Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

WATER RESEARCH

卷:138

Review

Hering, Daniel¹  Borja, Angel²  Jones, J. Iwan³  Pont, Didier^4,5  Boets, Pieter⁶  Bouchez, Agnes⁷  Bruce, Kat⁸  Drakare, Stina⁹  Hanfling, Bernd¹⁰  Kahlert, Maria⁹  Leese, Florian¹¹  Meissner, Kristian¹²  Mergen, Patricia^13,14  Reyjol, Yorick¹⁵  Segurado, Pedro¹⁶  Vogler, Alfried^17,18  Kelly, Martyn¹⁹ 

[1] Univ Duisburg Essen, Aquat Ecol, D-45117 Essen, Germany

[2] AZTI, Marine Res Div, Pasaia 20110, Spain

[3] Queen Mary Univ London, Sch Biol & Chem Sci, London E1 4NS, England

[4] Assoc VigiLIFE, 17 Rue Lac St Andre,Savoie Technolac BP 274, F-73375 Le Bourget Du Lac, France

[5] Univ Nat Resources & Life Sci, Inst Hydrobiol & Aquat Ecosyst Management, Gregor Mendel Str 33, A-1180 Vienna, Austria

[6] Prov Ctr Environm Res, PCM, Godshuizenlaan 95, B-9000 Ghent, Belgium

[7] INRA UMR CARRTEL, F-74200 Thonon Les Bains, France

[8] NatureMetrics Ltd, Egham TVV20 9TY, Surrey, England

[9] Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, POB 7050, SE-75007 Uppsala, Sweden

[10] Univ Hull, Sch Environm Sci, Evolutionary Biol Grp, Kingston Upon Hull HU6 7RX, N Humberside, England

[11] Univ Duisburg Essen, Aquat Ecosyst Res, D-45117 Essen, Germany

[12] Finnish Environm Inst, Freshwater Ctr, FI-40500 Jyvaskyla, Finland

[13] Bot Garden Meise, Nieuwelaan 38, B-1860 Meise, Belgium

[14] Royal Museum Cent Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium

[15] AFB, 5 Sq Felix Nadar, F-94300 Vincennes, France

[16] Univ Lisbon, Sch Agr, Forest Res Ctr, P-1349017 Lisbon, Portugal

[17] Imperial Coll London, Dept Life Sci, Cromwell Rd, London SW7 5BD, England

[18] Nat Hist Museum, Cromwell Rd, London SW7 5BD, England

[19] Bowburn Consultancy, 11 Monteigne Dr, Bowbum DH6 5QB, Durham, England

关键词: Meta-barcoding;    eDNA;    Biological quality elements;    Rivers;    Lakes;    Transitional and coastal waters;   

DOI  :  10.1016/j.watres.2018.03.003

来源: Elsevier

【 摘 要 】

Assessment of ecological status for the European Water Framework Directive (WFD) is based on Biological Quality Elements (BQEs), namely phytoplankton, benthic flora, benthic invertebrates and fish. Morphological identification of these organisms is a time-consuming and expensive procedure. Here, we assess the options for complementing and, perhaps, replacing morphological identification with procedures using eDNA, metabarcoding or similar approaches. We rate the applicability of DNA-based identification for the individual BQEs and water categories (rivers, lakes, transitional and coastal waters) against eleven criteria, summarised under the headlines representativeness (for example suitability of current sampling methods for DNA-based identification, errors from DNA-based species detection), sensitivity (for example capability to detect sensitive taxa, unassigned reads), precision of DNA-based identification (knowledge about uncertainty), comparability with conventional approaches (for example sensitivity of metrics to differences in DNA-based identification), cost effectiveness and environmental impact. Overall, suitability of DNA-based identification is particularly high for fish, as eDNA is a well-suited sampling approach which can replace expensive and potentially harmful methods such as gill-netting, trawling or electrofishing. Furthermore, there are attempts to replace absolute by relative abundance in metric calculations. For invertebrates and phytobenthos, the main challenges include the modification of indices and completing barcode libraries. For phytoplankton, the barcode libraries are even more problematic, due to the high taxonomic diversity in plankton samples. If current assessment concepts are kept, DNA-based identification is least appropriate for macrophytes (rivers, lakes) and angiosperms/macroalgae (transitional and coastal waters), which are surveyed rather than sampled. We discuss general implications of implementing DNA-based identification into standard ecological assessment, in particular considering any adaptations to the WFD that may be required to facilitate the transition to molecular data. (C) 2018 Elsevier Ltd. All rights reserved.

【 授权许可】

Free