With the increasing affordability of next-generation sequencing technologies, genotype-by-sequencing has become a cost-effective tool for ecologists and conservation biologists to describe a species' evolutionary history. For host–parasite interactions, genotype-by-sequencing can allow the simultaneous examination of host and parasite genomes and can yield insight into co-evolutionary processes. The eastern oyster, Crassostrea virginica, is among the most important aquacultured species in the United States. Natural and farmed oyster populations can be heavily impacted by ‘dermo’ disease caused by an alveolate protist, Perkinsus marinus. Here, we used restricted site-associated DNA sequencing (RADseq) to simultaneously examine spatial population genetic structure of host and parasite. We analysed 393 single-nucleotide polymorphisms (SNPs) for P. marinus and 52,100 SNPs for C. virginica from 36 individual oysters from the Gulf of Mexico (GOM) and mid-Atlantic coastline. All analyses revealed statistically significant genetic differentiation between the GOM and mid-Atlantic coast populations for both C. virginica and P. marinus, and genetic divergence between Chesapeake Bay and the outer coast of Virginia for C. virginica, but not for P. marinus. A co-phylogenetic analysis confirmed significant coupled evolutionary change between host and parasite across large spatial scales. The strong genetic divergence between marine basins raises the possibility that oysters from either basin would not be well adapted to parasite genotypes and phenotypes from the other, which would argue for caution with regard to both oyster and parasite transfers between the Atlantic and GOM regions. More broadly, our results demonstrate the potential of RADseq to describe spatial patterns of genetic divergence consistent with coupled evolution.

An increase in oyster aquaculture as a sustainable method of shellfish production is one response to overharvest and degradation of natural oyster reefs over the past century. Successful aquaculture production requires determining the environmental conditions optimal for oyster growth. In this study, the salinity, temperature, chlorophyll a concentration and the growth of Crassostrea virginica were monitored at four locations within the Mission-Aransas Estuary, Texas (USA), a shallow subtropical estuary influenced by relatively low freshwater inflow. Mean growth of the oyster shell (0.205 mm d–1 and 0.203 g d–1) and soft tissues (3.447 mg d–1) was highest when salinity was low (mean = 15.5) and chlorophyll a concentration was high (8.4 μg l–1). Oyster growth also varied temporally with periods of spawning. In low-inflow estuaries such as the Mission-Aransas Estuary, oyster farms should be sited close to river mouths so that oysters can benefit from freshwater inflows and lower salinities.

Understanding the effects of predicted rising sea levels, combined with changes in precipitation and freshwater inflow on key estuarine ecosystem engineers such as the eastern oyster would provide critical information to inform restoration design and predictive models. Using oyster ladders with shell bags placed at three heights to capture a range of inundation levels, oyster growth of naturally recruited spat was monitored over the course of 6 months. Oyster numbers and shell heights were consistently highest in bottom and mid bags experiencing greater than 50% inundation (mid: 63 ± 7%; bottom: 95 ± 3%). Identifying thresholds for optimal oyster growth and survival to enhance restoration engineering would require finer scale evaluation of inundation levels.

Radiocarbon dates from known age, pre-bomb eastern oyster (Crassostrea virginica) shells provide local marine reservoir corrections (ΔR) for Chesapeake Bay and the Middle Atlantic coastal area of eastern North America. These data suggest subregional variability in ΔR, ranging from 148±46 14C yr on the Potomac River to −109±38 14C yr at Swan Point, Maryland. The ΔR weighted mean for the Chesapeake's Western Shore (129±22 14C yr) is substantially higher than the Eastern Shore (−88±23 14C yr), with outer Atlantic Coast samples falling between these values (106±46 and 2±46 14C yr). These differences may result from a combination of factors, including 14C-depleted freshwater that enters the bay from some if its drainages, 14C-depleted seawater that enters the bay at its mouth, and/or biological carbon recycling. We advocate using different subregional ΔR corrections when calibrating 14C dates on aquatic specimens from the Chesapeake Bay and coastal Middle Atlantic region of North America.

