Genetic improvement for disease resistance in oysters: A review

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.

Resilience against the impacts of climate change in an ecologically and economically significant native oyster

Climate change is acidifying and warming our oceans, at an unprecedented rate posing a challenge for marine invertebrates vital across the globe for ecological services and food security. Here we show it is possible for resilience to climate change in an ecologically and economically significant oyster without detrimental effects to the energy budget. We exposed 24 pair-mated genetically distinct families of the Sydney rock oyster, Saccostrea glomerata to ocean acidification and warming for 4w and measured their resilience. Resilience was identified as the capacity to defend their acid-base balance without a loss of energy available for Scope for Growth (SFG). Of the 24 families, 13 were better able to defend their acid-base balance while eight had no loss of energy availability with a positive SFG. This study has found oyster families with reslience against climate change without a loss of SFG, is an essential mitigation strategy, in a critical mollusc.

Exploring PAH kinetics in wild vs. transplanted triploid and diploid oysters at a contaminated field site using immunological techniques

Crassostrea virginica is a well-established bivalve species for biomonitoring persistent organic pollutants such as polycyclic aromatic hydrocarbons (PAH) in aquatic environments. Differing biomonitoring methods employing either wild oysters inhabiting sites of interest or naïve cultured oysters deployed to sites for extended periods can be used for site evaluations. However, important differences in total contaminant concentrations accumulated have been observed between the wild and transplanted groups. Furthermore, although rearing cultured triploid oysters is widely popular in commercial farming, the difference in contaminant bioaccumulation potential between triploid and diploid cultured oysters is vastly understudied, particularly for organic contaminants such as PAH. This study explores differences in PAH kinetics between transplanted triploid and diploid cultured oysters and wild oysters at a PAH-impacted site during a 6-week field exposure study using novel immunological techniques: antibody-based biosensor technology and immunofluorescence visualization. Conventional chemical analysis of oyster tissue was also conducted for comparison. While differences were observed in the oyster interstitial fluid between the wild and transplanted oysters throughout the study, whole tissue analysis revealed differing trends at each time point. Our findings suggest that insufficient equilibration time may contribute to the differences observed between groups. Furthermore, when combined with visual evidence via immunofluorescence, internal partitioning of contaminants may be an important determinant for total concentrations measured. A better understanding of the differences observed between wild and transplanted oyster groups is necessary for improved biomonitoring. Our study highlights the value in employing novel immunological techniques to explore possible mechanisms driving these differences.

Understanding Crassostrea virginica tolerance of Perkinsus marinus through global gene expression analysis

Disease tolerance, a host's ability to limit damage from a given parasite burden, is quantified by the relationship between pathogen load and host survival or reproduction. Dermo disease, caused by the protozoan parasite P. marinus, negatively impacts survival in both wild and cultured eastern oyster (C. virginica) populations. Resistance to P. marinus has been the focus of previous studies, but tolerance also has important consequences for disease management in cultured and wild populations. In this study we measured dermo tolerance and evaluated global expression patterns of two sensitive and two tolerant eastern oyster families experimentally challenged with distinct doses of P. marinus (0, 10⁶, 10⁷, and 10⁸ parasite spores per gram wet weight, n = 3-5 individuals per family per dose). Weighted Gene Correlation Network Analysis (WGCNA) identified several modules correlated with increasing parasite dose/infection intensity, as well as phenotype. Modules positively correlated with dose included transcripts and enriched GO terms related to hemocyte activation and cell cycle activity. Additionally, these modules included G-protein coupled receptor, toll-like receptor, and tumor necrosis factor pathways, which are important for immune effector molecule and apoptosis activation. Increased metabolic activity was also positively correlated with treatment. The module negatively correlated with infection intensity was enriched with GO terms associated with normal cellular activity and growth, indicating a trade-off with increased immune response. The module positively correlated with the tolerant phenotype was enriched for transcripts associated with "programmed cell death" and contained a large number of tripartite motif-containing proteins. Differential expression analysis was also performed on the 10⁸ dosed group using the most sensitive family as the comparison reference. Results were consistent with the network analysis, but signals for "programmed cell death" and serine protease inhibitors were stronger in one tolerant family than the other, suggesting that there are multiple avenues for disease tolerance. These results provide new insight for defining dermo response traits and have important implications for applying selective breeding for disease management.

Comparative analysis of intestinal microbiota composition and transcriptome in diploid and triploid Carassius auratus

Polyploidy and the microbiome are crucial factors in how a host organism responds to disease. However, little is known about how triploidization and microbiome affect the immune response and disease resistance in the fish host. Therefore, this study aims to identify the relationship between intestinal microbiota composition, transcriptome changes, and disease resistance in triploid Carassius auratus (3nCC). In China's central Dongting lake water system, diploid (2nCC) and triploid Carassius auratus were collected, then 16S rRNA and mRNA sequencing were used to examine the microbes and gene expression in the intestines. 16S rRNA sequencing demonstrated that triploidization altered intestinal richness, as well as the diversity of commensal bacteria in 3nCC. In addition, the abundance of the genus Vibrio in 3nCC was increased compared to 2nCC (P < 0.05). Furthermore, differential expression analysis of 3nCC revealed profound up-regulation of 293 transcripts, while 324 were down-regulated. Several differentially expressed transcripts were related to the immune response pathway in 3nCC, including NLRP3, LY9, PNMA1, MR1, PELI1, NOTCH2, NFIL3, and NLRC4. Taken together, triploidization can alter bacteria composition and abundance, which can in turn result in changes in expression of genes. This study offers an opportunity for deciphering the molecular mechanism underlying disease resistance after triploidization.

Host-microbiota interactions play a crucial role in oyster adaptation to rising seawater temperature in summer

Climate change, represented by rising and fluctuating temperature, induces systematic changes in marine organisms and in their bacterial symbionts. However, the role of host-microbiota interactions in the host's response to rising temperature and the underlying mechanisms are incompletely understood in marine organisms. Here, the symbiotic intestinal microbiota and transcriptional responses between diploid and triploid oysters that displayed susceptible and resistant performance under the stress of rising temperature during a summer mortality event were compared to investigate the host-microbiota interactions. The rising and fluctuating temperatures triggered an earlier onset and higher mortality in susceptible oysters (46.7%) than in resistant oysters (17.3%). Correlation analysis between microbial properties and environmental factors showed temperature was strongly correlated with indices of α-diversity and the abundance of top 10 phyla, indicating that temperature significantly shaped the intestinal microbiota of oysters. The microbiota structure of resistant oysters exhibited more rapid changes in composition and diversity compared to susceptible oysters before peak mortality, indicating that resistant oysters possessed a stronger ability to regulate their symbiotic microbiota. Meanwhile, linear discriminant analysis effect size (LefSe) analysis found that the probiotics Verrucomicrobiales and Clostridiales were highly enriched in resistant oysters, and that potential pathogens Betaproteobacteriales and Acidobacteriales were enriched in susceptible oysters. These results implied that the symbiotic microbiota played a significant role in the oysters' adaptation to rising temperature. Accompanying the decrease in unfavorable bacteria before peak mortality, genes related to phagocytosis and lysozymes were upregulated and the xenobiotics elimination pathway was exclusively expressed in resistant oysters, demonstrating the validity of these immunological functions in controlling proliferation of pathogens driven by rising temperature. Compromised immunological functions might lead to proliferation of pathogens in susceptible oysters. This study might uncover a conserved mechanism of adaptation to rising temperature in marine invertebrates from the perspective of interactions between host and symbiotic microbiota.

