Metabarcoding of benthic ciliate communities shows high potential for environmental monitoring in salmon aquaculture

The backbone of benthic marine monitoring programs is the biological component, traditionally the macrofauna inventory. Such macrofauna-based environmental impact assessments (EIA), however, are very time consuming and expensive. To overcome these shortcomings, we used environmental metabarcoding to test the potential of protists as bioindicators in EIAs. Therefore, we analyzed taxonomic metabarcodes (V9 region of the SSU rRNA), obtained from sediment samples collected along a 400-m transect extending from below salmon cages towards the open sea along the predominant current flow. The obtained genetic data of protistan communities were compared to benchmark data obtained from traditional macrofauna surveys of the same samples. Ciliates emerged as the most powerful indicators mirroring the macrofauna benchmark patterns with statistical significance. Ordination analyses showed that ciliate communities resolved impacted sampling sites below and in immediate vicinity of the salmon cages even better than macrofauna communities. It can be concluded that ciliates allow for a better fine-scale resolution of impact conditions than traditional monitoring methods. Other protistan taxon groups such as diatoms and chrysophytes were not as successful as marine benthic indicators compared to ciliates. We conclude that the implementation of ciliate metabarcoding can substantially improve EIAs. We discuss further mandatory research needs to make ciliate metabarcoding a routine tool in official regulations for EIAs in salmon farming.