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Aims Given the pivotal role played by the gut microbiota in regulating the host immune system, great interest has arisen in the possibility of controlling fish health by modulating the gut microbiota. Hence, there is a need to better understand of the host–microbiota interactions after disease responses to optimize the use of probiotics to strengthen disease resilience and recovery. Methods and Results We tested the effects of a probiotic feed additive in rainbow trout and challenged the fish with the causative agent for enteric red mouth disease, Yersinia ruckeri. We evaluated the survival, host immune gene expression and the gut microbiota composition. Results revealed that provision of probiotics and exposure to Y. ruckeri induced immune gene expression in the host, which were associated with changes in the gut microbiota. Subsequently, infection with Y. ruckeri had very little effect on microbiota composition when probiotics were applied, indicating that probiotics increased stabilisation of the microbiota. Our analysis revealed potential biomarkers for monitoring infection status and fish health. Finally, we used modelling approaches to decipher interactions between gut bacteria and the host immune gene responses, indicating removal of endogenous bacteria elicited by non-specific immune responses. Conclusions We discuss the relevance of these results emphasizing the importance of host–microbiota interactions, including the protective potential of the gut microbiota in disease responses. Significance and Impact of the Study Our results highlight the functional consequences of probiotic-induced changes in the gut microbiota post infection and the resulting host immune response.

Haemal lordosis, a frequent skeletal deformity in teleost fish, has long been correlated with increased mechanical loads induced by swimming activity. In the present study, we examine whether juvenile zebrafish can recover from haemal lordosis and explore the musculoskeletal mechanisms involved. Juveniles were subjected to a swimming challenge test (SCT) that induced severe haemal lordosis in 49% of the animals and then immediately transferred them to 0.0 total body lengths (TL) per second of water velocity for a week. The recovery from lordosis was examined by means of whole mount staining, histology and gene expression analysis. Results demonstrate that 80% of the lordotic zebrafish are capable of internal and external recovery within a week after the SCT. Recovered individuals presented normal shape of the vertebral centra, maintaining though distorted internal tissue organization. Through the transcriptomic analysis of the affected haemal regions, several processes related to chromosome organization, DNA replication, circadian clock and transcription regulation were enriched within genes significantly regulated behind this musculoskeletal recovery procedure. Genes especially involved in adipogenesis, bone remodeling and muscular regeneration were regulated. A remodeling tissue-repair hypothesis behind haemal lordosis recovery is raised. Limitations and future possibilities for zebrafish as a model organism to clarify mechanically driven musculoskeletal changes are discussed.

The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here we examine a whitefish population introduced to northern Finnish Lake Tsahkal in late 1960’s, where three divergent morphs (viz. littoral, pelagic and profundal feeders) were found ten generations after. Using demographic modelling based on genomic data we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid symmetric speciation scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping three quantitative trait loci associated with gonad weight variation, a proxy for sexual maturity and spawning time, were identified. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.

In the face of the human-caused biodiversity crisis, understanding the theoretical basis of conservation ef-forts of endangered species and populations has become increasingly important. According to population genetics theory, population subdivision helps organisms retain genetic diversity, crucial for adaptation in a changing environment. Habitat topography is thought to be important for generating and maintaining popu-lation subdivision, but empirical cases are needed to test this assumption. We studied Saimaa ringed seals, landlocked in a labyrinthine lake and recovering from a drastic bottleneck, with additional samples from three other ringed seal subspecies. Using whole-genome sequences of 145 seals, we analyzed the distribution of variation and genetic relatedness among the individuals in relation to the habitat shape. Despite a severe his-tory of genetic bottlenecks with prevalent homozygosity in Saimaa ringed seals, we found evidence for the population structure mirroring the subregions of the lake. Our genome-wide analyses showed that the sub -populations had retained unique variation and largely complementary patterns of homozygosity, highlighting the significance of habitat connectivity in conservation biology and the power of genomic tools in under-standing its impact. The central role of the population substructure in preserving genetic diversity at the metapopulation level was confirmed by simulations. Integration of genetic analyses in conservation deci-sions gives hope to Saimaa ringed seals and other endangered species in fragmented habitats.

Microbiomes provide key ecological functions to their host; however, most host-associated microbiomes are too complicated to allow a model of essential host–microbe–microbe interactions. The intestinal microbiota of salmonids may offer a solution since few dominating species often characterize it. Healthy fish coexist with a mutualistic Mycoplasma sp. species, while stress allows the spread of pathogenic strains, such as Aliivibrio sp. Even after a skin infection, the Mycoplasma does not recover; Aliivibrio sp. often remains the dominant species, or Mycoplasma–Aliivibrio coexistence was occasionally observed. We devised a model involving interactions among the host immune system, Mycoplasma sp. plus a toxin-producing pathogen. Our model embraces a complete microbiota community and is in harmony with experimental results that host–Mycoplasma mutualism prevents the spread of pathogens. Contrary, stress suppresses the host immune system allowing dominance of pathogens, and Mycoplasma does not recover after stress disappears.

Comparing observed versus theoretically expected evolutionary responses is important for our understanding of the evolutionary process, and for assessing how species may cope with anthropogenic change. Here, we document directional selection for larger female size in Atlantic salmon, using pedigree-derived estimates of lifetime reproductive success as a fitness measure. We show the trait is heritable and, thus, capable of responding to selection. The Breeder's Equation, which predicts microevolution as the product of phenotypic selection and heritability, predicted evolution of larger size. This was at odds, however, with the observed lack of either phenotypic or genetic temporal trends in body size, a so-called "paradox of stasis." To investigate this paradox, we estimated the additive genetic covariance between trait and fitness, which provides a prediction of evolutionary change according to Robertson's secondary theorem of selection (STS) that is unbiased by missing variables. The STS prediction was consistent with the observed stasis. Decomposition of phenotypic selection gradients into genetic and environmental components revealed a potential upward bias, implying unmeasured factors that covary with trait and fitness. These results showcase the power of pedigreed, wild population studies-which have largely been limited to birds and mammals-to study evolutionary processes on contemporary timescales.

Microalgal cultivation in aquaculture wastewater (AWW) from recirculating aquaculture systems (RAS) is an approach for combined production of valuable algal biomass and AWW treatment. The growth, nutrient uptake, fatty acid (FA) profile, and tocopherol content of mixed algal cultures of Euglena gracilis with Selenastrum grown in AWWs from pikeperch (Sander lucioperca) and catfish (Clarias anguillaris) RAS were studied. The highest algal biomass (1.5gL(-1)), lipid (84.9mgL(-1)), and tocopherol (877.2gL(-1)) yields were achieved in sludge-amended pike perch AWW. Nutrient removal rates in experiments were 98.9-99.5 and 98.4-99.8% for NH4-N and PO4-P, and 75.4-89.2% and 84.3-95.7% for TN and TP, respectively, whereas the COD was reduced by 45.8-67.6%. Biomass EPA and DHA content met, while ARA and tocopherol content exceeded the requirements for fish feed. Algal cultivation in AWWs is a promising alternative for AWW treatment while providing a replacement for fish oil in feed.

