Characterization of a New Toti-like Virus in Sea Bass, Dicentrarchus labrax.

The European sea bass Dicentrarchus labrax is the main species reared in Mediterranean aquaculture. Its larval stage, which is very sensitive and highly affected by sanitary and environmental conditions, is particularly scrutinized in hatcheries. Recently, a Mediterranean sea bass farm had to deal with an abnormal increase in mortality, especially between 20 and 35 days post-hatching (dph). Biological investigations led to the observation of cytopathic effects on three different fish cell lines after almost 3 weeks of culture at 14 °C in contact with homogenized affected larvae, suggesting the presence of a viral agent. High-throughput sequencing revealed a 6818-nucleotide-long RNA genome with six putative ORFs, corresponding to the organization of viruses belonging to the Totiviridae family. This genome clustered with the newly described and suggested Pistolvirus genus, sharing 45.5% to 37.2% nucleotide identity with other piscine toti-like viruses such as Cyclopterus lumpus toti-like virus (CLuTLV) or piscine myocarditis virus (PMCV), respectively. Therefore, we propose to name this new viral agent sea bass toti-like virus (SBTLV). Specific real-time RT-PCR confirmed the presence of the viral genome in the affected larval homogenate from different production batches and the corresponding cell culture supernatant. Experimental infections performed on sea bass fingerlings did not induce mortality, although the virus could be detected in various organs and a specific immune response was developed. Additional studies are needed to understand the exact involvement of this virus in the mortality observed in hatcheries and the potential associated cofactors.

Whole-genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass.

BACKGROUND: Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustainability of production systems. The aim of this study was to identify genomic regions and genes that are associated with VNN resistance in sea bass. RESULTS: We generated a dataset of 838,451 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation of two commercial populations (A: 2371 individuals and B: 3428 individuals) of European sea bass with phenotypic records for binary survival in a VNN challenge. For each population, three cohorts were submitted to a red-spotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, quantitative trait loci (QTL) were mapped using a Bayesian sparse linear mixed model (BSLMM). We found several QTL regions that were specific to one of the populations on different linkage groups (LG), and one 127-kb QTL region on LG12 that was shared by both populations and included the genes ZDHHC14, which encodes a palmitoyltransferase, and IFI6/IFI27-like, which encodes an interferon-alpha induced protein. The most significant SNP in this QTL region was only 1.9 kb downstream of the coding sequence of the IFI6/IFI27-like gene. An unrelated population of four large families was used to validate the effect of the QTL. Survival rates of susceptible genotypes were 40.6% and 45.4% in populations A and B, respectively, while that of the resistant genotype was 66.2% in population B and 78% in population A. CONCLUSIONS: We have identified a genomic region that carries a major QTL for resistance to VNN and includes the ZDHHC14 and IFI6/IFI27-like genes. The potential involvement of the interferon pathway, a well-known anti-viral defense mechanism in several organisms (chicken, human, or fish), in survival to VNN infection is of particular interest. Our results can lead to major improvements for sea bass breeding programs through marker-assisted genomic selection to obtain more resistant fish.

Effects of dietary co-exposure to fungal and herbal functional feed additives on immune parameters and microbial intestinal diversity in rainbow trout (Oncorhynchus mykiss).

Misuse and overuse of antibiotics in aquaculture has proven to be an unsustainable practice leading to increased bacterial resistance. An alternative strategy involves the inclusion of immunostimulants in fish diets, especially fungal and herbal compounds already authorized for human consumption, hence without environmental or public health concerns. In this study, we used a holistic and cross-disciplinary pipeline to assess the immunostimulatory properties of two fungi: Trametes versicolor and Ganoderma lucidum; one herbal supplement, capsaicin in the form of Espelette pepper (Capsicum annuum), and a combination of these fungal and herbal additives on rainbow trout (Oncorhynchus mykiss). We investigated the impact of diet supplementation for 7 weeks on survival, growth performance, cellular, humoral, and molecular immune parameters, as well as the intestinal microbial composition of the fish. Uptake of herbal and fungal compounds influenced the expression of immune related genes, without generating an inflammatory response. Significant differences were detected in the spleen-tlr2 gene expression. Supplementation with herbal additives correlated with structural changes in the fish intestinal microbiota and enhanced overall intestinal microbial diversity. Results demonstrated that the different treatments had no adverse effect on growth performance and survival, suggesting the safety of the different feed additives at the tested concentrations. While the mechanisms and multifactorial interactions remain unclear, this study provides insights not only in regard to nutrition and safety of these compounds, but also how a combined immune and gut microbiota approach can shed light on efficacy of immunostimulant compounds for potential commercial inclusion as feed supplements.

