Nematode metabarcoding as an alternative to conventional benthic macrofauna monitoring of fish farming

Fish farming is the fastest-growing marine food industry. The environmental impacts of fish farming are well recognized, though tools to effectively assess them are quite limited. Benthic macroinvertebrates are currently the most used bioindicators of organic enrichment resulting from fish farming activities. However, the morphology-based analysis of benthic macrofauna is time-consuming and requires taxonomic knowledge, which is not readily available. Attempts to use sediment eDNA metabarcoding to assess benthic macrofauna have also been inconclusive. Here, we test nematode metabarcoding as an alternative method to monitor fish farming environmental impacts. We have analyzed nematode communities from over 100 million sequences of the 18S V1V2 marker from 274 sediment samples collected from ten salmon farms in Norway. Our data document consistent trends in nematode alpha diversity, exhibiting significant and strong positive correlations with distance from the cage and negative correlations with environmental parameters, such as total organic carbon, total organic matter, carbon-to‑nitrogen ratio, and trace metals (i.e., Cu and Zn). Nematode beta diversity also shows a strong correlation with the corresponding Ecological Quality Status categories. We identify several nematode amplicon sequence variants exhibiting significant response along gradients of pollution-related parameters and the AMBI index. The occurrence of nematode genera in metabarcoding data is congruent with their known ecological knowledge. Our study provides solid evidence that nematodes are as sensitive as benthic macrofauna to organic enrichment associated with salmon farming and suggests that nematode metabarcoding could be implemented in the environmental monitoring of salmon farms.