The aim of the present study was to evaluate the phospholipid requirements for gilthead seabream, fed with low-fish meal diets. A 70-day feeding trial was performed to evaluate the dietary effects of marine versus plant-based phospholipid sources in low-fish meal diets on growth, body composition, liver, muscle and intestinal fatty acid profiles (polar and neutral), as well as liver morphology. Three levels of krill (marine) or soy lecithin (plant) as phospholipid source, at 0.53%, 1% and 2%, were supplemented in diets with 10% fish meal inclusion. The effects were compared to a high-fish meal diet (65%) as a positive control, and a low-fish meal diet without addition of phospholipids as a negative control. Growth, feed and protein efficiency parameters were improved by the addition of phospholipids in the low-fish meal diets, irrespective of the source, but all parameters were lower compared to the positive control. Krill phospholipid supplementation showed optimal results at 0.5% levels and soybean lecithin supplementation at 1% level. Significant differences by the phospholipid supplementation were found in both the neutral and polar lipid profile in the liver and muscle, while only in the neutral lipids in the intestine. Evaluation of liver histology indicated mild improvement of steatosis symptoms. Overall, our results indicate that phospholipid supplementation in low-fish meal diets can improve the growth and liver status in gilthead seabream juveniles. EU 7th Framework Programme [288925] This study has received funding from the EU 7th Framework Programme, under the ARRAINA project (Grant agreement 288925): Advanced Research Initiatives for Nutrition & Aquaculture.

This work was supported by the BBSRC EastBio PhD studentship awarded to MC, the Danish Strategic Research Council grant No 060300449B HABFISH, and the European Maritime and Fisheries Fund and the Danish Fisheries Agency joint grant “Sundt Dambrug”. Molecular work at University of Aberdeen was funded by Scottish Aquaculture Innovation grant SL 2017 08. EK was supported by BBSRC grant BB/R018812/1. The gill of teleost fish is a multifunctional organ involved in many physiological processes, including protection of the mucosal gill surface against pathogens and other environmental antigens by the gill-associated lymphoid tissue (GIALT). Climate change associated phenomena, such as increasing frequency and magnitude of harmful algal blooms (HABs) put extra strain on gill function, contributing to enhanced fish mortality and fish kills. However, the molecular basis of the HAB-induced gill injury remains largely unknown due to the lack of high-throughput transcriptomic studies performed on teleost fish in laboratory conditions. We used juvenile rainbow trout (Oncorhynchus mykiss) to investigate the transcriptomic responses of the gill tissue to two (high and low) sublethal densities of the toxin-producing alga Prymnesium parvum, in relation to non-exposed control fish. The exposure time to P. parvum (4–5 h) was sufficient to identify three different phenotypic responses among the exposed fish, enabling us to focus on the common gill transcriptomic responses to P. parvum that were independent of dose and phenotype. The inspection of common differentially expressed genes (DEGs), canonical pathways, upstream regulators and downstream effects pointed towards P. parvum-induced inflammatory response and gill inflammation driven by alterations of Acute Phase Response Signalling, IL-6 Signalling, IL-10 Signalling, Role of PKR in Interferon Induction and Antiviral Response, IL-8 Signalling and IL-17 Signalling pathways. While we could not determine if the inferred gill inflammation was progressing or resolving, our study clearly suggests that P. parvum blooms may contribute to the serious gill disorders in fish. By providing insights into the gill transcriptomic responses to toxin-producing P. parvum in teleost fish, our research opens new avenues for investigating how to monitor and mitigate toxicity of HABs before they become lethal. Publisher PDF

Microalgae have been used as live food in aquatic species. In recent years, the interest in microalgae has considerably increased, thanks to the evolution of production techniques that have identified them as an ecologically attractive aquafeed ingredient. The present study provides the first data about the effects of dietary inclusion of a microalgae consortium grown in a high-rate algal pond system on zootechnical performance, morphometric indices, and dietary nutrient digestibility as well as morphology and functionality of the digestive system of European sea bass,Dicentrarchus labrax. A dietary treatment including a commercial mono-cultured microalgae (Nannochloropsissp.) biomass was used for comparison. Six hundred and thirty-six European sea bass juveniles (18 ± 0.28 g) were randomly allotted into 12 experimental groups and fed 4 different diets for 10 weeks: a control diet based on fish meal, fish oil, and plant protein sources; a diet including 10% ofNannochloropsisspp. biomass (100 g/kg diet); and two diets including two levels (10% and 20%) of the microalgal consortium (100 and 200 g/kg diet).Even at the highest dietary inclusion level, the microalgal consortium (200 g/kg diet) did not affect feed palatability and fish growth performance. A significant decrease in the apparent digestibility of dry matter, protein, and energy was observed in diets including 10 and 20% of the microalgal consortium, but all fish exhibited a well-preserved intestinal histomorphology. Moreover, dietary inclusion with the microalgal consortium significantly increased the enzymatic activity of maltase, sucrase-isomaltase, and ɤ-glutamil transpeptidase in the distal intestine of the treated European sea bass. Algal consortium grown using fish farm effluents represents an attempt to enhance the utilization of natural biomasses in aquafeeds when used at 10 % as substitute of vegetable ingredients in diet for European sea bass.

Enriched rearing has been demonstrated to shape the phenotype of hatchery-reared salmonids and improve their post-release survival in the wild, thus having an important applied value in conservation. However, it is unclear if rearing conditions or survival selection during the early life stages induce long-term fitness effects on adult phenotypes. Using a paired full-sib set-up, we investigated the influence of the environmental enrichment at the egg and fry stages on the milt quality and skin colouration of the adult brown trout (Salmo trutta L.). Overall, males had a higher number of skin spots than females. Notably, the total numbers of spots and black spots were significantly lower in fish raised in an enriched environment than in their full siblings reared in a conventional hatchery environment. However, neither sperm motility nor sperm swimming behaviour differed between full sib males reared in different environments. Our results suggest that rearing method may shape the colouration of brown trout, either by ecological carry-over effects or by selective survival during the rearing process. This, in turn, indicates that ecological conditions at early life can have long-prevailing phenotypically plastic or microevolutionary effects on the adult traits of fish. These effects should be taken into consideration to better understand the ecological role of rearing methodology in salmonid conservation.

