Showing papers on "Oyster published in 2019"

Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event.

Abstract: Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.

Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event

Abstract: The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013–2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1–V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.

The application of oyster reefs in shoreline protection: Are we over-engineering for an ecosystem engineer?

Abstract: Oyster reef living shorelines have been proposed as an effective alternative to traditional coastal defence structures (e.g. bulkheads, breakwaters), with the benefit that they may keep pace with sea‐level rise and provide co‐benefits, such as habitat provision. However, there remains uncertainty about the effectiveness of shoreline protection provided by oyster reefs, which limits their broader application. We draw evidence from studies along the east and gulf coasts of the United States, where much research and implementation of oyster reef restoration has occurred, to better define the existing gaps in our understanding of the use of restored oyster reefs for shoreline protection. We find potential disconnects between ecological and engineering functions of reefs. In response, we outline how engineering and ecological principles are used in the design of oyster reef living shorelines and highlight knowledge gaps where an integration of these disciplines will lead to their more effective application. Synthesis and applications. This work highlights the necessary steps to advance the application of oyster reef living shorelines. Importantly, future research should focus on appropriate designs and conditions needed for these structures to effectively protect our coasts from erosion, while supporting a sustainable oyster population, thereby providing actionable nature‐based alternatives for coastal defence to diverse end‐users.

Current Status of European Oyster Decline and Restoration in Germany

Abstract: Marine ecosystems of temperate regions are highly modified by human activity and far from their original natural status. The North Sea, known as an intensively used area, has lost its offshore oyster grounds due to overexploitation in a relatively short time. Native oyster beds as a once abundant and ecologically highly important biogenic reef-type have vanished from the North Sea ecosystem in most areas of both their former distribution and magnitude. Worldwide, oyster stocks have been severely exploited over the past centuries. According to estimates, about 85% of the worldwide oyster reef habitats have been destroyed over the course of the last century. This loss of oyster populations has meant far more than just the loss of a valuable food resource. Oyster reefs represent a characteristic benthic community which offers a variety of valuable ecosystem services: better water quality, local decrease of toxic algal blooms, increase in nutrient uptake, increase of bentho-pelagic coupling, increase in species richness, increase of multidimensional biogenic structures which provide habitat, food, and protection for numerous invertebrate and fish species. The aim of oyster restoration is to promote redevelopment of this valuable missing habitat. The development of strategies, methods, and procedures for a sustainable restoration of the European oyster Ostrea edulis in the German North Sea is currently a focus of marine nature conservation. Main drivers for restoring this ecological key species are the enhancement of biodiversity and ecosystem services in the marine environment. Results of these investigations will support the future development and implementation of a large-scale and long-term German native oyster restoration programme to re-establish a healthy population of this once-abundant species now absent from the region.

Oyster breakwater reefs promote adjacent mudflat stability and salt marsh growth in a monsoon dominated subtropical coast

Abstract: Oyster reefs have the potential as eco-engineers to improve coastal protection. A field experiment was undertaken to assess the benefit of oyster breakwater reefs to mitigate shoreline erosion in a monsoon-dominated subtropical system. Three breakwater reefs with recruited oysters were deployed on an eroding intertidal mudflat at Kutubdia Island, the southeast Bangladesh coast. Data were collected on wave dissipation by the reef structures, changes in shoreline profile, erosion-accretion patterns, and lateral saltmarsh movement and related growth. This was done over four seasons, including the rainy monsoon period. The observed wave heights in the study area ranged 0.1–0.5 m. The reefs were able to dissipate wave energy and act as breakwaters for tidal water levels between 0.5–1.0 m. Waves were totally blocked by the vertical relief of the reefs at water levels <0.5 m. On the lee side of the reefs, there was accretion of 29 cm clayey sediments with erosion reduction of 54% as compared to control sites. The changes caused by the deployed reefs also facilitated seaward expansion of the salt marsh. This study showed that breakwater oyster reefs can reduce erosion, trap suspended sediment, and support seaward saltmarsh expansion demonstrating the potential as a nature-based solution for protecting the subtropical coastlines.