Insight into selective breeding for robustness based on field survival records: New genetic evaluation of survival traits in pacific white shrimp (Penaeus vannamei) breeding line

Survival can be considered a relatively ‘old’ trait in animal breeding, yet commonly neglected in aquaculture breeding because of the simple binary records and generally low heritability estimates. Developing routine genetic evaluation systems for survival traits however, will be important for breeding robust strains based on valuable field survival data. In the current study, linear multivariate animal model (LMA) was used for the genetic analysis of survival records from 2-year classes (BL2019 and BL2020) of pacific white shrimp (Penaeus vannamei) breeding lines with data collection of 52, 248 individuals from 481 fullsib families. During grow-out test period, 10 days intervals of survival data were considered as separate traits. Two survival definitions, binary survivability (S) and continuous survival in days (SL), were used for the genetic analysis of survival records to investigate; 1) whether adding more survival time information could improve estimation of genetic parameters; 2) the trajectory of survival heritability across time, and 3) patterns of genetic correlations of survival traits across time. Levels of heritability estimates for both S and SL were low (0.005–0.076), 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 (r_g > 0.8). Heritability estimates of body weight (BW) for BL2019 and BL2020 were 0.486 and 0.373, respectively. Trajectories of survival heritability 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 on the trajectory of heritability estimates for survival traits across grow-out stage in aquaculture. Results will be useful for developing robust improved pacific white shrimp culture strains in selective breeding programs based on field survival data.

Life history of oysters influences Vibrio parahaemolyticus accumulation in Pacific oysters (Crassostrea gigas)

Vibrio parahaemolyticus infection in humans is associated with raw oyster consumption. Evaluation of V. parahaemolyticus presence in oysters is of most interest because of the economic and public health issues that it represents. To explore V. parahaemolyticus accumulation and depuration in adult Crassostrea gigas, we developed a GFP-tagged V. parahaemolyticus strain (IFVp201-gfp⁺ ), as well as a rapid and efficient quantification method in C. gigas oysters haemolymph by flow cytometry. Impact of the life history of C. gigas on accumulation and depuration of V. parahaemolyticus IFVp201 was subsequently investigated. We found that naive oysters, i.e. grown in controlled facilities with UV treated seawater, accumulated significantly more IFVp201 than environmental oysters, i.e. grown in intertidal environment. We hypothesized that environmental oysters could have been immune primed, thus could limit V. parahaemolyticus accumulation. Meanwhile, both naive and environmental oysters had similar depuration rates.

A Deterministic Model for Understanding Nonlinear Viral Dynamics in Oysters

Contamination of oysters with a variety of viruses is one key pathway to trigger outbreaks of massive oyster mortality as well as human illnesses, including gastroenteritis and hepatitis. Much effort has gone into examining the fate of viruses in contaminated oysters, yet the current state of knowledge of nonlinear virus-oyster interactions is not comprehensive because most studies have focused on a limited number of processes under a narrow range of experimental conditions. A framework is needed for describing the complex nonlinear virus-oyster interactions. Here, we introduce a mathematical model that includes key processes for viral dynamics in oysters, such as oyster filtration, viral replication, the antiviral immune response, apoptosis, autophagy, and selective accumulation. We evaluate the model performance for two groups of viruses, those that replicate in oysters (e.g., ostreid herpesvirus) and those that do not (e.g., norovirus), and show that this model simulates well the viral dynamics in oysters for both groups. The model analytically explains experimental findings and predicts how changes in different physiological processes and environmental conditions nonlinearly affect in-host viral dynamics, for example, that oysters at higher temperatures may be more resistant to infection by ostreid herpesvirus. It also provides new insight into food treatment for controlling outbreaks, for example, that depuration for reducing norovirus levels is more effective in environments where oyster filtration rates are higher. This study provides the foundation of a modeling framework to guide future experiments and numerical modeling for better prediction and management of outbreaks.

IMPORTANCE The fate of viruses in contaminated oysters has received a significant amount of attention in the fields of oyster aquaculture, food quality control, and public health. However, intensive studies through laboratory experiments and in situ observations are often conducted under a narrow range of experimental conditions and for a specific purpose in their respective fields. Given the complex interactions of various processes and nonlinear viral responses to changes in physiological and environmental conditions, a theoretical framework fully describing the viral dynamics in oysters is warranted to guide future studies from a top-down design. Here, we developed a process-based, in-host modeling framework that builds a bridge for better communications between different disciplines studying virus-oyster interactions.

Little evidence for genetic variation associated with susceptibility to sea star wasting syndrome in the keystone species Pisaster ochraceus

The keystone species Pisaster ochraceus suffered mass mortalities along the northeast Pacific Ocean from Sea Star Wasting Syndrome (SSWS) outbreaks in 2013-2016. SSWS causation remains of debate, leading to concerns as to whether outbreaks will continue to impact this species. Considering the apparent link between ocean temperature and SSWS, the future of this species and intertidal communities remains uncertain. Surveys of co-occurring apparently normal and wasting P. ochraceus along the central Oregon coast in 2016 allowed us to address whether variation in disease status showed genetic variation that may be associated with differences in susceptibility to SSWS. We performed restriction site-associated DNA sequencing (2bRAD-seq) to genotype ~72,000 single nucleotide polymorphism (SNP) loci across apparently normal and wasting sea stars. Locus-specific analyses of differentiation (F_ST ) between disease-status groups revealed no signal of genetic differences separating the two groups. Using a multivariate approach, we observed weak separation between the groups, but identified 18 SNP loci showing highest discriminatory power between the groups and scanned the genome annotation for linked genes. A total of 34 protein-coding genes were found to be located within 15 kb (measured by linkage disequilibrium decay) of at least one of the 18 SNPs, and 30 of these genes had homologies to annotated protein databases. Our results suggest that the likelihood of developing SSWS symptoms does not have a strong genetic basis. The few genomic regions highlighted had only modest levels of differentiation, but the genes associated with these regions may form the basis for functional studies aiming to understand disease progression.

Integrated Proteomic and Transcriptomic Analysis of Gonads Reveal Disruption of Germ Cell Proliferation and Division, and Energy Storage in Glycogen in Sterile Triploid Pacific Oysters (Crassostrea gigas)

Triploid oysters have poor gonadal development, which can not only bring higher economic benefits but also have a potential application in the genetic containment of aquaculture. However, the key factors that influence germ cell development in triploid oysters remain unclear. In this study, data-independent acquisition coupled to transcriptomics was applied to identify genes/proteins related to sterility in triploid Crassostrea gigas. Eighty-four genes were differentially expressed at both the protein and mRNA levels between fertile and sterile females. For male oysters, 207 genes were differentially expressed in the transcriptomic and proteomic analysis. A large proportion of downregulated genes were related to cell division, which may hinder germ cell proliferation and cause apoptosis. In sterile triploid females, a primary cause of sterility may be downregulation in the expression levels of certain mitotic cell cycle-related genes. In sterile triploid males, downregulation of genes related to cell cycle and sperm motility indicated that the disruption of mitosis or meiosis and flagella defects may be linked with the blocking of spermatogenesis. Additionally, the genes upregulated in sterile oysters were mainly associated with the biosynthesis of glycogen and fat, suggesting that sterility in triploids stimulates the synthesis of glycogen and energy conservation in gonad tissue.