The European Commission asked EFSA for a scientific opinion on the risks for animal and human health related to the presence of dioxins (PCDD/Fs) and DL‐PCBs in feed and food. The data from experimental animal and epidemiological studies were reviewed and it was decided to base the human risk assessment on effects observed in humans and to use animal data as supportive evidence. The critical effect was on semen quality, following pre‐ and postnatal exposure. The critical study showed a NOAEL of 7.0 pg WHO2005‐TEQ/g fat in blood sampled at age 9 years based on PCDD/F‐TEQs. No association was observed when including DL‐PCB‐TEQs. Using toxicokinetic modelling and taking into account the exposure from breastfeeding and a twofold higher intake during childhood, it was estimated that daily exposure in adolescents and adults should be below 0.25 pg TEQ/kg bw/day. The CONTAM Panel established a TWI of 2 pg TEQ/kg bw/week. With occurrence and consumption data from European countries, the mean and P95 intake of total TEQ by Adolescents, Adults, Elderly and Very Elderly varied between, respectively, 2.1 to 10.5, and 5.3 to 30.4 pg TEQ/kg bw/week, implying a considerable exceedance of the TWI. Toddlers and Other Children showed a higher exposure than older age groups, but this was accounted for when deriving the TWI. Exposure to PCDD/F‐TEQ only was on average 2.4‐ and 2.7‐fold lower for mean and P95 exposure than for total TEQ. PCDD/Fs and DL‐PCBs are transferred to milk and eggs, and accumulate in fatty tissues and liver. Transfer rates and bioconcentration factors were identified for various species. The CONTAM Panel was not able to identify reference values in most farm and companion animals with the exception of NOAELs for mink, chicken and some fish species. The estimated exposure from feed for these species does not imply a risk., This publication is linked to the following EFSA Supporting Publications articles: http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2018.EN-1136/full, http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2018.EN-1137/full, http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2018.EN-1374/full

The teleost zebrafish (Danio rerio), an established model for human skeletal diseases, is reared under controlled conditions with defined parameters for temperature and photoperiod. Studies aimed at defining the proper rearing density have been performed with regard to behavioural and physiological stress response, sex ratio and reproduction. Studies concerning the effect of rearing density on the skeletal phenotype are lacking. This study analyses the response of the skeleton to different rearing densities and describes the skeletal deformities. Wild-type zebrafish were reared up to 30 dpf (days post-fertilization) in a common environment. From 30 to 90 dpf, animals were reared at three different densities: high density (HD), 32 fish l(-1); medium density (MD), 8 fish l(-1) and low density (LD), 2 fish l(-1). Animals at 30 and 90 dpf were collected and whole-mount stained with Alizarin red S to visualize mineralized tissues. The entire skeleton was analysed for meristic counts and 172 types of deformities. The results showed that the rearing density significantly influenced the specimens' average standard length, which decreased with the increase in the rearing density. Differences in meristic counts among the three groups were not observed. Rearing density-independent malformations affected the ribs, neural arches and the spines of the abdominal region, as well as vertebrae of the caudal complex. The HD group showed the highest number of deformities per specimen, the highest number of observed types of deformities and, together with the MD group, the highest frequency of specimens affected by severe deformities. In particular, the HD group showed deformities affecting arches, spines and vertebral centra in the caudal region of the vertebral column. This study provides evidence of an effect of the rearing density on the development of different skeletal phenotypes.

Animal models are essential tools for addressing fundamental scientific questions about skeletal diseases and for the development of new therapeutic approaches. Traditionally, mice have been the most common model organism in biomedical research, but their use is hampered by several limitations including complex generation, demanding investigation of early developmental stages, regulatory restrictions on breeding, and high maintenance cost. The zebrafish has been used as an efficient alternative vertebrate model for the study of human skeletal diseases, thanks to its easy genetic manipulation, high fecundity, external fertilization, transparency of rapidly developing embryos, and low maintenance cost. Furthermore, zebrafish share similar skeletal cells and ossification types with mammals. In the last decades, the use of both forward and new reverse genetics techniques has resulted in the generation of many mutant lines carrying skeletal phenotypes associated with human diseases. In addition, transgenic lines expressing fluorescent proteins under bone cell- or pathway- specific promoters enable in vivo imaging of differentiation and signaling at the cellular level. Despite the small size of the zebrafish, many traditional techniques for skeletal phenotyping, such as x-ray and microCT imaging and histological approaches, can be applied using the appropriate equipment and custom protocols. The ability of adult zebrafish to remodel skeletal tissues can be exploited as a unique tool to investigate bone formation and repair. Finally, the permeability of embryos to chemicals dissolved in water, together with the availability of large numbers of small-sized animals makes zebrafish a perfect model for high-throughput bone anabolic drug screening. This review aims to discuss the techniques that make zebrafish a powerful model to investigate the molecular and physiological basis of skeletal disorders.

Stress triggers a battery of physiological responses in fish, including the activation of metabolic pathways involved in energy production, which helps the animal to cope with the adverse situation. Prolonged exposure to stressful farming conditions may induce adverse effects at the whole-animal level, impairing welfare. Fourier transform infrared (FTIR) spectroscopy is a rapid biochemical fingerprinting technique, that, combined with chemometrics, was applied to disclose the metabolic alterations in the fish liver as a result of exposure to standard stressful practices in aquaculture. Gilthead seabream (Sparus aurata) adults exposed to different stressors were used as model species. Spectra were preprocessed before multivariate statistical analysis. Principal components analysis (PCA) was used for pattern recognition and identification of the most discriminatory wavenumbers. Key spectral features were selected and used for classification using the k-nearest neighbour (KNN) algorithm to evaluate whether the spectral changes allowed for the reliable discrimination between experimental groups. PCA loadings suggested that major variations in the hepatic infrared spectra responsible for the discrimination between the experimental groups were due to differences in the intensity of absorption bands associated with proteins, lipids and carbohydrates. This broad-range technique can thus be useful in an exploratory approach before any targeted analysis. FCT: SFRH/BD/138884/2018/ SFRH/BD/136319/2018/ UIDB/04326/2020/ 16-02-05-FMP-12 info:eu-repo/semantics/publishedVersion

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F-ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.

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 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.

It is well known that healthy gut microbiota is essential to promote host health and well-being. The intestinal microbiota of endothermic animals as well as fish are classified as autochthonous or indigenous, when they are able to colonize the host’s epithelial surface or are associated with the microvilli, or as allochthonous or transient (associated with digesta or are present in the lumen). Furthermore, the gut microbiota of aquatic animals is more fluidic than that of terrestrial vertebrates and is highly sensitive to dietary changes. In fish, it is demonstrated that [a] dietary form (live feeds or pelleted diets), [b] dietary lipid (lipid levels, lipid sources and polyunsaturated fatty acids), [c] protein sources (soybean meal, krill meal and other meal products), [d] functional glycomic ingredients (chitin and cellulose), [e] nutraceuticals (probiotics, prebiotics, synbiotics and immunostimulants), [f] antibiotics, [g] dietary iron and [h] chromic oxide affect the gut microbiota. Furthermore, some information is available on bacterial colonization of the gut enterocyte surface as a result of dietary manipulation which indicates that changes in indigenous microbial populations may have repercussion on secondary host–microbe interactions. The effect of dietary components on the gut microbiota is important to investigate, as the gastrointestinal tract has been suggested as one of the major routes of infection in fish. Possible interactions between dietary components and the protective microbiota colonizing the digestive tract are discussed.

