Ecological quality in freshwater streams is reflected across all three domains of life. Freshwater stream A-B-E amplicon

Regular assessment of surface waters to monitor ecological status has become a priority in recent years. Stream water assessment require improved protocols and development of new methods on a large scale and at regular intervals as current methodologies rely on taxonomic expertise which can be costly and time-consuming. Next-generation sequencing approaches for high-throughput analyses of diverse ecosystems are increasingly used, and it has been shown that this type of methodology has potential for stream water quality assessments. The present study aimed to assess the potential of using an amplicon sequencing based approach that simultaneously targets the 16S (prokaryotes) and 18S (eukaryotes) rRNA genes in order to capture a snapshot of the quality in the whole ecosystem. Results based on the analysis of 50 randomly selected Danish water streams showed that the domain-specific profiles of the sampled water stream ecosystems were capable of separating the samples into their respective ecological status categories. Furthermore, it was possible to extract potential indicator organisms from all three domains associated to a single ecological status category, low and high quality ecosystems, as well as those with a high correlation to ecological status across all categories.