Aquaculture

In recent years many advances have been made towards developing cost-efficient low-density genomic tools for a wider implementation of genomic selection in aquaculture breeding programmes. Genotype imputation from very low-density (LD) SNP panels of just a few hundred markers to high-density (HD) SNP panels has become a promising strategy to reduce the cost of genotyping while maintaining accurate genomic prediction. The objective of this study is to assess the impact of the makeup of HD-genotyped reference populations on i) the accuracy of imputation for LD-genotyped individuals and ii) the accuracy of genomic prediction for three traits of importance in Atlantic salmon production: growth, resistance to cardiomyopathy syndrome and resistance to pancreas disease. An Atlantic salmon population genotyped with a 47K SNP array was used for the study, along with an in silico LD panel of 554 SNPs. Five reference population scenarios for imputation were tested, which could include only the parents of the candidates for selection, a combination of parents and candidates, or just candidates. All scenarios resulted in highly accurate imputation rates (over 80%) except when the HD reference population was only composed of selection candidates. Nonetheless, the accuracy of imputation barely had an impact on the accuracy of genomic prediction, as the imputed datasets performed very similarly to the HD-panel. Adding a proportion of the offspring to the reference population, in addition to the parents, did not result in any benefit in terms of genomic prediction. Imputation is a cost-effective and robust option for genomic selection in aquaculture.

Cleaner fish species have gained great importance in the control of sea lice, among them, lumpfish (Cyclopterus lumpus) has become one of the most popular. Lumpfish life cycle has been closed, and hatchery reproduction is now possible, however, current production is reliant on wild caught broodstock to meet the increasing demand. Selective breeding practices are called to play an important role in the successful breeding of most aquaculture species, including lumpfish. In this study we analysed a lumpfish population for the identification of genomic markers linked to production traits. Sequencing of RAD libraries allowed us to identify, 7,193 informative markers within the sampled individuals. Genome wide association analysis for sex, weight, condition factor and standard length was performed. One single major QTL region was identified for sex determination, while nine QTL regions were detected for weight, and three QTL regions for standard length. A total of 177 SNP markers of interest (from QTL regions) and 399 top Fst SNP markers were combined in a low-density panel, useful to obtain relevant genetic information from lumpfish populations. Moreover, a robust combined subset of 29 SNP markers (10 associated to sex, 14 to weight and 18 to standard length) provided over 90% accuracy in predicting the animals phenotype. Overall, our findings provide significant insights into the genetic control of important traits in lumpfish and deliver important genomic resources that will facilitate the establishment of selective breeding programs in lumpfish.

Survival is an old trait in animal breeding, yet commonly neglected nowadays for its simple binary records and low levels of heritability in aquaculture species. These traits however, can provide valuable field data when selecting for robustness in genetic improvement programs. In the current study, linear multivariate animal model (LMA) was used for the genetic analysis of survival records from two-year classes (BL2019 and BL2020) of white-leg shrimp (Penaeus vannamei) breeding lines with a total number of 52, 248 individuals from 481 fullsib families recorded for data collection. During grow-out test period, 10 day intervals of survival data were considered as independent traits. Two survival definitions, binary survivability (S) and continuous survival in days (SL), were used for the genetic analysis of survival records to investigate; i) whether adding more survival time information could improve estimation of genetic parameters; ii) the trajectory of survival heritability across time, and iii) patterns of genetic correlations of survival traits across time. Levels of heritability estimates for both S and SL were low (0.005 to 0.076), while heritability for survival day number was found to be similar with that of binary records at each observation time and were highly genetically correlated (rg >0.8). Heritability estimates of body weight (BW) for BL2019 and BL2020 were 0.486 and 0.373, respectively. Trajectories of survival heritability across time showed a gradual increase across the grow-out test period but slowed or reached a plateau during the later grow-out test period. Genetic correlations among survival traits in the grow-out tests were moderate to high, and the closer the times were between estimates, the higher were their genetic correlations. In contrast, genetic correlations between both survival traits and body weight were low but positive. Here we provide the first report of the trajectory of heritability estimates for survival traits across time in aquaculture. Results will be useful for developing robust improved white-leg shrimp culture strains in selective breeding programs based on field survival data.