Pradhan, Ajay/0000-0003-2305-8574, WOS: 000509791400034, PubMed ID: 31676350, In the present study, we investigated the detrimental effects of ethoxyquin (EQ) on zebrafish embryonic development using different endpoints including lethality, malformations, locomotion and gene expression. EQ is primarily used as a preservative in animal feed and it has been shown to have negative impacts on different laboratory animals. However, studies on the adverse effects of EQ in aquatic animals are still limited. In this study, zebrafish eggs were exposed to different concentrations of EQ ranging from 1 to 100 mu M for six days. In the 100 mu M treated groups 95 and 100% mortality was observed at 24 and 48 h, respectively. Delayed development, decreased pigmentation and pericardial edema were observed in larvae. Behavioral analysis of larvae demonstrated a distinct locomotive pattern in response to EQ both in light and dark indicating a possible developmental neurotoxicity and deficits in locomotion. The expression levels of genes involved in several physiological pathways including stress response, cell cycle and DNA damage were altered by EQ. Our results demonstrate that EQ could cause developmental and physiological toxicity to aquatic organisms. Hence, its toxic effect should be further analyzed and its use and levels in the environment must be monitored carefully., Knowledge Foundation, Sweden; Orebro University, This study was financed by Knowledge Foundation, Sweden, and Orebro University.

While evolutionary responses require heritable variation, estimates of heritability (h2) from wild fish populations remain rare. A 20-year molecular pedigree for a wild Scottish population of Atlantic salmon (Salmo salar) was used to investigate genetic contributions to (co)variation in two important, correlated, phenotypic traits: â sea ageâ (number of winters spent at sea prior to spawning) and size-at-maturity (body length just prior to spawning). Sea age was strongly heritable (h2 = 0.51) and size exhibited moderate heritability (h2 = 0.27). A very strong genetic correlation (rG = 0.96) between these traits implied the same functional loci must underpin variation in each. Indeed, body size within sea ages had much lower heritability that did not differ significantly from zero. Thus, within wild S. salar populations, temporal changes in sea age composition could reflect evolutionary responses, whereas rapid changes of body size within sea ages are more likely due to phenotypic plasticity. These inheritance patterns will influence the scope of evolutionary responses to factors such as harvest or climate change and, hence, have management implications for salmonid populations comprising a mix of sea ages. Si une variation héritable est nécessaire pour permettre des réactions évolutives, les estimations de l’héritabilité (h2) obtenues pour des populations sauvages demeurent rares. Un pedigree moléculaire de 20 ans pour une population sauvage écossaise de saumons atlantiques (Salmo salar) a été utilisé pour étudier les contributions génétiques à la (co)variation de deux caractères phénotypiques corrélés importants, à savoir « l’âge marin » (le nombre d’hivers passés en mer avant le frai) et la taille à la maturité (la longueur du corps juste avant le frai). L'âge marin est fortement héritable (h2 = 0,51) et la taille présente une héritabilité modérée (h2 = 0,27). Une corrélation génétique très forte (rG = 0,96) entre ces caractères indique que les mêmes sites fonctionnels doivent sous-tendre la variation des deux caractères. En effet, la taille du corps pour des âges marins donnés présente une héritabilité beaucoup plus faible qui n’est pas significativement différente de zéro. Ainsi, dans les populations sauvages de S. salar, les changements dans le temps de la composition des âges marins pourraient refléter des reactions évolutives, alors que des changements rapides de la taille du corps au sein de classes d’âge marin sont plus probablement le fait d’une plasticité phénotypique. Ces motifs d’hérédité influenceront la portée des réactions évolutives à des facteurs comme l’exploitation ou les changements climatiques, ce qui a des conséquences pour la gestion de populations de salmonidés composées d’un mélange d’âges marins. [Traduit par la Rédaction]

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 genomewide SNPs, and our findings highlight the potential of genomic selection to breed farmed European sea bass with improved resistance to VNN.

1. Inferring the dynamics of populations in time and space is a central challenge in ecology. Intra-specific structure (for example genetically distinct sub-populations or meta-populations) may require methods that can jointly infer the dynamics of multiple populations. This is of particular importance for harvested species, for which management must balance utilization of productive populations with protection of weak ones. 2. Here we present a novel method for simultaneous learning about the spatio-temporal dynamics of multiple populations that combines genetic data with prior information about abundance and movement, akin to an integrated population modelling approach. We apply the Bayesian genetic mixed stock analysis to 17 wild and 10 hatchery-reared Baltic salmon (S. salar) stocks, quantifying uncertainty in stock composition in time and space, and in population dynamics parameters such as migration timing and speed. 3. The genetic data were informative about stock-specific movement patterns, updating priors for migration path, timing and speed. Use of a population dynamics model allowed robust interpolation of expected catch composition at areas and times with no genetic observations. Our results indicate that the commonly used "equal prior probabilities" assumption may not be appropriate for all mixed stock analyses: incorporation of prior information about stock abundance and movement resulted in more plausible and precise estimates of mixture compositions in time and space. 4. The model we present here forms the basis for optimizing the spatial and temporal allocation of harvest to support the management of mixed populations of migratory species.

This work was supported by a grant from the European Fisheries Fund (European Union). Date of Acceptance: 14/04/2015 In studies of the population dynamics of parasitic sea lice and the implications of outbreaks for salmon farms, several types of mathematical models have been implemented. Delay differential equation models describe the temporal dynamics of average adult lice densities over many farm sites. In contrast, larval transport models consider the relative densities of lice at farm sites by modelling larval movements between them but do not account for temporal dynamics or feedbacks created by reproduction. Finally, several recent studies have investigated spatiotemporal variation in site lice abundances using statistical models and distance-based proxies for connectivity. We developed a model which integrates connectivity estimates from larval transport models into the delay differential equation framework. This allows representation of sea lice developmental stages, dispersal between sites, and the impact of management actions. Even with identical external infection rates, lice abundances differ dramatically between farms over a production cycle (dependent on oceanographic conditions and resulting between-farm connectivity). Once infected, lice dynamics are dominated by site reproduction and subsequent dispersal. Lice control decreases actual lice abundances and also reduces variation in abundance between sites (within each simulation) and between simulation runs. Control at sites with the highest magnitude of incoming connections, computed directly from connectivity modelling, had the greatest impact on lice abundances across all sites. Connectivity metrics may therefore be a reasonable approximation of the effectiveness of management practices at particular sites. However, the model also provides new opportunities for investigation and prediction of lice abundances in interconnected systems with spatially varying infection and management. Publisher PDF