Glyphosate-based herbicide exposure: effects on gill microbiota of rainbow trout (Oncorhynchus mykiss) and the aquatic bacterial ecosystem.

The herbicide glyphosate has been widely used in the past 40 years, under the assumption that side effects were minimal. In recent years, its impact on microbial compositions and potential indirect effects on plant, animal and human health have been strongly suspected. Glyphosate and co-formulates have been detected in various water sources, but our understanding of their potential effects on aquatic animals is still in its infancy compared with mammals. In this study, we investigated the effect of chronic exposure to an environmentally relevant concentration of glyphosate on bacterial communities of rainbow trout (Oncorhynchus mykiss). Gills, gut contents and gut epithelia were then analyzed by metabarcoding targeting the 16S rRNA gene. Our results revealed that rainbow trout has its own bacterial communities that differ from their surrounding habitats and possess microbiomes specific to these three compartments. The glyphosate-based herbicide treatment significantly affected the gill microbiome, with a decrease in diversity. Glyphosate treatments disrupted microbial taxonomic composition and some bacteria seem to be sensitive to this environmental pollutant. Lastly, co-occurrence networks showed that microbial interactions in gills tended to decrease with chemical exposure. These results demonstrate that glyphosate could affect microbiota associated with aquaculture fish.

Characterization of a novel picornavirus isolated from moribund gilthead seabream (Sparus aurata) larvae.

Gilthead seabream represents a species of importance in Mediterranean aquaculture. The larval stage is particularly sensitive and frequently impacted in suboptimal environmental or sanitary conditions. In the present study, investigations were carried out in a seabream hatchery following an unusual mortality reaching 70% among 50-day post-hatching. Anorexia, loss of appetite and abnormal swimming behaviour were observed in absence of parasites or pathogenic bacteria. Proliferation of rod-shaped bacteria in the gut lumen was associated with focal degeneration in the intestinal mucosa. Cytopathic effects on an EK-1 cell line after 21 days of culture at 14°C and 20°C in contact with homogenized affected larvae revealed the presence of a viral agent. Molecular characterization by high-throughput sequencing showed a typical picornavirus genome organization with a polyprotein precursor of 2276 amino acids sharing 46.3% identity with that of the Eel Picornavirus-1. A specific real-time PCR confirmed the presence of the viral genome in affected larval homogenate and corresponding cell culture supernatant. We propose the name Potamipivirus daurada for this novel species within the genus Potamipivirus. The etiological role of this virus remains uncertain at this time, and future studies will be necessary to investigate its prevalence in natural and aquaculture-reared populations as well as its ability to cause diseases in gilthead seabream.

Changes in defense capacity to infectious hematopoietic necrosis virus (IHNv) in rainbow trout intergenerationally exposed to glyphosate.