BackgroundCryopreservation is a valuable tool in aquaculture and conservation programs, yet it exposes spermatozoa to physiological and molecular stresses that may impair motility, fertilisation capacity, and genomic stability. In fishes, where sperm motility is brief and easily activated, post-thaw separation of high-quality sperm remains technically challenging and poorly understood. This study evaluated whether density-gradient centrifugation can isolate a functionally superior subpopulation of sterlet (Acipenser ruthenus) spermatozoa with enhanced motility, fertilising ability, and reduced cryopreservation-induced epigenetic alterations. We further examined whether the use of this selected fraction influences DNA methylation patterns in resulting embryos. ResultsCryopreservation substantially reduced the proportion of motile spermatozoa, while density-gradient centrifugation consistently enriched motile cells both before and after freezing. Motility enhancement reflected a higher proportion of cells capable of activation rather than changes in kinematic behaviour. Fertilisation trials confirmed that the selected post-thaw fraction produced fewer malformed embryos compared with unselected cryopreserved sperm. Cryopreservation and post-thaw selection induced small but significant methylation changes in sperm, predominantly in intergenic regions and promoter-proximal elements. However, these epigenetic differences were not maintained in embryos. Embryo methylomes showed minimal variation between treatments, no distinct clustering by sperm origin, and negligible numbers of differentially methylated regions. Thus, although cryopreservation and sperm selection influenced sperm DNA methylation, these alterations did not translate into measurable changes in embryo methylation patterns. ConclusionsDensity-gradient centrifugation effectively isolates a motile, functionally improved sterlet sperm fraction after cryopreservation, enhancing fertilisation outcomes and reducing developmental abnormalities. Cryopreservation and sperm selection introduce detectable but limited methylation variation in spermatozoa; however, these changes are not inherited by embryos. The findings highlight the utility of post-thaw sperm selection in aquaculture practice and indicate that cryopreservation-associated epigenetic variation in sterlet sperm does not propagate to early developmental stages.

The bacterial skin disease tenacibaculosis, caused by Tenacibaculum species, can compromise numerous species of economically important marine fish, including salmonids. While tenacibaculosis is a known threat to Atlantic salmon (Salmo salar) aquaculture, the pathogenesis of Tenacibaculum maritimum and Tenacibaculum dicentrarchi on Chinook salmon (Oncorhynchus tshawytscha) has not yet been investigated. In this study, three molecular O-AGC types of T. maritimum (O-AGC Type 3-0, Type 2-1 and Type 3-2) and T. dicentrarchi isolated during a disease outbreak of farmed Chinook salmon in Aotearoa New Zealand were assessed for their ability to induce tenacibaculosis in salmon smolts under controlled conditions. Naive Chinook salmon were exposed to T. maritimum or T. dicentrarchi by immersion. Clinical signs of tenacibaculosis were apparent post-exposure and observed in 100% of all three molecular O-AGC types of T.-maritimum-challenged fish, with 100% morbidity in O-AGC Type 2-1 and Type 3-2 and 60% in O-AGC Type 3-0. Chinook salmon exposed to T. dicentrarchi showed characteristic clinical signs of disease in 51% of the challenged population, with 28% morbidity. Common gross pathological signs observed for both Tenacibaculum species were congruent with observations on farmed fish in the field, including scale loss, erythematous skin lesion, skin ulcers, fin necrosis, mouth erosion and gill ulceration. Exophthalmia was observed only in T. maritimum-challenged fish, while skin ulcers appeared grossly more severe with exposed musculature in T. dicentrarchi-challenged fish. Pure T. maritimum and T. dicentrarchi cultures were reisolated from the skin and gills of the challenged fish and their identity was confirmed by species-specific PCR and molecular O-AGC typing. Challenge experiments and associated field surveillance (for T. maritimum) did not show the presence of culturable T. maritimum cells in the anterior kidney. This provides compelling evidence that tenacibaculosis in farmed Chinook salmon is an external infectious disease, and that Tenacibaculum is a marine obligate organism that is unable to survive in fish body fluids and does not cause septicaemia. This has repercussions for approaches to experimental challenges with Tenacibaculum species, which must occur by immersion rather than intraperitoneal or intramuscular inoculation, to replicate the natural transmission pathway and to ensure a successful challenge model. This study fulfilled modernised Kochs postulates for the three molecular O-AGC types of T. maritimum and single strain of T. dicentrarchi as aetiological agents of tenacibaculosis in Chinook salmon that cause mortalities with considerable external abnormalities. Author summaryChinook salmon, Oncorhynchus tshawytscha, is the most significant species of Pacific salmon for its large size and nutritional content which makes it a premium choice for aquaculture. In Aotearoa|New Zealand, Chinook salmon is the only marine salmon species farmed. For a decade, the industry was impacted by an undiagnosed skin disease resulting in high mortalities. Disease susceptibility in Chinook salmon is scarcely studied and added to the challenge for a timely diagnosis. This novel research provides insight on disease susceptibility of Chinook salmon and confirms Tenacibaculum species identified in New Zealand pose a high threat to the aquaculture industry. This research has global implications and contributes valuable insights and approaches to disease management that can be applied in British Columbia and Canada where Chinook salmon populations are in decline.