In the last 20 years, research has been directed towards possible differences in the mating behaviour of species belonging to the Salmonidae family that may reproductively isolate wild populations from escaped hatchery or farmed fish. Despite these studies, a detailed description of the overall behavioural repertoire of Salmonidae species from wild and farmed environments is still lacking. Furthermore, although Arctic charr has been described as the most variable between all vertebrate species, possible behavioural plasticity outside of the breeding season has not been widely investigated, and a complete ethogram for Arctic charr not in breeding condition is currently unavailable. This study presents the first complete ethogram of captive Arctic charr behaviour outside of the breeding season. The completeness of this ethogram was validated based on the Behavioural Accumulation Curves methodology, a reliable and easy to use tool for assessing the best compromise between sampling effort and ethogram completeness. Additionally, a new way of presenting an ethogram has been proposed and validated using a dichotomous key to describe behaviour types. This proved to be a more effective operational tool for identifying Arctic charr behaviour than the ethogram. The dichotomous key of behaviour led to a significantly less ambiguous identification of behavioural units, thus reducing observer, recording errors and enhancing accuracy. This study therefore represents an effective step forward to a more in-depth and rigorous comparison of Arctic charr behavioural adaptation between and within artificial and natural settings.

CD36 is a scavenger receptor which has been studied closely in mammals where it is expressed by many different cell types and plays a role in highly diverse processes, both homeostatic and pathologic. It is among other things important in the innate immune system, in angiogenesis, and in clearance of apoptotic cells, and it is also involved in lipid metabolism and atherosclerosis. Recently, in the cephalochordate amphioxus a primitive CD36 family member was described, which was present before the divergence of CD36 from other scavenger receptor B family members, SCARB1 and SCARB2. Not much is known on the Cd36 molecule in teleost fish. We therefore studied Cd36 in both zebrafish and common carp, two closely related cyprinid fish species. Whereas a single cd36 gene is present in zebrafish, carp has two cd36 genes, and all show conserved synteny compared to mammalian CD36. The gene expression of carp cd36 is high in brain, ovary and testis but absent in immune organs. Although in mammals CD36 expression in erythrocytes, monocytes and macrophages is high, gene expression studies in leukocyte subtypes of adult carp and zebrafish larvae, including thrombocytes and macrophages provided no indication for any substantial expression of cd36 in immune cell types. Surprisingly, analysis of the cd36 promoter region does show the presence of several binding sites for transcription factors known to regulate immune responses. Overexpression of carp cd36 locates the receptor on the cell surface of mammalian cell lines consistent with the predicted topology of cyprinid Cd36 with a large extracellular domain, two transmembrane domains, and short cytoplasmic tails at both ends. Gene expression of cd36 is down-regulated during infection of zebrafish with Mycobacterium marinum, whereas knockdown of cd36 in zebrafish larvae led to higher bacterial burden upon such infection. We discuss the putative role for Cd36 in immune responses of fish in the context of other members of the scavenger receptor class B family.

Homologous and heterologous (genogroup Ia) DNA vaccines against viral hemorrhagic septicemia virus (genogroup IVa) conferred partial protection in Pacific Herring Clupea pallasii. Early protection at 2 weeks postvaccination (PV) was low and occurred only at an elevated temperature (12.6°C, 189 degree days), where the relative percent survival following viral exposure was similar for the two vaccines (IVa and Ia) and higher than that of negative controls at the same temperature. Late protection at 10 weeks PV was induced by both vaccines but was higher with the homologous vaccine at both 9.0°C and 12.6°C. Virus neutralization titers were detected among 55% of all vaccinated fish at 10 weeks PV. The results suggest that the immune response profile triggered by DNA vaccination of herring was similar to that reported for Rainbow Trout Oncorhynchus mykiss by Lorenzen and LaPatra in 2005, who found interferon responses in the early days PV and the transition to adaptive response later. However, the protective effect was far less prominent in herring, possibly reflecting different physiologies or adaptations of the two fish species. Received August 1, 2016; accepted March 10, 2017.

International audience; The study tests the physiological responses of Persian sturgeon, Acipenser persicus, during the abrupt release of juveniles from freshwater (FW) into brackish waters (BW=11 parts per thousand) of the Caspian Sea. Fish weight at release was 2-3g (2.55 +/- 0.41g; 8.8 +/- 0.58cm TL). Totals of 160 individuals were randomly distributed into four fiber-glass aerated tanks (volume 60-L). Two tanks served as controls (FW groups), and two as exposure tanks for BW (Caspian Sea water=CSW). Fish were sampled at 0, 3, 6, 12, 24, 48 and 96hr after abrupt transfer to CSW. Plasma osmolality, immunolocalization of Na+, K+ -ATPase (NKA) and Na+/K+/2Cl(-) (NKCC) Co-transporter, NKA activity and the NKA -subunit mRNA expression were analyzed. Blood osmolality of fish transferred from FW to CSW increased significantly within hours post-transfer (p

[EN] Protocols for the cryopreservation of fish gametes have been developed for many different fish species, in special, freshwater salmonids and cyprinids. Methods for sperm freezing have progressed during the last decades due to the increasing number of potential applications: aquaculture (genetic improvement programs, broodstock management, helping with species having reproductive problems), biotechnology studies using model fish species (preservation of transgenic or mutant lines), cryobanking of genetic resources from endangered species, etc. This mini-review tries to give an overview of the present situation of this area of research, identifying the main challenges and perspectives, redirecting the reader to more in-depth reviews and papers., Partially funded by the European Training Network IMPRESS (Marie Sklodowska Curie Actions; Grant agreement nº: 642893), COST Office (Food and Agriculture COST Action FA1205: AQUAGAMETE), the Research Centre of Excellence- 9878-3/2016/FEKUT, KMR_12-1-2012-0436, NKFIH (OTKA) 109847, KLING 31-03-05-FEP-73, CRIOBIV 31-03-05-FEP-59, REPLING 31-03-05-FEP-69 all from PROMAR programme.

