Towards a standardized operating procedure for eDNA-based biomonitoring in coastal marine salmon aquaculture

The marine aquaculture industry and regulators are in the process of implementing eDNA metabarcoding of microbial communities for compliance monitoring. This requires standardization of sampling, laboratory, and data analysis protocols. Towards this goal we in this study completed two further milestones using samples collected from two Scottish salmon farms; (i) We tested the effect of different DNA polymerases used in the PCR amplification of the taxonomic marker gene (V3-V4 hypervariable region of the bacterial 16S rRNA gene) which are frequently being used in eDNA biomonitoring of aquaculture installations. (ii) We quantified sampling background noise obtained from eDNA samples and statistically compared results with the sampling bias obtained for macrofaunal samples of the same source sediments. We detected differences in bacterial community structures resulting from the performance of different DNA polymerases, which could influence the interpretation of biomonitoring results. Furthermore, we found that sampling-induced errors for eDNA samples were similar to errors for macrofaunal samples collected according to compliance monitoring protocol (ca. 25% noise in both cases). Finally, we showed that within-grab variances of microbial community structures were in the same order of magnitude (less than 10 times difference in all cases) as the one obtained from replicate grabs collected from the same locale (impact category). Based on our findings, we make a recommendation for a PCR protocol, which allows to obtain comparable results in case of different service providers conducting biomonitoring. Also, we propose a sampling scheme for eDNA biomonitoring which minimizes sampling-induced errors and makes upcoming eDNA-based monitoring results comparable with previous compliance monitoring results obtained from macrofaunal data.