KWR Anthony Verschoor by KWR Anthony Verschoor
13 June 2018

DNA-based assessment of freshwater resources and ecosystems

Following the European Water Framework Directive (WFD), the status of European freshwater resources and ecosystems is monitored by counting the numbers of different organisms: phytoplankton, phytobenthos, larger aquatic plants, benthic invertebrates and fish. Some member states have now developed new (DNA-based) methods to do these assessments.This article describes the possibilities to complement or replace the traditional (visual) observation methods with DNA-based techniques, and suggests adaptations to the WFD to apply such techniques in current monitoring schemes. This may lead to less labour-intensive, faster and more robust status assessments across the EU....

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

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...

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