Discussion
The present study aimed to characterise the domain-specific diversity profiles of 53 Danish stream water sampling locations using an amplicon sequencing based method simultaneously targeting the bacterial, archaeal and eukaryotic composition. The purpose was to explore this method as a low cost and high throughput alternative to conventional stream-water quality assessments based on macroinvertebrates as BQE. The obtained domain-specific diversity profiles were able to separate the sampled streams based on their respective ecological status and revealed potential indicator organisms for further studies.