This study investigated the effect of dietary astaxanthin supplementation on egg quality and juvenile growth of long snout seahorse (Hippocampus guttulatus). Captive breed seahorse broodstock were fed four diets composed of frozen shrimp [Atlantic ditch shrimp, Palaemonetes varians) used as a vector to deliver artificial diets with increasing levels of astaxanthin (0, 75, 100 and 125 mg kg(-1) dry weight)]. The results indicated that the astaxanthin uptake into eggs from the enriched shrimp diets was highly efficient. Females fed unsupplemented astaxanthin diet produced similar-sized eggs with lower concentration of astaxanthin than females fed diets with astaxanthin. The lower concentration of astaxanthin in the eggs was correlated with the production of smaller juveniles in comparison with the juveniles hatched from parents fed supplemented astaxanthin diets. Juvenile growth and survival was limited by their size on release from the male's pouch as at the end of 28-day postparturition juveniles produced with the diet with no astaxanthin were still significantly smaller (P < 0.05) than those produced from parents fed astaxanthin-supplemented diets. These results demonstrate a significant benefit of dietary astaxanthin supplementation in long snout seahorse diets in terms of improved egg quality and juvenile growth and survival. FCT - Portugal [BPD/34816/2007] info:eu-repo/semantics/publishedVersion

Individual differences in physiological and behavioural responses to stressors are increasingly recognised as adaptive variation and thus raw material for evolution and fish farming improvements including selective breeding. Such individual variation has been evolutionarily conserved and is present in all vertebrate taxa including fish. In farmed animals, the interest in consistent trait associations, that is coping styles, has increased dramatically over the last years because many studies have demonstrated links to performance traits, health and disease susceptibility and welfare. This study will review (i) the main behavioural, neuroendocrine, cognitive and emotional differences between reactive and proactive coping styles in farmed fish; (ii) the methodological approaches used to identify coping styles in farmed fish, including individual (group) mass-screening tests; and (iii) how knowledge on coping styles may contribute to improved sustainability of the aquaculture industry, including welfare and performance of farmed fish. Moreover, we will suggest areas for future research, where genetic basis (heritability/epigene tic) of coping styles, and the neuroendocrine mechanisms behind consistent as well as flexible behavioural patterns are pinpointed as central themes. In addition, the ontogeny of coping styles and the influence of age, social context and environmental change in coping styles will also be discussed. European Commission under the 7th Framework Programme FP7-KBBE [265957]

Fish are continuously forced to actively absorb or expel water and ions through epithelia. Most studies have focused on the gill due to its role in Na+ and Cl- trafficking. However, comparatively few studies have focused on the changing function of the intestine in response to external salinity. Therefore, the present study investigated the main intestinal changes of long-term acclimation of the Senegalese sole (Solea senegalensis) to 5,15, 38 and 55 ppt. Through the measurement of short-circuit current (Isc) in Ussing chambers and biochemical approaches, we described a clear anterior/posterior functional regionalization of the intestine in response to salinity. The use of specific inhibitors in Ussing chamber experiments, revealed that the bumetanide-sensitive Na+/K+/Cl- co-transporters are the main effectors of Cl- uptake in both anterior intestine and rectum. Additionally, the use of the anion exchanger specific inhibitor, DIDS, showed a salinity/region dependency of anion exchanger function. Moreover, we also described ouabain-sensitive Na+/K+-ATPase (NKA) and Bafilomycin Al-sensitive H-ATPase activities (HA), which displayed changes related to salinity and intestinal region. However, the most striking result of the present study is the description of an omeprazole-sensitive H+/K+-ATPase (HKA) in the rectum of Senegalese sole. Its activity was consistently measurable and increased at lower salinities, reaching rates even higher than those of the NKA. Together our results provide new insights into the changing role of the intestine in response to external salinity in teleost fish. The rectal activity of HKA offers an alternative/cooperative mechanism with the HA in the final processing of intestinal water absorption by apical titration of secreted bicarbonate. (C) 2016 Elsevier Inc. All rights reserved. Ministry of Science and Education, Spain [AGL2010-14876] Ministry of Science and Higher Education European Social Funds through the Portuguese National Science Foundation (FCT) [PTDC/MAR-BIO/3811/2012, PTDC/MAR-BIO/3034/2014] Portuguese Foundation for Science and Technology (FCT) [UID/Multi/04326/2013]

Background The identification of DNA methyltransferases (Dnmt) expression patterns during development and their regulation is important to understand the epigenetic mechanisms that modulate larval plasticity in marine fish. In this study, dnmt1 and dnmt3 paralogs were identified in the flatfish Solea senegalensis and expression patterns in early developmental stages and juveniles were determined. Additionally, the regulation of Dnmt transcription by a specific inhibitor (5-aza-2′-deoxycytidine) and temperature was evaluated. Results Five paralog genes of dnmt3, namely dnmt3aa, dnmt3ab, dnmt3ba, dnmt3bb.1 and dnmt3bb.2 and one gene for dnmt1 were identified. Phylogenetic analysis revealed that the dnmt gene family was highly conserved in teleosts and three fish-specific genes, dnmt3aa, dnmt3ba and dnmt3bb.2 have evolved. The spatio-temporal expression patterns of four dnmts (dnmt1, dnmt3aa, dnmt3ab and dnmt3bb.1) were different in early larval stages although all of them reduced expression with the age and were detected in neural organs and dnmt3aa appeared specific to somites. In juveniles, the four dnmt genes were expressed in brain and hematopoietic tissues such as kidney, spleen and gills. Treatment of sole embryos with 5-aza-2′-deoxycytidine down-regulated dntm1 and up-regulated dntm3aa. Moreover, in lecithotrophic larval stages, dnmt3aa and dnmt3ab were temperature sensitive and their expression was higher in larvae incubated at 16 °C relative to 20 °C. Conclusion Five dnmt3 and one dnmt1 paralog were identified in sole and their distinct developmental and tissue-specific expression patterns indicate that they may have different roles during development. The inhibitor 5-aza-2′-deoxycytidine modified the transcript abundance of dntm1 and dntm3aa in embryos, which suggests that a regulatory feedback mechanism exists for these genes. The impact of thermal regime on expression levels of dnmt3aa and dnmt3ab in lecithotrophic larval stages suggests that these paralogs might be involved in thermal programing.

Post-prandial changes in plasma mineral levels and utilisation of minerals in rainbow trout fed complete plant ingredient based diets with or without supplemental di-calcium phosphate (DCP) were studied over an 8 week period. Three diets were used: diet M was FM and fish oil (FO) based diet (control); diets VP0 and VP + (V diets) were completely based on plant derived protein and lipid sources. One of the V diets (VP +) was supplemented with DCP to supply 5 g kg− 1 dry matter available phosphorus (P); while the other diet (VP0) was not supplemented with DCP. Change in dietary protein source significantly affected the post-prandial pattern in plasma levels of P (p < 0.05), Ca (p < 0.007), Mg (p < 0.001) and Zn (p < 0.03). Area under the curve analysis indicated that compared to VP0, DCP supplementation in VP + improved plasma levels of P (p < 0.01) and K (p < 0.05); Cu (p < 0.002), Se (p < 0.009) and Zn (p < 0.001) levels were reduced while Ca, Mg and Fe levels were unaffected (p > 0.05). Based on measurement of apparent digestibility, growth and whole body composition analyses, mineral balances were established showing that supplementation of DCP led to significant increase in whole body P concentration and P retention in VP +, comparable to fish fed diet M with significantly (p < 0.05) reduced faecal and non-faecal P losses. There was improved post-absorptive retention (as % of available intake) of Ca (p < 0.05), Mg (p < 0.05) and K (p < 0.05) in VP + compared to VP0. Utilisation of Cu (p < 0.05) and Zn (p < 0.01) was negatively affected. DCP supplementation to complete plant ingredient based diet increased the post-prandial plasma levels, whole body concentration and utilisation of macro-minerals (P, Ca, Mg and K) whereas that of micro-minerals especially Zn and Cu were negatively affected