Aquatic pathogens and biofouling: pilot study of ostreid herpesvirus 1 translocation by bivalves

Ostreid herpesvirus 1 (OsHV-1) has caused mass mortalities in Pacific oysters (Crassostrea gigas) in Europe, Australia, and New Zealand. While aquaculture-associated movements of infected Pacific oysters are a well-known cause of OsHV-1 spread once established in a region, translocation via biofouling of aquaculture equipment or vessels needs further investigation to explain the more distant spread of OsHV-1. Laboratory experiments were designed to test for transmission of OsHV-1 between infected and naïve Pacific oysters via a simulated biofouling translocation scenario. Three common biofouling species [Sydney rock oysters (Saccostrea glomerata), Mediterranean mussels (Mytilus galloprovincialis) and Pacific oysters] were tested as intermediaries using a cohabitation challenge with Pacific oysters infected by injection. Transmission occurred, albeit for one of eight replicates when Pacific oysters were the intermediary species. This demonstrated a possible pathway for pathogen spread via biofouling containing Pacific oysters while highlighting the complexity of OsHV-1 transmission. Such complexities require further investigation to inform future risk assessments and management of fouled aquaculture equipment and vessels.

Physiological Variation in Response to Vibrio and Hypoxia by Aquacultured Eastern Oysters in the Southeastern United States

Eastern oysters (Crassostrea virginica) have long been recognized as model organisms of extreme environmental tolerance, showing resilience to variation in temperature, salinity, hypoxia and microbial pathogens. These phenotypic responses, however, show variability between geographic locations or habitats (e.g., tidal). Physiological, morphological and genetic differences occur in populations throughout a species' geographical range, which may have been shaped by regional abiotic and biotic variations. Few studies of C. virginica have explored the combined factors of physiological mechanisms of divergent phenotypes between locations and the genetic relationships of individuals between these locations. To characterize genetic relationships of four locations with aquacultured oysters along the North Carolina and Virginia coast, we sequenced a portion of cytochrome oxidase subunit I (COI) that revealed significant variation in haplotype distribution between locations. We then measured mitochondrial physiology and expression of the innate immunity response of hemocytes to lab acclimation and combined stress conditions to compare basal expression and stress response in oysters between these locations. For stress sensing genes, toll-like receptors had the strongest location-specific response to hypoxia and Vibrio, whereas mannose receptor and a stress-receptor were specific to hypoxia and bacteria, respectively. The expression of stress response genes also showed location-specific and stressor-specific changes in expression, particularly for big defensin and the complement gene Cq3. Our results further suggested that genetic similarity of oysters from different locations was not clearly related to physiological and molecular responses. These results are informative for understanding the range of physiological plasticity for stress responses in this commercially important oyster species. They also have implications in the oyster farming industry as well as conservation efforts to restore endangered native oyster beds.

Contemporary Oyster Reef Restoration: Responding to a Changing World

Globally, there is growing interest in restoring previously widespread oyster reefs to reinstate key ecosystem services such as shoreline protection, fisheries productivity and water filtration. Yet, since peak expiration of oysters in the 1800s, significant and ongoing environmental change has occurred. Estuaries and coasts are undergoing some of the highest rates of urbanization, warming and ocean acidification on the planet, necessitating novel approaches to restoration. Here, we review key design considerations for oyster reef restoration projects that maximize the probability that they will meet biological and socio-economic goals not only under present-day conditions, but into the future. This includes selection of sites, and where required, substrates and oyster species and genotypes for seeding, not only on the basis of their present and future suitability in supporting oyster survival, growth and reproduction, but also based on their match to specific goals of ecosystem service delivery. Based on this review, we provide a road map of design considerations to maximize the success of future restoration projects.

Potential of genomic technologies to improve disease resistance in molluscan aquaculture

Molluscan aquaculture is a major contributor to global seafood production, but is hampered by infectious disease outbreaks that can cause serious economic losses. Selective breeding has been widely used to improve disease resistance in major agricultural and aquaculture species, and has clear potential in molluscs, albeit its commercial application remains at a formative stage. Advances in genomic technologies, especially the development of cost-efficient genomic selection, have the potential to accelerate genetic improvement. However, tailored approaches are required owing to the distinctive reproductive and life cycle characteristics of molluscan species. Transgenesis and genome editing, in particular CRISPR/Cas systems, have been successfully trialled in molluscs and may further understanding and improvement of genetic resistance to disease through targeted changes to the host genome. Whole-organism genome editing is achievable on a much greater scale compared to other farmed species, making genome-wide CRISPR screening approaches plausible. This review discusses the current state and future potential of selective breeding, genomic tools and genome editing approaches to understand and improve host resistance to infectious disease in molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Transcriptomic responses of saline-adapted Nile tilapia (Oreochromis niloticus) to rearing in both saline and freshwater

The Nile tilapia, Oreochromis niloticus, is an important species for global aquaculture. Recently, a single genetic line of Nile tilapia was developed using estimated breeding values (EBVs) for body weight under moderately saline water that showed significant improvement in growth performance. To explore the molecular mechanisms underlying this enhanced growth capacity, RNA-Seq was used to profile differences in gene expression in the liver and pituitary gland of high- and low-growth performance families of male Nile tilapia progeny, reared in either saline or freshwater environments. Comparisons of tissues from high- and low-EBV families, and also between fish reared in either saline or freshwater, revealed 142 and 2208 differentially expressed genes (DEGs), respectively. DEGs identified between the EBV groups comprised a number of genes involved in the regulation of growth and reproduction. We found an overexpression of hormone genes involved in growth-inhibition in the pituitary of Low-EBV tilapia including 2 somatostatin genes (GHIH), corticoliberin (CRH) and tachykinin-3-like protein. Furthermore, several genes associated with the cAMP pathway were underexpressed in low-EBV tilapia pituitary together with several early response genes. This study provides insight into the transcriptomic factors associated with growth performance in saline-adapted Nile tilapia reared in environments with high and low salinity levels and provides valuable knowledge for the future development of selection strategies to improve growth performance in this species.

Susceptibility variation to the main pathogens of Crassostrea gigas at the larval, spat and juvenile stages using unselected and selected oysters to OsHV-1 and/or V. aestuarianus

French commercial hatcheries are massively producing Crassostrea gigas selected for their higher resistance to OsHV-1, and soon should also implement selection for increasing resistance to Vibrio aestuarianus. The first objective of this study was to optimize the breeding programs for dual resistance to OsHV-1 and V. aestuarianus to determine the earliest life stage for which oysters are able to develop disease resistance. Wild stocks and selected families were tested using experimental infections by both pathogens at the larval, spat and juvenile stages. Oyster families could be evaluated for OsHV-1 as soon as the larval stage by a bath method, but this only highlighted the most resistant families; those that showed the highest resistance to V. aestuarianus could be determined using the cohabitation method at the juvenile stage. The second objective of this study was to determine if selection to increase/decrease the resistance to OsHV-1 and V. aestuarianus could have an impact on other major pathogens currently detected in hatchery at the larval stage, and in nursery and field at the spat/juveniles stages (V. coralliilyticus, V. crassostreae, V. tasmaniensis, V. neptunius, V. europaeus, V. harveyi, V. chagasi). No relationship was found between mortality caused by V. aestuarianus/OsHV-1 and the mortality caused by the other virulent bacterial strains tested regardless the stages, except between OsHV-1 and V. tasmaniensis at the juvenile stage. Finally, miscellaneous findings were evidenced such as (1) bath for bacterial challenges was not adapted for spat, (2) the main pathogens at the larval stage were OsHV-1 and V. coralliilyticus using bath, while it was V. coralliilyticus, V. europaeus, and V. neptunius at the juvenile stage by injection, and (4) variation in mortality was observed among families/wild controls for all pathogens at larval and juvenile stages, except for V. harveyi for larvae.