Glyphosate, the most widely used herbicide active substance worldwide, has raised many scientific, political and public debates in the context of its recent re-registration in the European Union, highlighting in particular a lack of data concerning its potential generational effects. In this study, we investigated the intergenerational toxicity of this active substance used alone or coformulated in glyphosate-based herbicides (GBHs) on the ability of rainbow trout (Oncorhynchus mykiss) to face a viral challenge. Juvenile trout from parents exposed for eight months to four different chemical exposure conditions (non-exposed control, pure glyphosate, Roundup Innovert®, and Viaglif Jardin® were experimentally infected with the infectious hematopoietic necrosis virus (IHNv). Various enzymatic and hemato-immunological markers were assessed before and after the viral challenge. Chemical contamination with GBHs strongly modulated viral trout susceptibility. Pure glyphosate induced a cumulative mortality of 35.8%, comparable to the control (37.0%), which was significantly reduced with Roundup Innovert® (-9.9%) and increased (+14.8%) with Viaglif Jardin®. No modification was observed for the biomarkers analysed for any conditions. These results demonstrate that the nature of the co-formulants associated to glyphosate in GHBs can modulate the susceptibility of fish to pathogens.

Corrigendum: Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, The European Sea Bass (Dicentrarchus labrax) and the Gilthead Sea Bream (Sparus aurata).

[This corrects the article DOI: 10.3389/fgene.2021.665920.].

Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, the European Sea Bass (Dicentrarchus labrax) and the Gilthead Sea Bream (Sparus aurata).

Disease outbreaks are a major threat to the aquaculture industry, and can be controlled by selective breeding. With the development of high-throughput genotyping technologies, genomic selection may become accessible even in minor species. Training population size and marker density are among the main drivers of the prediction accuracy, which both have a high impact on the cost of genomic selection. In this study, we assessed the impact of training population size as well as marker density on the prediction accuracy of disease resistance traits in European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata). We performed a challenge to nervous necrosis virus (NNV) in two sea bass cohorts, a challenge to Vibrio harveyi in one sea bass cohort and a challenge to Photobacterium damselae subsp. piscicida in one sea bream cohort. Challenged individuals were genotyped on 57K-60K SNP chips. Markers were sampled to design virtual SNP chips of 1K, 3K, 6K, and 10K markers. Similarly, challenged individuals were randomly sampled to vary training population size from 50 to 800 individuals. The accuracy of genomic-based (GBLUP model) and pedigree-based estimated breeding values (EBV) (PBLUP model) was computed for each training population size using Monte-Carlo cross-validation. Genomic-based breeding values were also computed using the virtual chips to study the effect of marker density. For resistance to Viral Nervous Necrosis (VNN), as one major QTL was detected, the opportunity of marker-assisted selection was investigated by adding a QTL effect in both genomic and pedigree prediction models. As training population size increased, accuracy increased to reach values in range of 0.51-0.65 for full density chips. The accuracy could still increase with more individuals in the training population as the accuracy plateau was not reached. When using only the 6K density chip, accuracy reached at least 90% of that obtained with the full density chip. Adding the QTL effect increased the accuracy of the PBLUP model to values higher than the GBLUP model without the QTL effect. This work sets a framework for the practical implementation of genomic selection to improve the resistance to major diseases in European sea bass and gilthead sea bream.

Generational effects of a chronic exposure to a low environmentally relevant concentration of glyphosate on rainbow trout, Oncorhynchus mykiss.

In the past few decades, glyphosate became the most used herbicide substance worldwide. As a result, the substance is ubiquitous in surface waters. Concerns have been raised about its ecotoxicological impact, but little is known about its generational toxicity. In this study, we investigate the impact of an environmentally relevant concentration of glyphosate and its co-formulants on an F2 generation issued from exposed generations F0 and F1. Trans, inter and multigenerational toxicity of 1 µgL-1 of the active substance was evaluated on early stages of development and juvenile rainbow trout (Oncorhynchus mykiss) using different molecular, biochemical, immuno-hematologic, and biometric parameters, behavior analysis, and a viral challenge. Reproductive parameters of generation F1 were not affected. However, developmental toxicity in generation F2 due to glyphosate alone or co-formulated was observed with head size changes (e.g. head surface up to +10%), and metabolic disruptions (e.g. 35% reduction in cytochrome-c-oxidase). Moreover, larvae exposed transgenerationally to Viaglif and intergenerationally to glyphosate and Roundup presented a reduced response to light, potentially indicating altered escape behavior. Overall methylation was, however, not altered and further experiments using gene-specific DNA metylation analyses are required. After several months, biochemical parameters measured in juvenile fish were no longer impacted, only intergenerational exposure to glyphosate drastically increased the susceptibility of rainbow trout to hematopoietic necrosis virus. This result might be due to a lower antibody response in exposed fish. In conclusion, our results show that generational exposure to glyphosate induces developmental toxicity and increases viral susceptibility. Co-formulants present in glyphosate-based herbicides can modulate the toxicity of the active substance. Further investigations are required to study the specific mechanisms of transmission but our results suggest that both non-genetic mechanisms and exposure during germinal stage could be involved.

