Taxonomic composition of eDNA metabarcoding data
There were 42.30 million eukaryote sequences in the OTUAtable, which clustered into 2,239 OTUs. The number of eukaryotic reads per sample varied from 43,498 to 355,828, with an average of 167,872. The most dominant taxon was Ochrophyta, represented by 26.72 million reads and accounting for 63.2% of total reads; the majority of them (26.64 million) were assigned to diatoms (Diatomea). Metazoa was the next most dominant taxon in the OTUA table, with 12.57 million sequences accounting for 29.7% of total reads across samples. Within the OTUA table, there were 6,371 reads assigned to Atlantic salmon and 9,959 reads assigned to chicken (a common ingredient in fish food). When chicken reads were detected, they tended to be present at stations close to cage edge, with more reads detected at cage edge (i.e. 0 m) than other stations (Table S6). Atlantic salmon reads had a similar pattern at most farm sites.
Excluding non-metazoan reads and presumed farm contamination reads (i.e. from salmon and chicken), there were 12.55 million metazoan reads in the OTUM table, which clustered into 400 metazoan OTUs. Metazoan sequences numbered 1.60, 1.51, 1.91, 1.17, 1.65, and 4.71 million at BI, BS, MI, MR, PP and VP farm sites, respectively, which accounted for 20.5%, 26.3%, 30.6%, 17.7%, 16.8%, 77.4% of total reads per farm, respectively (Table1). Most metazoan reads were Calanoida (pelagic copepods), which had 9.11 million reads across samples.
Benthic metazoans were represented by 3.42 million reads clustered into 367 OTUs (Table S7). The number of benthic metazoan sequences was 913,866, 163,707, 646,120, 253,574, 58,500, and 1,388,311 at BI, BS, MI, MR, PP and VP, respectively. In the OTUBM table, Nematoda was the most abundant phylum at BI, BS, MI and MR, accounting for 30.9%-62.5% of reads, while Arthropoda and Annelida were most abundant at PP and VP, respectively (Figure 1). At the order level, the most abundant order of Polychaeta was Capitellida in both DNA barcoding and eDNA metabarcoding data (Table S8).