Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi.

The sea louse Caligus rogercresseyi has become one of the main constraints for the sustainable development of salmon aquaculture in Chile. Although this parasite's negative impacts are well recognized by the industry, some novel potential threats remain unnoticed. The recent sequencing of the C. rogercresseyi genome revealed a large bacterial community associated with the sea louse, however, it is unknown if these microorganisms should become a new focus of sanitary concern. Herein, chromosome proximity ligation (Hi-C) coupled with long-read sequencing were used for the genomic reconstruction of the C. rogercresseyi microbiota. Through deconvolution analysis, we were able to assemble and characterize 413 bacterial genome clusters, including six bacterial genomes with more than 80% of completeness. The most represented bacterial genome belonged to the fish pathogen Tenacibacullum ovolyticum (97.87% completeness), followed by Dokdonia sp. (96.71% completeness). This completeness allowed identifying 21 virulence factors (VF) within the T. ovolyticum genome and four antibiotic resistance genes (ARG). Notably, genomic pathway reconstruction analysis suggests putative metabolic complementation mechanisms between C. rogercresseyi and its associated microbiota. Taken together, our data highlight the relevance of Hi-C techniques to discover pathogenic bacteria, VF, and ARGs and also suggest novel host-microbiota mutualism in sea lice biology.

METALLOTHIONEIN EXPRESSION IN A PARASITIC CRUSTACEAN, LAMPROGLENA CLARIAE (CRUSTACEA: COPEPODA), ON CLARIAS GARIEPINUS (TELOESTEI: CLARIIDAE) CORRESPONDS TO WATER QUALITY.

Globally, parasites are sensitive toward environmental changes, and, in some cases, they are even more sensitive than their hosts. However, there is limited knowledge on the physiological responses of parasites and their effects on their hosts in relation to environmental degradation. In this study, metallothioneins (MTs) were isolated and compared between the ectoparasite Lamproglena clariae and its host fish Clarias gariepinus. Differences in the levels of MTs in the parasite and host were compared to physicochemical water quality variables and metals to determine if MT expression was linked with changes in water quality. Clarias gariepinus individuals were sampled from 2 sites of differing water quality along the Vaal River using gill nets and assessed for L. clariae. Gill, muscle, and liver tissue of the host and L. clariae were collected and stored in liquid nitrogen for analysis of MT. Water and sediment samples were collected for metal analysis by inductively coupled plasma-optical emission spectrometry and inductively coupled plasma-mass spectrometry. Nutrient levels and water hardness in water samples were assessed using spectrophotometry. MTs were quantified using spectrophotometry and size exclusion chromatography in the host and parasite, respectively. Infections by L. clariae differed between sites, with higher parasite intensity at the unpolluted Vaal Dam site. Concentrations of MT in host tissues and L. clariae were significantly higher at the polluted site, below the Vaal River Barrage, compared to the Vaal Dam site. Parasite MT concentrations were significantly lower compared to concentrations in the liver and gill tissue of C. gariepinus individuals. In conclusion, differences in the concentrations of MT and infection biology of L. clariae reflected the state of the environment and support the usefulness of this parasite and other Lamproglena spp. as bioindicators.

Potential negative effects and heterogeneous distribution of a parasitic copepod Salmincola edwardsii (Copepoda: Lernaeopodidae) on Southern Asian Dolly Varden Salvelinus curilus in Hokkaido, Japan.

The genus Salmincola is an ectoparasitic copepod group commonly infesting the branchial and buccal cavities of salmonids. While negative impacts on hatchery fishes have been reported, their impacts on wild fish populations and distribution patterns are critically understudied. In the Shiretoko Peninsula, Hokkaido, Japan, we found parasites belonging to this genus on the branchial cavity of a stream salmonid, Southern Asian Dolly Varden Salvelinus curilus. All parasites recovered were identified as Salmincola edwardsii based on morphological characteristics and partial 28S rDNA sequences. Prevalence was highly heterogeneous even among neighboring streams (0-54.8%, < 10 km) with the mean intensity among streams being generally low (2.19 parasites/infeted fish). Despite the low intensity, quantile regression analysis showed negative trends between parasite intensity and host condition, suggesting that the infestation of S. edwardsii has a potential negative impact on the host salmonid. In addition, a single copepod was found from an anadromous fish, which could indicate some salinity tolerance of the copepods. It is important to evaluate the effects of Salmincola spp. on host species and determine the limiting factors on the parasite's distribution for proper management.

Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis.

Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry.

Caligus madeirensis sp. nov. (Copepoda: Caligidae) Parasitic on Pompano, Trachinotus ovatus (Linnaeus, 1758), from Eastern Atlantic Waters, Surrounding the Madeira Archipelago, Portugal.

INTRODUCTION: A new species of the genus Caligus is described based on specimens collected from pompano, Trachinotus ovatus (Linnaeus), caught in eastern Atlantic waters, near the Madeira archipelago. METHODS: Pompano (n = 21) were purchased from the local fish market and examined for parasitic copepods. Morphological features of the copepods were examined and drawn using an Olympus BX51 equipped with a drawing tube. Key diagnostic characters were scanned using a confocal laser scanning microscope and a scanning electron microscope. RESULTS: Caligus madeirensis sp. nov., can be distinguished from all congeners (270 spp.) by the combination of the following characters: (i) an accessory process on the 3 outer terminal spines located on the distal exopodal segment of leg 1, (ii) a mandible with 14 teeth, (iii) a sternal furca with parallel, spatulate tines, (iv) a maxilliped with 2 simple setae at base of a claw, (v) a leg 3 with second endopodal segment with 5 pinnate setae, (vi) a 2-segmented leg 4 exopod with I; III spine formula, (vii) a male antenna with 4 overlapping plates on the distal segment, (viii) a male maxilliped corpus bearing a prominent myxal process ornamented with dense corrugations along inner margin. CONCLUSION: Together with Caligus madeirensis sp. nov., the Caligus fauna of Portugal consists of 13 species reported from 17 Portuguese marine fishes. Considering the large number of marine fish species (510 spp.) currently recorded from Portuguese waters it seems that only 3.3% of the Portuguese marine fishes have been found to be infested with species of the genus Caligus O.F. Müller, 1758, the result of which, however, might be due to limited sampling.

Transcriptomic Profiling in Fins of Atlantic Salmon Parasitized with Sea Lice: Evidence for an Early Imbalance Between Chalimus-Induced Immunomodulation and the Host's Defense Response.

Parasitic sea lice (e.g., Lepeophtheirus salmonis) cause costly outbreaks in salmon farming. Molecular insights into parasite-induced host responses will provide the basis for improved management strategies. We investigated the early transcriptomic responses in pelvic fins of Atlantic salmon parasitized with chalimus I stage sea lice. Fin samples collected from non-infected (i.e. pre-infected) control (PRE) and at chalimus-attachment sites (ATT) and adjacent to chalimus-attachment sites (ADJ) from infected fish were used in profiling global gene expression using 44 K microarrays. We identified 6568 differentially expressed probes (DEPs, FDR < 5%) that included 1928 shared DEPs between ATT and ADJ compared to PRE. The ATT versus ADJ comparison revealed 90 DEPs, all of which were upregulated in ATT samples. Gene ontology/pathway term network analyses revealed profound changes in physiological processes, including extracellular matrix (ECM) degradation, tissue repair/remodeling and wound healing, immunity and defense, chemotaxis and signaling, antiviral response, and redox homeostasis in infected fins. The QPCR analysis of 37 microarray-identified transcripts representing these functional themes served to confirm the microarray results with a significant positive correlation (p < 0.0001). Most immune/defense-relevant transcripts were downregulated in both ATT and ADJ sites compared to PRE, suggesting that chalimus exerts immunosuppressive effects in the salmon's fins. The comparison between ATT and ADJ sites demonstrated the upregulation of a suite of immune-relevant transcripts, evidencing the salmon's attempt to mount an anti-lice response. We hypothesize that an imbalance between immunomodulation caused by chalimus during the early phase of infection and weak defense response manifested by Atlantic salmon makes it a susceptible host for L. salmonis.

Effect of cleaner fish on sea lice in Norwegian salmon aquaculture: a national scale data analysis.