Developmental effect of parental or direct chronic exposure to environmental concentration of glyphosate on the larvae of rainbow trout, Oncorhynchus mykiss.

The environmental safety profile of glyphosate, the most commonly used herbicide worldwide, is still a subject of debate and little is known about the generational toxicity of this active substance (AS) and the associated commercial formulations called "glyphosate-based herbicides" (GBHs). This study investigated the impact of parental and direct exposure to 1µgL-1 of glyphosate using the AS alone or one of two GBH formulations (i.e. Roundup Innovert® and Viaglif Jardin®) in the early developmental stages of rainbow trout. Three different modes of exposure on the F1 generation were studied: (1) intergenerational (i.e. fish only exposed through their parents); (2) direct (i.e. fish exposed only directly) and (3) multigenerational (i.e. fish both exposed intergenerationally and directly). The impact of chemical treatments on embryo-larval development (survival, biometry and malformations), swimming behaviour, biochemical markers of oxidative stress equilibrium (TBARS and catalase), acetylcholine esterase (AChE) and energy metabolism (citrate synthase, CS; cytochrome-c oxidase, CCO; lactate dehydrogenase, LDH; glucose-6-phosphate dehydrogenase, G6PDH) was explored. Chemical exposure did not affect the survival of F1 embryos or malformation rates. Direct exposure to the AS induced some biometric changes, such as reduction in head size (with a 10% decrease in head length), independently of co-formulants. Intergenerational exposure to the AS or the Roundup GBH increased swimming activity of the larvae, with increase of between 78 and 102% in travel speeds. Viaglif co-formulants appear to have counteracted this behavioural change. The minor changes detected in the assayed biochemical markers suggested that observed effects were not due to oxidative damage, AChE inhibition or alterations to energy metabolism. Nonetheless, multi- and intergenerational exposure to Roundup increased CS:CCO and LDH:CS ratios by 46% and 9%, respectively, with a potential modification of the aerobic-to-anaerobic energy production balance. These biochemical effects were not correlated with those observed on individual level of biological organization. Therefore, further studies on generational toxicity of glyphosate and its co-formulants are needed to identify the other mechanisms of glyphosate toxicity at the cellular level.

Immunological and metabolic effects of acute sublethal exposure to glyphosate or glyphosate-based herbicides on juvenile rainbow trout, Oncorhynchus mykiss.

Glyphosate is a commonly used agrochemical active substance co-formulated in glyphosate-based herbicides (GBHs) whose environmental safety is still a subject of debate in the European Union. We evaluated the effects of acute sublethal exposure to glyphosate on rainbow trout by measuring changes in their metabolic and hemato-immunologic functions and their ability to survive a viral challenge. Juvenile fish were exposed for 96 h to 500 µg L-1 of glyphosate through the active substance alone or two GHBs, Roundup Innovert® and Viaglif Jardin®, and fish were then infected with the infectious hematopoietic necrosis virus. Red and white blood cell counts (RBCC and WBCC), as well as several enzymatic activities (citrate synthase, CS; cytochrome-c oxidase, CCO; lactate dehydrogenase, LDH; glucose-6-phosphate dehydrogenase, G6PDH; acetylcholinesterase, AChE), were measured 96 h after chemical contamination (S1), and 96 h post-viral infection (S2). Mortality rates were monitored, and virus titers at the mortality peaks and seropositivity of the survivors were analyzed at 60 days post-viral infection (S3). Cumulative mortalities, viral titers, and seropositivity induced by virus infection were similar among conditions. Hematological analysis revealed significant increases of 30% for RBCC for Roundup at S1, and of 22% for WBCC at S2. No changes were observed in metabolic enzyme activities at S1. At S2, CCO and G6PDH activities were significantly higher than controls in all the chemically contaminated groups (+61 to 62% and +65 to 138%, respectively). LDH and AChE activities were increased for the Viaglif (p = 0.07; +55%) and for glyphosate and Roundup conditions (p < 0.05, +62 to 79%), respectively. Rainbow trout acutely exposed to glyphosate or GBHs presented no major physiological changes. Viral infection revealed disruptions, potentially modulated by co-formulants, of hematological and metabolic parameters, showing that it is essential to consider the stressful natural environment of fish in the chemical assessment.