Differential Mortality and High Viral Load in Naive Pacific Oyster Families Exposed to OsHV-1 Suggests Tolerance Rather than Resistance to Infection

Pacific oysters, Crassostrea gigas, are one of the most productive aquaculture species in the world. However, they are threatened by the spread of Ostreid herpesvirus-1 (OsHV-1) and its microvariants (collectively "µvars"), which cause mass mortalities in all life stages of Pacific oysters globally. Breeding programs have been successful in reducing mortality due to OsHV-1 variants following viral outbreaks; however, an OsHV-1-resistant oyster line does not yet exist in the United States (US), and it is unknown how OsHV-1 µvars will affect US oyster populations compared to the current variant, which is similar to the OsHV-1 reference, found in Tomales Bay, CA. The goals of this study were to investigate the resistance of C. gigas juveniles produced by the Molluscan Broodstock Program (MBP) to three variants of OsHV-1: a California reference OsHV-1, an Australian µvar, and a French µvar. This is the first study to directly compare OsHV-1 µvars to a non-µvar. The survival probability of oysters exposed to the French (FRA) or Australian (AUS) µvar was significantly lower (43% and 71%, respectively) than to the reference variant and controls (96%). No oyster family demonstrated resistance to all three OsHV-1 variants, and many surviving oysters contained high copy numbers of viral DNA (mean ~3.53 × 108). These results indicate that the introduction of OsHV-1 µvars could have substantial effects on US Pacific oyster aquaculture if truly resistant lines are not achieved, and highlight the need to consider resistance to infection in addition to survival as traits in breeding programs to reduce the risk of the spread of OsHV-1 variants.

Unraveling concordant and varying responses of oyster species to Ostreid Herpesvirus 1 variants

The Ostreid herpesvirus 1 (OsHV-1) and variants, particularly the microvariants (μVars), are virulent and economically devastating viruses impacting oysters. Since 2008 OsHV-1 μVars have emerged rapidly having particularly damaging effects on aquaculture industries in Europe, Australia and New Zealand. We conducted field trials in Tomales Bay (TB), California where a non-μVar strain of OsHV-1 is established and demonstrated differential mortality of naturally exposed seed of three stocks of Pacific oyster, Crassostrea gigas, and one stock of Kumamoto oyster, C. sikamea. Oysters exposed in the field experienced differential mortality that ranged from 64 to 99% in Pacific oysters (Tasmania>Midori = Willapa stocks), which was much higher than that of Kumamoto oysters (25%). Injection trials were done using French (FRA) and Australian (AUS) μVars with the same oyster stocks as planted in the field and, in addition, two stocks of the Eastern oyster, C. virginica. No mortality was observed in control oysters. One C. virginica stock suffered ~10% mortality when challenged with both μVars tested. Two Pacific oyster stocks suffered 75 to 90% mortality, while one C. gigas stock had relatively low mortality when challenged with the AUS μVar (~22%) and higher mortality when challenged with the French μVar (~72%). Conversely, C. sikamea suffered lower mortality when challenged with the French μVar (~22%) and higher mortality with the AUS μVar (~44%). All dead oysters had higher viral loads (~1000×) as measured by quantitative PCR relative to those that survived. However, some survivors had high levels of virus, including those from species with lower mortality. Field mortality in TB correlated with laboratory mortality of the FRA μVar (69% correlation) but not with that of the AUS μVar, which also lacked correlation with the FRA μVar. The variation in response to OsHV-1 variant challenges by oyster species and stocks demonstrates the need for empirical assessment of multiple OsHV-1 variants.

Haplosporidian host:parasite interactions

The host:parasite interactions of the 3 serious haplosporidian pathogens of oysters, on which most information exists, are reviewed. They are Bonamia ostreae in Ostrea spp. and Crassostrea gigas; Bonamia exitiosa in Ostrea spp.; and Haplosporidium nelsoni in Crassostrea spp. Understanding the haemocytic response to pathogens is constrained by lack of information on haematopoiesis, haemocyte identity and development. Basal haplospridians in spot prawns are probably facultative parasites. H. nelsoni and a species infecting Haliotis iris in New Zealand (NZAP), which have large extracellular plasmodia that eject haplosporosomes or their contents, lyse surrounding cells and are essentially extracellular parasites. Bonamia spp. have small plasmodia that are phagocytosed, haplosporosomes are not ejected and they are intracellular obligate parasites. Phagocytosis by haemocytes is followed by formation of a parasitophorous vacuole, blocking of haemocyte lysosomal enzymes and the endolysosomal pathway. Reactive oxygen species (ROS) are blocked by antioxidants, and host cell apoptosis may occur. Unlike susceptible O. edulis, the destruction of B. ostreae by C. gigas may be due to higher haemolymph proteins, higher rates of granulocyte binding and phagocytosis, production of ROS, the presence of plasma β-glucosidase, antimicrobial peptides and higher levels of haemolymph and haemocyte enzymes. In B.exitiosa infection of Ostrea chilensis, cytoplasmic lipid bodies (LBs) containing lysosomal enzymes accumulate in host granulocytes and in B. exitiosa following phagocytosis. Their genesis and role in innate immunity and inflammation appears to be the same as in vertebrate granulocytes and macrophages, and other invertebrates. If so, they are probably the site of eicosanoid synthesis from arachidonic acid, and elevated numbers of LBs are probably indicative of haemocyte activation. It is probable that the molecular interaction, and role of LBs in the synthesis and storage of eicosanoids from arachidonic acid, is conserved in innate immunity in vertebrates and invertebrates. However, it seems likely that haplosporidians are more diverse than realized, and that there are many variations in host parasite interactions and life cycles.

First comparison of French and Australian OsHV-1 µvars by bath exposure

Economically devastating mortality events of farmed and wild shellfish due to infectious disease have been reported globally. Currently, one of the most significant disease threats to Pacific oyster Crassostrea gigas culture is the ostreid herpesvirus 1 (OsHV-1), in particular the emerging OsHV-1 microvariant genotypes. OsHV-1 microvariants (OsHV-1 µvars) are spreading globally, and concern is high among growers in areas unaffected by OsHV-1. No study to date has compared the relative virulence among variants. We provide the first challenge study comparing survival of naïve juvenile Pacific oysters exposed to OsHV-1 µvars from Australia (AUS µvar) and France (FRA µvar). Oysters challenged with OsHV-1 µvars had low survival (2.5% exposed to AUS µvar and 10% to FRA µvar), and high viral copy number as compared to control oysters (100% survival and no virus detected). As our study was conducted in a quarantine facility located ~320 km from the ocean, we also compared the virulence of OsHV-1 µvars using artificial seawater made from either facility tap water (3782 µmol kg-1 seawater total alkalinity) or purchased distilled water (2003 µmol kg-1). Although no differences in survival or viral copy number were detected in oysters exposed to seawater made using tap or distilled water, more OsHV-1 was detected in tanks containing the lower-alkalinity seawater, indicating that water quality may be important for virus transmission, as it may influence the duration of viral viability outside of the host.

Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

In genomic selection (GS), genome-wide SNP markers are used to generate genomic estimated breeding values 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). In the current study, we evaluated the potential of genomic selection for host resistance to OsHV-1 in Pacific oysters, and compared it with pedigree-based approaches. An OsHV-1 disease challenge was performed using an immersion-based virus exposure treatment for oysters for 7 days. A total of 768 samples were genotyped using the medium-density SNP array for oysters. A 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 ± SE) 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 approximately 500 SNPs. This demonstrates the potential for GS in Pacific oyster breeding programmes, and importantly, demonstrates that a low number of SNPs might suffice to obtain accurate genomic estimated breeding values, thus potentially making the implementation of GS more cost effective.

Genetic diversity and phenotypic variation within hatchery-produced oyster cohorts predict size and success in the field

The rapid growth of the aquaculture industry to meet global seafood demand offers both risks and opportunities for resource management and conservation. In particular, hatcheries hold promise for stock enhancement and restoration, yet cultivation practices may lead to enhanced variation between populations at the expense of variation within populations, with uncertain implications for performance and resilience. To date, few studies have assessed how production techniques impact genetic diversity and population structure, as well as resultant trait variation in and performance of cultivated offspring. We collaborated with a commercial hatchery to produce multiple cohorts of the eastern oyster (Crassostrea virginica) from field-collected broodstock using standard practices. We recorded key characteristics of the broodstock (male : female ratio, effective population size), quantified the genetic diversity of the resulting cohorts, and tested their trait variation and performance across multiple field sites and experimental conditions. Oyster cohorts produced under the same conditions in a single hatchery varied almost twofold in genetic diversity. In addition, cohort genetic diversity was a significant positive predictor of oyster performance traits, including initial size and survival in the field. Oyster cohorts produced in the hatchery had lower within-cohort genetic variation and higher among-cohort genetic structure than adults surveyed from the same source sites. These findings are consistent with "sweepstakes reproduction" in oysters, even when manually spawned. A readily measured characteristic of broodstock, the ratio of males to females, was positively correlated with within-cohort genetic diversity of the resulting offspring. Thus, this metric may offer a tractable way both to meet short-term production goals for seafood demand and to ensure the capacity of hatchery-produced stock to achieve conservation objectives, such as the recovery of self-sustaining wild populations.

A scaling down mapping of Pinna nobilis (Linnaeus, 1758) through the combination of scientific literature, NATURA 2000, grey literature and citizen science data

This research investigates the occurrence of Pinnanobilis (Linnaeus, 1758) in the Mediterranean Sea, where it is an endemic and the largest bivalve species. Such a species is protected under the European Council Directive 92/43/EEC since 1992, being exposed to anthropogenic impacts. The distribution of this species has been known, in the past, only from reports in scientific literature. Presently, the concerns, threats and risks for P.nobilis are increasing and a more detailed mapping of the actual distribution from a largest to a local spatial scale is essential for the implementation of monitoring, management and conservation actions. Here we provide a systematic review on the occurrence of P.nobilis, employing and combining different sources of information, such as scientific and grey literature, NATURA 2000 geodata and citizen science records. The methodological approach is a pilot test based on a scaling down of the geographical area of study, from the whole of the Mediterranean Sea to the Italian and Apulian coastline (South-East Italy); accordingly, the above mentioned sources of data have been gradually included. The results show that the combination of multiple sources of information provide a more exact determination of the species distribution at a local scale, identifying sites where in-depth actions are required to ensure the species conservation and restoration. Also, the IUCN has recently underlined that the conservation of P.nobilis has become a difficult challenge, so that each of the spatial scales for the investigation is crucial to enable a better preservation and conservation of the species in the Mediterranean Sea.

The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves

Oysters are keystone species in estuarine ecosystems and are of substantial economic value to fisheries and aquaculture worldwide. Contending with disease and environmental stress are considerable challenges to oyster culture. Here we report a draft genome of the Sydney Rock Oyster, Saccostrea glomerata, an iconic and commercially important species of edible oyster in Australia known for its enhanced resilience to harsh environmental conditions. This is the second reference genome to be reported from the family Ostreidae enabling a genus-level study of lophotrochozoan genome evolution. Our analysis of the 784-megabase S. glomerata genome shows extensive expansions of gene families associated with immunological non-self-recognition. Transcriptomic analysis revealed highly tissue-specific patterns of expression among these genes, suggesting a complex assortment of immune receptors provide this oyster with a unique capacity to recognize invading microbes. Several gene families involved in stress response are notably expanded in Saccostrea compared with other oysters, and likely key to this species’ adaptations for improved survival higher in the intertidal zone. The Sydney Rock Oyster genome provides a valuable resource for future research in molluscan biology, evolution and environmental resilience. Its close relatedness to Crassostrea will further comparative studies, advancing the means for improved oyster agriculture and conservation.

Testing plasma subtilisin inhibitory activity as a selective marker for dermo resistance in eastern oysters

Recent findings have suggested that eastern oyster plasma possesses inhibitors of the protease subtilisin, which play a role in the host defense against Perkinsus marinus, a protist parasite causing dermo. A study was conducted to determine whether plasma subtilisin inhibitory activity (PSIA) could be used as a selective marker in breeding programs for dermo resistance. Eastern oysters Crassostrea virginica from 2 wild Louisiana populations shown to differ in dermo resistance were collected and their PSIA was measured. Three groups of oysters were established to spawn from each population. One group was composed of randomly sampled oysters (i.e. unselected) and the other 2 groups were composed of oysters with the highest or lowest PSIA. After spawning, progenies were deployed in October 2014 in a dermo endemic area and sampled quarterly for 2 yr to measure their mortality, growth, P. marinus infection intensity, condition index, PSIA, and the gene expression of 3 subtilisin inhibitors (cvSI-1, cvSI-2, and cvSI-3). Oyster cumulative mortalities of the progenies of all groups increased both years from April to October, concomitant with increasing P. marinus infection intensities. Mortalities and P. marinus infection intensities differed markedly between the 2 populations, but differences between the unselected and selected groups of each population were limited. Measurements of PSIA and cvSI-1, cvSI-2, and cvSI-3 gene expressions between the progenies of all groups showed few differences. CvSI-1 gene expression in surviving oysters of the most susceptible population was increased at the end of the study, adding additional support to the potential role of cvSI-1 defense against P. marinus.

Transgenerational plasticity and antiviral immunity in the Pacific oyster (Crassostrea gigas) against Ostreid herpesvirus 1 (OsHV-1)

The oyster's immune system is capable of adapting upon exposure to a pathogen-associated molecular pattern (PAMP) to have an enhanced secondary response against the same type of pathogen. This has been demonstrated using poly(I:C) to elicit an antiviral response in the Pacific oyster (Crassostrea gigas) against Ostreid herpesvirus (OsHV-1). Improved survival following exposure to poly(I:C) has been found in later life stages (within-generational immune priming) and in the next generation (transgenerational immune priming). The mechanism that the oyster uses to transfer immunity to the next generation is unknown. Here we show that oyster larvae have higher survival to OsHV-1 when their mothers, but not their fathers, are exposed to poly(I:C) prior to spawning. RNA-seq provided no evidence to suggest that parental exposure to poly(I:C) reconfigures antiviral gene expression in unchallenged larvae. We conclude that the improved survival of larvae might occur via maternal provisioning of antiviral compounds in the eggs.

