Evaluating the potential of DNA metabarcoding for ecological status assessment under the Water Framework Directive: A case study on benthic invertebrates from Western Carpathian streams

Routine biomonitoring under the Water Framework Directive (WFD) follows a conventional methodology primarily based on the morphological identification of taxa within the five biological quality elements (phytoplankton, phytobenthos, macrozoobenthos, macrophytes and fish). This identification is particularly challenging for macrozoobenthos due to their high taxonomic diversity. Moreover, this approach is time-consuming and resource intensive. Our current study aims to: (i) evaluate the implementation of DNA metabarcoding in long-term monitored sites to assess the effectiveness of three sample types (bulk samples of macrozoobenthos, and eDNA from water and sediments), (ii) evaluate the ecological status of water bodies using metabarcoding data, and (iii) compare ecological metrics values using conventional and molecular approaches. Sampling was conducted at 17 localities in Slovakia, covering eight stream types. DNA metabarcoding detected 30% more species than conventional monitoring performed over 15 years without needing time-intensive sample processing and morphological identification. At the same time, the bulk samples captured more macrozoobenthos taxa than the other sample types. On average, the bulk samples detected 85% of the taxa captured by DNA metabarcoding. The differences in values of ecological metrics obtained within the conventional approach and between the conventional and metabarcoding approaches were relatively small, typically corresponding to differences within one ecological quality class. However, more pronounced differences were observed in non-abundance-based metrics, such as EPT and BMWP, indicating higher sensitivity of species detection with DNA metabarcoding. This study demonstrates the effectiveness of DNA metabarcoding across multiple metrics and highlights its potential to enhance routine biomonitoring.