Successful reproduction is a key factor for efficient breeding schemes and sustainable animal farming. Aquaculture breeding programs rely heavily on small fractions of selected breeders to yield large production stocks, given the high fecundity typically observed in these species. In Sweden, Arctic charr (Salvelinus alpinus) is a salmonid with notable commercial potential, with a selective breeding program operating for ten generations under a growth-rate focused breeding goal. Despite significant gains, the nucleus faces challenges with low and fluctuating fertility impeding expansion efforts. In this study, we estimate genetic parameters for charr milt quality phenotypes measured with specialized cytometry and Computer-Assisted Sperm Analysis (CASA). At the same time, we assess the sex-specific architecture governing egg count and sperm concentration along body size. Finally, we propose a novel analytical framework for the analysis of realized fertilization success rates by considering a multiplicative system of latent maternal and paternal contributions. Low to moderate heritability estimates and genetic correlations were obtained from multi-trait modelling for traits reflecting sperm quality along with high estimates for fork length. Genetic correlations among sperm kinematic parameters appeared strong, while the same traits showed weak positive and weak negative correlations with sperm concentration and fork length, respectively. Furthermore, a negative genetic correlation between sperm concentration and both male body size and egg count suggests a complex interplay of a possible trade-off and sexual antagonism. Our latent fertility analytical approach returned low to moderate heritability estimates depending on the modelling configuration. Overall, our study demonstrated the complexity characterizing the heritable portions of reproductive traits in Arctic charr and tested alternative tools that have the potential for integration into selective breeding programs.

In genomic selection (GS), genome-wide SNP markers are used to generate genomic estimated breeding values (gEBVs) for selection candidates. The application of GS in shellfish looks promising and has the potential to help in dealing with one of the main issues currently affecting Pacific oyster production worldwide, which is the \"summer mortality syndrome\". This causes periodic mass mortality in farms worldwide and has mainly been attributed to a specific variant of the Ostreid herpesvirus (OsHV-1-var). In the current study, we evaluated the potential of genomic selection for host resistance OsHV in Pacific oysters, and compared it to pedigree-based approaches. An OsHV-1 disease challenge was performed using an immersion-based virus exposure treatment for oysters for seven days. 768 samples were genotyped using the medium density SNP array for oysters. GWAS was performed for the survival trait using a GBLUP approach in BLUPF90 software. Heritability ranged from 0.25{+/-}0.05 to 0.37{+/-}0.05 (mean{+/-}s.e) based on pedigree and genomic information, respectively. Genomic prediction was more accurate than pedigree prediction, and SNP density reduction had little impact on prediction accuracy until marker densities dropped below [~]500 SNPs. This demonstrates the potential for GS in Pacific oyster breeding programs and importantly, demonstrates that a low number of SNPs might suffice to obtain accurate gEBVs, thus potentially making the implementation of GS more cost effective.