Oyster population reproductive capacity and dynamics are controlled at the most basic level by the observed sex-ratios. Since oysters are sequential, protandric hermaphrodites the population sex-ratio is related to the demographics (shell length, age, and biomass). Oysters were collected from June through to August 2008 at twelve bars in the James, Rappahannock and Great Wicomico Rivers, Virginia, USA. Bars were aggregated into five groups on the basis of similar age–length relationships. Sex-ratios (fraction female), age–length, and biomass–length relationships were determined for each group. The fraction female increased within increasing shell length, age, and biomass at all sites. Simultaneous hermaphrodites were rarely observed. Group specific differences in shell length (SL, mm) and age (yr) for the timing of the protandric shift were observed with the earliest shift from male to female occurring at ~60 mm SL and ~1.6 yr. The proportion of females observed in the larger or older individuals was at least 70–80%. Sex-ratios from summer 2008 were used to develop sex–length, sex–age, and sex–biomass keys that were applied to autumn-survey data from 2006, 2007, 2008 and 2009. In these years, sex-ratios by shell length and age were strongly biased towards males while the sex-ratio by biomass was strongly biased towards females. Disease mortality compounds natural and fishing mortality resulting in age/size specific cropping yielding truncated population demographics and an earlier protandric shift in populations on the extremes of the range examined. Regardless of location, market (>76 mm SL) oysters are predominantly female.

In this paper, biochemical and physiological analyses were used to characterize changes associated with mortality event occurred during veliger development of American oyster, Crassostrea virginica. Biochemical analyses included the evaluation of lipid classes, fatty acid composition and total protein content. Larval physiology was evaluated by studying feeding activity, enzymes related to energy metabolism, oxidative stress levels and enzymatic antioxidant defenses. These analyses were complemented by bacterial community analyses as well as by measuring larval oyster performance. We observed that mortality events coincided with (1) strong changes in the surrounding bacterial community; (2) a progressive decrease in feeding activity; (3) higher levels of some lipid classes (free fatty acids, diglycerides, and acetone mobile phospholipids); (4) lower levels of phospholipids and protein; (5) higher contents of non-methylene interrupted dienoic fatty acids (22:2 NMI); (6) a decrease in energy metabolism activity (citrate synthase and cytochrome oxidase activities); (7) a higher oxidative stress (lipid peroxidation level); and (8) an activation of antioxidant defences before mortality (glutathione peroxidase and superoxide dismutase). We hypothesized that mortality emergence was related to higher energy consumption coupled with the progressive decline in feeding activity, lowered energy reserves and a decrease in energy metabolism activity. Thus, the low energy availability limited the efficiency of antioxidant defenses, resulting in a higher oxidative stress.

Restoration of shellfish populations is becoming an increasingly common practice worldwide, as natural fisheries succumb to pressures of overharvesting, habitat loss or degradation, and challenges from invasive competitors and pathogens. Primary genetic concerns relevant to shellfish restoration projects are reviewed, using the cupped oysters Crassostrea gigas and Crassostrea virginica as case studies. Molecular genetic tools can be used to delineate the geographic distribution of germ plasm diversity at the species and intraspecific levels, enabling more informed selection of genetic material for hatchery breeding and production. Maintenance of genetic variability and prevention of excessive inbreeding in hatchery stocks may be facilitated by the use of genetic markers for regular pedigree monitoring. The effect of hatchery supplementation on the effective population size of a recipient wild population (Ryman-Laikre effect) is reviewed in light of the population biology of bivalve molluscs, and appears to be minimal. Deployment of selected enhancement stocks may be a valuable tool for improvement of degraded wild populations, reversing the negative effects of generations of selective harvesting. Molecular genetic tools can be used effectively to monitor restoration programs, when the discriminatory power of the marker(s) is high and high-throughput scoring methods currently available are used.

Perkinsus marinus is a severe pathogen of the oyster Crassostrea virginica on the East Coast of the United States. Transmission dynamics of this parasite were investigated in situ for 2 consecutive years (May through October) at 2 lower Chesapeake Bay sites. Compared to previous studies where seasonal infection patterns in oysters were measured, this study also provided parasite water column abundance data measured using real-time PCR. As previously observed, salinity and temperature modulated parasite transmission dynamics. Using regression analysis, parasite prevalence, oyster mortalities and parasite water column abundance were significantly positively related to salinity. Perkinsus marinus weighted prevalence in wild oysters and parasite water column abundance both were significantly related to temperature, but the responses lagged 1 month behind temperature. Parasite water column abundance was the highest during August (up to 1200 cells/l) and was significantly related to P. marinus weighted prevalence in wild oysters, and to wild oyster mortality suggesting that parasites are released in the environment via both moribund and live hosts (i.e. through feces). Incidence was not significantly related to parasite water column abundance, which seems to indicate the absence of a linear relationship or that infection acquisition is controlled by a more complex set of parameters.

