Transcription expression of immune-related genes from Caligus rogercresseyi evidences host-dependent patterns on Atlantic and coho salmon

Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations

The fish's immune response is affected by different factors, including a wide range of environmental conditions that can also disrupt or promote changes in the host-pathogen interactions. How environmental conditions modulate the salmon genome during parasitism is poorly understood here. This study aimed to explore the environmental influence on the Salmo salar transcriptome and methylome infected with the sea louse Caligus rogercresseyi. Atlantic salmon were experimentally infected with lice at two temperatures (8 and 16 °C) and salinity conditions (32 and 26PSU). Fish tissues were collected from the infected Atlantic salmon for reduced representation bisulfite sequencing (RRBS) and whole transcriptome sequencing (RNA-seq) analysis. The parasitic load was highly divergent in the evaluated environmental conditions, where the lowest lice abundance was observed in fish infected at 8 °C/26PSU. Notably, transcriptome profile differences were statistically associated with the number of alternative splicing events in fish exposed to low temperature/salinity conditions. Furthermore, the temperature significantly affected the methylation level, where high values of differential methylation regions were observed at 16 °C. Also, the association between expression levels of spliced transcripts and their methylation levels was determined, revealing significant correlations with Ferroptosis and TLR KEEG pathways. This study supports the relevance of the environmental conditions during host-parasite interactions in marine ecosystems. The discovery of alternative splicing transcripts associated with DMRs is also discussed as a novel player in fish biology.

Heritability of Immunity Traits and Resistance of Atlantic Salmon against the Sea Louse Caligus rogercresseyi

The immune response of Atlantic salmon to sea lice has been extensively studied, but we still do not know the mechanisms by which some fish become resistant and others do not. In this study, we estimated the heritabilities of three key proteins associated with the innate immunity and resistance of Salmo salar against the sea louse Caligus rogercresseyi. In particular, we quantified the abundance of 2 pro-inflammatory cytokines, Tnfα and Il-8, and an antioxidant enzyme, Nkef, in Atlantic salmon skin and gill tissue from 21 families and 268 individuals by indirect ELISA. This covers a wide parasite load range from low or resistant (mean sea lice ± SE = 8.7 ± 0.9) to high or susceptible (mean sea lice ± SE = 43.3 ± 2.0). Our results showed that susceptible fish had higher levels of Nkef and Tnfα than resistant fish in their gills and skin, although gill Il-8 was higher in resistant fish, while no significant differences were found in the skin. Furthermore, moderate to very high heritable genetic variation was estimated for Nkef (h2 skin: 0.96 ± 0.14 and gills: 0.97 ± 0.11) and Tnfα (h2 skin: 0.53 ± 0.17 and gills: 0.32 ± 0.14), but not for Il-8 (h2 skin: 0.22 ± 0.12 ns and gills: 0.09 ± 0.08 ns). This work provides evidence that Nkef and Tnfα protein expressions are highly heritable and related to resistance against sea lice in Atlantic salmon.

Applying genetic technologies to combat infectious diseases in aquaculture

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

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.

Transcriptome and morphological analysis in Caligus rogercresseyi uncover the effects of Atlantic salmon vaccination with IPath®

It is known that iron transporter proteins and their regulation can modulate the fish's immune system, suggesting these proteins as a potential candidate for fish vaccines. Previous studies have evidenced the effects of Atlantic salmon immunized with the chimeric iron-related protein named IPath® against bacterial and ectoparasitic infections. The present study aimed to explore the transcriptome modulation and the morphology of the sea louse Caligus rogercresseyi in response to Atlantic salmon injected with IPath®. Herein, Atlantic salmon were injected with IPath® and challenged to sea lice in controlled laboratory conditions. Then, female adults were collected after 25 days post-infection for molecular and morphological evaluation. Transcriptome analysis conducted in lice collected from immunized fish revealed high modulation of transcripts compared with the control groups. Notably, the low number of up/downregulated transcripts was mainly found in lice exposed to the IPath® fish group. Among the top-25 differentially expressed genes, Vitellogenin, Cytochrome oxidases, and proteases genes were strongly downregulated, suggesting that IPath® can alter lipid transport, hydrogen ion transmembrane transport, and proteolysis. The morphological analysis in lice collected from IPath® fish revealed abnormal embryogenesis and inflammatory processes of the genital segment. Furthermore, head kidney, spleen, and skin were also analyzed in immunized fish to evaluate the transcription expression of immune and iron homeostasis-related genes. The results showed downregulation of TLR22, MCHII, IL-1β, ALAs, HO, BLVr, GSHPx, and Ferritin genes in head kidney and skin tissues; meanwhile, those genes did not show significant differences in spleen tissue. Overall, our findings suggest that IPath® can be used to enhance the fish immune response, showing a promissory commercial application against lice infections.