Biogeography of resistance to paralytic shellfish toxins in softshell clam, Mya arenaria (L.), populations along the Atlantic coast of North America

Blooms of Alexandrium spp., the causative agent of paralytic shellfish poisoning (PSP), recur with varying frequency and intensity on the Northwest Atlantic coast of North America, from New York, USA, to northern Canadian waters. Along this latitudinal range blooms co-occur with abundant, intertidal populations of softshell clams, Mya arenaria. Prior work identified a naturally-occurring genetic mutation in Domain II α-subunit of the clams' voltage-gated sodium channels (Na_V), which significantly reduces the binding affinity of the paralytic shellfish toxin, saxitoxin (STX). This mutation provides clams with resistance to the deleterious effects of STX, allowing them to continue feeding during Alexandrium spp. blooms and attain very high tissue toxicities. This study used genetic sequencing of the Na_V mutation locus in clams from four coastal regions of the Bay of Fundy-Gulf of Maine and the mid-Atlantic to determine the percentage of clams in each region that possess the resistant Na_V mutation. The genotype composition was related to the occurrence and magnitude of PSP outbreaks based on shellfish toxicity, primarily that of mussels, Mytilus edulis, used as a proxy for the prevalence and severity of Alexandrium blooms in each region. As hypothesized, the proportion of clams bearing the resistant mutation generally matched up well with the historical incidence and intensity of Alexandrium spp. blooms. The highest percentage of homozygote resistant clams (RR = 70.0%), and the lowest percentage of sensitive clams (SS = 4.5%) were found in eastern Gulf of Maine populations. Exceptions at a few sites where anomalously high numbers of M. arenaria with the resistant mutation were found despite the absence of blooms, may be attributable to larval gene flow. There was no evidence that Alexandrium blooms occurring in Northport Harbor, Long Island, have resulted in a shift in genotypic composition of the local clam population, presumably due to their low cell toxicity. Seasonal mismatch of highly vulnerable M. arenaria postset with toxic blooms at this latitude may also partly explain this result. This study provides strong supporting evidence that Alexandrium blooms can select for resistance to PSP-toxins in M. arenaria populations and proposes a mechanism for the persistence of the sensitive allele throughout the region. Implications for clam aquaculture (seeding) efforts, as well as for shellfish toxicity monitoring are discussed.

Effect of antiprotozoal molecules on hypnospores of Perkinsus spp. parasite

Perkinsus protozoan parasites have been associated with high mortality of bivalves worldwide, including Brazil. The use of antiproliferative drugs to treat the Perkinsosis is an unusual prophylactic strategy. However, because of their environment impact it could be used to control parasite proliferation in closed system, such as hatchery. This study evaluated the anti-Perkinsus activity potential of synthesized and commercial compounds. Viability of hypnospores of Perkinsus spp. was assessed in vitro. Cells were incubated with three 2-amino-thiophene (6AMD, 6CN, 5CN) and one acylhydrazone derivatives (AMZ-DCL), at the concentrations of 31.25; 62.5; 125; 250 and 500 μM and one commercial chlorinated phenoxy phenol derivative, triclosan (2, 5, 10 and 20 μM), for 24-48 h. Two synthetic molecules (6CN and AMZ-DCL) caused a significant decline (38 and 39%, respectively) in hypnospores viability, at the highest concentration (500 μM), after 48 h. Triclosan was the most cytotoxic compound, causing 100% of mortality at 20 μM after 24 h and at 10 μM after 48 h. Cytotoxic effects of the compounds 6CN, AMZ-DCL, and triclosan were investigated by measuring parasite's zoosporulation, morphological changes and metabolic activities (esterase activity, production of reactive oxygen species and lipid content). Results showed that zoosporulation occurred in few cell. Triclosan caused changes in the morphology of hypnospores. The 6CN and AMZ-DCL did not alter the metabolic activities studied whilst Triclosan significantly increased the production of reactive oxygen species and changed the amount and distribution of lipids in the hypnospores. These results suggest that three compounds had potential to be used as antiprotozoal drugs, although further investigation of their mechanism of action must be enlightened.

High turnover of faecal microbiome from algal feedstock experimental manipulations in the Pacific oyster (Crassostrea gigas)

The composition of digestive microbiomes is known to be a significant factor in the health of a variety of hosts, including animal livestock. Therefore, it is important to ascertain how readily the microbiome can be significantly altered. To this end, the role of changing diet on the digestive microbiome of the Pacific oyster (Crassostrea gigas) was assessed via weekly faecal sampling. Over the course of 12 weeks, isolated individual oysters were fed either a control diet of Tetraselmis algae (Tet) or a treatment diet which shifted in composition every 4 weeks. Weekly faecal samples from all oysters were taken to characterize their digestive bacterial microbiota. Concurrent weekly sampling of the algal feed cultures was performed to assess the effect of algal microbiomes, independent of the algal type, on the microbiomes observed in the oyster samples. Changing the algal feed was found to be significantly associated with changes in the faecal microbiome over a timescale of weeks between control and treatment groups. No significant differences between individual microbiomes were found within control and treatment groups. This suggests the digestive microbiome of the Pacific oyster can be quickly and reproducibly manipulated.

Antiviral Defense and Innate Immune Memory in the Oyster

The Pacific oyster, Crassostrea gigas, is becoming a valuable model for investigating antiviral defense in the Lophotrochozoa superphylum. In the past five years, improvements to laboratory-based experimental infection protocols using Ostreid herpesvirus I (OsHV-1) from naturally infected C. gigas combined with next-generation sequencing techniques has revealed that oysters have a complex antiviral response involving the activation of all major innate immune pathways. Experimental evidence indicates C. gigas utilizes an interferon-like response to limit OsHV-1 replication and spread. Oysters injected with a viral mimic (polyI:C) develop resistance to OsHV-1. Improved survival following polyI:C injection was found later in life (within-generational immune priming) and in the next generation (multi-generational immune priming). These studies indicate that the oyster's antiviral defense system exhibits a form of innate immune-memory. An important priority is to identify the molecular mechanisms responsible for this phenomenon. This knowledge will motivate the development of practical and cost-effective treatments for improving oyster health in aquaculture.