Anti-Bacillus megaterium activity was measured in unfractionated plasma withdrawn from three common US East Coast bivalve molluscs: an oyster Crassostrea virginica and the mussels Geukensia demissa and Mytilus edulis. The activities of the plasma samples from these bivalves were also measured against a C. virginica pathogen Perkinsus marinus. Strong anti-B. megaterium activity was measured in plasma from C. virginica and M. edulis, but was not detected in G. demissa. Bactericidal activity was found in hemocyte extracts from all bivalves in this study, suggesting a cellular origin of cytotoxic humoral factors. Peptides (< 10 kDa) were separated from the plasma samples by ultrafiltration; weak antibacterial peptide activity was quantified in C. virginica peptides, but not in peptides from the mussels. In the case of P. marinus, plasma from M. edulis or G. demissa was boldly cidal as compared to plasma from C. virginica. This difference in activity probably reflects the low pathogenicity of this oyster parasite for the mussel species tested. In summary, the bactericidal activity of plasma proteins from these bivalves showed considerable interspecies variation and did not necessarily correlate directly with antiprotistan activity. When present, antibacterial and antiprotistan activities seemed to be associated with plasma proteins rather than < 10-kDa plasma peptides, with the possible exception of C. virginica anti-B. megaterium activity and the occasionally expressed anti-P. marinus activity of M. edulis peptides. The precise identity of the plasma protein(s) responsible for the antimicrobial activities measured have yet to be determined, but it is likely that agents other than, or in addition to, lysozyme play significant roles in the process.

Juvenile oyster disease (JOD) in the eastern oyster, Crassostrea virginica, is characterized by a conchiolin deposit on the inner surface of the valves. Similarities to pathological syndromes affecting other oysters (pearl oyster mortality) and clams (brown ring disease), has suggested an infectious origin and a possible bacterial etiology. Bacteriological analysis (Total Heterotrophic Bacteria, THB and Total Vibrio sp., TVS) of oyster soft tissues, shell fluid and inner shell surfaces were monitored during the course of JOD onset and development. A significant increase in THB (but not TVS) occurred in shell fluid and at thesurface of the inner shell of JOD affected oysters. At the same time, changes in cytometric parameters (Total Hemocyte Counts, THC; Differential Hemocyte Counts, DHC) in hemolymph and shell fluid were documented in symptomatic oysters. THC in the shell fluid showed a decrease in late-stage JOD oysters. The disease was also correlated with altered cell ratios in both hemolymph and shell fluid, resulting in an increase in the percentage of the granulocytes in both locations. Our results have showed that main pathological changes associated with JOD occurred in extrapallial region rather than in the soft tissues. The disease was transmitted in the laboratory by extracts from diseased oysters: anomalous conchiolin developed within 4 weeks and the prevalence was higher when two inoculations were performed rather than one. A number of bacterial strains were found at high levels in diseased oysters and isolated. However, none produced the JOD deposit when injected into asymptomatic oysters. The bacterial etiology hypothesis for JOD should be explored further, expanded beyond the family Vibrionaceae, and should include consideration of a multiple etiology.

In the late 1980's juvenile oysters, Crassostrea virginica, spawned and cultured in New England and New York, began experiencing up to nearly 100% mortalities in some batches of juveniles. The cause of these mortalities was not ascertained immediately, but examination of dead and dying oysters did not reveal a previously recognized disease syndrome. Early studies showed that it was not an environmental or genetic problem, thus we hypothesized that a new, transmissible disease agent caused the observed mortality. This was verified under laboratory conditions where the disease was readily transmissible. Transmission was enhanced by warm water temperatures, 22–26 °C, and salinities of 18–30 ppt. Also, the infectious agent was filterable and sensitive to erythromycin, supporting the hypothesis that the causative agent may be a protistan parasite in the 2–6 μm size range. No evidence to support a viral or bacterial etiology was found.

A description is provided of the anomalous conchiolin deposits which are formed by Pinctada maxima and which are associated with unusual mortalities. Comparisons are made with brown ring disease found in Ruditapes philippinarum and juvenile Crassostrea virginica. In P. maxima, the deposits are not organized into a ring but rather are broad-based and result in retraction of the mantle with the deposits lying outside the edge of the mantle. Vibrio sp. have been implicated in causing the diseases of P. maximaand R. philippinarum whereas the etiological agent of the disease in C. virginica is unknown. It is suggested that the coccoid bodies formed in the mantle of C. virginica, but not in affected P. maxima and R. philippinarum, are sequestered portions of cytoplasm formed as a result autophagocytosis. Stimuli which could be responsible for inducing sequestration are discussed. The ultrastructure of the presumptive autophagosomes is described and compared to similar bodies found in C. gigas infected with a herpes-like virus.