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.