Results
Amplicon sequencing of 53 bulk samples from Danish freshwater streams yielded a total of 2,416,798 high quality sequence reads. The obtained sequencing depth was assessed using a rarefaction curve (Figure S1), and based on this, a minimum 10,000 sequences per sample was set as the criterion for inclusion in the analysis. Three samples were removed from the dataset as they did not meet this threshold, and 50 samples across all five ecological status categories entered the analysis with an average of 41,684 ± 7628 sequences per sample. A total of 13,446 ZOTUs were detected across all samples, with the majority representing the domain Bacteria (11,672 ZOTUs, 87.8 % of total reads, followed by Eukaryota (282 ZOTUs, 7.3 % of total reads) andArchaea (233 ZOTUs, 0.8 % of total reads). A total of 1259 ZOTUs (4.1 % of total reads) could not be classified and were removed from subsequent analyses.