Electronic Supplementary Materials

Electronic Supplementary Materials for the article "Evaluating the potential of DNA metabarcoding for ecological status assessment under the Water Framework Directive: A case study from streams in the Western Carpathians".Supplementary material 1. List of sampling sites and their detailed characteristics processed using DNA metabarcoding in this study. (Supplementary Material 1.xlsx)Supplementary material 2. List of sampling sites with a chronological framework for the data collected by the Slovak Water Research Institute (WRI). (Supplementary Material 2.xlsx)Supplementary material 3. Composition of the reaction mixture and PCR protocols used for DNA fragment amplification. (Supplementary Material 3.xlsx)Supplementary material 4. The list of species (conventional dataset) identified by the Water Research Institute (WRI) by compliance with the Water Framework Directive (WFD) and conventional approach. Each species is annotated with its presence (1) or absence (0) at the sampling sites. (Supplementary Material 4.xlsx)Supplementary material 5. The list of species (DNA dataset) obtained by this study using the DNA metabarcoding approach. The data contains results for individual replicates, with species presence represented by the number of reads and absence, indicated as 0. (Supplementary Material 5.xlsx)Supplementary material 6. Reference values for metrics used in partial EQR (Ecological Quality Ratio) calculations by stream type. The abbreviations for the different stream types are explained below the table. (Supplementary Material 6.xlsx)Supplementary material 7. Venn diagrams demonstrating species overlap among the three sample types (eDNA from water, sediments, and bulk samples) for each study site. Coloured rectangles represent the corresponding stream types. (Supplementary Material 7.tif)Supplementary material 8. A parallel analysis of the taxonomic classes detected in the three sample types (eDNA from water, eDNA from sediments, and bulk samples). The analysis highlights the overlap and unique records of taxonomic classes across sample types. (Supplementary Material 8.tiff)Supplementary material 9. The percentual proportion of reads of sequences assigned to higher taxonomic groups (classes) for the three sample types (eDNA from water, eDNA from sediments, and bulk samples). The visualisation provides a comparative insight into the taxonomic composition at the class level and highlights differences in the detection efficiency of each sample type. (Supplementary Material 9.tif)Supplementary material 10. Number of recorded species and their percentage representation within three types of samples (eDNA from water, sediments, and bulk samples) at the sampling sites. (Supplementary Material 10.xlsx)Supplementary material 11. Venn diagrams demonstrating species level overlap between DNA metabarcoding (bulk samples) and the conventional approach. Coloured rectangles indicate the corresponding stream types. (Supplementary Material 11.tif)Supplementary material 12. A. The values of individual metrics calculated using the ASTERICS software for both conventional and DNA-based datasets. B. Recalculated partial EQR (Ecological Quality Ratio) values relative to reference values for each metric. The total EQR for each sample is highlighted in red. (Supplementary Material 12.xlsx)Supplementary material 13. The results of the individual metrics used to calculate the overall ecological status for 17 sampling sites representing eight stream types obtained from 57 conventional samples conducted by WRI and 17 DNA metabarcoding samples gained in this study. (Supplementary Material 13.tif)