Tissue distribution, metabolism, and elimination of Victoria Pure Blue BO in rainbow trout: Main metabolite as an appropriate residue marker.

Victoria Pure Blue BO is a dye that bears some therapeutic activity and that can be retrieved in effluent or may be used in aquaculture as a prohibited drug. In this study, the metabolism and tissue distribution during uptake and depuration of VPBO were investigated in order to propose a residue marker of illegal treatment in fish. The dye was administered to rainbow trout (oncorhynchus mykiss) for one day by water bath at a dose of 0.1 mg.L-1. The concentrations of VPBO in all tissues increased rapidly during the treatment period, reaching a Cmax of 567 ± 301 µg.L-1 in plasma and 1846 µg kg-1 ±517 for liver after 2 h. After placing the rainbow trout in a clean water bath for a 64 day-period of depuration, the concentrations in the tissues and plasma decreased to reach comparable levels for muscle and for skin after 33 days. The concentrations measured were still above the LOQ at 2.26 ± 0.48 µg kg-1 for muscle and 2.85 ± 1.99 µg kg-1 for skin at the end of the depuration period. The results indicated the existence of 14 phase I metabolites and one glucuronide conjugated metabolite. Non-compartmental analysis was applied to assess the pharmacokinetic parameters. The half-life in edible muscle of the main metabolite detected, deethyl-leuco-VPBO, was found to be 22.5 days compared to a half-life of 19.7 days for the parent VPBO. This study provides new information to predict a VPBO drug treatment of aquacultured species via a proposed new residue marker.

Comparative analysis of the course of infection and the immune response in rainbow trout (Oncorhynchus mykiss) infected with the 5 genotypes of infectious hematopoietic necrosis virus.

Infectious hematopoietic necrosis virus (IHNV) is a pathogen of importance for salmonid aquaculture. In this study, we aimed to characterize virus behavior and defense mechanisms developed in rainbow trout (RT, Oncorhynchus mykiss) experimentally infected with isolates belonging to the five described genotypes of IHNV, i.e. L, U, M, E and J. Mortality was monitored for two months, and blood and target organs were sampled at different times post-infection to assess viral load and cellular and humoral immune responses. Profiles of virulence were highly linked to precocious viral replication but also to the innate and specific immunity elicited in the host. Seroneutralization test (SNT) used for specific antibodies detection exhibited reliable results, with efficient cross-neutralization observed in heterologous systems except for the Asian representative. These data bring new insights about IHNV/RT interaction and reinforce the interest of SNT as preventive and epidemiological tool.

Impact of chronic exposure of rainbow trout, Oncorhynchus mykiss, to low doses of glyphosate or glyphosate-based herbicides.