The salmon aquaculture industry has adopted the use of invertivorous 'cleaner fishes' (CF) for biological control of sea louse infestations on farmed salmon. At present, ~50 million CF are used annually in Norway alone, with variable success in experimental and industrial contexts. We used a national scale database of louse counts, delousing treatments and CF stocking events on Norwegian salmon farms to test for evidence of CF efficacy at 488 sites that completed a grow-out cycle within 2016-2018. Our analysis revealed that sites using more CF over the duration of a grow-out cycle did not have fewer lice on average, likely because CF use is reactive and in proportion to the scale of the louse problem. Over time within sites, we found that (i) sites using more CF early in the grow-out cycle were able to wait slightly longer (conservatively, a 5.2 week delay with 5000 CF stocked week-1) before conducting the first delousing treatment, and (ii) CF stocking events were followed, on average, by a small reduction in louse population growth rates. However, both effects were small and highly variable, and louse population growth rates remained positive on average, even when large numbers of CF were used (tens of thousands per site). Moreover, effects of CF on louse density tended to be short-lived, likely reflecting mortality and escape of stocked CF. Overall, the data indicate that while some sites consistently obtain good results from CF, there is also widespread suboptimal use. A better understanding of factors affecting CF efficacy in commercial sea cages is required to inform legislation and drive more efficient and ethical use of CF by the salmon aquaculture industry.

A Next-Generation Approach to Calculate Source-Sink Dynamics in Marine Metapopulations.

In marine systems, adult populations confined to isolated habitat patches can be connected by larval dispersal. Source-sink theory provides effective tools to quantify the effect of specific habitat patches on the dynamics of connected populations. In this paper, we construct the next-generation matrix for a marine metapopulation and demonstrate how it can be used to calculate the source-sink dynamics of habitat patches. We investigate the effect of environmental variables on the source-sink dynamics and demonstrate how the next-generation matrix can provide useful biological insight into transient as well as asymptotic dynamics of the model.

Ecological Factors Mediate Immunity and Parasitic Co-Infection in Sea Fan Octocorals.

The interplay among environment, demography, and host-parasite interactions is a challenging frontier. In the ocean, fundamental changes are occurring due to anthropogenic pressures, including increased disease outbreaks on coral reefs. These outbreaks include multiple parasites, calling into question how host immunity functions in this complex milieu. Our work investigates the interplay of factors influencing co-infection in the Caribbean sea fan octocoral, Gorgonia ventalina, using metrics of the innate immune response: cellular immunity and expression of candidate immune genes. We used existing copepod infections and live pathogen inoculation with the Aspergillus sydowii fungus, detecting increased expression of the immune recognition gene Tachylectin 5A (T5A) in response to both parasites. Cellular immunity increased by 8.16% in copepod infections compared to controls and single Aspergillus infections. We also detected activation of cellular immunity in reef populations, with a 13.6% increase during copepod infections. Cellular immunity was similar in the field and in the lab, increasing with copepod infections and not the fungus. Amoebocyte density and the expression of T5A and a matrix metalloproteinase (MMP) gene were also positively correlated across all treatments and colonies, irrespective of parasitic infection. We then assessed the scaling of immune metrics to population-level disease patterns and found random co-occurrence of copepods and fungus across 15 reefs in Puerto Rico. The results suggest immune activation by parasites may not alter parasite co-occurrence if factors other than immunity prevail in structuring parasite infection. We assessed non-immune factors in the field and found that sea fan colony size predicted infection by the copepod parasite. Moreover, the effect of infection on immunity was small relative to that of site differences and live coral cover, and similar to the effect of reproductive status. While additional immune data would shed light on the extent of this pattern, ecological factors may play a larger role than immunity in controlling parasite patterns in the wild. Parsing the effects of immunity and ecological factors in octocoral co-infection shows how disease depends on more than one host and one parasite and explores the application of co-infection research to a colonial marine organism.

Parasite induced mortality is context dependent in Atlantic salmon: insights from an individual-based model.

An individual-based model was parameterized to explore the impact of a crustacean ectoparasite (sea louse, Lepeophtheirus salmonis & Caligus spp.) on migrating Atlantic salmon smolt. The model explores how environmental and intrinsic factors can modulate the effect of sea lice on survival, growth and maturation of Atlantic salmon at sea. Relative to other effects, the parasite infestation pressure from fish farms and the encounter process emerge as the most important parameters. Although small variations in parasite-induced mortality may be masked by variable environmental effects, episodes of high infestation pressure from fish farms should be observable in wild populations of Atlantic salmon if laboratory studies accurately reflect the physiological effects of sea lice. Increases in temperature in the model negatively influenced fish survival by affecting the development time of the parasite at a rate that was not compensated for by the growth of the host. Discharge from rivers was parameterized to increase migration speed and influenced parasite induced mortality by decreasing time spent in areas with increased infestation pressure. Initial size and growth of the host was inversely related to the impact of the parasite because of size-dependent parasite-induced mortality in the early phase of migration. Overall, the model illustrates how environmental factors modulate effects on the host population by impacting either the parasite load or the relative effect of the parasite. The results suggest that linking population-level effects to parasite infestation pressure across climatic and environmental gradients may be challenging without correctly accounting for these effects.

