Salmon lice--impact on wild salmonids and salmon aquaculture

De novo transcriptomic analysis to identify candidate genes potentially related to host recognition during infective stage of Caligus fugu (Crustacea: Copepoda)

Attachment site recognition for infecting a definite host is crucial for obligate ectoparasites. Caligus fugu, a marine copepod parasite primarily found on pufferfishes, has a unique host-/organ-specificity. The infective stage of the species exclusively infects host fins as the attachment site. However, so far, little is known about the mechanism underlying the specificity of C. fugu. In this study, transcriptomic profiles of the infective first copepodid stage (CI) along with the pre- and a post-infective stage, i.e., second nauplii (NII) and second copepodids (CII), respectively, were investigated. The de novo assembled transcriptome of C. fugu showed that a high number of transcripts showed high homology to those of relative species, Caligus rogercresseyi (94.7 %) and Lepeophtheirus salmonis (91.0 %), suggesting that only a small portion of species-specific genes contribute to interspecific differences, such as host-seeking. Importantly, no gene was noted from the odorant receptors and gustatory receptors families in C. fugu transcripts, similar to L. salmonis genome. Genes related to chemosensing such as the ionotropic glutamate receptors (iGluR) or ionotropic receptors (IRs), viz., GRIA2, GRIA3, GRID2, GRIK2, GRIK3, IR21a, IR25a, IR40a, and IR93a, likely involved in host-seeking, were highly expressed during CI among the three stages. In addition, inositol 1,4,5-triphosphate receptor-associated 2, another potential candidate gene involved in host-seeking, was significantly upregulated in CI compared with that in NII and maintained at the same level in CII. Our present transcriptomic data should offer a foundation for further investigations on various biological aspects, such as the host-/organ-specificity of sea lice.

The digestion time for salmon louse (Lepeoptheirus salmonis) in lumpfish (Cyclopterus lumpus) in relation to freshness, developmental stage, and temperature

Sea lice infestations cause significant economic losses in the Atlantic salmon aquaculture industry. To biologically control sea lice at farming sites, cleaner fish such as lumpfish are employed. However, the efficacy of lumpfish is under constant debate, primarily due to limited knowledge of digestion times, which makes it difficult to interpret the number of salmon lice found in the stomach contents of dissected lumpfish. The aim of this study was to provide quantitative estimates of the degradation of salmon lice over a period of 12 days. After an acclimation period of approximately one week, batches of eight lumpfish (average weight 94.3 g, SD ± 33.2) were fed salmon lice and arranged in tanks. Each batch received six large mobile lice and two adult female lice. Samplings were conducted at 24-hour intervals during the first four days and at 48-hour intervals over the remaining eight days. The experiment was conducted twice, each at a different temperature regime (6°C and 9°C), using live lice in both trials. To investigate if the freshness of the louse influenced degradation and digestion, the setup was replicated in the 9°C experiment with lice that had been stored frozen at -80°C, with an additional 12-hour sampling point for comprehensive observation. The analysis of salmon lice revealed expected digestion times of 6.4 days and 12.9 days for large mobile and adult female salmon lice, respectively. Temperature and lice freshness did not seem to influence digestion times, but the developmental stage of the lice did. The findings of this study can be used to estimate the cleaning efficacy of lumpfish based on the stomach contents.

Transcriptomic insights into the low-salinity tolerance of the sea louse Caligus elongatus

Caligus elongatus is a marine copepod ectoparasite on a wide variety of fish species. It has also been observed on fish farms cultivating Atlantic salmon and reports shows that this parasite can be a problem for the industry and for the fish's welfare. Freshwater is used as one of the non-medical treatment methods against the salmon louse (Lepeophtheirus salmonis). However, the efficacy of freshwater treatment against C. elongatus is still unknown. This study aims to fill this gap by examining the salinity tolerance limits of both adult and copepodid life stages of C. elongatus. Our findings reveal that detached adult C. elongatus exhibit low tolerance to reduced salinity, with mortality occurring within hours at salinities below 20 ppt. In contrast, copepodid stages demonstrated a slightly higher tolerance, surviving at salinities as low as 15 ppt for one day. Adult lice attached to a host quickly detached from the fish as soon as the salinity was lower than 20 ppt, suggesting that freshwater delousing might be effective in this species. To further understand the genetic basis of acclimation to reduced salinities, we performed RNA-sequencing to assemble the first transcriptome of this species and identify differentially expressed genes. Several genes regulated upon low-salinity transfer were identified. These include genes involved in proline metabolism, energy metabolism, and the transport of various ions and betaine, an osmolyte. The potential roles of these genes in salinity acclimation are discussed within an evolutionary context, providing valuable insights into the survival mechanisms of C. elongatus under low-salinity conditions.

QTL mapping provides new insights into emamectin benzoate resistance in salmon lice, Lepeophtheirus salmonis

BACKGROUND

The salmon louse (Lepeophtheirus salmonis) is a parasite of wild and farmed salmonid fish, causing huge economic damage to the commercial farming of Atlantic salmon (Salmo salar) in the northern hemisphere. The avermectin emamectin benzoate (EMB) is widely used for salmon delousing. While resistance to EMB is widespread in Atlantic populations of L. salmonis, the molecular mechanisms of resistance remain to be elucidated. The aim of the present work was to obtain insights into potential EMB resistance mechanisms by identifying genetic and transcriptomic markers associated with EMB resistance.

RESULTS

Crosses were performed between EMB-susceptible and -resistant L. salmonis, sourced from two parental strains isolated in Scotland, producing fully pedigreed families. The EMB susceptibility of individual parasites was characterised using time-to-response bioassays. Parasites of two families were subjected to double digest restriction site-associated DNA sequencing (ddRAD-seq) for simultaneous discovery of single nucleotide polymorphisms (SNPs) and genotyping. Data analysis revealed that EMB resistance is associated with one quantitative trait locus (QTL) region on L. salmonis chromosome 5. Marker-trait association was confirmed by genotyping assays for 7 SNPs in two additional families. Furthermore, the transcriptome of male parasites of the EMB-susceptible and -resistant L. salmonis parental strains was assessed. Among eighteen sequences showing higher transcript expression in EMB-resistant as compared to drug-susceptible lice, the most strongly up-regulated gene is located in the above QTL region and shows high homology to β spectrin, a cytoskeleton protein that has roles in neuron architecture and function. Further genes differentially regulated in EMB-resistant lice include a glutathione S-transferase (GST), and genes coding for proteins with predicted roles in mitochondrial function, intracellular signalling or transcription.

CONCLUSIONS

Major determinants of EMB resistance in L. salmonis are located on Chromosome 5. Resistance can be predicted using a limited number of genetic markers. Genes transcriptionally up-regulated in EMB resistant parasites include a β spectrin, a cytoskeletal protein with still incompletely understood roles in neuron structure and function, as well as glutathione S-transferase, an enzyme with potential roles in the biochemical defence against toxicants.

Fishy business in Seattle: Salmon mislabeling fraud in sushi restaurants vs grocery stores

Salmon is the most commonly consumed finfish in the United States of America (USA), and the mislabeling of salmon is a widespread problem. Washington State is a global supplier of wild-caught Pacific salmon and local salmon mislabeling results in substantial economic, ecological, and cultural impacts. Previous studies in Washington State identified high levels of mislabeled salmon in both markets and restaurants, resulting in local legislation being passed that requires proper labeling of salmon products, including identifying it as wild-caught or farm-raised. To investigate whether recent legislative efforts reduced salmon fraud rates, we acquired and genetically barcoded salmon samples from 67 grocery stores and 52 sushi restaurants in Seattle, Washington. DNA from each salmon sample was isolated and the cytochrome c oxidase gene was sequenced to identify the fish species. Our study, conducted from 2022-2023, revealed 18% of salmon samples from both grocery stores and sushi restaurants were mislabeled. While most samples were acquired during the fall months when wild salmon is in season, we still observed a high salmon mislabeling rate. Unlike grocery stores, Seattle sushi restaurants often sold farmed salmon mislabeled as wild salmon. Specifically, substitutions of vendor-claimed wild salmon with farmed salmon occurred in 32.3% of sushi restaurant samples compared to 0% of grocery store samples. Additionally, occurrences of wild salmon being substituted with another salmon species (wild or farmed) occurred in 38.7% of sushi restaurant samples compared to 11.1% of grocery store samples. All salmon substitutions in sushi restaurants harmed the customer financially as they were given a cheaper market-priced fish. In grocery stores, however, we did not detect significant economic loss to customers due to salmon mislabeling. Taken together, it is important to continue to develop and enforce legislation in Washington State that prevents salmon fraud and promotes ecologically sustainable fishing practices.