Glyphosate is an herbicidal active substance (AS) entering in the composition of a large diversity of pesticide products (glyphosate-based herbicides; GBH) used in modern intensive agriculture. This compound has a favorable environmental safety profile but was suspected to induce deleterious effects in aquatic organisms, with a potential effect of some associated co-formulants. This study aimed to assess the impact of direct and chronic exposure to glyphosate on the health status of rainbow trout, Oncorhynchus mykiss. A total of 36 genitors were exposed daily for 10 months to a dose of glyphosate representative of environmental concentrations (around 1 µg L-1) using the AS alone or two GBHs formulations (i.e. Roundup Innovert® and Viaglif Jardin®) and findings were compared to an unexposed control group (n=12). The effects of chemical exposure on the reproductive capacities, hemato-immunologic functions, energetic metabolism, oxidative stress and specific biomarkers of exposure were analyzed over a period of 4 months covering spawning. A limited mortality between 15% and 30% specific to the spawning occurred under all conditions. No differences were observed in reproduction parameters i.e. mean weights, relative fertility and fecundity. Red blood cell count, hematocrit index, mean corpuscular volume and white blood cell counts were similar for all the sampling dates. Significant changes were observed two months before spawning with a 70% decrease of the proportion of macrophages in trout exposed to Viaglif only and a reduction of 35% of the phagocytic activity in fish exposed to the two GBHs. Trends towards lower levels of expression of tumor necrosis factor-α (between 38% and 66%) were detected one month after the spawning for all contaminated conditions but without being statistically significant. Biomarkers of exposure, i.e. acetylcholine esterase and carbonic anhydrase activities, were not impacted and none of the chemical contaminants disturbed the oxidative stress or metabolism parameters measured. These results suggest that a 10 months exposure of rainbow trout to a concentration of 1 µg L-1 of glyphosate administered using the pure active substance or two GBHs did not significantly modify their global health including during the spawning period. The immunological disturbances observed will need to be further explored because they could have a major impact in response to infectious stress.

The Viral Hemorrhagic Septicemia Virus (VHSV) Markers of Virulence in Rainbow Trout (Oncorhynchus mykiss).

Viral hemorrhagic septicemia virus (VHSV) is a highly contagious virus leading to high mortality in a large panel of freshwater and marine fish species. VHSV isolates originating from marine fish show low pathogenicity in rainbow trout. The analysis of several nearly complete genome sequences from marine and freshwater isolates displaying varying levels of virulence in rainbow trout suggested that only a limited number of amino acid residues might be involved in regulating the level of virulence. Based on a recent analysis of 55 VHSV strains, which were entirely sequenced and phenotyped in vivo in rainbow trout, several amino acid changes putatively involved in virulence were identified. In the present study, these amino acid changes were introduced, alone or in combination, in a highly-virulent VHSV 23-75 genome backbone by reverse genetics. A total of 35 recombinant VHSV variants were recovered and characterized for virulence in trout by bath immersion. Results confirmed the important role of the NV protein (R116S) and highlighted a major contribution of the nucleoprotein N (K46G and A241E) in regulating virulence. Single amino acid changes in these two proteins drastically affect virus pathogenicity in rainbow trout. This is particularly intriguing for the N variant (K46G) which is unable to establish an active infection in the fins of infected trout, the main portal of entry of VHSV in this species, allowing further spread in its host. In addition, salmonid cell lines were selected to assess the kinetics of replication and cytopathic effect of recombinant VHSV and discriminate virulent and avirulent variants. In conclusion, three major virulence markers were identified in the NV and N proteins. These markers explain almost all phenotypes (92.7%) observed in trout for the 55 VHSV strains analyzed in the present study and herein used for the backward validation of virulence markers. The identification of VHSV specific virulence markers in this species is of importance both to predict the in vivo phenotype of viral isolates with targeted diagnostic tests and to improve prophylactic methods such as the development of safer live-attenuated vaccines.

VHSV Single Amino Acid Polymorphisms (SAPs) Associated With Virulence in Rainbow Trout.

