3. Results
We obtained 372,431,352 reads and 4,702 OTUs for the 102 eDNA samples
after quality filtering and excluding OTUs with read abundance
<0.01 % per sample. Reads among samples were unevenly
distributed ranging from 88,446 to 4,451,399 with a mean read number of
1,880,966. We excluded two samples that had only 3,282 and 7,928 reads,
respectively, to avoid unrepresentative biodiversity data due to too low
sequencing depth. These two samples were therefore excluded from the
dataset to prevent distorting results due to these outliers. After the
database and taxonomist checks, 2,840 OTUs remained which were assigned
to 506 species. The uneven read distribution was no concern as neither
OTU richness nor species richness were correlated with read numbers (see
S1 & S2). Eight controls with no DNA were also included to test for
contamination during field or laboratory proceedings. Their read numbers
ranged from zero to four, indicating no substantial contamination. The
vast majority of reads was assigned to metazoans, especially arthropods
and annelids, with <1 % of reads assigned to non-metazoan
taxa. In all samples, chironomids had the highest read numbers and
constitued 55 to 95 % of every sample.