Cell death induced by Lepeophtheirus salmonis labial gland protein 3 in salmonid fish leukocytes: A mechanism for disabling host immune responses

The salmon louse (Lepeophtheirus salmonis) is an ectoparasite feeding on mucus, skin, and blood of salmonids. On parasitised fish erosions and, at later lice stages, ulcerations appear at the louse feeding site. In susceptible species like Atlantic salmon (Salmo salar) with a limited rejection of lice, only a mild inflammatory response with minor influx of immune cells is seen at these lesions, as the salmon louse secrete proteins that can dampen immune responses. In a previous study, Lepeophtheirus salmonis labial gland protein 3 (LsLGP3) was suggested to dampen cellular responses, and the present study aimed at increasing our understanding of its mode of action. LsLGP3 was found to be secreted on to the host skin, and both in vivo and in vitro experiments were performed to elucidate its function. Histological analysis of the louse attachment site revealed an epidermal and dermal influx of mainly macrophages and granulocytes after 5 days post infestation. The immune cell influx was deeper in the dermis throughout the louse infestation, and LsLGP3 may be involved in dampening this response. Enriched populations of Atlantic salmon B-cells, T-cells, granulocytes, and monocytes were exposed to recombinant LsLGP3 (recLGP3) in vitro, resulting in a significant decrease in cell viability compared to non-exposed controls. An apoptotic cell morphology with "beads-on-a-string" like protrusions was seen in all leukocyte cell fractions after recLGP3 exposure, but not in erythrocytes or keratocytes. A decreased viability was also detected in pink salmon leucocytes, which was not in leucocytes from non-salmonid species. These functional insights suggest that LsLGP3 specifically induces apoptosis of salmonid leukocytes and is likely a key protein secreted by the lice that disables the Atlantic salmon ability to mount an adequate immune response towards the salmon louse. In vivo LsLGP3 knock down studies indicated that the effect is localised primarily at the lice feeding site, without affecting immune cells that are not situated adjacent to the lice-inflicted lesion. The findings from this study could significantly aid in the development of new immune based anti-salmon louse prophylactic measures and treatments.

Algal protein-based 3D-printed fish-analogs as a new approach for sustainable seafood

Rising global demand for animal-products exceeds human-population growth. This unsustainable trend causes harmful ecological effects. Overfishing causes extinction of aquatic animals and a dangerous biodiversity loss harming aquatic ecosystems. Hence, replacing animal-based food, particularly beef and fish, with sustainable alternatives is an urgent vital global mission. Analogs of animal-based products include plant-based, tissue-culture-based and fermentation-based products. Fish analogs have mainly been based on plant-protein, fungi, tissue-culture, but to our knowledge, fish analogs made of algae, particularly macroalgae, as the major component and protein-source have not been reported. 3D-food-printing is a fast-developing technology, enabling formation of complex three-dimensional structures with various heterogeneous topologies and tailorable compositions. Herein, we report the co-extraction of proteins and polysaccharides from the red marine-macroalgae Gracilaria cornea, and using the extract in injection-based 3D-printing to form prototypes of salmon-fillet. Two bioinks were used: a red bioink dyed with microalgal-astaxanthin, for the muscle tissue, and a white bioink dyed with CaCO3, for the intramuscular fatty-tissue. Algal proteins have excellent nutritional amino-acid composition, and the co-extraction with agar facilitates 3D-printing thanks to its pseudoplastic and gelling properties. This study highlights macroalgae as an exciting natural raw-material for fish analogs towards sustainable seafood production, thereby decreasing harm to ocean fisheries.

Why aquaculture may not conserve wild fish

We review literature on the displacement paradox and the Jevons paradox, with consideration of their implications for the potential effects of aquaculture on wild fisheries. The Jevons paradox refers to circumstances where improvements in the efficiency of resource use lead to growth in consumption and therefore undermine conservation. The displacement paradox refers to circumstances where increasing use of a potential substitute for a resource (e.g., farmed fish) does not lead to proportionate reduction in consumption of the other resource (e.g., wild fish). The literature on the displacement paradox and the Jevons paradox suggests that there may be unanticipated consequences from the rise of aquaculture that may be detrimental for fisheries conservation. Here, we present theoretical explanations, drawing on the tragedy of the commodity, for understanding the tendencies for these technological paradoxes to occur and emphasize their relevance for concerns associated with fisheries and aquaculture systems.

Diseases of marine fish and shellfish in an age of rapid climate change

A recurring trend in evidence scrutinized over the past few decades is that disease outbreaks will become more frequent, intense, and widespread on land and in water, due to climate change. Pathogens and the diseases they inflict represent a major constraint on seafood production and yield, and by extension, food security. The risk(s) for fish and shellfish from disease is a function of pathogen characteristics, biological species identity, and the ambient environmental conditions. A changing climate can adversely influence the host and environment, while augmenting pathogen characteristics simultaneously, thereby favoring disease outbreaks. Herein, we use a series of case studies covering some of the world's most cultured aquatic species (e.g., salmonids, penaeid shrimp, and oysters), and the pathogens (viral, fungal, bacterial, and parasitic) that afflict them, to illustrate the magnitude of disease-related problems linked to climate change.

Wild salmon migration routes influence sea lice infestations: An agent-based model predicting farm-related infestations on juvenile salmon

This study presents an Agent-Based Model (ABM) simulation to assess the impact of varying migration routes on sea lice (Caligus clemensi) infestation levels in juvenile wild sockeye salmon (Oncorhynchus nerka) in the Discovery Islands, British Columbia, Canada. This research highlights the importance of migratory routes in determining the extent of exposure to sea lice originating from nearby salmon farms. Three northward out-migration routes were modelled, each exposing the fish to different levels of infestation pressure based on proximity to salmon farms. The ABM incorporates spatially explicit migration patterns of juvenile sockeye salmon using a detailed raster map of the Discovery Islands. Key variables such as swimming speed, progression rate, and infestation levels were integrated into the model, offering a comprehensive analysis of migration and infestation dynamics. The study revealed that infestation rate is highly variable, depending on migration routes. Specifically, salmon traveling longer migration routes with lower infestation pressure may experience higher sea lice loads compared to those on shorter routes with higher infestation pressure. This underscores the role of low infestation pressures and the critical influence of swimming speed, which affects exposure time, and thus infestation rates. Additionally, the study conducted a sensitivity analysis to understand the influence of various parameters on infestation rates. This analysis highlighted the importance of swimming speed and progression rate, particularly in routes closer to the farms. The findings suggest that slower swimming speeds and meandering routes increase exposure to lice, thereby elevating infestation levels. The research contributes to understanding the dynamics of sea lice transmission and its relationship with salmon migration patterns. It underscores the necessity of considering migratory routes and farm proximity in managing and mitigating the impact of sea lice infestation on wild salmon populations. This study's insights are crucial for developing strategies to balance aquaculture practices with the conservation of wild salmon.

Transcriptomic response of lumpfish (Cyclopterus lumpus) head kidney to viral mimic, with a focus on the interferon regulatory factor family

The economic importance of lumpfish (Cyclopterus lumpus) is increasing, but several aspects of its immune responses are not well understood. To discover genes and mechanisms involved in the lumpfish antiviral response, fish were intraperitoneally injected with either the viral mimic polyinosinic:polycytidylic acid [poly(I:C)] or phosphate-buffered saline (PBS; vehicle control), and head kidneys were sampled 24 hours post-injection (hpi) for transcriptomic analyses. RNA sequencing (RNA-Seq) (adjusted p-value <0.05) identified 4,499 upregulated and 3,952 downregulated transcripts in the poly(I:C)-injected fish compared to the PBS-injected fish. Eighteen genes identified as differentially expressed by RNA-Seq were included in a qPCR study that confirmed the upregulation of genes encoding proteins with antiviral immune response functions (e.g., rsad2) and the downregulation of genes (e.g., jarid2b) with potential cellular process functions. In addition, transcript expression levels of 12 members of the interferon regulatory factor (IRF) family [seven of which were identified as poly(I:C)-responsive in this RNA-Seq study] were analyzed using qPCR. Levels of irf1a, irf1b, irf2, irf3, irf4b, irf7, irf8, irf9, and irf10 were significantly higher and levels of irf4a and irf5 were significantly lower in the poly(I:C)-injected fish compared to the PBS-injected fish. This research and associated new genomic resources enhance our understanding of the genes and molecular mechanisms underlying the lumpfish response to viral mimic stimulation and help identify possible therapeutic targets and biomarkers for viral infections in this species.