The Viral Hemorrhagic Septicemia Virus (VHSV) is an OIE notifiable pathogen widespread in the Northern Hemisphere that encompasses four genotypes and nine subtypes. In Europe, subtype Ia impairs predominantly the rainbow trout industry causing severe rates of mortality, while other VHSV genotypes and subtypes affect a number of marine and freshwater species, both farmed and wild. VHSV has repeatedly proved to be able to jump to rainbow trout from the marine reservoir, causing mortality episodes. The molecular mechanisms regulating VHSV virulence and host tropism are not fully understood, mainly due to the scarce availability of complete genome sequences and information on the virulence phenotype. With the scope of identifying in silico molecular markers for VHSV virulence, we generated an extensive dataset of 55 viral genomes and related mortality data obtained from rainbow trout experimental challenges. Using statistical association analyses that combined genetic and mortality data, we found 38 single amino acid polymorphisms scattered throughout the complete coding regions of the viral genome that were putatively involved in virulence of VHSV in trout. Specific amino acid signatures were recognized as being associated with either low or high virulence phenotypes. The phylogenetic analysis of VHSV coding regions supported the evolution toward greater virulence in rainbow trout within subtype Ia, and identified several other subtypes which may be prone to be virulent for this species. This study sheds light on the molecular basis for VHSV virulence, and provides an extensive list of putative virulence markers for their subsequent validation.

Cellular, humoral and molecular responses in rainbow trout (Oncorhynchus mykiss) exposed to a herbicide and subsequently infected with infectious hematopoietic necrosis virus.

Aquatic ecosystems are now chronically polluted by a cocktail of many chemical substances. There is now clear evidence of associations between exposure to pollutants and greater susceptibility to pathogens. The aim of the present study was to characterize the defense capacities of rainbow trout (Oncorhynchus mykiss), chronically exposed to pendimethalin (PD), to subsequent experimental challenge with the infectious hematopoietic necrosis virus (IHNV). Immunological responses were examined at different organizational levels, from individuals to gene expression. No negative effects of PD were noted on the Fulton index nor on the liver or spleen somatic indices (LSI; SSI) before viral infection, but the infectious stress seems to generate a weak but significant decrease in Fulton and LSI values, which could be associated with consumption of energy reserves. During the viral challenges, the distribution of cumulative mortality was slightly different between infected groups. The impact of the virus on fish previously contaminated by PD started earlier and lasted longer than controls. The proportion of seropositive fish was lower in the fish group exposed to PD than in the control group, with similar quantities of anti-IHNV antibodies secreted in positive fish, regardless of the treatment. While no significant differences in C3-1 expression levels were detected throughout the experiment, TNF1&2, TLR3, Il-1ß and IFN expression levels were increased in all infected fish, but the difference was more significant in fish groups previously exposed to herbicide. On the other hand, ß-def expression was decreased in the pendimethalin-IHNV group compared to that in fish only infected by the virus (control-IHNV group).

Transchem project - Part II: Transgenerational effects of long-term exposure to pendimethalin at environmental concentrations on the early development and viral pathogen susceptibility of rainbow trout (Oncorhynchus mykiss).

In the Transchem project, rainbow trout genitors were exposed to environmental concentrations of pendimethalin over a period of 18 months and two new first generations of offspring, F1_2013 and F1_2014, were obtained. We investigated the impact of direct chemical exposure on juveniles as well as the potential cumulative transgenerational and direct effects on the larval development and on the pathogen susceptibility of offspring. Depending on the chemical treatment or not of the adults, their offspring were distributed in the tanks of our experimental system, in two batches i.e. juveniles from the control genitors (G-) and others from the contaminated ones (G+), and then, half of the tanks were exposed daily to pendimethalin (Off+) while the others were used as controls (Off-). Viral challenges were performed on the offspring, before and after three months of direct chemical exposure, with strains of infectious hematopoietic necrosis virus (IHNV), viral haemorrhagic septicemia virus (VHSV) and sleeping disease alphavirus (SDV). Direct and transgenerational macroscopic effects were observed on offspring, with a percentage of abnormalities in offspring derived from the genitors exposed to pendimethalin (G+) significantly higher compared to those from the genitors from non-exposed group (G-). Before the direct chemical exposure, similar kinetics of mortality was observed between the offspring from the contaminated or control genitors after VHSV infection. With IHNV, the G+ group died in a slightly larger proportion compared to the G- group and seroconversion was greater for the G- group. For the SDV challenge, the mortality was delayed for the G+ offspring compared to the G- and seroconversion reached 65% in the G+ group compared to 45% in the G-, with similar antibody titres. After three months of direct chemical exposure, kinetics of mortality induced by IHNV infection were similar for all groups studied. Infection with SDV resulted in a cumulative mortality of 40% for the G- groups (Off- and Off+), significantly higher than those observed from the contaminated genitors G+. Proportion of seropositivity for SDV varied from 24 to 47% depending on the group, with very low quantities of secreted antibodies. Lastly, the direct exposure of offspring could impact the capacity of fish to adapt their haematological parameters to environmental and physiological changes, and underlines the potential toxic effects on the next generations.