Chimeric Protein IPath® with Chelating Activity Improves Atlantic Salmon's Immunity against Infectious Diseases

Infection processes displayed by pathogens require the acquisition of essential inorganic nutrients and trace elements from the host to survive and proliferate. Without a doubt, iron is a crucial trace metal for all living organisms and also a pivotal component in the host–parasite interactions. In particular, the host reduces the iron available to face the infectious disease, increasing iron transport proteins’ expression and activating the heme synthesis and degradation pathways. Moreover, recent findings have suggested that iron metabolism modulation in fish promotes the immune response by reducing cellular iron toxicity. We hypothesized that recombinant proteins related to iron metabolism could modulate the fish’s immune system through iron metabolism and iron-responsive genes. Here a chimeric iron transport protein (IPath^®) was bioinformatically designed and then expressed in a recombinant bacterial system. The IPath^® protein showed a significant chelating activity under in vitro conditions and biological activity. Taking this evidence, a vaccine candidate based on IPath^® was evaluated in Atlantic salmon challenged with three different fish pathogens. Experimental trials were conducted using two fish groups: one immunized with IPath^® and another injected with adjutant as the control group. After 400 accumulated thermal units (ATUs), two different infection trials were performed. In the first one, fish were infected with the bacterium Aeromonas salmonicida, and in a second trial, fish were exposed to the ectoparasite Caligus rogercresseyi and subsequently infected with the intracellular bacterium Piscirickettsia salmonis. Fish immunized with IPath^® showed a significant delay in the mortality curve in response to A. salmonicida and P. salmonis infections. However, no significant differences between infected and control fish groups were observed at the end of the experiment. Notably, sea lice burden reduction was observed in vaccinated Atlantic salmon. Transcriptional analysis evidenced a high modulation of iron-homeostasis-related genes in fish vaccinated with IPath^® compared to the control group during the infection. Moreover, increasing expression of Atlantic salmon IgT was associated with IPath^® immunization. This study provides evidence that the IPath^® protein could be used as an antigen or booster in commercial fish vaccines, improving the immune response against relevant pathogens for salmon aquaculture.

Experimental transmission of Caligus rogercresseyi between two different fish species

Caligus rogercresseyi is the dominant sea louse parasite affecting the salmon and trout industry in southern Chile. This parasite has a wide range of native and endemic fish hosts. The Patagonian blenny Eleginops maclovinus, which is parasitized mostly by the caligid species Lepeophtheirus spp. and C. rogercresseyi, is presumably responsible for the transmission of C. rogercresseyi to salmonids. The aim of this study was to characterize the transmission of parasites between different fish species and parasite cohort development under laboratory conditions. Parasite abundances and intensities were quantified. Transmission of parasites from Patagonian blenny to Atlantic salmon Salmo salar was lower (~9%, mainly corresponding to C. rogercresseyi) than from salmon to Patagonian blenny (14.7-26.9%, where only C. rogercresseyi were observed). This suggests that the transmission of C. rogercresseyi from salmon individuals is higher than the transmission from a native fish. Parasite cohorts developed successfully on both fish species, but apparently under different developmental rates. Water temperature, oxygen, and juvenile abundances were the variables that better explained cohort development success and variation in C. rogercresseyi adult abundances over time.

Modulation of the Expression of Immune-related Gene in Atlantic and Coho Salmon during Infestation with the Sea lice Caligus rogercresseyi

Caligus rogercresseyi, a marine ectoparasite, causes notable economic losses for the Chilean salmonid industry. Nevertheless, the immunological responses of infected fish remain poorly understood, including proinflammatory cytokine generation and the respective modulatory effects of various cytokine receptors. This study evaluated mRNA expression of the NLRC5, major histocompatibility complex (MHC) class II, I-kappa-B-alpha, a regulatory that inhibits NF-kappa-B, and proinflammatory cytokines (IL-1β and IL-18) in the liver and muscle of Atlantic salmon (Salmo salar) and Coho salmon (Oncorhynchus kisutch) during a time-course C. rogercresseyi infestation trial. All assessed mRNA were strongly regulated during infestation, but S. salar showed up-regulated expression, possibly accounting for the high infestation vulnerability of this salmonid. In conclusion, this work helps to understand the modulation of the expression of different transcripts involved over short periods of C. rogercresseyi infestation in two salmonid species (S. salar and O. kisutch).