Toll like receptors (TLRs) are present in many different fish families from several different orders, including cyprinid, salmonid, perciform, pleuronectiform and gadiform representatives, with at least some conserved properties among these species. However, low conservation of the leucine-rich repeat ectodomain hinders predictions of ligand specificities of fish TLRs based on sequence information only. We review the presence of a TLR genes, and changes in their gene expression profiles as result of infection, in the context of different fish orders and fish families. The application of RT-qPCR and availability of increasing numbers of fish genomes has led to numerous gene expression studies, including studies on TLR gene expression, providing the most complete dataset to date. Induced changes of gene expression may provide (in)direct evidence for the involvement of a particular TLR in the reaction to a pathogen. Especially when findings are consistent across different studies on the same fish species or consistent across different fish species, up-regulation of TLR gene expression could be a first indication of functional relevance. We discuss TLR1, TLR2, TLR4, TLR5 and TLR9 as presumed sensors of bacterial ligands and discuss as presumed sensors of viral ligands TLR3 and TLR22, TLR7 and TLR8. More functional studies are needed before conclusions on ligands specific to (groups of) fish TLRs can be drawn, certainly true for studies on non-mammalian TLRs. Future studies on the conservation of function of accessory molecules, in conjunction with TLR molecules, may bring new insight into the function of fish TLRs.

In fish farming, economic values (EV) of breeding goal traits are lacking, even though they are key parameters when defining selection objectives. The aim of this study was to develop a bioeconomic model to estimate EV of 2 traits representing production performances in fish farming: the thermal growth coefficient (TGC) and the feed conversion ratio (FCR). This approach was applied to a farm producing African catfish (Clarias gariepinus) in a recirculating aquaculture system (RAS). In the RAS, 2 factors could limit production level: the nitrogen treatment capacity of the biofilter or the fish density in rearing tanks at harvest. Profit calculation includes revenue from fish sales, cost of juveniles, cost of feed, cost of waste water treatment, and fixed costs. In the reference scenario, profit was modeled to zero. EV were calculated as the difference in profit per kilogram of fish between the current population mean for both traits (µt) and the next generation of selective breeding (µt + ¿t) for either TGC or FCR. EV of TGC and FCR were calculated for three generations of hypothetical selection on either TGC or FCR (respectively 6.8% and 7.6% improvement per generation). The results show that changes in TGC and FCR can affect both the number of fish that can be stocked (number of batches per year and number of fish per batch) and the factor limiting production. The EV of TGC and FCR vary and depend on the limiting factors. When dissolved NH3-N is the limiting factor for both µt and µt + ¿t, increasing TGC decreases the number of fish that can be stocked but increases the number of batches that can be grown. As a result, profit remains constant and EVTGC is zero. Increasing FCR, however, increases the number of fish stocked and the ratio of fish produced per kilogram of feed consumed (“economic efficiency”). The EVFCR is 0.14 €/kg of fish, and profit per kilogram of fish increases by about 10%. When density is the limiting factor for both µt and µt + ¿t, the number of fish stocked per batch is fixed; therefore, extra profit is obtained by increasing either TGC, which increases the annual number of batches, or by decreasing FCR, which decreases annual feed consumption. EVTGC is 0.03 €/kg of fish and EVFCR is 0.05–0.06 €/kg of fish. These results emphasize the importance of calculating economic values in the right context to develop efficient future breeding programs in aquaculture.

The alimentary tract is a possible site where pathogens and toxins can enter. The alimentary tract is protected, amongst others, by mucus. In this study, tissue samples and crude mucus preparations from different parts of the intestinal tract of Cyprinus carpio (from intestinal bulb onto the hindgut) were examined using histological, histochemical and biochemical techniques. Furthermore, the response of the intestinal mucosal layer and intestinal mucus of C. carpio to acute soybean meal (SBM)-induced enteritis was investigated. In the present study, an indication for a different protein core of mucus high molecular weight glycoproteins (HMGs) for first and second segment could not be found. However, differences in mucus glycosylation could be found. Along the gut axis, the size of the major protein peaks were not similar, which can be caused by a different glycosylation. Also, differences in staining for the antimicrobial peptide beta-defensin 2 were found. Furthermore, changes in HMGs upon SBM diet were found similar to those found in inflammatory bowel disease (IBD) in humans. Initial changes include: changes in mucin composition, the presence of BD3 and of bacteria in internal organs. After the initial changes, all values measured returned back to the initial pre-SBM diet values.

International audience; This study examined the trophic ecology of three sympatric tropical tuna species (bigeye BET, skipjack SKJ, and yellowfin YFT) sampled in the Western Indian Ocean throughout 2013. Specifically we explored inter-specific resource partitioning and ontogenetic variability using neutral fatty acids and stable isotope analysis of liver and muscle from small (100 cm FL) tuna collected in mixed schools at the surface by purse-seine. Both biochemical tracers were used to calculate trophic niche indices that collectively revealed high potential for resource overlap, especially among small tuna. Resource overlap appeared strongest between BET and YFT, with SKJ tissues having high carbon isotope (delta C-13) values (-17 +/- 0.3 parts per thousand), lower nitrogen isotope (delta N-15) values (11.4 +/- 0.6 parts per thousand), and higher relative proportion of poly-unsaturated fatty acids (PUFA) than the two other species, indicating a different diet. Size was found to be a strong predictor for most biochemical tracers in the three species with delta C-13, delta N-15 and total lipid content in the liver. In the larger species (YFT and BET), proportions of mono-unsaturated fatty acids typically increased with size, while quantities of PUFA decreased. In addition to ontogenetic variability, trophic markers were shown to vary between sampling area and season: higher lipid reserves and delta N-15 values, and lower delta C-13 values occurred during monsoon periods around Seychelles than in the Mozambique Channel (parted from about 1500 km). Our multi-tracer approach reveals the magnitude of potential competitive interactions in mixed tropical tuna schools at both small and large sizes and demonstrates that ontogenetic niche differentiation acts as a major factor of coexistence in tropical tuna