Muscle lipid content was shown to affect many quality features in salmonids in both raw and processed fillets. The objective of the present work was to assess the consequences of 7 generations of divergent selection for muscle adiposity on some rainbow trout flesh quality and muscle parameters. Fish from Lean (L) and Fat (F) lines had a similar body weight but L fish were longer and had consequently lower condition factor values. Carcass yield was not affected by selective breeding, but L fish had lower hepato- and gonado-somatic indexes, a bigger head, and lower fillet yield than F fish. A difference of more than 15 points in mean fat-meter(R) values (genetic selection criteria) was measured between the two lines. Mean muscle lipid content was 5.0{+/-}1.0% for L line vs 13.5{+/-}2.2% for F line. An absolute difference of more than 6% was measured in fillet dry matter content between the two lines, for raw, cooked, and smoked fillets. Raw fillets from F fish were lighter (L*>) and more colorful (a* and b*>), but softer than those from the L line. Quality parameters of cooked fillets were very similar between the two lines, whereas smoked fillets exhibited, between the two lines, similar differences than raw fillets. A large difference in white muscle fiber size was observed, fish from F line having higher fiber mean diameter, a lower proportion of small fibers, and a higher proportion of large fibers. Sex effects were observed on these immature fish, on classically sex-related traits (GSI and head development), but also on muscle fiber size. Moreover, these effects were more marked in F line. Correlation analysis showed that raw fillet color was positively related to muscle adiposity whereas mechanical resistance was negatively related. Raw fillet mechanical resistance was also negatively correlated to white muscle fiber size. Moreover, smoked fillet quality parameters were correlated to raw fillet ones. The relationships between muscle adiposity, but also muscle cellularity, and fillet quality were discussed. HighlightsO_LI7 generations of adiposity divergent selection affect raw and smoked fillet quality. C_LIO_LISelective breeding led to a noteworthy response in white muscle cellularity. C_LIO_LISome differences between male and female was measured in immature pan-size trout. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/569019v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@10b25f6org.highwire.dtl.DTLVardef@e9402aorg.highwire.dtl.DTLVardef@173b1f9org.highwire.dtl.DTLVardef@a9898b_HPS_FORMAT_FIGEXP M_FIG C_FIG

Wild Atlantic salmon migrate to sea following completion of a developmental process known as parr - smolt transformation (PST), which establishes a seawater (SW) tolerant phenotype. Effective imitation of this aspect of anadromous life-history is a crucial aspect of commercial salmon production, with current industry practice being marred by significant losses during transition from the freshwater (FW) to SW phase of production. The natural photoperiodic control of PST can be mimicked by exposing farmed juvenile fish to a reduced duration photoperiod for at least 6 weeks before increasing the photoperiod in the last 1 - 2 months before SW transfer. While it is known that variations in this general protocol affect subsequent SW performance, there is no uniformly accepted industry standard; moreover, reliable prediction of SW performance from fish attributes in the FW phase remains a major challenge. Here we describe an experiment in which we took gill biopsies 1 week prior to SW transfer from 3000 individually tagged fish raised on 3 different photoperiod regimes during the FW phase. Biopsies were subjected to RNA profiling by Illumina sequencing, while individual fish growth and survival was monitored over 300 days in a SW cage environment, run as a common garden experiment. Using a random forest machine learning algorithm, we developed gene expression-based predictive models for initial survival and stunted growth in SW. Stunted growth phenotypes could not be predicted based on gill transcriptomes, but survival the first 40 days in SW could be predicted with moderate accuracy. While several previously identified marker genes contribute to this model, a surprisingly low weighting is ascribed to sodium potassium ATPase subunit genes, contradicting advocacy for their use as SW readiness markers. However, genes with photoperiod-history sensitive regulation were highly enriched among the genes with highest importance in the prediction model. This work opens new avenues for understanding and exploiting developmental changes in gill physiology during smolt development.