Catching the complexity of salmon-louse interactions

The study of host-parasite relationships is an integral part of the immunology of aquatic species, where the complexity of both organisms has to be overlayed with the lifecycle stages of the parasite and immunological status of the host. A deep understanding of how the parasite survives in its host and how they display molecular mechanisms to face the immune system can be applied for novel parasite control strategies. This review highlights current knowledge about salmon and sea louse, two key aquatic animals for aquaculture research worldwide. With the aim to catch the complexity of the salmon-louse interactions, molecular information gleaned through genomic studies are presented. The host recognition system and the chemosensory receptors found in sea lice reveal complex molecular components, that in turn, can be disrupted through specific molecules such as non-coding RNAs.

Iron metabolism modulation in Atlantic salmon infested with the sea lice Lepeophtheirus salmonis and Caligus rogercresseyi: A matter of nutritional immunity?

Sea lice are copepodid ectoparasites that produce high economic losses and environmental issues, thus impacting the salmon aquaculture worldwide. Atlantic salmon (Salmo salar) from Northern and Southern Hemispheres are primarily parasitized by Lepeophtheirus salmonis and Caligus rogercresseyi, respectively. To cope L. salmonis infestation, studies suggest that Atlantic salmon can restrict iron availability as a mechanism of nutritional immunity. However, no molecular studies of iron regulation from salmonids infected with C. rogercresseyi have been reported. The aim of this study was to determine if there are differences in the regulation of iron metabolism in Atlantic salmon infested with L. salmonis or C. rogercresseyi. For comparisons, skin and head kidney were profiled using qPCR of 15 genes related to iron regulation in Atlantic salmons infected with each sea louse species in Norway and Chile, respectively. Prior to infestation, no significant differences were observed between fish group. However, genes involved in iron transport and Heme biosynthesis were highly upregulated in Atlantic salmon infested with L. salmonis. Interestingly, hepcidin and Heme oxygenase, a component of the Heme degradation pathway, were upregulated during C. rogercresseyi infestation. Oxidative stress related genes were also evaluated, showing higher transcription activity in the head kidney than in the skin of Atlantic salmon infested with L. salmonis. These comparative results suggest pathogen-specific responses in infected Atlantic salmon, where iron metabolism is primarily regulated during the infestation with L. salmonis than C. rogercresseyi. Feeding behavior, for instance haematophagy, of the infesting sea lice species in relation to iron modulation is discussed.

Comparative immunity of Salmo salar and Oncorhynchus kisutch during infestation with the sea louse Caligus rogercresseyi: An enrichment transcriptome analysis

Caligus rogercresseyi, an ectoparasite affecting the Chilean salmon industry, can cause immunosuppression and physiological stress in farmed fish. Interestingly, coho salmon (Oncorhynchus kisutch) are notably resistant to infestation, whereas Atlantic salmon (Salmo salar) are phenotypically more susceptible to sea lice. However, comparative studies on immune responses to C. rogercresseyi have not been conducted. In this study, Illumina sequencing was conducted to evaluate head kidney and skin samples taken 7 and 14 days post-infestation, yielding a total of 1492 and 1522 contigs annotated to immune-related genes for Atlantic and coho salmon, respectively. Both species evidenced an upregulation of inflammatory genes. Atlantic salmon had highly upregulated TLR22 and MHCII at 14 days post-infestation, while coho salmon had highly upregulated stat5 and il1r transcripts. Fourteen transcripts related to T_H1, T_H2, TLR, and macrophage responses were corroborated via RT-qPCR. Statistical analyses indicated an upregulation of mmp13, cox2, il10, ccr3, tlr22a2, and tlr21 in Atlantic salmon and of ifnγ, cd83, T-bet, tlr13, and tlr19 in coho salmon. These results suggest strong differences between the Atlantic and coho salmon immune responses, where coho salmon, the more resistant species, presented a primary T_H1 response. Additionally, putative roles of TLRs in salmonids against sea lice were evidenced. This study is the first comparative transcriptome analysis that reveals species-specific immune responses in salmons infected with C. rogercresseyi.