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).