Although disease and infection is associated with attenuated growth, the molecular pathways involved are poorly characterized. We postulated that the IGF axis, a central governor of vertebrate growth, is repressed during infection to promote resource reallocation towards immunity. This hypothesis was tested in rainbow trout (Oncorhynchus mykiss) challenged by Aeromonas salmonicida (AS), a Gram-negative bacterial pathogen, or viral hemorrhagic septicemia virus (VHSv) at hatch, first feeding, and 3 weeks after first feeding. Quantitative transcriptional profiling was performed for genes encoding both IGF hormones, 19 salmonid IGF binding proteins (IGFBPs) and a panel of marker genes for growth and immune status. There were major differences in the developmental response of the IGF axis to AS and VHSv, with the VHSv challenge causing strong down-regulation of many genes. Despite this, IGFBP-1A1 and IGFBP-6A2 subtypes, each negative regulators of IGF signaling, were highly induced by AS and VHSv in striking correlation with host defense genes regulated by cytokine pathways. Follow-up experiments demonstrated a highly significant coregulation of IGFBP-1A1 and IGFBP-6A2 with proinflammatory cytokine genes in primary immune tissues (spleen and head kidney) when trout were challenged by a different Gram-negative bacterium, Yersinia ruckeri. Based on our findings, we propose a model where certain IGFBP subtypes are directly regulated by cytokine signaling pathways, allowing immediate modulation of growth and/or immune system phenotypes according to the level of activation of immunity. Our findings provide new and comprehensive insights into cross talk between conserved pathways regulating teleost growth, development, and immunity.

Background The correct evaluation of mineralization is fundamental for the study of skeletal development, maintenance, and regeneration. Current methods to visualize mineralized tissue in zebrafish rely on: 1) fixed specimens; 2) radiographic and μCT techniques, that are ultimately limited in resolution; or 3) vital stains with fluorochromes that are indistinguishable from the signal of green fluorescent protein (GFP)-labelled cells. Alizarin compounds, either in the form of alizarin red S (ARS) or alizarin complexone (ALC), have long been used to stain the mineralized skeleton in fixed specimens from all vertebrate groups. Recent works have used ARS vital staining in zebrafish and medaka, yet not based on consistent protocols. There is a fundamental concern on whether ARS vital staining, achieved by adding ARS to the water, can affect bone formation in juvenile and adult zebrafish, as ARS has been shown to inhibit skeletal growth and mineralization in mammals. Results Here we present a protocol for vital staining of mineralized structures in zebrafish with a low ARS concentration that does not affect bone mineralization, even after repetitive ARS staining events, as confirmed by careful imaging under fluorescent light. Early and late stages of bone development are equally unaffected by this vital staining protocol. From all tested concentrations, 0.01 % ARS yielded correct detection of bone calcium deposits without inducing additional stress to fish. Conclusions The proposed ARS vital staining protocol can be combined with GFP fluorescence associated with skeletal tissues and thus represents a powerful tool for in vivo monitoring of mineralized structures. We provide examples from wild type and transgenic GFP-expressing zebrafish, for endoskeletal development and dermal fin ray regeneration.

Pulse trawling is the most promising alternative to conventional beam trawls targeting Sole Solea solea (also known as Solea vulgaris), but due to the electric fields created by electrotrawls spinal injuries are reported in gadoid round fishes such as Atlantic Cod Gadus morhua. This study aimed to investigate the variability in the occurrence of electric-induced spinal injuries in cod. Four groups of cod, each originating from a different wild or farmed stock, were exposed to the pulses used by electrotrawls targeting Sole. Effects were analyzed based on behavior, mortality, and lesions up to 14 d after exposure, and morphological characteristics such as size, somatic weight, muscularity, the number of vertebral bodies, and the vertebral mineral contents of animals were compared among different cohorts. Second, the influence of factors such as water temperature, electrode diameter, and pulse type and amplitude were tested. Electrode diameter and pulse amplitude showed a positive correlation with the intensity of the fish’s reaction. However, the present experiments confirmed that cod also show variable vulnerability, with injury rates ranging from 0% to 70% after (almost) identical exposures near the electrode. This indicates that these injuries are not only determined by the pulse parameter settings but also by subtle, fish-specific factors. Although the absence of a sensitive group of cod did not enable the elucidation of the conclusive factor, the effect of physiological and morphological factors such as intervertebral ligaments and rearing conditions during early life merit further attention in future research.

International audience; This study investigated the consequences of passive ecological restoration on a riparian habitat and on water quality. The restoration plan consists of excluding livestock by constructing fences along an entire stream 1 m from the stream bed, with the assumption that recovering riparian habitat will restore their ecological processes (e.g., filtration, soil stabilization). We measured responses of riparian plant communities and physico-chemical water quality. We presented data from an 8-year before-after control-impact design across a reference stream and a restored stream in a rural landscape in Normandy, France. Restoration appeared to modify plant communities. After 8 years of restoration, the restored stream had a complex riparian bank, similar to that of the reference stream, with an increase in the number of trees, a decrease in bare soil, and an increase in habitat heterogeneity. Despite this modification, water quality did not improve. The same low water quality in the reference stream demonstrated the need for a watershed-scale approach and for actions to improve agricultural practices before implementing restoration practices at a smaller scale. Nonetheless, the lack of improved water quality does not necessarily mean that the restoration failed. Other functions and services can be provided by excluding livestock.

This study was funded by the 'Region Bretagne', the MAVA Foundation and 'Bretagne Grands Migrateurs'. The surveys and sampling were organised and operated by the company FISH PASS and the association 'Coeur Emeraude' in the Fremur River, and the INRA-Rennes and ONEMA in the Oir River. We are especially grateful to Frederic Marchand (INRA), Julien Tremblay (INRA), Richard Delanoe (ONEMA), Virgile Mazel (FISH PASS), Sebastien Quinot (FISH PASS) and all the people that helped with sampling and data gathering. We are also grateful to ORE PFC for the salmonids data. We are grateful to the two referees and to Anne Lize for their helpful comments.; As a key parameter in the management of fish populations, individual growth rate (GR) variations were examined in the European eel (Anguilla anguilla; >150mm) using extensive mark-recapture surveys in the lotic habitats of two small rivers of western France: the Fremur, supposed to be saturated, and at the same latitude, the Oir with densities fivefold lower than those of the Fremur. In both systems, generalised linear models were used to test whether spatiotemporal factors such as dominant habitat type or local density affect GR variability. In the presumed unsaturated system, the Oir, GR variability is mainly explained by a set of habitat suitability drivers (density, dominant habitat type). In the Fremur, GRs appear independent of differences in habitat density or productivity. Below saturation, an increase in density will decrease the GR through intraspecific competition. At saturation, intraspecific competition reaches such high levels that regardless of eel density and productivity, the resources available by individual are similar throughout the system. In these circumstances, the effect of density on growth was presumed undetectable. Despite these contrasted results, mean GRs observed in both catchments were closed (similar to 20mmyear(-1)). This is an unexpected result as GR is expected to be higher in unsaturated systems. This similarity could be explained by the difference between the two systems in terms of: (i) sex ratio (the Fremur is dominated by male, whereas the female is dominant in the Oir), (ii) habitat type distribution or (iii) possible interspecific competition (important salmonid populations in the Oir).