Nile tilapia (Oreochromis niloticus) is one of the most important aquaculture species in the world. When bacteria are present in cultured tilapia but do not cause a declared disease, it makes them asymptomatic carrier organisms. Once environmental or nutritional conditions change, an outbreak may occur. This is why it is so important to detect pathogens before outbreaks occur. This is the first study that use molecular techniques based on PCR to estimate prevalence of fish pathogens in southwest Mexico. During 2018, 2019, 2020 and 2022 samples of internal organs and lesions of Nile tilapia were taken and analyzed for detection of the main bacterial tilapia pathogens using one-step PCR or qPCR. A total of 2396 samples from the internal organs of Nile tilapia pond and cage cultured come from the Mexican Pacific southwest states of Guerrero, Oaxaca and Chiapas were analyzed. Most of the sampled tilapias were apparently healthy and had no relation between the clinical signs and the pathogens detection was found. No Francisella sp. was detected in any sample, Staphylococcus sp. was the most prevalent bacterial genus from the three states over time (from 0 to 64 %). Prevalence of Aeromonas sp. was from 0 to 4.3 %, although the fish pathogen A. dhakensis was not detected. Meanwhile, S. iniae was only detected in Chiapas in 2019 at low prevalence (1.4 %) and S. agalactiae was detected in the three sites at high prevalence (from 0 to 59 %). Both Streptococcus can cause streptococcosis, the most dangerous re-emergent disease to cultured tilapia, which means a great risk for tilapia farming in Mexico.

A systematic review and meta-analysis of genetic parameters underlying inheritance and complex biological relationships for quantitative traits are not available for aquatic animal species. I synthesised and conducted a comprehensive meta-analysis of the published information from 1985 to 2017 on heritability, common full-sib effects and genetic correlations for quantitative characters of biological importance (growth, carcass and flesh quality, disease resistance, deformity and reproduction) for aquaculture species. A majority of the studies (73.5%) focussed on growth related traits (body weight), followed by those on disease resistance (15.9%), whereas only a limited number of studies (10.6%) reported heritability estimates for carcass and flesh quality, deformity or reproduction characteristics. The weighted means of heritability for growth (weight, food utilisation efficiency, maturity) and carcass (fillet weight and yield) traits were moderate. Resistance against various bacteria, virus and parasites were moderately to highly heritable. Across aquatic animal species, the weighted heritability for a range of deformity measures and reproductive traits (fecundity, early survival) was low and not significantly different from zero. The common full-sibs (c2) accounted for a large proportion of total variance for body traits but it was of smaller magnitude in later phase of the growth development. The c2 effects however were not significant or in many cases they were not reported for carcass and flesh quality attributes as well as survival and deformity. The maternal genetic effects were not available for all traits studied especially for reproductive and early growth characters. Genetic correlations between body and carcass traits were high and positive, suggesting that selection for rapid growth can improve fillet weight, a carcass trait of paramount importance. Body weight, the most commonly used selection criterion in aquatic animals, showed non-significant genetic correlation with disease resistance, likely because both positive and negative genetic associations between the two types of traits. Interestingly the genetic associations between growth and reproductive performance (fecundity) and fry traits (fry weight, fry survival) were favourable. To date, there are still no published data on genetic relationships of carcass and flesh quality with disease resistance or reproductive performance in any aquaculture species. Additionally, the present study discussed new traits, including functional, immunological, behavioural and social interaction as well as uniformity that are emerging as potential selection criteria and which can be exploited in future genetic improvement programs for aquatic animals.