The Three-spined Stickleback, Gasterosteus aculeatus Linnaeus 1758, plays a minor role as a host of Lepeophtheirus salmonis (Krøyer 1837) in the Gulf of Maine.

The sea louse, Lepeophtheirus salmonis (Krøyer 1837), is a significant parasite of farmed salmon throughout the Northern Hemisphere. Management of on-farm louse populations can be improved by understanding the role that wild fish play in sustaining and providing refuge for the local population of sea lice. In this study, 1,064 sticklebacks were captured. Of these animals, 176 individuals were carrying a total of 238 sea lice, yielding a prevalence and intensity of 16.5% and 1.4 lice per fish, respectively. Detailed examination of the sea lice on the three-spined sticklebacks captured in Cobscook Bay found two L. salmonis individuals using three-spined sticklebacks as hosts. A 2012 survey of wild fish in Cobscook Bay, Maine, found multiple wild hosts for Caligus elongatus (von Nordmann 1832), including three-spined sticklebacks (Gasterosteus aculeatus L.), but no L. salmonis were found in this earlier study.

Synergistic osmoregulatory dysfunction during salmon lice (Lepeophtheirus salmonis) and infectious hematopoietic necrosis virus co-infection in sockeye salmon (Oncorhynchus nerka) smolts.

While co-infections are common in both wild and cultured fish, knowledge of the interactive effects of multiple pathogens on host physiology, gene expression and immune response is limited. To evaluate the impact of co-infection on host survival, physiology and gene expression, sockeye salmon Oncorhynchus nerka smolts were infected with the salmon louse Lepeophtheirus salmonis (V-/SL+), infectious hematopoietic necrosis virus (IHNV; V+/SL-), both (V+/SL+), or neither (V-/SL-). Survival in the V+/SL+ group was significantly lower than the V-/SL- and V-/SL+ groups (p = 0.024). Co-infected salmon had elevated osmoregulatory indicators and lowered haematocrit values as compared to the uninfected control. Expression of 12 genes associated with the host immune response was analysed in anterior kidney and skin. The only evidence of L. salmonis-induced modulation of the host antiviral response was down-regulation of mhc I although the possibility of modulation cannot be ruled out for mx-1 and rsad2. Co-infection did not influence the expression of genes associated with the host response to L. salmonis. Therefore, we conclude that the reduced survival in co-infected sockeye salmon resulted from the osmoregulatory consequences of the sea lice infections which were amplified due to infection with IHNV.

Derivation of the economic value of R0 for macroparasitic diseases and application to sea lice in salmon.

BACKGROUND: Macroparasites, such as ticks, lice, and helminths, are a concern in livestock and aquaculture production, and can be controlled by genetic improvement of the host population. Genetic improvement should aim at reducing the rate at which parasites spread across the farmed population. This rate is determined by the basic reproduction ratio, i.e. [Formula: see text], which is the appropriate breeding goal trait. This study aims at providing a method to derive the economic value of [Formula: see text]. METHODS: Costs of a disease are the sum of production losses and expenditures on disease control. Genetic improvement of [Formula: see text] lowers the loss-expenditure frontier. Its economic effect depends on whether the management strategy is optimized or not. The economic value may be derived either from the reduction in losses with constant expenditures or from the reduction in expenditures with constant losses. RESULTS: When [Formula: see text] ≤ 1, the economic value of a further reduction is zero because there is no risk of a major epidemic. When [Formula: see text] > 1 and management is optimized, the economic value increases with decreasing values of [Formula: see text], because both the mean number of parasites per host and frequency of treatments decrease at an increasing rate when [Formula: see text] decreases. When [Formula: see text] > 1 and management is not optimized, the economic value depends on whether genetic improvement is used for reducing expenditures or losses. For sea lice in salmon, the economic value depends on a reduction in expenditures with constant losses, and is estimated to be 0.065€/unit [Formula: see text]/kg production. DISCUSSION: Response to selection for measures of disease prevalence cannot be predicted from quantitative genetic theory alone. Moreover, many studies fail to address the issue of whether genetic improvement results in reduced losses or expenditures. Using [Formula: see text] as the breeding goal trait, weighed by its appropriate economic value, avoids these issues. CONCLUSION: When management is optimized, the economic value increases with decreasing values of [Formula: see text] (until the threshold of [Formula: see text], where it drops to zero). When management is not optimized, the economic value depends on whether genetic improvement is used for reduced expenditures or production losses. For sea lice in salmon, the economic value is estimated to be 0.065 €/unit [Formula: see text]/kg production.