The toxicity of chlorine dioxide to clownfish and its bactericidal capability to pathogenic strains of vibrio spp

Global ornamental fish transportation ranging from hours to days can produce multiple stress factors impact fish health and cause mortality. Clownfish, particularly Amphiprion ocellaris, are among the most traded saltwater ornamental fish. Vibrio includes several pathogenic strains that affect aquatic animals. Consequently, prophylactic treatment of the water or fish is recommended. In this study, six Vibrio strains including V. alginolyticus, V. parahaemolyticus and V. harveyi isolated from sick A. ocellaris and one V. harveyi strain from a sick East Asian fourfinger threadfin (Eleutheronema rhadinum) were tested for their sensitivity to a popular disinfectant, chlorine dioxide (ClO2). The results showed that 0.25 ppm ClO2 effectively suppressed five of the seven tested Vibrio strains for 24 h; however, 0.1 ppm ClO2 is safer for A. ocellaris. Meanwhile, ClO2 2.5 ppm reduced the bacterial counts to below 3.3 × 105 CFU/mL for 24 hours. The LC50 of ClO2 for A. ocellaris was 0.87 ppm at 10 min and 0.72 ppm at 24 h post treatment. Mild changes in water quality, including dissolved oxygen (DO), temperature and pH, were recorded during the trial. More research is necessary to understand the sensitivity of various aquatic animal pathogens to ClO2 and its toxicity to different aquatic animals.

Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon

BACKGROUND

Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown.

RESULTS

We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite.

CONCLUSIONS

Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

Inactivated Aeromonas salmonicida impairs adaptive immunity in lumpfish (Cyclopterus lumpus)

Aeromonas salmonicida, a widely distributed aquatic pathogen causing furunculosis in fish, exhibits varied virulence, posing challenges in infectious disease and immunity studies, notably in vaccine efficacy assessment. Lumpfish (Cyclopterus lumpus) has become a valuable model for marine pathogenesis studies. This study evaluated several antigen preparations against A. salmonicida J223, a hypervirulent strain of teleost fish, including lumpfish. The potential immune protective effect of A. salmonicida bacterins in the presence and absence of the A-layer and extracellular products was tested in lumpfish. Also, we evaluated the impact of A. salmonicida outer membrane proteins (OMPs) and iron-regulated outer membrane proteins (IROMPs) on lumpfish immunity. The immunized lumpfish were intraperitoneally (i.p.) challenged with 104 A. salmonicida cells/dose at 8 weeks-post immunization (wpi). Immunized and non-immunized fish died within 2 weeks post-challenge. Our analyses showed that immunization with A. salmonicida J223 bacterins and antigen preparations did not increase IgM titres. In addition, adaptive immunity biomarker genes (e.g., igm, mhc-ii and cd4) were down-regulated. These findings suggest that A. salmonicida J223 antigen preparations hinder lumpfish immunity. Notably, many fish vaccines are bacterin-based, often lacking efficacy evaluation. This study offers crucial insights for finfish vaccine approval and regulations.

Lufenuron treatment temporarily represses gene expression and affects the SUMO pathway in liver of Atlantic salmon

Lufenuron is a benzoylurea insecticide currently in use to combat sea lice infestation in salmon aquaculture in Chile. With pending approval in Norway, the aim of this work was to study the uptake and toxicity of lufenuron in liver tissue of Atlantic salmon. Juvenile salmon weighing 40 g were given a standard 7-day oral dose, and bioaccumulation and transcriptional responses in the liver were examined 1 day after the end-of-treatment (day 8) and after 1 week of elimination (day 14). Bioaccumulation levels of lufenuron were 29 ± 3 mg/kg at day 8 and 14 ± 1 mg/kg at day 14, indicating relatively rapid clearance. However, residues of lufenuron were still present in the liver after 513 days of depuration. The exposure gave a transient inhibition of transcription in the liver at day 8 (2437 significant DEGs, p-adj < .05), followed by a weaker compensatory response at day 14 (169 significant DEGs). Pathways associated with RNA metabolism such as the sumoylation pathway were most strongly affected at day 8, while the apelin pathway was most profoundly affected at day 14. In conclusion, this study shows that lufenuron easily bioaccumulates and that a standard 7-day oral dose induces a transient inhibition of transcription in liver of salmon.

Does sedation with AQUI-S® mitigate transport stress and post transport mortality in ballan wrasse (Labrus bergyltae)?

Ballan wrasse (Labrus bergylta) are commonly used as cleaner fish in salmon farms as a biological treatment to mitigate sea lice infestation. Improved welfare for cleaner fish both during production of these fish and when in sea-cages with salmon is crucial for the industry's development. A common operational procedure in ballan wrasse production is transporting juveniles from one land-based farm to another for further on-growing. Episodes of increased mortality have been reported after such transportations. In this study, the relationship between transport stress and post-transport mortality at the on-growing facility was examined. It was also investigated if light sedation with AQUI-S® can mitigate stress during transport. Stress was quantified by measuring cortisol release rate to the tank water during transport. This was investigated in 10 commercial live carrier truck transports (6 without AQUI-S® sedation and 4 with sedation during loading and transport). The total time of transport varied between 12 and 21 h. In general, mortality was significantly higher (1.0 ± 0.6% day-1) the first five days post-transport compared to 15-20 days post transport (0.5% day-1). There was also a strong relationship between fish weight at transport and post-transport mortality, where higher mean weight at transport reduced mortality. In contrast to what was expected, AQUI-S® treatment during transport procedures increased cortisol excretion rate, suggesting a stimulating effect of AQUI-S® on the stress axis in ballan wrasse. Considering these results, the value of using AQUI-S® to reduce stress during transport of juvenile ballan wrasse might be questioned. However, there was no relationship between cortisol release rate during transport and post-transport mortality. Furthermore, this study emphasizes that water cortisol measurements can be used as a none-invasive tool for monitoring stress and can be integrated into the welfare evaluation during commercial fish transports.

Effects of the sea lice chemotherapeutant, emamectin benzoate, on metabolism and behaviour of the sea-pen Pennatula phosphorea

Chemotherapeutants used to control infestations by sea lice can be released into the marine environment surrounding aquaculture farms. Among these therapeutic agents, emamectin benzoate is extensively utilized even though its impact on non-target taxa has not been thoroughly examined. In this context, we explored the effects of emamectin benzoate on a common Norwegian habitat-forming species: the phosphorescent sea-pen Pennatula phosphorea. Specifically, we examined P. phosphorea metabolic and responses before, during and after exposure to emamectin benzoate. Results indicate that an 8-day emamectin benzoate exposure (0.8 mg/L) did not induce P. phosphorea mortality or significant behavioural or metabolic modifications. However, we highlighted the presence and persistence of emamectin benzoate in exposed P. phosphorea tissue. These results indicate that emamectin benzoate is unlikely to adversely impact P. phosphorea populations in the environment. However, persistence of emamectin benzoate in tissue constitutes a potential for bioaccumulation with repeated treatments and should be examined in further studies.

Occurrence of salmonid alphavirus and piscine orthoreovirus-1 infections in migrating salmon (Salmo salar L.) post-smolt in western Norway

Viral diseases are a serious problem in Atlantic salmon (Salmo salar L.) farming in Norway, often leading to reduced fish welfare and increased mortality. Disease outbreaks in salmon farms may lead to spread of viruses to the surrounding environment. There is a public concern that viral diseases may negatively affect the wild salmon populations. Pancreas disease (PD) caused by salmonid alphavirus (SAV) and heart and skeletal muscle inflammation (HSMI) caused by piscine orthoreovirus-1 (PRV-1) are common viral diseases in salmon farms in western Norway. In the current study, we investigated the occurrence of SAV and PRV-1 infections in 651 migrating salmon post-smolt collected from three fjord systems (Sognefjorden, Osterfjorden and Hardangerfjorden) located in western Norway in 2013 and 2014 by real-time RT-PCR. Of the collected post-smolts, 303 were of wild origin and 348 were hatchery-released. SAV was not detected in any of the tested post-smolt, but PRV-1 was detected in 4.6% of them. The Ct values of PRV-1 positive fish were usually high (mean 32.0; range: 20.1-36.8). PRV-1 prevalence in post-smolts from the three fjords was 6.1% in Sognefjorden followed by 4.8% in Osterfjorden and 2.3% in Hardangerfjorden. The prevalence PRV-1 was significantly higher in wild (6.9%) compared to hatchery-released post-smolt (2.6%). The occurrence of PRV-1 infection in the fish was lowest in the Hardangerfjorden which has the highest fish farming intensity. Our results suggest that SAV infection are uncommon in migrating smolt while PRV-1 infection can be detected at low level. These findings suggest that migrating smolts were at low risk from SAV or PRV-1 released from salmon farms located in their migration routes in 2013 and 2014.