Transchem project - Part I: Impact of long-term exposure to pendimethalin on the health status of rainbow trout (Oncorhynchus mykiss L.) genitors.

Pendimethalin is a herbicide active substance commonly used in terrestrial agricultural systems and is thus detected at high concentrations in the surface water of several European countries. Previous studies reported several histopathological changes, enzymatic antioxidant modulation and immunity disturbance in fish exposed to this pesticide. The objective of this work was to investigate the direct effects of long-term exposure to environmental concentrations of pendimethalin over a period of 18 months in rainbow trout (Oncorhynchus mykiss) genitors. To do so, an experimental system consisting of eight similar 400 L tanks with a flow-through of fresh river water was used to perform daily chemical contamination. Fish were exposed to 850 ng/L for one hour and the pendimethalin concentration was then gradually diluted during the day to maintain optimal conditions for the fish throughout the experiment and to achieve a mean theoretical exposure level of around 100 ng L-1 per day. Every November, males and females were stripped to collect eggs and sperm and two new first generations of offspring were obtained. Kinetic sampling revealed differences in immune system parameters and antioxidative defences in the contaminated trout compared to the controls, due to pesticide exposure combined with seasonal changes related to gamete maturation. Moreover, reproductive capacity was significantly affected by exposure to the herbicide; a time lag of more than five weeks was observed for egg maturation in contaminated females and high bioconcentrations of pendimethalin were measured in eggs and sperm. Chemical transfer from genitors to offspring via gametes may affect embryo development and negatively impact the early stages of development.

Genome-wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing.

BACKGROUND: European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can result in high levels of morbidity and mortality, mainly during the larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance offers a promising strategy to control this disease. Our study aimed at investigating genetic resistance to VNN and genomic-based approaches to improve disease resistance by selective breeding. A population of 1538 sea bass juveniles from a factorial cross between 48 sires and 17 dams was challenged with RGNNV with mortalities and survivors being recorded and sampled for genotyping by the RAD sequencing approach. RESULTS: We used genome-wide genotype data from 9195 single nucleotide polymorphisms (SNPs) for downstream analysis. Estimates of heritability of survival on the underlying scale for the pedigree and genomic relationship matrices were 0.27 (HPD interval 95%: 0.14-0.40) and 0.43 (0.29-0.57), respectively. Classical genome-wide association analysis detected genome-wide significant quantitative trait loci (QTL) for resistance to VNN on chromosomes (unassigned scaffolds in the case of 'chromosome' 25) 3, 20 and 25 (P < 1e06). Weighted genomic best linear unbiased predictor provided additional support for the QTL on chromosome 3 and suggested that it explained 4% of the additive genetic variation. Genomic prediction approaches were tested to investigate the potential of using genome-wide SNP data to estimate breeding values for resistance to VNN and showed that genomic prediction resulted in a 13% increase in successful classification of resistant and susceptible animals compared to pedigree-based methods, with Bayes A and Bayes B giving the highest predictive ability. CONCLUSIONS: Genome-wide significant QTL were identified but each with relatively small effects on the trait. Tests of genomic prediction suggested that incorporating genome-wide SNP data is likely to result in higher accuracy of estimated breeding values for resistance to VNN. RAD sequencing is an effective method for generating such genome-wide SNPs, and our findings highlight the potential of genomic selection to breed farmed European sea bass with improved resistance to VNN.