The Atlantic salmon (Salmo salar) antimicrobial peptide cathelicidin-2 is a molecular host-associated cue for the salmon louse (Lepeophtheirus salmonis).

Chemical signals are a key element of host-parasite interactions. In marine ecosystems, obligate ectoparasites, such as sea lice, use chemical cues and other sensory signals to increase the probability of encountering a host and to identify appropriate hosts on which they depend to complete their life cycle. The chemical compounds that underlie host identification by the sea lice are not fully described or characterized. Here, we report a novel compound - the Atlantic salmon (Salmo salar) antimicrobial peptide cathelicidin-2 (Cath-2) - that acts as an activation cue for the marine parasitic copepod Lepeophtheirus salmonis. L. salmonis were exposed to 0, 7, 70 and 700 ppb of Cath-2 and neural activity, swimming behaviour and gene expression profiles of animals in response to the peptide were evaluated. The neurophysiological, behavioural and transcriptomic results were consistent: L. salmonis detects Cath-2 as a water-soluble peptide released from the skin of salmon, triggering chemosensory neural activity associated with altered swimming behaviour of copepodids exposed to the peptide, and chemosensory-related genes were up-regulated in copepodids exposed to the peptide. L. salmonis are activated by Cath-2, indicating a tight link between this peptide and the salmon louse chemosensory system.

Swimming Endurance in Juvenile Chinook Salmon Infected with Salmincola californiensis.

Juvenile Chinook Salmon Oncorhynchus tshawytscha moving downstream through tributaries of the upper Willamette River basin can spend months in reservoirs created by dams. While residing in the reservoirs, they often obtain heavy infections of the freshwater parasitic copepod Salmincola californiensis. The physiologic effect these parasites have on salmonids is poorly understood. We developed a method to infect juvenile Chinook Salmon in a laboratory with the copepodid stage of S. californiensis. Infected and uninfected fish were subjected to a swimming challenge to ascertain swimming endurance. Severity of gill damage was assessed using a dissecting microscope. Juvenile Chinook Salmon naturally infected with S. californiensis in Cougar Reservoir, Oregon, were also challenged and compared with their lab-infected counterparts. Copepod infection greatly impaired the swimming ability of laboratory fish, and the naturally infected fish were entirely incapable of swimming at low velocity. Chinook Salmon collected in the wild were more heavily infected than the laboratory fish and had trouble surviving collection and transport to our laboratory. The intensity of infection and severity of gill damage were positively correlated with diminished swimming ability, suggesting that heavy infection with copepods impairs gas exchange and osmotic regulation, which likely results in diminished fitness and decreased survival of infected fish.

Chitosan-silver nanocomposites in goldfish aquaria: A new perspective in Lernaea cyprinacea control.

Nanomedicine is a promising new research area in human and veterinary science. Metal nanoparticles have shown high biocidal activity against bacteria, fungi and viruses, few studies have focused on antiparasitic action. Therefore, this study aims to investigate the influence of chitosan-silver nanocomposites on the fish crustacean parasite Lernaea cyprinacea. The disease was detected in goldfish (Carassius auratus) aquaria during the spring. Molecular and morphometric characterizations of the parasite were performed using polymerase chain reaction for rRNA and scanning electron microscopy. Chitosan-silver nanocomposites were characterized using transmission electron microscopy and Zetasizer. Probit analysis of parasite mortality versus the logarithmic concentrations of the composites indicated that the 1h/LC50 was 5.495ppm. Parasites exposed to the chitosan-silver nanocomposites showed severe pathological alterations and adsorbed the composite particles on their cuticles. After aqueous exposure of the infected fish to the compound at its LC50 for 24h, the female lernaeids were completely dislodged. Moreover, the pathological findings indicated rapid skin wound healing and renewal at the parasitic injury site. Therefore, we concluded that chitosan-silver nanocomposites are potential parasitic control agents for ornamental glass aquaria, as they have detrimental effects on aquatic predators, such as copepods.

Histopathological changes on the gills of asp (Aspius aspius) and European catfish (Silurus glanis) caused by Lamproglena pulchella and a Lamproglena sp. (Copepoda: Lernaeidae), respectively.