Evolutionary predictions for a parasite metapopulation: Modelling salmon louse resistance to pest controls in aquaculture

Pests often evolve resistance to pest controls used in agriculture and aquaculture. The rate of pest adaptation is influenced by the type of control, the selective pressure it imposes, and the gene flow between farms. By understanding how these factors influence evolution at the metapopulation level, pest management strategies that prevent resistance from evolving can be developed. We developed a model for the metapopulation and evolutionary dynamics of the salmon louse (Lepeophtheirus salmonis), which is a major parasite affecting salmon aquaculture. Different management scenarios were simulated across a network of salmon farms covering half of Norway, and their effects on louse epidemiology and evolution were investigated. We compared louse controls that differed in how they were deployed through time (discrete vs. continuous), how they impacted the louse life cycle, and in their overall efficacy. We adjusted the strength of selection imposed by treatments, the dominance effect of the resistant allele, and the geographic location at which resistance originated. Continuously acting strategies (e.g., louse-resistant salmon) were generally more effective than discrete strategies at controlling lice, especially when they increased louse mortality during early developmental stages. However, effective strategies also risked imposing frequent and/or strong selection on lice, thus driving rapid adaptation. Resistant alleles were more likely to be lost through genetic drift when they were recessive, had a low-fitness advantage, or originated in low-farm-density areas. The north-flowing current along the Norwegian coastline dispersed resistant genes from south to north, and limited gene flow in the opposite direction. We demonstrate how evolutionary models can produce quantitative predictions over large spatial and temporal scales and for a range of pest control scenarios. Quantitative outputs can be translated into practical management decisions applied at a regional level to minimise the risk of resistance developing.

A modeling study of the impact of treatment policies on the evolution of resistance in sea lice on salmon farms

Salmonid aquaculture is an important source of nutritious food with more than 2 million tonnes of fish produced each year (Food and Agriculture Organisation of the United Nations, 2019). In most salmon producing countries, sea lice represent a major barrier to the sustainability of salmonid aquaculture. This issue is exacerbated by widespread resistance to chemical treatments on both sides of the Atlantic. Regulation for sea lice management mostly involves reporting lice counts and treatment thresholds, which depending on interpretation may encourage preemptive treatments. We have developed a stochastic simulation model of sea lice infestation including the lice life-cycle, genetic resistance to treatment, a wildlife reservoir, salmon growth and stocking practices in the context of infestation, and coordination of treatment between farms. Farms report infestation levels to a central organisation, and may then cooperate or not when coordinated treatment is triggered. Treatment practice then impacts the level of resistance in the surrounding sea lice population. Our simulation finds that treatment drives selection for resistance and coordination between managers is key. We also find that position in the hydrologically-derived network of farms can impact individual farm infestation levels and the topology of this network can impact overall infestation and resistance. We show how coordination and triggering of treatment alongside varying hydrological topology of farm connections affects the evolution of lice resistance, and thus optimise salmon quality within socio-economic and environmental constraints. Network topology drives infestation levels in cages, treatments, and hence treatment-driven resistance. Thus farmer behaviour may be highly dependent on hydrologically position and local level of infestation.

Welfare and performance of ballan wrasse (Labrus bergylta) reared at two different temperatures after a preparatory feeding trial with enhanced dietary eicosapentaenoic acid

Concerns have long been raised about the welfare of ballan wrasse (Labrus bergylta) used for the biological control of sea lice in Atlantic salmon (Salmo salar) aquaculture. This study assessed the effect of increased dietary eicosapentaenoic acid (EPA) levels and initial condition factor (CF) on the subsequent performance and welfare of ballan wrasse farmed in high and low water temperatures. Fish were fed a diet with either commercial or high EPA levels for 3 months at 15°C. Subsequently, fish were tagged with a passive integrated transponder, measured for their CF and divided into two groups consisting of fish from both treatments and reared for 4.5 months at either 15 or 6°C fed a commercial diet. Each fish was categorized as high (≥2.7) or low CF (<2.7) fish based on the calculated average CF of the population. Dietary composition influenced the fatty acid (FA) profile of the stored lipids without affecting the growth or welfare of ballan wrasse. Fish reared at 15°C showed higher growth, more fat and energy reserves and less ash content. Fish reared at 6°C lost weight, using up their body lipids at the end of the temperature trial. Gene expression analyses showed upregulation of the positive growth marker (GHrα) and two genes involved in the synthesis and oxidation of FAs (elovl5, cpt1) and downregulation of the negative growth marker (mstn) in fish reared at 15°C compared to those reared at 6°C. Fish reared at 6°C showed upregulated levels of il-6 compared to those reared at 15°C, suggesting an enhanced immune reaction in response to low temperature. Fish with high CF showed better survival, growth and performance compared to those with low CF. External welfare scoring showed higher prevalence and severity in emaciation, scale loss and the sum index score (of all measured welfare parameters) in fish reared at 6°C compared to those reared at 15°C and better welfare in fish with high CF compared to those with low CF. Histological examination of the skin showed that fish reared at 6°C had decreased epidermal thickness, a lower overall number of mucous cells in the inner and outer epidermis and a different organization of mucous cells compared to fish reared at 15°C, indicating stress in fish reared at 6°C. Overall, low water temperatures had profound effects on the performance and external and internal welfare parameters of ballan wrasse and can be considered a stressor likely affecting the delousing efficacy. These findings support the seasonal use of different cleaner fish species. High CF, but not increased dietary EPA levels, appeared to help fish cope better with low water temperatures and should thus be assessed and considered before deploying them in salmon cages.

Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish-Implications for Broodstock Provenance Sourcing and Larval Production

Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for "cleaner fish" to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype-environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our 'global' sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.

Repeated exposure affects susceptibility and responses of Atlantic salmon (Salmo salar) towards the ectoparasitic salmon lice (Lepeophtheirus salmonis)

Atlantic salmon (Salmo salar) is repeatedly exposed to and infected with ectoparasitic salmon lice (Lepeophtheirus salmonis) both in farms and in nature. However, this is not reflected in laboratory experiments where fish typically are infected only once. To investigate if a previous lice infection affects host response to subsequent infections, fish received 4 different experimental treatments; including 2 groups of fish that had previously been infected either with adult or infective salmon lice larvae (copepodids). Thereafter, fish in all treatment groups were infected with either a double or a single dose of copepodids originating from the same cohort. Fish were sampled when lice had developed into the chalimus, the pre-adult and the adult stage, respectively. Both the specific growth rate and cortisol levels (i.e. a proxy for stress) of the fish differed between treatments. Lice success (i.e. ability to infect and survive on the host) was higher in naïve than in previously infected fish (pre-adult stage). The expression of immune and wound healing transcripts in the skin also differed between treatments, and most noticeable was a higher upregulation early in the infection in the group previously infected with copepodids. However, later in the infection, the least upregulation was observed in this group, suggesting that previous exposure to salmon lice affects the response of Atlantic salmon towards subsequent lice infections.

Rejection of Lepeophtheirus salmonis driven in part by chitin sensing is not impacted by seawater acclimitization in Coho salmon (Oncorhynchus kisutch)

There is tremendous variation in life-history strategies among anadromous salmonids. Species that enter the ocean environment at small sizes (< 20 g) are likely under more physiological pressure from pathogens; however, little data is available on responses at these early stages. With this in mind, we performed salmon louse challenges with Coho salmon either immediately after seawater entry (SW; ca. 10 g) or after 30 days in SW (ca. 20 g). Irrespective of size or time in SW, parasites were rapidly rejected by the host, with > 90% of all parasites lost by 16 days post-infection (dpi). Rejection was concomitant with host epithelial granulomatous infiltrations that initially targeted the embedded frontal filament (4 dpi) and the entire parasite by 10 dpi. Illumina sequencing, followed by functional enrichment analysis, revealed a concerted defense response in the fin within 1 dpi that included multiple innate and adaptive immunity components. Strikingly, early indications of an allergic-type inflammatory response were associated with chitin sensing pathways orchestrated by early overexpression of the IgE-receptor, fcer1g. Additionally, there was profound overexpression of several classes of c-type lectin receptors, including dectin-2, mincle, and dc-sign at 1 dpi onward. These profiles and upregulation of cellular effector markers were corroborated by histopathological evaluation, revealing the simultaneous presence of mast cell/eosinophilic granular cells, sacciform cells, macrophages/histiocytes, and granulocytes in fin. At 10 dpi and concurrent with parasite expulsion, there was evidence of immunoregulation in addition to tissue remodelling pathways. At 16 dpi, the response was effectively abrogated. Simultaneous profiling of the parasite transcriptome revealed early induction of chitin metabolism and immunomodulation, toxin production and ECM degradation; however, after 7 dpi, these were replaced with overexpression of stress and immune defense genes. These data present the first evidence for Coho salmon demonstrating chitin- and sugar moiety-sensing as key drivers of salmon louse rejection.