Wave Attenuation by Oyster Reefs in Shallow Coastal Bays

Abstract: Oyster reef restoration in shallow estuarine environments has been thought to have the potential to provide shoreline protection as well as oyster habitat. This study was designed to address the question of how effective oyster reefs are at attenuating wave energy in shallow coastal bays. Measurements were made of waves on both sides of four restored intertidal oyster reefs and at a control site with no reef; mean water depths ranged from 0.9 to 1.3 m. The reefs differed in composition and position relative to the shoreline, but all had reef crest elevations between 0.3 and 0.5 m below mean sea level. Differences in wave heights between the exposed/sheltered sides and upwind/downwind sides of the reefs were used to quantify the effects of the reefs on waves under varying tidal and wind conditions. All four reefs were able to reduce wave heights by an average of 30–50% for water depths of 0.5–1.0 m (bracketing the heights of reef crests) and 0–20% for water depths of 1.0–1.5 m (reef crests > 0.25 m below the water surface). For water depths greater than 1.5 m, there was < 10% change in wave heights. In contrast, there was no average decrease in wave height from the more seaward (exposed) to the more landward wave gauge at the control site regardless of water depth. Based on our results, we conclude that fringing oyster reefs can reduce the wave energy reaching the shoreline of marshes with edge elevations close to mean sea level. However, reefs like those in our study have little effect on waves during deeper water conditions, which allow for the largest waves, and are therefore less likely to offer protection to marshes characterized by high edge scarps and marsh surface elevations well above mean sea level.

Dynamics of the Pacific oyster pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next-generation sequencing strategy.

Abstract: Infectious agents such as the bacteria Vibrio aestuarianus or Ostreid herpesvirus 1 have been repeatedly associated with dramatic disease outbreaks of Crassostrea gigas beds in Europe. Beside roles played by these pathogens, microbial infections in C. gigas may derive from the contribution of a larger number of microorganisms than previously thought, according to an emerging view supporting the polymicrobial nature of bivalve diseases. In this study, the microbial communities associated with a large number of C. gigas samples collected during recurrent mortality episodes at different European sites were investigated by real-time PCR and 16SrRNA gene-based microbial profiling. A new target enrichment next-generation sequencing protocol for selective capturing of 884 phylogenetic and virulence markers of the potential microbial pathogenic community in oyster tissue was developed allowing high taxonomic resolution analysis of the bivalve pathobiota. Comparative analysis of contrasting C. gigas samples conducted using these methods revealed that oyster experiencing mortality outbreaks displayed signs of microbiota disruption associated with the presence of previously undetected potential pathogenic microbial species mostly belonging to genus Vibrio and Arcobacter. The role of these species and their consortia should be targeted by future studies aiming to shed light on mechanisms underlying polymicrobial infections in C. gigas.

Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) and the Blue Mussel (Mytilus edulis): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities.

Abstract: Gut microbial community structure was evaluated for two species of bivalve molluscs, the eastern oyster (Crassostrea virginica) and the blue mussel (Mytilus edulis) collected from Long Island Sound, Connecticut, over the course of a year. These bivalves utilize a shared feeding mechanism, which may result in similar gut microbial communities. Their particle diet, marine aggregates, and surrounding environment, aggregate-free seawater (AFSW), were also collected for comparison. Due to the suspension-feeding activities of bivalves, the potential for aggregate- and AFSW-associated microbiota to influence their microbial communities may be significant. Both taxonomic and functional diversity of the samples were assessed. 16S rRNA gene amplicon sequencing indicated that oysters and mussels maintained similar, but not identical, gut microbiomes, with some temporal variation. Throughout the year, bivalve species had gut microbial community compositions that were more similar to one another than to aggregates. Within a month, bivalves shared on average a quarter of their total operational taxonomic units (OTUs) with each other and a 10th of their total OTUs with aggregates. During months with warm water temperatures, individuals within each of the four sample types had similar alpha diversity, but again, temporal variation was observed. On a functional level, bivalve gut microbial communities exhibited variation attributed to host species and season. Unlike oysters, mussel gut bacterial communities maintained high richness and evenness values throughout the year, even when values for the particle diet and AFSW were reduced. Overall, a core gut bivalve microbiome was present, and it was partially influenced by the marine aggregate microbial community.IMPORTANCE This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment.

