garden and Botanical Museum Berlin Dahlem, Freie Universitat Berlin, Konigin Luise Str. 6 8, Berlin, 14195, , Germany; University of Duisburg Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, Essen, 45141, , Germany; Musee National d Histoire Naturelle, 25 Rue Munster, Luxembourg, 2160, , Luxembourg; Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, Uppsala, SE 750 07, , Sweden 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. 637 638 Published version http //www.scopus.com/inward/record.url eid=2 s2.0 85047091292 partnerID=q2rCbXpz Articolo 2018_Science_of_the_Total_Environment_637_638_1295_1310.pdf Articolo in rivista Elsevier 0048 9697 Science of the total environment Science of the total environment Sci. total environ. angela.boggero BOGGERO ANGELA |