Does pre-spawning catch and release angling affect offspring telomere dynamics in Atlantic salmon?

The practice of 'catch and release' (C&R) angling confers a balance between animal welfare, conservation efforts and preserving the socio-economic interests of recreational angling. However, C&R angling can still cause exhaustion and physical injury, and often exposes the captured fish to the stress of air exposure. Therefore, the true conservation success of C&R angling depends on whether the angled individuals then survive to reproduction and whether there are any persisting effects on subsequent generations. Here we tested the hypothesis that the stress of C&R angling is then passed on to offspring. We experimentally manipulated the C&R experience of wild adult salmon prior to the spawning season. These parental fish either underwent a C&R simulation (which involved exercise with/without air exposure) or were left as control individuals. We then measured the telomere length of the arising offspring (at the larval stage of development) since previous studies have linked a shorter telomere length with reduced fitness/longevity and the rate of telomere loss is thought to be influenced by stress. Family-level telomere length was positively related to rate of growth. However, the telomere lengths of the salmon offspring were unrelated to the C&R experience of their parents. This may be due to there being no intergenerational effect of parental stress exposure on offspring telomeres, or to any potential effects being buffered by the significant telomere elongation mechanisms that are thought to occur during the embryonic and larval stages of development. While this may suggest that C&R angling has a minimal intergenerational effect on offspring fitness, there have been numerous other reports of negative C&R effects, therefore we should still be aiming to mitigate and refine such practices, in order to minimize their impacts on fish populations.

A new family of glutamate-gated chloride channels in parasitic sea louse Caligus rogercresseyi: A subunit refractory to activation by ivermectin is dominant in heteromeric assemblies

Sea louse ectoparasitosis is a major threat to fish aquaculture. Avermectins such as ivermectin and emamectin have been effectively used against sea louse infestation, but the emergence of resistance has limited their use. A better understanding of the molecular targets of avermectins is essential to the development of novel treatment strategies or new, more effective drugs. Avermectins are known to act by inhibiting neurotransmission through allosteric activation of glutamate-gated chloride channels (GluCls). We have investigated the GluCl subunit present in Caligus rogercresseyi, a sea louse affecting aquaculture in the Southern hemisphere. We identify four new subunits, CrGluCl-B to CrGluCl-E, and characterise them functionally. CrGluCl-A (previously reported as CrGluClα), CrGluCl-B and CrGluCl-C all function as glutamate channel receptors with different sensitivities to the agonist, but in contrast to subunit -A and -C, CrGluCl-B is not activated by ivermectin but is rather antagonised by the drug. CrGluCl-D channel appears active in the absence of any stimulation by glutamate or ivermectin and CrGluCl-E does not exhibit any activity. Notably, the expression of CrGluCl-B with either -A or -C subunits gives rise to receptors unresponsive to ivermectin and showing altered response to glutamate, suggesting that coexpression has led to the preferential formation of heteromers to which the presence of CrGluCl-B confers the property of ivermectin-activation refractoriness. Furthermore, there was evidence for heteromer formation with novel properties only when coexpressing pairs E/C and D/B CrGluCl subtypes. Site-directed mutagenesis shows that three transmembrane domain residues contribute to the lack of activation by ivermectin, most crucially Gln 15' in M2, with mutation Q15'T (the residue present in ivermectin-activated subunits A and C) conferring ivermectin activation to CrGluCl-B. The differential response to avermectin of these Caligus rogercresseyi GluClsubunits, which are highly conserved in the Northern hemisphere sea louse Lepeophtheirus salmonis, could have an influence on the response of these parasites to treatment with macrocyclic lactones. They could serve as molecular markers to assess susceptibility to existing treatments and might be useful molecular targets in the search for novel antiparasitic drugs.

A century of parasitology in fisheries and aquaculture

Fish parasitological research associated with fisheries and aquaculture has expanded remarkably over the past century. The application of parasites as biological tags has been one of the fields in which fish parasitology has generated new insight into fish migration and stock assessments worldwide. It is a well-established discipline whose methodological issues are regularly reviewed and updated. Therefore, no concepts or case-studies will be repeated here; instead, we summarize some of the main recent findings and achievements of this methodology. These include the extension of its use in hosts other than bony fishes; the improvements in the selection of parasite tags; the recognition of the host traits affecting the use of parasite tags; and the increasingly recognized need for integrative, multidisciplinary studies combining parasites with classical methods and modern techniques, such as otolith microchemistry and genetics. Archaeological evidence points to the existence of parasitic problems associated with aquaculture activities more than a thousand years ago. However, the main surge of research within aquaculture parasitology occurred with the impressive development of aquaculture over the past century. Protozoan and metazoan parasites, causing disease in domesticated fish in confined environments, have attracted the interest of parasitologists and, due to their economic importance, funding was made available for basic and applied research. This has resulted in a profusion of basic knowledge about parasite biology, physiology, parasite-host interactions, life cycles and biochemistry. Due to the need for effective control methods, various solutions targeting host-parasite interactions (immune responses and host finding), genetics and pharmacological aspects have been in focus.

Dual RNA-Seq Analysis Reveals Transcriptome Effects during the Salmon–Louse Interaction in Fish Immunized with Three Lice Vaccines

Due to the reduced efficacy of delousing drugs used for sea lice control in salmon aquaculture, fish vaccines have emerged as one of the most sustainable strategies in animal health. Herein, the availability of C. rogercresseyi and Salmo salar genomes increases the capability of identifying new candidate antigens for lice vaccines using RNA sequencing and computational tools. This study aimed to evaluate the effects of two recombinant antigens characterized as peritrophin and cathepsin proteins on the transcriptome profiling of Atlantic salmon during a sea lice infestation. Four experimental groups were used: Peritrophin, cathepsin, and peritrophin/cathepsin (P/C), and PBS as the control. C. rogercresseyi female, S. salar head kidney, and skin tissue samples were sampled at 25 days post-infestation (dpi) for Illumina sequencing and RNA-seq analysis. Differential gene expression, gene ontology, and chromosomal expression analyses were performed. Furthermore, the dual RNA-seq analysis approach was performed to simultaneously explore host and pathogen transcriptomes, identifying functional associations for vaccine design. The morphometry of female sea lice exposed to immunized fish was also evaluated. The RNA-Seq analysis exhibited prototype-dependent transcriptome modulation, showing a conspicuous competition for metal ions during the infestation. Moreover, Dual RNA-seq analysis revealed vaccine-dependent gene patterns in both the host and the pathogen. Notably, significant morphometric differences between lice collected from immunized and control fish were observed, where cathepsin and P/C showed 57% efficacy. This study showed the potential of two proteins as lice vaccines for the salmon industry, suggesting novel molecular mechanisms between host–parasite interactions.

Peritrophin-like Genes Are Associated with Delousing Drug Response and Sensitivity in the Sea Louse Caligus rogercresseyi

Caligus rogercresseyi is the main ectoparasite that affects the salmon industry in Chile. The mechanisms used by the parasite to support its life strategy are of great interest for developing control strategies. Due to the critical role of insect peritrophins in host–parasite interactions and response to pest control drugs, this study aimed to identify and characterize the peritrophin-like genes present in C. rogercresseyi. Moreover, the expression of peritrophin-like genes was evaluated on parasites exposed to delousing drugs such as pyrethroids and azamethiphos. Peritrophin genes were identified by homology analysis among the sea louse transcriptome database and arthropods peritrophin-protein database obtained from GenBank and UniProt. Moreover, the gene loci in the parasite genome were located. Furthermore, peritrophin gene expression levels were evaluated by RNA-Seq analysis in sea louse developmental stages and sea lice exposed to delousing drugs deltamethrin, cypermethrin, and azamethiphos. Seven putative peritrophin-like genes were identified in C. rogercresseyi with high homology with other crustacean peritrophins. Differences in the presence of signal peptides, the number of chitin-binding domains, and the position of conserved cysteines were found. In addition, seven peritrophin-like gene sequences were identified in the C. rogercresseyi genome. Gene expression analysis revealed a stage-dependent expression profile. Notably, differential regulation of peritrophin genes in resistant and susceptible populations to delousing drugs was found. These data are the first report and characterization of peritrophin genes in the sea louse C. rogercresseyi, representing valuable knowledge to understand sea louse biology. Moreover, this study provides evidence for a deeper understanding of the molecular basis of C. rogercresseyi response to delousing drugs.

Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon

Background

Rapidly spreading parasitic infections like amoebic gill disease (AGD) are increasingly problematic for Atlantic salmon reared in aquaculture facilities and potentially pose a risk to wild fish species in surrounding waters. Currently, it is not known whether susceptibility to AGD differs between wild and farmed salmon. Wild Atlantic salmon populations are declining and this emerging disease could represent an additional threat to their long-term viability. A better understanding of how AGD affects fish health is therefore relevant for the accurate assessment of the associated risk, both to farming and to the well-being of wild populations. In this study, we assessed the impact of natural exposure to AGD on wild, hybrid and farmed post-smolt Atlantic salmon reared in a sea farm together under common garden conditions.

Results

Wild fish showed substantially higher mortality levels (64%) than farmed fish (25%), with intermediate levels for hybrid fish (39%) suggesting that AGD susceptibility has an additive genetic basis. Metabolic rate measures representing physiological performance were similar among the genetic groups but were significantly lower in AGD-symptomatic fish than healthy fish. Gut microbial diversity was significantly lower in infected fish. We observed major shifts in gut microbial community composition in response to AGD infections. In symptomatic fish the relative abundance of key taxa Aliivibrio, Marinomonas and Pseudoalteromonas declined, whereas the abundance of Polaribacter and Vibrio increased compared to healthy fish.

Conclusions

Our results highlight the stress AGD imposes on fish physiology and suggest that low metabolic-rate fish phenotypes may be associated with better infection outcomes. We consider the role increased AGD outbreak events and a warmer future may have in driving secondary bacterial infections and in reducing performance in farmed and wild fish.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00203-x.

Effects of tag type and surgery on migration of Atlantic salmon (Salmo salar) smolts

Tagging salmon smolts to provide information about the timing of outmigration has been a common approach to monitor phenology and model the risk of encountering stressors. However, the validity of tagging has come under scrutiny because of the sensitivity of this parameter in various management systems. We studied the probability of migration, timing of migration and growth during migration for Atlantic salmon smolts tagged with three different tags in the River Dale, western Norway. Two groups were tagged with passive integrated transponder (PIT) tags via a small ventral nonsurgical incision, either a 12 mm or a new 16 mm PIT tag. Two groups were subjected to surgical implantation of either a dummy acoustic transmitter or a 12 mm PIT tag (a sham surgery). Overall, 71% of the tagged smolts were recaptured at the downstream Wolf trap. Smolts from the sham tagged group were recaptured most frequently (78%) compared to dummy acoustic transmitters and 16 mm PIT tags (both 68%), but the differences were not significant. Results agree with prior assessments that longer smolts migrated earlier, with about half a day earlier migration for each millimetre total length of the smolt, but did not suggest any difference in time of migration among the tag types. Growth in length was evident from release to recapture, with smaller smolts exhibiting greater growth and no effect of tagging treatment. Our findings suggest that inferences about the timing of outmigration for salmon smolts based on acoustic tagging should be made cautiously because of the relationship among tag size, suitable fish size and the timing of a tagged individual's migration.

The effect of different intensities of the ectoparasitic salmon lice (Lepeophtheirus salmonis) on Atlantic salmon (Salmo salar)

The effect of different intensities of the ectoparasitic salmon lice (Lepeophtheirus salmonis) on stress, growth and the expression of immune and wound healing transcripts in the skin of Atlantic salmon (Salmo salar) was investigated. Lice infection success and survival were similar at the chalimus and preadult stage in the low and high dose group, but infection success and survival were significantly lower in the high than in the low dose group at the adult stage. The expression of investigated transcripts was not correlated to lice intensities, but several of them were significantly differently expressed locally in the skin at the site of lice attachment in infected fish compared to controls. This included an up-regulation of pro-inflammatory markers at the site of lice attachment (e.g., interleukin 1-beta, interleukin 8 and the acute phase protein serum amyloid A), a reduction of markers of adaptive immunity (cluster of differentiation 8-alpha and immunoglobulin M) and decreased expression of the anti-inflammatory cytokine interleukin 10.

Acoustic Delicing of Atlantic Salmon (Salmo salar): Fish Welfare and Salmon Lice (Lepeophtheirus salmonis) Dynamics

Acoustic lice treatment (AcuLice) is a newly developed system, which uses a composite acoustic sound image with low-frequency sound to remove salmon lice (Lepeophtheirus salmonis) from Atlantic salmon (Salmo salar). This field study documents the stress effects on Atlantic salmon and the effect on salmon lice dynamics during large-scale use of the AcuLice system. The effect of the AcuLice treatment on salmon lice dynamics was measured by weekly salmon lice counting at the facilities from mid-summer 2019 to late-spring 2020. The number of salmon lice treatments in the same period was also compared to a reference group. In addition, the number of weeks until the first salmon lice treatment (mechanical treatment) was compared between the two groups. Apart from a slight increase in plasma glucose, no significant differences were observed in the primary, secondary, or tertiary stress responses measured. For the mature female salmon lice, a significantly lower number (mean ± SEM) was shown for the AcuLice group (0.24 ± 0.03) compared to the reference group (0.44 ± 0.04). In addition, a lower number (mean ± SEM) of salmon lice treatments and a longer production period before the first salmon lice treatment occurred was observed at the AcuLice facilities (33.2 ± 3 weeks) compared to the reference facilities (20.3 ± 2 weeks). These data suggest that the use of the AcuLice system reduces the need for traditional salmon lice treatments with no added stress to the fish.

Temperature affects settlement success of ectoparasitic salmon lice (Lepeophtheirus salmonis) and impacts the immune and stress response of Atlantic salmon (Salmo salar)

In this study, the effect of temperature on Atlantic salmon (Salmo salar) stress and immune response to the ectoparasitic salmon lice (Lepeophtheirus salmonis) was investigated. We found that infestation affected the expression of several immune and wound healing transcripts in the skin especially at the site of lice attachment compared to un-infested control fish. Moreover, expression patterns in the skin of infested fish suggest that host immune responses towards salmon lice are impaired at low temperatures. However, reduced lice infestation success and survival at the lowest investigated temperatures suggest that cold water temperatures are more detrimental to the lice than their fish hosts. Finally, temperature affected the stress response of the fish and infected fish had a higher increase in cortisol levels in response to handling (a stressor) than un-infested controls.

Exploring Sea Lice Vaccines against Early Stages of Infestation in Atlantic Salmon (Salmo salar)

The sea louse Caligus rogercresseyi genome has opened the opportunity to apply the reverse vaccinology strategy for identifying antigens with potential effects on lice development and its application in sea lice control. This study aimed to explore the efficacy of three sea lice vaccines against the early stage of infestation, assessing the transcriptome modulation of immunized Atlantic salmon. Therein, three experimental groups of Salmo salar (Atlantic salmon) were vaccinated with the recombinant proteins: Peritrophin (prototype A), Cathepsin (prototype B), and the mix of them (prototype C), respectively. Sea lice infestation was evaluated during chalimus I-II, the early-infective stages attached at 7-days post infestation. In parallel, head kidney and skin tissue samples were taken for mRNA Illumina sequencing. Relative expression analyses of genes were conducted to identify immune responses, iron transport, and stress responses associated with the tested vaccines during the early stages of sea lice infection. The vaccine prototypes A, B, and C reduced the parasite burden by 24, 44, and 52% compared with the control group. In addition, the RNA-Seq analysis exhibited a prototype-dependent transcriptome modulation. The high expression differences were observed in genes associated with metal ion binding, molecular processes, and energy production. The findings suggest a balance between the host’s inflammatory response and metabolic process in vaccinated fish, increasing their transcriptional activity, which can alter the early host–parasite interactions. This study uncovers molecular responses produced by three vaccine prototypes at the early stages of infestation, providing new knowledge for sea lice control in the salmon aquaculture.

Key role of mitochondrial mutation Leu107Ser (COX1) in deltamethrin resistance in salmon lice (Lepeophtheirus salmonis)

The pyrethroid deltamethrin (DTM) is used to treat Atlantic salmon (Salmo salar) against salmon louse (Lepeophtheirus salmonis) infestations. However, DTM resistance has evolved in L. salmonis and is currently common in the North Atlantic. This study aimed to re-assess the association between DTM resistance and mitochondrial (mtDNA) mutations demonstrated in previous reports. Among 218 L. salmonis collected in Scotland in 2018–2019, 89.4% showed DTM resistance in bioassays, while 93.6% expressed at least one of four mtDNA single nucleotide polymorphisms (SNPs) previously shown to be resistance associated. Genotyping at further 14 SNP loci allowed to define three resistance-associated mtDNA haplotypes, named 2, 3 and 4, occurring in 72.0%, 14.2% and 7.3% of samples, respectively. L. salmonis strains IoA-02 (haplotype 2) and IoA-10 (haplotype 3) both showed high levels (~ 100-fold) of DTM resistance, which was inherited maternally in crossing experiments. MtDNA haplotypes 2 and 3 differed in genotype for 17 of 18 studied SNPs, but shared one mutation that causes an amino acid change (Leu107Ser) in the cytochrome c oxidase subunit 1 (COX1) and was present in all DTM resistant while lacking in all susceptible parasites. We conclude that Leu107Ser (COX1) is a main genetic determinant of DTM resistance in L. salmonis.