Anti-Inflammatory Activity of β-thymosin Peptide Derived from Pacific Oyster (Crassostrea gigas) on NO and PGE₂ Production by Down-Regulating NF-κB in LPS-Induced RAW264.7 Macrophage Cells.

Abstract: β-thymosin is known for having 43 amino acids, being water-soluble, having a light molecular weight and ubiquitous polypeptide. The biological activities of β-thymosin are diverse and include the promotion of wound healing, reduction of inflammation, differentiation of T cells and inhibition of apoptosis. Our previous studies showed that oyster β-thymosin originated from the mantle of the Pacific oyster, Crassostrea gigas and had antimicrobial activity. In this study, we investigated the anti-inflammatory effects of oyster β-thymosin in lipopolysaccharide (LPS)-induced RAW264.7 macrophage cells using human β-thymosin as a control. Oyster β-thymosin inhibited the nitric oxide (NO) production as much as human β-thymosin in LPS-induced RAW264.7 cells. It also showed that oyster β-thymosin suppressed the expression of prostaglandin E₂ (PGE₂), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Moreover, oyster β-thymosin reduced inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) and interleukin-6 (IL-6). Oyster β-thymosin also suppressed the nuclear translocation of phosphorylated nuclear factor-κB (NF-κB) and degradation of inhibitory κB (IκB) in LPS-induced RAW264.7 cells. These results suggest that oyster β-thymosin, which is derived from the mantle of the Pacific oyster, has as much anti-inflammatory effects as human β-thymosin. Additionally, oyster β-thymosin suppressed NO production, PGE₂ production and inflammatory cytokines expression via NF-κB in LPS-induced RAW264.7 cells.

Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease.

Abstract: Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or detrimental role in OsHV-1 μvar disease outbreaks.

Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada.

Abstract: Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11,321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean FST = 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDAs) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype-environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster.

Low Greenhouse Gas Emissions from Oyster Aquaculture.

Abstract: Production of animal protein is associated with high greenhouse gas (GHG) emissions. Globally, oyster aquaculture is increasing as a way to meet growing demands for protein, yet its associated GHG-emissions are largely unknown. We quantified oyster aquaculture GHG-emissions from the three main constituents of GHG-release associated with terrestrial livestock production: fermentation in the animal gut, manure management, and fodder production. We found that oysters release no methane (CH4) and only negligible amounts of nitrous oxide (0.00012 ± 0.00004 μmol N2O gDW-1 hr-1) and carbon dioxide (3.556 ± 0.471 μmol CO2 gDW-1 hr-1). Further, sediment fluxes of N2O and CH4 were unchanged in the presence of oyster aquaculture, regardless of the length of time it had been in place. Sediment CO2 release was slightly stimulated between 4 and 6 years of aquaculture presence and then returned to baseline levels but was not significantly different between aquaculture and a control site when all ages of culture were pooled. There is no GHG-release from oyster fodder production. Considering the main drivers of GHG-release in terrestrial livestock systems, oyster aquaculture has less than 0.5% of the GHG-cost of beef, small ruminants, pork, and poultry in terms of CO2-equivalents per kg protein, suggesting that shellfish aquaculture may provide a a low GHG alternative for future animal protein production compared to land based sources. We estimate that if 10% of the protein from beef consumption in the United States was replaced with protein from oysters, the GHG savings would be equivalent to 10.8 million fewer cars on the road.

Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling.

Abstract: Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world’s most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster Pinctada margaritifera, a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from P. margaritifera individuals: the gill, gonad, byssus gland, haemolymph, mantle, adductor muscle, mucus, and gut. Richness of bacterial Operational Taxonomic Units (OTUs) and phylogenetic diversity differed between host tissues, with mucous layers displaying the highest richness and diversity. This multi-tissues approach permitted the identification of consistent microbial members, together constituting the core microbiome of P. margaritifera, including Alpha- and Gammaproteobacteria, Flavobacteriia, and Spirochaetes. We also found a high representation of Endozoicimonaceae symbionts, indicating that they may be of particular importance to oyster health, survival and homeostasis, as in many other coral reef animals. Our study demonstrates that the microbial communities and their associated predicted functional profiles are tissue specific. Inferred physiological functions were supported by current physiological data available for the associated bacterial taxa specific to each tissue. This work provides the first baseline of microbial community composition in P. margaritifera, providing a solid foundation for future research into this commercially important species and emphasises the important effects of tissue differentiation in structuring the oyster microbiome.

Active management is required to turn the tide for depleted Ostrea edulis stocks from the effects of overfishing, disease and invasive species.

Abstract: The decline of the European oyster Ostrea edulis across its biogeographic range has been driven largely by over-fishing and anthropogenic habitat destruction, often to the point of functional extinction. However, other negatively interacting factors attributing to this catastrophic decline include disease, invasive species and pollution. In addition, a relatively complex life history characterized by sporadic spawning renders O. edulis biologically vulnerable to overexploitation. As a viviparous species, successful reproduction in O. edulis populations is density dependent to a greater degree than broadcast spawning oviparous species such as the Pacific oyster Crassostrea (Magallana) gigas. Here, we report on the benthic assemblage of O. edulis and the invasive gastropod Crepidula fornicata across three actively managed South coast harbors in one of the few remaining O. edulis fisheries in the UK. Long-term data reveals that numbers of O. edulis sampled within Chichester Harbour have decreased by 96%, in contrast numbers of C. fornicata sampled have increased by 441% over a 19-year period. The recent survey data also recorded extremely low densities of O. edulis, and extremely high densities of C. fornicata, within Portsmouth and Langstone Harbours. The native oyster's failure to recover, despite fishery closures, suggests competitive exclusion by C. fornicata is preventing recovery of O. edulis, which is thought to be due to a lack of habitat heterogeneity or suitable settlement substrate. Large scale population data reveals that mean O. edulis shell length and width has decreased significantly across all years and site groups from 2015 to 2017, with a narrowing demographic structure. An absence of juveniles and lack of multiple cohorts in the remaining population suggests that the limited fishing effort exceeds biological output and recruitment is poor. In the Langstone & Chichester 2017 sample 98% of the population is assigned to a single cohort (modal mean 71.20 ± 8.78 mm, maximum length). There is evidence of small scale (<5 km) geographic population structure between connected harbors; the 2015 Portsmouth and Chichester fishery populations exhibited disparity in the most frequent size class with 36% within 81-90 mm and 33.86% within 61-70 mm, respectively, the data also indicates a narrowing demographic over a short period of time. The prevalence of the disease Bonamiosis was monitored and supports this microgeographic population structure. Infection rates of O. edulis by Bonamia ostreae was 0% in Portsmouth Harbor (n = 48), 4.1% in Langstone (n = 145) and 21.3% in Chichester (n = 48) populations. These data collectively indicate that O. edulis is on the brink of an ecological collapse within the Solent harbors. Without effective intervention to mitigate the benthic dominance by C. fornicata in the form of biologically relevant fishery policy and the management of suitable recruitment substrate these native oyster populations could be lost.

Bacterial Community Dynamics in an Oyster Hatchery in Response to Probiotic Treatment.

