TY - JOUR
T1 - Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive
AU - Hering, Daniel
AU - Borja, Angel
AU - Jones, J. Iwan
AU - Pont, Didier
AU - Boets, Pieter
AU - Bouchez, Agnes
AU - Bruce, Kat
AU - Drakare, Stina
AU - Hänfling, Bernd
AU - Kahlert, Maria
AU - Leese, Florian
AU - Meissner, Kristian
AU - Mergen, Patricia
AU - Reyjol, Yorick
AU - Segurado, Pedro
AU - Vogler, Alfried
AU - Kelly, Martyn
N1 - Funding Information:
This paper is a result of the COST Action CA15219 “Developing new genetic tools for bioassessment of aquatic ecosystems in Europe” (DNAqua-Net), funded by the European Union . We are grateful to Alexander Weigand and Sarah Kückmann for their valuable support throughout the Action. We greatly appreciated the comments of three anonymous reviewers, who contributed a lot to improving the paper.
Publisher Copyright:
© 2018 Elsevier Ltd
PY - 2018/7/1
Y1 - 2018/7/1
N2 - 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.
AB - 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.
KW - Biological quality elements
KW - eDNA
KW - Lakes
KW - Meta-barcoding
KW - Rivers
KW - Transitional and coastal waters
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U2 - 10.1016/j.watres.2018.03.003
DO - 10.1016/j.watres.2018.03.003
M3 - Review article
C2 - 29602086
AN - SCOPUS:85044585777
SN - 0043-1354
VL - 138
SP - 192
EP - 205
JO - Water Research
JF - Water Research
ER -