Lepeophtheirus (Copepoda: Caligidae) associated with fish: global infection patterns, parasite-host interactions and geographic range

Lepeophtheirus Nordmann, 1832 is a genus of sea lice that have been reported to cause parasitic disease problems for fish farming and the fishery industry. This first global investigation on Lepeophtheirus species associated with fish and infestation patterns, parasite-host interactions and geographic ranges linked to these ectoparasites covered articles published from 1940 to 2022. The total of 481 samples of Lepeophtheirus spp. comprised 49 species of these ectoparasites and were found parasitizing 100 teleost fish species from 46 families and 15 orders. Globally, a total of 9 Lepeophtheirus species were found in farmed fish (1 species occurred only in farmed fish and 8 species in both farmed and wild fish) and 48 in wild fish. The highest numbers of occurrences of Lepeophtheirus were in Serranidae and Pleuronectidae. L. pectoralis and L. salmonis were the species with widest geographic distribution. Host specificity was an important factor in the geographic distribution of L. salmonis. Most of the parasite species showed specificity for host fish families, as well as specificity for geographic regions. Little is known about many Lepeophtheirus species compared to the economical important L. salmonis. This could be an obstacle to developing improved management control strategies for the parasite in the fish farming industry, in addition to the diminishing knowledge of parasite taxonomy in many regions.

Larval salmon lice Lepeophtheirus salmonis exhibit behavioral responses to conspecific pre-adult and adult cues

In the larval stage of the parasitic copepod Lepeophtheirus salmonis, the free-living copepodid must locate and settle on a salmonid host. Chemosensory mechanisms play a role in determining whether a potential host is suitable for attachment, yet the full suite of chemical cues and resulting behavioral mechanisms used are unknown. After maturing, pre-adult female and adult male salmon lice aggregate upon salmonid hosts for reproduction. Copepodid salmon lice have been observed preferentially infesting hosts that harbor conspecific adults. The aim of this study was to investigate the possibility that salmon lice copepodids perceive and respond to cues from pre-adult female, adult-male, and/or gravid female salmon lice. Behavioral bioassays were conducted in vitro with copepodids exposed to water conditioned with 3 stages of conspecific lice (pre-adult female, adult male, or gravid female), and seawater conditioned with Atlantic salmon Salmo salar Linnaeus, 1758. Experiments demonstrated that copepodids exposed to water conditioned with the salmon host, pre-adult female, or adult male salmon lice significantly altered their behavior, whereas salmon lice exposed to water conditioned with gravid females did not. These results are potentially valuable in the development of novel methods for mitigation of L. salmonis in the salmon aquaculture industry.

New strategy for the design, production and pre-purification of chimeric peptide with immunomodulatory activity in Salmosalar

The intensive salmon farming is associated with massive outbreaks of infections. The use of antibiotics for their prevention and control is related to damage to the environment and human health. Antimicrobial peptides (AMPs) have been proposed as an alternative to the use of antibiotics for their antimicrobial and immunomodulatory activities. However, one of the main challenges for its massive clinical application is the high production cost and the complexity of chemical synthesis. Thus, recombinant DNA technology offers a more sustainable, scalable, and profitable option. In the present study, using an AMPs function prediction methodology, we designed a chimeric peptide consisting of sequences derived from cathelicidin fused with the immunomodulatory peptide derived from flagellin. The designed peptide, CATH-FLA was produced by recombinant expression using an easy pre-purification system. The chimeric peptide was able to induce IL-1β and IL-8 expression in Salmo salar head kidney leukocytes, and prevented Piscirickettsia salmonis-induced cytotoxicity in SHK-1 cells. These results suggest that pre-purification of a recombinant AMP-based chimeric peptide designed in silico allow obtaining a peptide with immunomodulatory activity in vitro. This could solve the main obstacle of AMPs for massive clinical applications.

Effect of sea lice chemotherapeutant hydrogen peroxide on the photosynthetic characteristics and bleaching of the coralline alga Lithothamnion soriferum

The proliferation of sea lice (Lepeophtheirus salmonis) represents a major challenge for the salmonid aquaculture industry in Norway. Hydrogen peroxide (H₂O₂) is a chemotherapeutant frequently used on Norwegian farms, however, its toxicity to non-target benthic species and habitats remains poorly understood. Maerl beds are constructed by the accumulation of non-geniculate coralline algae and provide important ecological functions. Due to the rapid expansion of aquaculture in Norway and the continued use of H₂O₂ as an anti-sea lice treatment, it is crucial to understand the impact of H₂O₂ on the physiology of maerl-forming species. The effects of a 1 h exposure to H₂O₂ on the photophysiology and bleaching of the coralline alga Lithothamnion soriferum were examined here through a controlled time-course experiment. PAM fluorimetry measurements showed that H₂O₂ concentrations ≥ 200 mg l^-1 negatively affected photosystem II (PSII) in thalli immediately after exposure, which was observed through a significant decline in maximum photochemical efficiency (F_v/F_m) and relative electron transport rate (rETR). The negative effects on PSII induced by oxidative stress, however, appear to be reversible, and full recovery of photosynthetic characteristics was observed 48 h to 28 days after exposure to 200 mg H₂O₂ l^-1 and 2000 mg H₂O₂ l^-1, respectively. At 28 days after exposure, there was evidence of two- to four-times more bleaching in thalli treated with concentrations ≥ 200 mg H₂O₂ l^-1 compared to those in the control. This indicates that despite the recovery of PSII, persistent damages can occur on the structural integrity of thalli, which may considerably increase the vulnerability of coralline algae to further exposure to H₂O₂ and other chemical effluents from salmonid farms.

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 > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3-1.6 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 ≈ 60% of the genome assemblies.

Draft Genome Sequences of 23 Tenacibaculum Isolates from Farmed Norwegian Lumpfish, Cyclopterus lumpus

Draft genome sequences of 23 Tenacibaculum sp. strains that were isolated from Cyclopterus lumpus (lumpfish) were investigated to elucidate possible routes of transmission between Salmo salar (Atlantic salmon) and lumpfish.

Cohabitation With Atlantic Salmon (Salmo salar) Affects Brain Neuromodulators But Not Welfare Indicators in Lumpfish (Cyclopterus lumpus)

Lumpfish are utilized to combat ectoparasitic epidemics in salmon farming. Research gaps on both cleaning behavior and client preferences in a natural environment, emphasizes the need to investigate the physiological impacts on lumpfish during cohabitation with piscivorous Atlantic salmon. Lumpfish (39.9 g, S.D ± 8.98) were arranged in duplicate tanks (n = 40 per treatment) and exposed to Live Atlantic salmon (245.7 g, S.D ± 25.05), salmon Olfaction or lifelike salmon Models for 6 weeks. Growth and health scores were measured every second week. In addition, the final sampling included measurements of neuromodulators, body color, and plasma cortisol. A stimulation and suppression test of the hypothalamic-pituitary-interrenal (HPI) axis was used for chronic stress assessment. Results showed that growth, health scores, and body color remained unaffected by treatments. Significant reductions in levels of brain dopamine and norepinephrine were observed in Live compared to Control. Plasma cortisol was low in all treatments, while the stimulation and suppression test of the HPI axis revealed no indications of chronic stress. This study presents novel findings on the impact on neuromodulators from Atlantic salmon interaction in the lumpfish brain. We argue that the downregulation of dopamine and norepinephrine indicate plastic adjustments to cohabitation with no negative effect on the species. This is in accordance with no observed deviations in welfare measurements, including growth, health scores, body color, and stress. We conclude that exposure to salmon or salmon cues did not impact the welfare of the species in our laboratory setup, and that neuromodulators are affected by heterospecific interaction.

