Sample collection

Sample processing and morphological identification

Experimental set-up and library preparation

Processing of raw reads

Alpha diversity of DNA metabarcoding datasets

Beta diversity analyses of DNA metabarcoding datasets

Species composition based on morphological identification

Processing of raw reads

Alpha diversity based on DNA metabarcoding

Betadiversity analysis of the DNA metabarcoding datasets

High number of unique ASVs per sample does not show the genetic diversity, but reflects PCR or sequencing errors

DNA replicates from bulk DNA samples increase macrobenthos species detection

Pooling DNA replicates does not change alpha and beta diversity patterns

PCR replicates from bulk DNA samples substantially differ in the detection of rare species

Comparison between morphological identification and the metabarcoding method