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

Abstract

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 targeting L. salmonis DNA in environmental samples. Here, we developed and tested a new L. salmonis specific 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 different L. salmonis isolates. Seawater was spiked with known numbers of nauplii and copepodite free-swimming (planktonic) stages of L. salmonis to 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 for L. salmonis detection and quantification. The assay specificity was high and a high correlation between MGC and planktonic stages of L. salmonis was established in the laboratory conditions. In the field, L. salmonis DNA was consequently detected, but with MGC number below that expected for one copepodite or nauplii. We concluded that only L. salmonis tissue or eDNA residues were detected. This novel study opens for a fully automatized L. salmonis DNA quantification using ESP robotic to monitor the parasitic load, but challenges remain to exactly transfer information about eDNA quantities to decisions by the farmers and possible interventions.

High resolution longitudinal molecular and morphological tracking of planktonic threats to salmon aquaculture: new candidates and old players

“…Cunea, Parvamoeba ), and the read depths required to per sample to ‘sequence through’ this biological noise using universal metabarcoding markers are impractical. As such, monitoring of specific planktonic threats by molecular means may be better achieved by targeted —for example qPCR (Bridle et al, 2010; Krolicka et al, 2022) —and semi-targeted —e.g. clade-specific— metabarcoding approaches (Dario et al, 2017).…”

“…DNA from adult and juvenile lice should also be abundant in the water column (e.g. Krolicka et al, 2022). However, unambiguous N. perurans reads were extremely rare in the dataset (19 total, see supplementary data), as were those for L. salmonis (976 total) and C. elongatus (18 total).…”

Molecular identification and environmental DNA detection of gill lice ectoparasites associated with Brook Trout declines

“…Although eDNA analysis has been successful in detecting several groups of salmonid parasites, including protozoans (Bastos Gomes et al 2017), flatworms (Rusch et al 2018;Fossøy et al 2020), and cnidarians (Richey et al 2020), few studies have utilized this approach for the detection of parasitic copepods. Peters et al (2018) and Krolicka et al (2022) were able to detect Lepeophtheirus salmonis, a marine salmonid parasitic copepod, with eDNA isolated from seawater samples using single-species quantitative polymerase chain reaction (qPCR) and multispecies metabarcoding approaches, respectively. These studies suggest that eDNA shows great promise in improving surveys for salmonid parasites, but it has yet to be applied for monitoring parasitic copepods in freshwater systems.…”

“…(2018) and Krolicka et al. (2022) were able to detect Lepeophtheirus salmonis , a marine salmonid parasitic copepod, with eDNA isolated from seawater samples using single‐species quantitative polymerase chain reaction (qPCR) and multispecies metabarcoding approaches, respectively. These studies suggest that eDNA shows great promise in improving surveys for salmonid parasites, but it has yet to be applied for monitoring parasitic copepods in freshwater systems.…”

Molecular quantification of parasitic sea louse larvae depends on species and life stage

“…Molecular methods have been proposed as a cost‐effective solution for directly measuring sea louse larval quantity in plankton and water samples collected at fish farms or the open sea (Bui et al., 2021; Krolicka et al., 2022). To date, these methods have only been utilized for relative quantification of L. salmonis (Bui et al., 2021; Krolicka et al., 2022; McBeath et al., 2006; Peters et al., 2018; Turon et al., 2022), where the measured DNA quantities generated by qPCR and metabarcoding cannot be accurately converted to an exact biomass or number of individuals. Current molecular methodologies also lack the capability to distinguish between infective copepodid and non‐infective nauplii life stages of sea lice, limiting their use to studies where total larval abundance is of interest (Byrne et al., 2018).…”