Research Before Policy: Identifying Gaps in Salmonid Welfare Research That Require Further Study to Inform Evidence-Based Aquaculture Guidelines in Canada

Aquaculture is a growing industry worldwide and Canadian finfish culture is dominated by marine salmonid farming. In part due to increasing public and stakeholder concerns around fish welfare protection, the first-ever Canadian Code of Practice for the Care and Handling of Farmed Salmonids was recently completed, following the National Farm Animal Care Council's (NFACC) rigorous Code development process. During this process, both the Scientific (responsible for reviewing existing literature and producing a peer-reviewed report that informs the Code) and Code Development (a diverse group of stakeholders including aquaculture producers, fish transporters, aquaculture veterinarians, animal welfare advocates, food retailers, government, and researchers) Committees identified research gaps in tandem, as they worked through the literature on salmonid physiology, health, husbandry, and welfare. When those lists are combined with the results of a public "top-of-mind" survey conducted by NFACC, they reveal several overlapping areas of scientific, stakeholder, and public concern where scientific evidence is currently lacking: (1) biodensity; (2) health monitoring and management, with a focus on sea lice infection prevention and management; (3) feed quality and management, particularly whether feed restriction or deprivation has consequences for welfare; (4) enclosure design, especially focused on environmental enrichment provision and lighting design; and (5) slaughter and euthanasia. For each of these five research areas, we provide a brief overview of current research on the topic and outline the specific research gaps present. The final section of this review identifies future research avenues that will help address these research gaps, including using existing paradigms developed by terrestrial animal welfare researchers, developing novel methods for assessing fish welfare, and the validation of new salmonid welfare indices. We conclude that there is no dearth of relevant research to be done in the realm of farmed salmonid welfare that can support crucial evidence-based fish welfare policy development.

Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus

Simple Summary

Lumpfish (Cyclopterus lumpus) is an emergent aquaculture species, and its miRNA repertoire is still unknown. miRNAs are critical post-transcriptional modulators of teleost gene expression. Therefore, a lumpfish reference miRNAome was characterized by small RNA sequencing and miRDeep analysis of samples from different organs and developmental stages. The resulting miRNAome, an essential reference for future expression analyses, consists of 443 unique mature miRNAs from 391 conserved and eight novel miRNA genes. Enrichment of specific miRNAs in particular organs and developmental stages indicates that some conserved lumpfish miRNAs regulate organ and developmental stage-specific functions reported in other teleosts.

Abstract

MicroRNAs (miRNAs) are endogenous small RNA molecules involved in the post-transcriptional regulation of protein expression by binding to the mRNA of target genes. They are key regulators in teleost development, maintenance of tissue-specific functions, and immune responses. Lumpfish (Cyclopterus lumpus) is becoming an emergent aquaculture species as it has been utilized as a cleaner fish to biocontrol sea lice (e.g., Lepeophtheirus salmonis) infestation in the Atlantic Salmon (Salmo salar) aquaculture. The lumpfish miRNAs repertoire is unknown. This study identified and characterized miRNA encoding genes in lumpfish from three developmental stages (adult, embryos, and larvae). A total of 16 samples from six different adult lumpfish organs (spleen, liver, head kidney, brain, muscle, and gill), embryos, and larvae were individually small RNA sequenced. Altogether, 391 conserved miRNA precursor sequences (discovered in the majority of teleost fish species reported in miRbase), eight novel miRNA precursor sequences (so far only discovered in lumpfish), and 443 unique mature miRNAs were identified. Transcriptomics analysis suggested organ-specific and age-specific expression of miRNAs (e.g., miR-122-1-5p specific of the liver). Most of the miRNAs found in lumpfish are conserved in teleost and higher vertebrates, suggesting an essential and common role across teleost and higher vertebrates. This study is the first miRNA characterization of lumpfish that provides the reference miRNAome for future functional studies.

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.

Two apolipoproteins in salmon louse (Lepeophtheirus salmonis), apolipoprotein 1 knock down reduces reproductive capacity

The salmon louse, Lepeophtheirus salmonis is an ectoparasite of salmonid fish in the Northern Hemisphere, causing large economical losses in the aquaculture industry and represent a threat to wild populations of salmonids. Like other oviparous animals, it is likely that female lice use lipoproteins for lipid transport to maturing oocytes and other organs of the body. As an important component of lipoproteins, apolipoproteins play a vital role in the transport of lipids through biosynthesis of lipoproteins. Apolipoproteins have been studied in detail in different organisms, but no studies have been done in salmon lice. Two apolipoprotein encoding genes (LsLp1 and LsLp2) were identified in the salmon lice genome. Transcriptional analysis revealed both genes to be expressed at all stages from larvae to adult with some variation, LsLp1 generally higher than LsLp2 and both at their highest levels in adult stages of the louse. In adult female louse, the LsLp1 and LsLp2 transcripts were found in the sub-epidermal tissue and the intestine. RNA interference-mediated knockdown of LsLp1 and LsLp2 in female lice resulted in reduced expression of both transcripts. LsLp1 knockdown female lice produced significantly less offspring than control lice, while knockdown of LsLp2 in female lice caused no reduction in the number of offspring. These results suggest that LsLp1 has an important role in reproduction in female salmon lice.

•

Salmon lice are ectoparasites and a major threat to aquaculture industry and wild salmon.

•

Two apolipoproteins in salmon louse (Lepeophtheirus salmonis).

•

Expressed at all stages from larvae to adult, sub-epidermal tissue and the intestine .

•

RNA interference-mediated knockdown of LsLp1 and LsLp2.

•

LsLp1 knockdown female lice produced significantly less offspring than control lice.

Effects of simulated environmental discharges of the salmon lice pesticides deltamethrin and azamethiphos on the swimming behaviour and survival of adult Northern shrimp (Pandalus borealis)

Swimming behaviour was investigated in adult egg-carrying northern shrimp (Pandalus borealis) exposed to dilute concentrations of the pesticides Alpha Max® (active ingredient deltamethrin) and Salmosan® (active ingredient azamethiphos) used to control parasitic copepods in salmon aquaculture. These treatments are applied topically within fish nets or well boats. Following a short treatment period, the pesticides are directly discharged to sea, exposing non-target organisms such as P. borealis to diluted concentrations of these chemicals. Locomotor activity was measured continuously in individual shrimp over several days within which they were exposed to treatments of diluted AlphaMax® or Salmosan®. Dilutions were based on modelling and dispersion studies from the literature and were considered environmentally realistic for greater than 1 km from point of discharge. 24 h continuous flow treatments were delivered within a 3.5-day monitoring period to observe the timeline of events following the release of treatment water, addressing questions of temporal responses in locomotor activity, recognising key time points of significant events and assessing the survival capacity of the shrimp. Exposure of shrimp to 1 ng l^-1 deltamethrin triggered an immediate increase in swimming activity which reduced in intensity over the following 22 h leaving all shrimp either moribund or dead. A further exposure trial exposing shrimp to 0.2 ng l^-1 deltamethrin (nominal) showed an increase in activity at the start of exposure that continued throughout the 24 h delivery, returning to previous levels by the end of the 3.5-day monitoring period. All these shrimps survived for at least four weeks after exposure, putting the threshold concentration of deltamethrin leading to immobility or death in adult P. borealis within this study at greater than 0.2 ng l^-1 (nominal) and less than 1 ng l ^- 1 (measured). Exposure of P. borealis to azamethiphos at 30 ng l^-1 induced several periods of significantly increased activity within the first 10 h of exposure and an extended period of reduced activity during post exposure, though no morbidity was observed with this treatment. No significant increase in activity or morbidity was observed in shrimp during a water vehicle control assessment. Shrimps exposed to a combination of 30 ng l^-1 azamethiphos and 1 ng l^-1 deltamethrin broadly followed the response pattern shown by shrimp exposed to 1 ng l^-1 deltamethrin alone. Pesticide residues were not detected in post exposure tissue analyses for either chemical. The potential ecological significance of increased swimming activity at the start of pesticide exposures is discussed.

Simulated effects of increasing salmonid production on sea lice populations in Norway

Norway produces more than one million tonnes of salmonids every year, almost exclusively in open-water net pens. In 2014, the Norwegian government announced plans to increase salmonid production. However, increasing the number of farmed salmonids can have negative effects on the marine environment that threaten the industry's sustainability. In particular, production growth can lead to an increase in density-dependent diseases, including parasitic sea lice. The aim of this study was to simulate the effects of increased salmonid production on sea lice abundance using different scenarios for increasing the number of fish and for the management of sea lice. We used a previously developed, partly stage-structured model based on Norwegian production and environmental data to simulate the different scenarios. Our results show that increasing the marine farmed salmonid population at a national level by two or five times the current production leads to an increase in the sea lice abundance by 3.5% and 7.1%, respectively. We also found that by lowering the maximum allowable level of sea lice to an average of 0.049 adult females per fish, weekly treatments can be used to control sea lice population growth with a five times increase in production. However, this increases the number of farms treating per week by as much as 281.3%, which can lead to high costs and increased mortality among farmed salmonids. Overall, the results from our study shed light on the effects of increasing salmonid production in Norway with respect to the ongoing threat of sea lice infestations.