Sexual maturation is a critical developmental transition in abalone, yet its molecular basis remains unclear. Understanding the mechanisms underlying maturation is essential for improving the yield and quality of aquaculture production. This study employed transcriptomic analysis to identify key genes involved in the early stages of sexual maturation in the greenlip abalone (Haliotis laevigata), a commercially and ecologically important species native to Australia. Among the most significantly differentially expressed genes were members of the 5-hydroxytryptamine receptor, cytochrome P450, and HSP70 families, which are associated with neuroendocrine signalling, steroid metabolism, and cellular stress response, respectively. Gene regulatory network analysis further predicted their upstream and downstream interactions, suggesting potential signalling pathways that may coordinate reproductive initiation. These findings provide new insights into the molecular mechanisms underlying early maturation in abalone and establish a foundation for future functional investigations.

The Yesso scallop Mizuhopecten yessoensis is an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic differences among hatchery stocks. In this study, we compare cultured Canadian and wild Japanese populations of Yesso scallop using double-digest restriction site-associated DNA (ddRAD)-sequencing to genotype 21,048 variants in 71 wild-caught scallops from Japan, 65 scallops from the Vancouver Island University breeding population, and 37 scallops obtained from a commercial farm off Vancouver Island, British Columbia. The wild scallops are largely comprised of equally unrelated individuals, whereas cultured scallops are comprised of multiple families of related individuals. The polymorphism rate estimated in wild scallops was 1.7%, whereas in the cultured strains it ranged between 1.35% and 1.07%. Interestingly, heterozygosity rates were highest in the cultured populations, which is likely due to shellfish hatchery practices of crossing divergent strains to gain benefits of heterosis and to avoid inbreeding. Evidence of founder effects and drift were observed in the cultured strains, including high genetic differentiation between cultured populations and between cultured populations and the wild population. Cultured populations had effective population sizes ranging from 9-26 individuals whereas the wild population was estimated at 25-50K individuals. Further, a depletion of low frequency variants was observed in the cultured populations. These results indicate significant genetic diversity losses in cultured scallops in Canadian breeding programs. Article SummaryYesso scallop was introduced to breeding programs in Canada around 40 years ago and has become a valuable aquaculture species in the country with little information regarding its genetic diversity. This work genotypes over 20K genetic variants in wild Yesso scallops from Japan and compares to a major broodstock collection in British Columbia, Canada, as well as a commercial farm in the same region. Reduced polymorphism but elevated heterozygosity indicates value of using genetic information to guide breeding programs.

Breeding programs are essential in aquaculture, improving economically and environmentally important traits. In aquaculture systems, animals are raised in large groups, where social interactions are frequent and can influence individual performance. In these circumstances, indirect genetic effects can play an important role in the response to selection, and consequently, their effects on selection outcomes must be analyzed. This study aimed to evaluate the implications of heterogeneous social interaction effects on fish breeding programs using stochastic simulations. We simulated a fish breeding program with 2000 selection candidates from 1000 families formed by a partial mating design of 100 males and 100 females. Social interactions were simulated, affected by the target phenotype and two latent-personality traits. We investigated how genetic gains and phenotypic variances are affected by the magnitude and direction of social interaction effects on the target phenotype, different selection strategies, and the genetic correlations between the target phenotype and personality traits. Our results showed that increased social interaction effects lead to greater phenotypic variability in the target trait. Under mass selection, the genetic means of personality traits change, and these changes depend on the strength and direction of genetic correlations between the focal and personality traits. Conversely, group selection did not increase phenotypic variability but reduced genetic gain for the focal trait compared to mass selection. Moreover, group selection did not alter the genetic means of personality traits. However, this approach increased the rate of inbreeding per generation, which could be mitigated by optimizing the number of families per group.

Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on a regional, rather than at a stock-specific, level. Within British Columbia, chum salmon regional groupings were described at the conservation unit (CU) level, and there may be substructure within particular CUs. Genome wide associations of phenotypic sex to SNP genetic markers identified two clear peaks, a very strong peak on Linkage Group 15, and another on Linkage Group 3. With these new resources, we were better able to characterize the sex-determining region and gain further insights into sex determination in chum salmon and the general biology of this species.

BackgroundRecently, the frequency and severity of marine diseases have increased in association with global changes, and molluscs of economic interest are particularly concerned. Among them, the Pacific oyster (Crassostrea gigas) production faces challenges from several diseases such as the Pacific Oyster Mortality Syndrome (POMS) or vibriosis. Various strategies such as genetic selection or immune priming have been developed to fight some of these infectious diseases. The microbial education, which consist of exposing the host immune system to beneficial microorganisms during early life stages is a promising approach against diseases. This study explores the concept of microbial education using controlled and pathogen-free bacterial communities and assesses its protective effects against POMS and Vibrio aestuarianus infections, highlighting potential applications in oyster production. ResultsWe demonstrate that it is possible to educate the oyster immune system by adding microorganisms during the larval stage. Adding culture based bacterial mixes to larvae protects only against the POMS disease while adding whole microbial communities from oyster donors protects against both POMS and vibriosis. The efficiency of the immune protection depends both on oyster origin and on the composition of the bacterial mixes used for exposure. No preferential protection was observed when the oysters were stimulated with their sympatric strains. We further show that the added bacteria were not maintained in the oyster microbiota after the exposure, but this bacterial addition induced long term changes in the microbiota composition and oyster immune gene expression. ConclusionOur study reveals successful immune system education of oysters by introducing beneficial micro-organisms during the larval stage. We improved the long-term resistance of oysters against critical diseases (POMS disease and Vibrio aestuarianus infections) highlighting the potential of microbial education in aquaculture.

Atlantic salmon (Salmo salar) when exposed to heat stress have reduced voluntary feeding and exhibit changes in digesta consistency. This study was performed to determine what bacterial species occur and the overall bacterial abundance in the gut microbiome in heat stressed Atlantic salmon. For this Atlantic salmon in seawater tanks at 15{degrees}C were fed for 2 to 4 weeks. Tank temperatures were increased to 19{degrees}C until voluntary feeding abated at which point tank temperatures were cooled to 15{degrees}C for 4 weeks. At the end of each temperature phase the fish were stripped of feces and microbiome profiles were determined using 16S rRNA V1-V3 metabarcoding. The tank experiment was repeated three times in successive years. Vibrionaceae comprised most reads after the warm phase completed. The prominent levels of Vibrionaceae were accompanied by a large predominance of cast (sloughed intestinal mucosa) containing fecal samples. qPCR estimated Vibrionaceae cell populations increased 1.9-3.4 log units/g after the warm phase but and slightly decreased by 0.3-1.1 log units/g after the 15{degrees}C recovery phase. The results indicated heat stress induced inappetence corresponds to increased cast production accompanied by predominance of Vibrionaceae. Vibrionaceae colonizing the Atlantic salmon gut should be the focus of studies on the microbiology of thermally induced inappetence and dysbiosis in Atlantic salmon. Key ContributionThe experiments confirm that thermal stress increased cast production in Atlantic salmon. The increase in cast production coincides with increased predominance of Vibrionaceae. Though the growth of Vibrionaceae in the gut of salmon is not associated with acute disease it may represent a dysbiosis effect. The results suggest extended summers in regions where sea surface temperatures are at the tolerance limits require increased husbandry management of farmed fish. In addition, more studies are needed to determine if novel approaches can limit overgrowth of Vibrionaceae.