Abstract: Larval oysters in hatcheries are susceptible to diseases caused by bacterial pathogens, including Vibrio spp. Previous studies have shown that daily addition of the probiotic Bacillus pumilus RI06-95 to water in rearing tanks increases larval survival when challenged with the pathogen Vibrio coralliilyticus. We propose that the presence of probiotics causes shifts in bacterial community structure in rearing tanks, leading to a net decrease in the relative abundance of potential pathogens. During three trials spanning the 2012-2015 hatchery seasons, larvae, tank biofilm, and rearing water samples were collected from control and probiotic-treated tanks in an oyster hatchery over a 12-day period after spawning. Samples were analyzed by 16S rRNA sequencing of the V4 or V6 regions followed by taxonomic classification, in order to determine bacterial community structures. There were significant differences in bacterial composition over time and between sample types, but no major effect of probiotics on the structure and diversity of bacterial communities (phylum level, Bray-Curtis k = 2, 95% confidence). Probiotic treatment, however, led to a higher relative percent abundance of Oceanospirillales and Bacillus spp. in water and oyster larvae. In the water, an increase in Vibrio spp. diversity in the absence of a net increase in relative read abundance suggests a likely decrease in the abundance of specific pathogenic Vibrio spp., and therefore lower chances of a disease outbreak. Co-occurrence network analysis also suggests that probiotic treatment had a systemic effect on targeted members of the bacterial community, leading to a net decrease in potentially pathogenic species.

Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): New genomic tools for breeding programs and management of natural resources

Abstract: The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non-native species, and epidemic outbreaks have severely affected this important resource, particularly, the protozoan parasite Bonamia ostreae, which is the main concern affecting its production and conservation. In order to identify genomic regions and markers potentially associated with bonamiosis resistance, six oyster beds distributed throughout the European Atlantic coast were sampled. Three of them have been exposed to this parasite since the early 1980s and showed some degree of innate resistance (long-term affected group, LTA), while the other three were free of B. ostreae at least until sampling date (naive group, NV). A total of 14,065 SNPs were analyzed, including 37 markers from candidate genes and 14,028 from a medium-density SNP array. Gene diversity was similar between LTA and NV groups suggesting no genetic erosion due to long-term exposure to the parasite, and three population clusters were detected using the whole dataset. Tests for divergent selection between NV and LTA groups detected the presence of a very consistent set of 22 markers, located within a putative single genomic region, which suggests the presence of a major quantitative trait locus associated with B. ostreae resistance. Moreover, 324 outlier loci associated with factors other than bonamiosis were identified allowing fully discrimination of all the oyster beds. A practical tool which included the 84 highest discriminative markers for tracing O. edulis populations was developed and tested with empirical data. Results reported herein could assist the production of stocks with improved resistance to bonamiosis and facilitate the management of oyster beds for recovery production and ecosystem services provided by this species.

Comparative Transcriptome Analysis Reveals Molecular Basis Underlying Fast Growth of the Selectively Bred Pacific Oyster, Crassostrea gigas.

Abstract: Fast growth is one of the most desired traits for all food animals, which affects the profitability of animal production. The Pacific oyster, Crassostrea gigas, is an important aquaculture shellfish around the world with the largest annual production. Growth of the Pacific oyster has been greatly improved by artificial selection breeding, but molecular mechanisms underlying growth remains poorly understood, which limited the molecular integrative breeding of fast growth with other superior traits. In this study, comparative transcriptome analyses between the fast-growing selectively bred Pacific oyster and unselected wild Pacific oysters were conducted by RNA-Seq. A total of 1,303 protein-coding genes differentially expressed between fast-growing oysters and wild controls were identified, of which 888 genes were expressed at higher levels in the fast-growing oysters. Functional analysis of the differentially expressed genes (DEGs) indicated that genes involved in microtubule motor activity and biosynthesis of nucleotides and proteins are potentially important for growth in the oyster. Positive selection analysis of genes at the transcriptome level showed that a significant number of ribosomal protein genes had undergone positive selection during the artificial selection breeding process. These results also indicated the importance of protein biosynthesis and metabolism for the growth of oysters. The alternative splicing (AS) of genes was also compared between the two groups of oysters. A total of 3,230 differential alternative splicing events (DAS) were identified, involved in 1,818 genes. These DAS genes were associated with specific functional pathways related to growth, such as "long-term potentiation," "salivary secretion," and "phosphatidylinositol signaling system." The findings of this study will be valuable resources for future investigation to unravel molecular mechanisms underlying growth regulation in the oyster and other marine invertebrates and to provide solid support for breeding application to integrate fast growth with other superior traits in the Pacific oyster.

Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas : genetic effect and interaction network

Abstract: Oyster is rich in glycogen and free amino acids and is called “the milk of sea”. To understand the main genetic effects of these traits and the genetic networks underlying their correlation, we have conducted the whole genome resequencing with 427 oysters collected from the world-wide scale. After association analysis, 168 clustered significant single nucleotide polymorphism (SNP) loci were identified for glycogen content and 17 SNPs were verified with 288 oyster individuals in another wide populations. These were the most important candidate loci for oyster breeding. Among 24 genes in the 100-kb regions of the leading SNP loci, cytochrome P450 17A1 (CYP17A1) contained a non-synonymous SNP and displayed higher expressions in high glycogen content individuals. This might enhance the gluconeogenesis process by the transcriptionally regulating the expression of phosphoenolpyruvate carboxykinase (PEPCK) and glucose 6-phosphatase (G6Pase). Also, for amino acids content, 417 clustered significant SNPs were identified. After genetic network analysis, three node SNP regions were identified to be associated with glycogen, protein, and Asp content, which might explain their significant correlation. Overall, this study provides insights into the genetic correlation among complex traits, which will facilitate future oyster functional studies and breeding through molecular design.

Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii

Abstract: The pearl oyster Pinctada fucata martensii (Pfu.), widely cultured in the South China Sea, is a precious source of sea pearls and calcifying materials. A yellow shell variety of Pfu. was obtained after years of artificial breeding. To identify differentially expressed genes between yellow shell and normal black shell pearl oysters, we performed transcriptomic sequencing and proteomic analyses using mantle edge tissues. A total of 56,969 unigenes were obtained from transcriptomic, of which 21,610 were annotated, including 385 annotated significant up-regulated genes and 227 significant down-regulated genes in yellow shell oysters (| log2 (fold change) | ≥2 and false discovery rate < 0.001). Tyrosine metabolism, calcium signalling pathway, phototransduction, melanogenesis pathways and rhodopsin related Gene Ontology (GO) terms were enriched with significant differentially expressed genes (DEGs) in transcriptomic. Proteomic sequencing identified 1769 proteins, of which 51 were significantly differentially expressed in yellow shell oysters. Calmodulin, N66 matrix protein, nacre protein and Kazal-type serine protease inhibitor were up-regulated in yellow shell oysters at both mRNA and protein levels, while glycine-rich protein shematrin-2, mantle gene 4, and sulphide: quinone oxidoreductase were down-regulated at two omics levels. Particularly, calmodulin, nacre protein N16.3, mantle gene 4, sulphide: quinone oxidoreductase, tyrosinase-like protein 3, cytochrome P450 3A were confirmed by quantitative real-time PCR. Yellow shell oysters possessed higher total carotenoid content (TCC) compared than black shell oyster based on spectrophotography. The yellow phenotype of pearl oysters, characterised by higher total carotenoids content, may reflect differences in retinal and rhodopsin metabolism, melanogenesis, calcium signalling pathway and biomineralisation. These results provide insights for exploring the relationships between calcium regulation, biomineralisation and yellow shell colour pigmentation.