First insight into the heritable variation of the resistance to infection with the bacteria causing the withering syndrome disease in Haliotis rufescens abalone

Withering syndrome disease has experienced worldwide spread in the last decade. This fatal disease for abalone is produced by a rickettsia-like organism (WS-RLO), the bacterium "Candidatus Xenohaliotis californiensis". To evaluate the potential of the red abalone (Haliotis rufescens) to improve its resistance to infection by WS-RLO, the additive genetic component in the variation of this trait was estimated. For this, the variation in infection intensity with WS-RLOs and WS-RLOv (phage-infected RLOs) was analyzed in 56 families of full-sibs maintained for three years in a host-parasite cohabitation aquaculture system. A WS-RLO prevalence of 65% was observed in the analysed population; and from the total WS-RLO inclusions 60% were hyperparasited with the phage (WS-RLOv). The decrease in the food ingestion rate was the sole negative effect associated with increasing WS-RLO intensity of infection, suggesting that the high level of WS-RLOv load may have diminished the symptoms of WS disease in the analyzed abalones. The estimated heritabilities were moderate to mid, but significant, varying from 0.21 to 0.23 and 0.36 for WS-RLO and WS-RLOv infections, respectively. This suggests that variation in resistance to infection with WS-RLO may respond to selection in the evaluated red abalone population. Estimated response to selection (G) for the level of infection by WS-RLO indicated that if the 10% of red abalone with the lowest infection level is selected as broodstock, a 90% reduction in the intensity of infection in the progeny can be expected, even with the lowest estimation of heritability (h²=0.21). This strong response would be also due to the large phenotypic variance of this trait. Strong positive correlations, both phenotypic and genotypic, were observed between infection intensities with WS-RLO and WS-RLOv, indicating that selection to increase resistance to one of the types of RLOs will affect resistance in the other in the same direction. This is the first study that demonstrates the existence of additive genetic variation for resistance to WS-RLO in abalone. Consequently, it is possible to increase the resistance to WS-RLO in H. rufescens by selective breeding, which can be an economically attractive and environmentally friendly manner to reduce mortalities and growth effects caused by WS in abalone farms.

Several strains, one disease: experimental investigation of Vibrio aestuarianus infection parameters in the Pacific oyster, Crassostrea gigas

This study investigated oyster infection dynamics by different strains of Vibrio aestuarianus isolated before and after the apparent re-emergence of this pathogen observed in France in 2011. We conducted experiments to compare minimal infective dose, lethal dose 50 and bacterial shedding for six V. aestuarianus strains. Whatever the strain used, mortality was induced in juvenile oysters by intramuscular injection and reached 90–100% of mortality within 5 days. Moreover, bacterial shedding was comparable among strains and reached its maximum after 20 h (≈10 EXP5 bacteria/mL/animal). Similarly, our first estimations of lethal dose 50 were comparable among strains (minimal infective dose around 0.4 × 10EXP5 bacteria/mL and LD50 around 10EXP5 bacteria/mL) by using seawater containing freshly shed bacteria. These results indicate that, at least with these criteria, despite V. aestuarianus strains genetic diversity, the disease process is similar. The strains isolated after the apparent re-emergence of the bacteria in 2011, do not present a more acute virulence phenotype than the reference strains isolated between 2002 and 2007. Finally, our study provides original and noteworthy data indicating that infected oysters shed bacteria at a level above the threshold of LD50 a few days before they die, meaning that infection is expected to spread in a susceptible population.

A Production Calendar Based on Water Temperature, Spat Size, and Husbandry Practices Reduce OsHV-1 μvar Impact on Cultured Pacific Oyster Crassostrea gigas in the Ebro Delta (Catalonia), Mediterranean Coast of Spain

Since 2006, the production of Pacific oyster Crassostrea gigas in the Ebro Delta area has dramatically declined from around 800 metric tons (MT) per year to 138 MT in 2011. This decline in production has had a significant socio-economic impact in a region where the shellfish sector is a traditional economic activity for many families. The identified agent responsible for this reduction in C. gigas production was Ostreid Herpesvirus microvar (OsHV-1 μvar), which has been associated with C. gigas spat mortalities in France, and in many other countries. In Spain the episodes of mortality became critical for the regional shellfish production between 2008 until 2014, with mortality percentage up to 100%. In this study, local hatchery C. gigas spat was used as sentinel animals for epidemiological studies and management tests carried out with the aim of reducing oyster mortality in the Ebro Delta area. A production calendar mainly based on water temperature dynamics was designed around an optimal schedule for spat immersion. The immersion calendar included two optimal periods for spat immersion, in summer when temperatures are ≥25°C and at the end of autumn and beginning of winter when they are ≤13°C. Such production planning has reduced mortalities from 80% (in 2014 and previous years) to 2-7.5% in 2015 in cemented oysters. Furthermore, other recommendations related to spat immersion size, culture density and methodology, and cementing calendar, which helped to achieve the results presented, were also recorded and transferred to local producers. This work presents a successfully tested management strategy reducing OsHV-1 μvar impact by designing new field management practices mainly focused on the handling and timing of spat immersion. This approach could be used as a management model in areas presenting similar production practices and environmental characteristics.

Genetic parameters of resistance to Vibrio aestuarianus, and OsHV-1 infections in the Pacific oyster, Crassostrea gigas, at three different life stages

Background

In France, two main diseases threaten Pacific oyster production. Since 2008, Crassostrea gigas spat have suffered massive losses due to the ostreid herpesvirus OsHV-1, and since 2012, significant mortalities in commercial-size adults have been related to infection by the bacterium Vibrio aestuarianus. The genetic basis for resistance to V. aestuarianus and OsHV-1 and the nature of the genetic correlation between these two traits were investigated by using 20 half-sib sire families, each containing two full-sib families. For each disease, controlled infectious challenges were conducted using naïve oysters that were 3 to 26 months old. In addition, siblings were tested under field, pond and raceway conditions to determine whether laboratory trials reflected mortality events that occur in the oyster industry.

Results

First, we estimated the genetic basis of resistance to V. aestuarianus in C. gigas. Susceptibility to the infection was low for oysters in spat stage but increased with later life stages. Second, we confirmed a strong genetic basis of resistance to OsHV-1 infection at early stages and demonstrated that it was also strong at later stages. Most families had increased resistance to OsHV-1 infection from the spat to adult stages, while others consistently showed low or high mortality rates related to OsHV-1 infection, regardless of the life stage. Our third main finding was the absence of genetic correlations between resistance to OsHV-1 infection and resistance to V. aestuarianus infection.

Conclusions

Selective breeding to enhance resistance to OsHV-1 infection could be achieved through selective breeding at early stages and would not affect resistance to V. aestuarianus infection. However, our results suggest that the potential to select for improved resistance to V. aestuarianus is lower. Selection for dual resistance to OsHV-1 and V. aestuarianus infection in C. gigas might reduce the impact of these two major diseases by selecting families that have the highest breeding values for resistance to both diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0297-2) contains supplementary material, which is available to authorized users.

Viruses infecting marine molluscs

Although a wide range of viruses have been reported in marine molluscs, most of these reports rely on ultrastructural examination and few of these viruses have been fully characterized. The lack of marine mollusc cell lines restricts virus isolation capacities and subsequent characterization works. Our current knowledge is mostly restricted to viruses affecting farmed species such as oysters Crassostrea gigas, abalone Haliotis diversicolor supertexta or the scallop Chlamys farreri. Molecular approaches which are needed to identify virus affiliation have been carried out for a small number of viruses, most of them belonging to the Herpesviridae and birnaviridae families. These last years, the use of New Generation Sequencing approach has allowed increasing the number of sequenced viral genomes and has improved our capacity to investigate the diversity of viruses infecting marine molluscs. This new information has in turn allowed designing more efficient diagnostic tools. Moreover, the development of experimental infection protocols has answered some questions regarding the pathogenesis of these viruses and their interactions with their hosts. Control and management of viral diseases in molluscs mostly involve active surveillance, implementation of effective bio security measures and development of breeding programs. However factors triggering pathogen development and the life cycle and status of the viruses outside their mollusc hosts still need further investigations.

