3.1 Effect of sampling day, sampling position, and environment  
Sampling day affected the detection of both species (F = 5.933, p-value = <0.001, ndf = 4.055, ddf = 90.945) and OTU (F = 2.765, p-value = 0.030, ndf = 3.32, ddf = 91.68) richness. In contrast, neither temperature, discharge, nor sampling position had an effect on species or OTU richness. Highest species and OTU richness was detected in spring with lowest numbers in the summer months for all three sampling positions (Figure 2 and Figure S3). Conversely, sampling positions exhibited little difference in read richness, with 99 % of reads shared among the different positions in the stream and only a small fraction of reads being exclusively detected per sampling position (≤0.1 %) (Figure 2). The sampling positions showed high overlap of reads for shared species (99.14 %) and only a small fraction of reads was assigned to the exclusively detected species per sampling position (≤0.1 %) (Figure 2). Although some species were exclusively found at one of the three sampling positions (Figure 2), relative occurrence of these species was low in contrast to shared species (Figure S4). We found no significant differences between surface, riverbed or riverbank samples based on OTU richness (Kruskal-Wallis rank sum test: chi-squared = 0.085, p-value = 0.957, ndf = 2, ddf = 97) or read abundance (Kruskal-Wallis rank sum test: chi-squared = 0.774, p-value = 0.679, ndf = 2, ddf = 97).