In a parasitology survey of Hungarian fishes, heavy infections of parasitic copepods Lamproglena pulchella and a Lamproglena sp. were found in the gills of the asp and the European catfish, respectively. Individuals of both fish species were emaciated and infected with hundreds of Lamproglena. Copepods located close to the tip of gill filaments and formed a depression at the attachment sites. In histological sections, cell degenerations and local haemorrhages were present adjacent to the maxillipeds and where the maxillary claws pierced the gill tissue. Around maxillae and in the midgut of the Lamproglena, damaged piscine blood cells and remains of the gill tissue were observed. Host reaction was expressed by proliferation of epithelioid cells, increase in both number and size of goblet and mast cells and formation of giant cells.

Statistical modelling of sea lice count data from salmon farms in the Faroe Islands.

Fiskaaling regularly counts the number of sea lice in the attached development stages (chalimus, mobiles and adult) for the salmon farms in the Faroe Islands. A statistical model of the data is developed. In the model, the sea-lice infection is represented by the chalimus (or mobile) lice developing into adult lice and is used to simulate past and current levels of adult lice-including treatments-as well as to predict the adult sea lice level 1-2 months into the future. Time series of the chalimus and adult lice show cross-correlations that shift in time and grow in size with temperature. This implies in situ the temperature-dependent development times of about 56 down to 42 days and the inverted development times (growth rates) of 0.018 up to 0.024 lice/day at 8-10°C. The temperature dependence DT=α1T+α2α3=17,840T+7.439-2.128is approximated byD1T=105.2-6.578T≈49 days at the mean temperature 8.5°C-similar to DchaT=100.6-6.507T≈45 days from EWOS data. The observed development times at four sites for a year (2010-11) were 49, 50, 51 and 52 days, respectively. Finally, we estimate the sea lice production from fish farms to discuss approaches to control the sea lice epidemics-preferably by natural means. This study is useful for understanding sea lice levels and treatments, and for in situ analysis of the sea-lice development times and growth rates.

Evolution of virulence under intensive farming: salmon lice increase skin lesions and reduce host growth in salmon farms.

Parasites rely on resources from a host and are selected to achieve an optimal combination of transmission and virulence. Human-induced changes in parasite ecology, such as intensive farming of hosts, might not only favour increased parasite abundances, but also alter the selection acting on parasites and lead to life-history evolution. The trade-off between transmission and virulence could be affected by intensive farming practices such as high host density and the use of antiparasitic drugs, which might lead to increased virulence in some host-parasite systems. To test this, we therefore infected Atlantic salmon (Salmo salar) smolts with salmon lice (Lepeophtheirus salmonis) sampled either from wild or farmed hosts in a laboratory experiment. We compared growth and skin damage (i.e. proxies for virulence) of hosts infected with either wild or farmed lice and found that, compared to lice sampled from wild hosts in unfarmed areas, those originating from farmed fish were more harmful; they inflicted more skin damage to their hosts and reduced relative host weight gain to a greater extent. We advocate that more evolutionary studies should be carried out using farmed animals as study species, given the current increase in intensive food production practices that might be compared to a global experiment in parasite evolution.

Parasitism perturbs the mucosal microbiome of Atlantic Salmon.

Interactions between parasite, host and host-associated microbiota are increasingly understood as important determinants of disease progression and morbidity. Salmon lice, including the parasitic copepod Lepeophtheirus salmonis and related species, are perhaps the most important problem facing Atlantic Salmon aquaculture after feed sustainability. Salmon lice parasitize the surface of the fish, feeding off mucus, scales and underlying tissue. Secondary bacterial infections are a major source of associated morbidity. In this study we tracked the diversity and composition of Salmo salar skin surface microbiota throughout a complete L. salmonis infection cycle among 800 post-smolts as compared to healthy controls. Among infected fish we observed a significant reduction in microbial richness (Chao1, P = 0.0136), raised diversity (Shannon, P < 7.86e-06) as well as highly significant destabilisation of microbial community composition (Pairwise Unifrac, beta-diversity, P < 1.86e-05; P = 0.0132) by comparison to controls. While undetectable on an individual level, network analysis of microbial taxa on infected fish revealed the association of multiple pathogenic genera (Vibrio, Flavobacterium, Tenacibaculum, Pseudomonas) with high louse burdens. We discuss our findings in the context of ecological theory and colonisation resistance, in addition to the role microbiota in driving primary and secondary pathology in the host.