Senegalese sole is a promising European aquaculture species whose main challenge is that captive-born males (F1) are unable to reproduce in farms, hindering breeding programs. Chemical communication through the olfactory system is hypothesized to stem this issue. Although significant advancement in genomic resources has been made over the past decade, scarce information exists on the genomic basis of olfaction, a special sensory system for demersal species like flatfish, which could play a prominent role in reproduction, social and environmental interactions. A full-length transcriptome of the olfactory rosettes including females, males, juveniles and adults, of both F1 and wild origins, was generated at the isoform-level by combining Oxford Nanopore long-read and Illumina short-read sequencing technologies. A total of 20,670 transcripts actively expressed were identified: 13,941 were known transcripts, 5,758 were novel transcripts from known genes, and 971 were novel genes encoding novel transcripts. Special attention was paid to the olfactory receptor gene families (OlfC, OR, ORA and TAAR) expression. Our comprehensive olfactory transcriptome of Senegalese sole provides a foundation for delving into the functional basis of this complex organ in teleost and flatfish. Furthermore, it provides a valuable resource for addressing reproductive management challenges in Senegalese sole aquaculture.

This study investigates the molecular responses of Chinese shrimp (Fenneropenaeus chinensis) to low salinity stress, employing RNA-seq and functional enrichment analyses. A total of 12,332 expressed genes were identified, with 227 differentially expressed genes (DEGs) detected, revealing intricate adaptive responses in gill tissues. Functional enrichment analysis highlighted DEGs associated with ion-transport regulation, bio-metabolism and detoxification (based on GO terms). The upregulation of ATP1A1, SLC26A2, and STK39 suggested a pivotal role of ion-transport regulation, emphasizing the importance of maintaining osmotic balance. In terms of bio-metabolism, ENPP6, GLS, and DMGDH exhibited significant upregulation, indicating adjustments in energy metabolism for low-salinity adaptation. Notably, the downregulation of GSTO1 and CTH raised questions about detoxification pathways, potentially reflecting adaptations or compromises in response to low salinity. Further correlation network analysis highlighted key genes like GLS, STK39, SESN1, and SARDH, revealing intricate relationships among DEGs. RT-qPCR validation confirmed the consistency of gene expression patterns with RNA-seq results. In conclusion, this study provides a comprehensive understanding of the molecular mechanisms underlying Chinese shrimp responses to low salinity stress. The identified genes lay the groundwork for targeted interventions and strategies to enhance shrimp aquaculture system resilience amid changing salinity levels.

Enterocytozoon hepatopenaei (EHP) is a shrimp pathogen that causes huge economic losses. In the present study, the hosts of EHP were investigated using polymerase chain reaction (PCR) in an aquaculture farm located in Maoming, China. EHP was detected in Litopenaeus vannamei, Penaeus monodon, crab, false mussel, and three dragonfly species (Anax parthenope, Pantala flavescens, and Ischnura senegalensis). In the histopathological examination using hematoxylin-eosin staining, EHP spores were found in nymphs and adult dragonflies naturally infected with EHP that were collected from the shrimp farm. Fluorescence in situ hybridization results showed a positive signal for EHP infection in the fat body of dragonfly nymphs. Immature and mature microsporidian spores and late sporogonial plasmodium were observed in the cytoplasm of dragonfly nymphs using transmission electron microscopy. The transmission of EHP from shrimp to dragonfly nymphs was confirmed via cohabitation challenge experiments in which EHP-free dragonfly nymphs were cohabited with EHP-infected shrimp, and the transmission of EHP from dragonfly nymphs to shrimp was demonstrated via the cohabitation of EHP-infected dragonfly nymphs with EHP-free shrimp and oral administration challenge experiments. This study confirms that dragonflies can act as natural EHP hosts, and a novel EHP horizontal transmission route exists between dragonflies and shrimp. Author summaryTo the authors knowledge, this study presents the first report of microsporidia (EHP) infecting both crustaceans and insects (A. parthenope, P. flavescens, and I. senegalensis). The horizontal transmission of EHP between dragonfly nymphs and shrimp was confirmed through cohabitation and oral administration challenge experiments. EHP has become a globally significant threat to shrimp aquaculture. The findings of the present study will help to design prevention strategies, such as the use of nets to prevent dragonflies from entering shrimp ponds.