Infectious diseases in oyster aquaculture require a new integrated approach

Emerging diseases pose a recurrent threat to bivalve aquaculture. Recently, massive mortality events in the Pacific oyster Crassostrea gigas associated with the detection of a microvariant of the ostreid herpesvirus 1 (OsHV-1µVar) have been reported in Europe, Australia and New Zealand. Although the spread of disease is often viewed as a governance failure, we suggest that the development of protective measures for bivalve farming is presently held back by the lack of key scientific knowledge. In this paper, we explore the case for an integrated approach to study the management of bivalve disease, using OsHV-1 as a case study. Reconsidering the key issues by incorporating multidisciplinary science could provide a holistic understanding of OsHV-1 and increase the benefit of research to policymakers.

Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray

The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in response to B. ostreae through massively sequencing and has aided to improve our knowledge of the immune mechanisms of flat oyster. The validated oligo-microarray and the establishment of a reference transcriptome will be useful for large-scale gene expression studies in this species.

Single or dual experimental infections with Vibrio aestuarianus and OsHV-1 in diploid and triploid Crassostrea gigas at the spat, juvenile and adult stages

French production of the Pacific cupped oyster, Crassostrea gigas, is currently threatened by two pathogens, OsHV-1 and V. aestuarianus. While oysters selected for their higher resistance to OsHV-1 are now available for the industry, the impact of V. aestuarianus on such oysters is unknown, especially for triploids. In addition, experimental infection has used the virus or the bacteria alone, but there have been no investigations of dual exposure to these pathogens. This study is the first report of single or dual exposure in spat (Spat1 and Spat2), juvenile and adult naïve oysters. For each of the two stocks evaluated, unselected oysters and oysters selected for their higher resistance to OsHV-1 infection were tested, as well as their triploid siblings of the selected oysters produced using cytochalasin B. We confirmed that resistance to OsHV-1 infection and susceptibility to V. aestuarianus increased with age and size, although selected oysters were not significantly impacted by OsHV-1 whatever their ploidy, size or age. We found different mortality patterns depending on the pathogen tested. The mortality pattern was similar for oysters exposed to OsHV-1 or to both pathogens in the Spat1 trial (4months old and 1.9g). The mortality pattern was similar for oysters exposed to V. aestuarianus or to both pathogens in the Adult trial (25months old and 63.1g). Surprisingly, mortality was much higher (ranging from 75.9% to 100%), in particular for the selected oysters, for the Spat2 (8months old/3.9g) and Juvenile trials (16months old/18.4g) given a dual exposure, regardless of the level of selection for OsHV-1 and the ploidy state. Our findings highlight an important threat for oyster farmers: oysters exposed to both pathogens could experience dramatic mortality rates, even in oysters selected for their higher resistance to OsHV-1. Finally, our study demonstrated for the first time that triploid oysters were more susceptible to experimental challenges with V. aestuarianus at the spat stage than their diploid siblings. However, the difference in mortality between the triploids and diploids remained limited and ranged from 22.9% to 6.6% for spat and adults, respectively with a relatively regularly decrease in the difference with increased age.

Oysters and Vibrios as a Model for Disease Dynamics in Wild Animals

Disease dynamics in the wild are influenced by a number of ecological and evolutionary factors not addressed by traditional laboratory-based characterization of pathogens. Here we propose the oyster, Crassostrea gigas, as a model for studying the interaction of the environment, bacterial pathogens, and the host in disease dynamics. We show that an important first step is to ask whether the functional unit of pathogenesis is a bacterial clone, a population, or a consortium in order to assess triggers of disease outbreaks and devise appropriate monitoring tools. Moreover, the development of specific-pathogen-free (SPF) oysters has enabled assessment of the infection process under natural conditions. Finally, recent results show the importance of microbial interactions and host genetics in determining oyster health and disease.

Can selection for resistance to OsHV-1 infection modify susceptibility to Vibrio aestuarianus infection in Crassostrea gigas? First insights from experimental challenges using primary and successive exposures

Since 2008, the emergent virus OsHV-1µvar has provoked massive mortality events in Crassostrea gigas spat and juveniles in France. Since 2012, mortality driven by the pathogenic bacteria Vibrio aestuarianus has stricken market-sized adults. A hypothesis to explain the sudden increase in mortality observed in France since 2012 is that selective pressure due to recurrent viral infections could have led to a higher susceptibility of adults to Vibrio infection. In our study, two OsHV-1-resistant lines (AS and BS) and their respective controls (AC and BC) were experimentally challenged in the laboratory to determine their level of susceptibility to V. aestuarianus infection. At the juvenile stage, the selected lines exhibited lower mortality (14 and 33%) than the control lines (71 and 80%), suggesting dual-resistance to OsHV-1 and V. aestuarianus in C. gigas. Interestingly, this pattern was not observed at the adult stage, where higher mortality was detected for AS (68%) and BC (62%) than AC (39%) and BS (49%). These results were confirmed by the analysis of the expression of 31 immune-related genes in unchallenged oysters. Differential gene expression discriminated oysters according to their susceptibility to infection at both the juvenile and adult stages, suggesting that resistance to V. aestuarianus infection resulted in complex interactions between the genotype, stage of development and immunity status. Finally, survivors of the V. aestuarianus challenge at the juvenile stage still exhibited significant mortality at the adult stage during a second and third V. aestuarianus challenge, indicating that these survivors were not genetically resistant.

The ecology, evolution, impacts and management of host-parasite interactions of marine molluscs

Molluscs are economically and ecologically important components of aquatic ecosystems. In addition to supporting valuable aquaculture and wild-harvest industries, their populations determine the structure of benthic communities, cycling of nutrients, serve as prey resources for higher trophic levels and, in some instances, stabilize shorelines and maintain water quality. This paper reviews existing knowledge of the ecology of host-parasite interactions involving marine molluscs, with a focus on gastropods and bivalves. It considers the ecological and evolutionary impacts of molluscan parasites on their hosts and vice versa, and on the communities and ecosystems in which they are a part, as well as disease management and its ecological impacts. An increasing number of case studies show that disease can have important effects on marine molluscs, their ecological interactions and ecosystem services, at spatial scales from centimeters to thousands of kilometers and timescales ranging from hours to years. In some instances the cascading indirect effects arising from parasitic infection of molluscs extend well beyond the temporal and spatial scales at which molluscs are affected by disease. In addition to the direct effects of molluscan disease, there can be large indirect impacts on marine environments resulting from strategies, such as introduction of non-native species and selective breeding for disease resistance, put in place to manage disease. Much of our understanding of impacts of molluscan diseases on the marine environment has been derived from just a handful of intensively studied marine parasite-host systems, namely gastropod-trematode, cockle-trematode, and oyster-protistan interactions. Understanding molluscan host-parasite dynamics is of growing importance because: (1) expanding aquaculture; (2) current and future climate change; (3) movement of non-native species; and (4) coastal development are modifying molluscan disease dynamics, ultimately leading to complex relationships between diseases and cultivated and natural molluscan populations. Further, in some instances the enhancement or restoration of valued ecosystem services may be contingent on management of molluscan disease. The application of newly emerging molecular tools and remote sensing techniques to the study of molluscan disease will be important in identifying how changes at varying spatial and temporal scales with global change are modifying host-parasite systems.