![]() ![]() The distance between the observed conditions to defined undisturbed reference water bodies (i.e. ![]() This directive changed the focus of water management from simple pollution control to measuring aquatic ecosystem integrity and health, by using five “biological quality elements” (BQEs): fishes, aquatic macroinvertebrates, phytoplankton, macroalgae, and macrophytes, supplemented by chemical and hydromorphological quality indicators (see annex II and V). In the European Union the required aquatic quality assessment became legally binding through the Water Framework Directive, which aims to restore in all member states a ‘good ecological status’ of each surface waterbody at the latest by 2027. The resulting programs–implemented for example in the USA (the National Aquatic Resources Survey (NARS previously known as EMAP)), in Canada (the Canadian Aquatic Biomonitoring Network (CABIN)), in South Africa (the National Aquatic Ecosystem Health Monitoring Program (NAEHMP)) or in Australia (the AUStralian RIVer Assessment System (AUSRIVAS))–have all in common that they aim to acquire detailed data that describe the ecological health and trends of freshwater bodies, ideally based on continuous monitoring of aquatic indicator taxa. The international Convention on Biological Diversity defined a general framework for counteracting degradation through restoration and management of aquatic ecosystems, followed by national and regional conservation strategies and action plans. Therefore, protection of aquatic habitats and their functions, combined with prevention of further deterioration and initiation of restoration, has become an important task in Europe and elsewhere. Species richness in freshwater ecosystems is increasingly endangered by the consequences of climate change, environmental pollution, overexploitation, river fragmentation or flow regulation, and invasive species. The provided reference DNA barcodes help building the foundation for metabarcoding approaches, which provide faster sample processing and more cost-efficient ecological status determination. Although the cost-benefit analysis of both methods showed that DNA barcoding is still more expensive (5.30–8.60€ per sample) and time consuming (12.5h), the results emphasize the potential to increase taxonomic resolution and gain a more complete profile of biodiversity, especially in invertebrates. The 18 fish species were assigned to 20 molecular barcode index numbers, the 104 aquatic invertebrate taxa to 113 molecular entities. Dissimilarities between the two approaches occurred in 7% of the invertebrates and in 1% of the fishes. In 18% of the invertebrates morphology allowed only assignments to higher systematic entities, but DNA barcoding lead to species-level assignment. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. morphology-based identification in monitoring routines. Here, we focus on the freshwater fauna of the River Sieg (Germany) to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. ![]() Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss.
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