The salmon louse genome may be much larger than sequencing suggests

The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding over 92% of expected genes and transcriptome datasets routinely mapping over 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements in the range of 1.3 to 1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up approx. 60% of the genome assemblies.

Protective Immunization of Atlantic Salmon (Salmo salar L.) against Salmon Lice (Lepeophtheirus salmonis) Infestation

Vaccination against salmon lice (Lepeophtheirus salmonis) is a means of control that averts the negative effects of chemical approaches. Here, we studied the immunogenicity and protective effect of a vaccine formulation (based on a salmon lice-gut recombinant protein [P33]) against Lepeophtheirus salmonis infestation in Atlantic salmon in a laboratory-based trial. Our findings revealed that P33 vaccine can provide a measure of protection against immature and adult salmon lice infestation. This protection seemed to be vaccine dose-dependent, where higher doses resulted in lower parasitic infestation rates. We also provide immunological evidence confirming that P33-specific immune response can be triggered in Atlantic salmon after P33 vaccination, and that production of P33-specific antibodies in blood can be detected in vaccinated fish. The negative correlation between P33-specific IgM in salmon plasma and salmon lice numbers on vaccinated fish suggests that protection against lice can be mediated by the specific antibody in salmon plasma. The success of P33 vaccination in protecting salmon against lice confirms the possibility of employing the hematophagous nature of the parasite to deliver salmon-specific antibodies against lice-gut proteins.

Key Role of Mitochondrial Mutation Leu107Ser (COX1) in Deltamethrin Resistance in Salmon Lice (Lepeophtheirus Salmonis)

Deltamethrin (DTM) is used to treat Atlantic salmon (Salmon salar) against salmon lice (Lepeophtheirus salmonis) infestations. However, development of DTM resistance has been reported from North Atlantic L. salmonis populations, in which resistance is associated with mitochondrial (mtDNA) mutations. This study investigated the relationship between DTM resistance and mtDNA single nucleotide polymorphisms (SNPs). A total of 188 L. salmonis collected from Scottish aquaculture sites were assessed using DTM bioassays and genotyped at 18 SNP loci. Genotyping further included archived parasites of known DTM susceptibility status. The results identified eleven mtDNA haplotypes, three of which were associated with DTM resistance. Phylogenetic analyses of haplotypes suggested multiple origins of DTM resistance. L. salmonis laboratory strains IoA-00 and IoA-10 showed similarly high levels (~100-fold) of DTM resistance in bioassays. Both strains differed strongly in mtDNA haplotype, but shared the missense mutation Leu107Ser in the mitochondrial gene cytochrome c oxidase subunit 1 (COX1), which was detected in all further DTM resistant L. salmonis isolates assessed. In crossing experiments with a DTM-susceptible strains, maternal inheritance of DTM resistance is apparent with both IoA-10 (this study) and IoA-02 (earlier reports). We conclude that Leu107Ser (COX1) is a main genetic determinant of DTM resistance in L. salmonis.

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 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 the challenge remains the adequate sampling of a volume of seawater sufficiently large to be representative of outbreaks and load around fish farms.

Breeding for chemical camouflage the case of salmon kairomones and resistance to salmon lice infectivity

Salmon lice are ectoparasites that threaten wild and farmed salmonids. Artificial selection of salmon for resistance to the infectious copepodid lice stage currently relies on in vivo challenge trials on thousands of salmon a year. We found that salmon emit a bouquet of kairomones which the lice use to find and infect the salmon. Some of these compounds vary between families and could be used as a more direct and ethical measurements of lice resistance for breeding farmed salmon.

Breeding for chemical camouflage the case of salmon kairomones and resistance to salmon lice infectivity

Salmon lice are ectoparasites that threaten wild and farmed salmonids. Artificial selection of salmon for resistance to the infectious copepodid lice stage currently relies on in vivo challenge trials on thousands of salmon a year. We found that salmon emit a bouquet of kairomones which the lice use to find and infect the salmon. Some of these compounds vary between families and could be used as a more direct and ethical measurements of lice resistance for breeding farmed salmon.

Inclusion of photoautotrophic cultivated diatom biomass in salmon feed can deter lice

The aim of this study was to evaluate the potential of diatom (microalgae) biomass as a lice-reducing ingredient in salmon feed. The original hypothesis was based on the fact that polyunsaturated aldehydes (PUAs), e.g. 2-trans, 4-trans decadenial (A3) produced by diatoms can function as grazing deterrents and harm copepod development. Salmon lice (Lepeophtheirus salmonis) is a copepod, and we intended to test if inclusion of diatom biomass in the feed could reduce the infestation of lice on salmon. We performed experiments where salmon kept in tanks were offered four different diets, i.e. basic feed with diatoms, fish oil, Calanus sp. oil or rapeseed oil added. After a feeding period of 67 days a statistically representative group of fishes, tagged with diet group origin, were pooled in a 4000L tank and exposed to salmon lice copepodites whereafter lice infestation was enumerated. Salmon from all four diet groups had good growth with SGR values from 1.29 to 1.44% day-1 (increase from ca. 130 g to 350 g). At the termination of the experiment the number of lice on salmon offered diatom feed were statistically significantly lower than on salmon fed the other diets. Mean lice infestation values increased from diatom feed through Calanus and fish oil to standard feed with terrestrial plant ingredients. Analysis of the chemical composition of the different diets (fatty acids, amino acids) failed to explain the differences in lice infestation. The only notable result was that diatom and Calanus feed contained more FFA (free fatty acids) than feed with fish oil and the control feed. None of the potential deleterious targeted polyunsaturated aldehydes could be detected in skin samples of the salmon. What was exclusive for salmon that experienced reduced lice was diatom inclusion in the feed. This therefore still indicates the presence of some lice deterring ingredient, either in the feed, or an ingredient can have triggered production of an deterrent in the fish. An obvious follow up of this will be to perform experiments with different degrees of diatom inclusion in the feeds, i.e. dose response experiments combined with targeted PUA analyses, as well as to perform large scale experiments under natural conditions in aquaculture pens.

Principles and Methods of Counteracting Harmful Salmon–Arthropod Interactions in Salmon Farming: Addressing Possibilities, Limitations, and Future Options

The arthropod salmon louse (Lepeophtheirus salmonis) is a major threat to Atlantic salmon aquaculture and wild salmonids. Essentially like in monoculture, very high concentrations of susceptible hosts may result in high reproduction and severe production of waves of pests. Pest management is crucial both for fish health and protection of wild fish populations from aquaculture influence. Various methods have been utilized to control salmon lice infestations, such as pesticide use, physical treatments, construction modifications, fallowing, breeding, vaccination, and biological control. Most of the methods are partially successful, but none completely fulfills the necessary pest control strategy. Like in agriculture, lice/pest management is an arms race, but the marine environment makes it even more difficult to precisely hit the target pest and avoid unintended negative effects on general wildlife. In this study, we provide an overview of the methods and principles of salmon lice management and address current possibilities and limitations. We also highlight the potential of emerging strategies and enabling technologies, like genome editing, RNA interference, and machine learning, in arthropod management in aquaculture.