Sea lice(Lepeophtherius salmonis)detection and quantification around aquaculture installations using environmental DNA

The naturally occurring ectoparasite salmon lice (Lepeophtherirus salmonis) poses a great challenge for the salmon farming industry, as well as for wild salmonids in the Northern hemisphere. To better control the infestation pressure and protect the production, there is a need to provide fish farmers with sensitive and efficient tools for rapid early detection and monitoring of the parasitic load. This can be achieved by targetingL. salmonisDNA in environmental samples. Here, we developed and tested a newL. salmonisspecific DNA-based assay (qPCR assay) for detection and quantification from seawater samples using an analytical pipeline compatible with the Environmental Sample Processor (ESP) for autonomous water sample analysis of gene targets. Specificity of the L. salmonis qPCR assay was demonstrated through in-silico DNA analyses covering sequences of differentL. salmonisisolates. Seawater was spiked with known numbers of nauplii and copepodite free-swimming (planktonic) stages ofL. salmonisto investigate the relationship with the number of marker gene copies (MGC). Finally, field samples collected at different times of the year in the vicinity of a salmon production farm in Western Norway were analyzed forL. salmonisdetection and quantification. The assay specificity was high and a high correlation between MGC and planktonic stages ofL. salmoniswas established in the laboratory conditions. In the field,L. salmonisDNA was consequently detected, but with MGC number below that expected for one copepodite or nauplii. We concluded that onlyL. salmonistissue or eDNA residues were detected. This novel study opens for a fully automatizedL. salmonisDNA quantification using ESP robotic to monitor the parasitic load, but the challenge remains the adequate sampling of a volume of seawater sufficiently large to be representative of outbreaks and load around fish farms.