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Non-consumptive effects of predators on prey populations have received increased interest in recent years. For Crassostrea virginica (Eastern Oyster), much of the focus has been on induced morphological defenses (e.g., shell thickening). Here, we provide in situ documentation of a behavioral response of Eastern Oysters (valve closure) to the threat of predation on a natural reef. This behavioral response, while intuitive, has been largely ignored in the literature despite potential impacts on individual oyster health by affecting feeding and subsequently energy assimilation, reproductive condition, and growth. In situ photographs revealed that, under natural conditions, Eastern Oysters closed during the passive presence of a crab mate-guarding pair and took ∼5 minutes to reopen to pre-predator gapes. Given that multiple oysters in our photos reacted similarly, this behavioral response may scale up to have effects on the population and the ecosystem services that Eastern Oysters provide. Ultimately, our observations open the door to a number of testable hypotheses regarding a predator's non-consumptive effects on oyster reefs.

The Eastern oyster Crassostrea virginica (Family Ostreidae) is one of the most important fishery and aquaculture species in the U.S. and is a keystone species for coastal reefs. A breeding program was initiated in 2019 to support the fast-growing aquaculture industry culturing this species in the Gulf of Mexico. Oysters from 17 wild populations in embayment along the U.S. Gulf of Mexico coast from southwest Florida to the Matagorda Bay, Texas were used as broodstock for the program to maximize genetic diversity in the base population. A sperm repository of the broodstock was established to support the breeding project. The goal of this study was to demonstrate the sperm sample collection, processing, cryopreservation, and the data management plan involved in the establishment of a sperm germplasm repository of base populations. The supporting objectives were to: (1) develop a data management plan for the sperm repository; (2) streamline the procedure for sample collection, processing, and cryopreservation; (3) incorporate sperm quality analysis into the procedure, and (4) archive the cryopreserved samples as a repository for future use in the breeding program. This sperm repository included a total of 102 male oysters from the 17 collection sites (six oysters per site). A data management plan was developed with six categories, including sample collection, phenotype, fresh sperm, genotype, cryopreservation, and post-thaw sperm, as guide for data collection. Sperm collection was accomplished by strip spawn, and fresh sperm production, motility, and fertility were recorded for quality analysis. Cryopreserved sperm samples were sorted, labelled, archived, and stored in liquid nitrogen for future use. Post-thaw motility (1–30%) and plasm membrane integrity (15.34–70.36%) were recorded as post-thaw quality parameters. Overall, this study demonstrated a streamlined procedure of oyster sperm collection, processing, and cryopreservation for establishing a sperm repository that can serve as a template for construction of oyster germplasm repositories for breeding programs.

Oysters are ecosystem engineers that create biogenic reef habitat important to estuarine biodiversity, benthic-pelagic coupling, and fishery production. Prevailing explanations for the dramatic decline of eastern oysters (Crassostrea virginica) during the last century overlook ecosystem complexity by ignoring interactions among multiple environmental disturbances. To explain oyster loss, we tested whether (1) mortality of oysters on natural oyster reefs varies with water depth (3 m vs. 6 m), (2) harvesting by oyster dredges reduces the height of oyster reefs, and (3) bottom-water hypoxia/anoxia and reduction in reef height through fishery disturbance interact to enhance mortality of oysters in the Neuse River estuary, North Carolina, USA. The percentage of oysters found dead (mean ± 1 SD) during a survey of natural reefs in May 1993 was significantly greater at 6-m (92 ± 10%) than at 3-m (28 ± 9%) water depth. Less than one scason's worth of oyster dredging reduced the height of restored oyster reefs by ∼30%. During stratification of the water column in summer, oxygen depletion near the seafloor at 6 m caused mass mortality of oysters, other invertebrates, and fishes on short, deep experimental reefs, while oysters and other reef associates elevated into the surface layer by sufficient reef height or by location in shallow water survived. Highly mobile blue crabs (Callinectes sapidus) abandoned burrows located in hypoxic/anoxic bottom waters but remained alive in shallow water. Our results indicate that interaction of reef habitat degradation (height reduction) through fishery disturbance and extended bottom-water hypoxia/anoxia caused the pattern of oyster mortality observed on natural reefs and influences the abundance and distribution of fish and invertebrate species that utilize this temperate reef habitat. Interactions among environmental disturbances imply a need for the integrative approaches of ecosystem management to restore and sustain estuarine habitat.

Coastal ecosystem restoration is accelerating globally as a means of enhancing shoreline protection, carbon storage, water quality, fisheries, and biodiversity. Among the most substantial of these efforts have been those focused on re-establishing oyster reefs across the US Atlantic and Gulf coasts. Despite considerable investment, it is unclear how the scale of and approaches toward oyster restoration have evolved. A synthesis of 1768 projects undertaken since 1964 reveals that oyster substrate restoration efforts have primarily been concentrated in the Chesapeake Bay and the Gulf Coast, have been heavily reliant on oyster shell, and have re-established 4.5% of the reef area that has been lost across all regions. By comparing costs to ecosystem service benefits, we discovered that the return-on-investment of oyster restoration varies widely, but generally increases with project size. To facilitate the recovery of coastal ecosystems and their services, scientists and resource managers must adopt a new restoration paradigm prioritizing investment in sites that maximize economic and ecological benefits and minimize construction costs.

Genomic structural variation is an important source of genetic and phenotypic diversity, playing a critical role in evolution. The recent availability of a high-quality reference genome for the eastern oyster, Crassostrea virginica , and whole-genome sequence data of samples from across the species range in the USA, provides an opportunity to explore structural variation across the genome of this species. Our analysis shows significantly greater individual-level duplications of regions across the genome than that of most model vertebrate species. Duplications are widespread across all ten chromosomes with variation in frequency per chromosome. The eastern oyster shows a large interindividual variation in duplications as well as particular chromosomal regions with a higher density of duplications. A high percentage of duplications seen in C. virginica lie completely within genes and exons, suggesting the potential for impacts on gene function. These results support the hypothesis that structural changes may play a significant role in standing genetic variation in C. virginica , and potentially have a role in their adaptive and evolutionary success. Altogether, these results suggest that copy number variation plays an important role in the genomic variation of C. virginica . This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

Autogenic ecosystem engineers are critically important parts of many marine and estuarine systems because of their substantial effect on ecosystem services. Oysters are of particular importance because of their capacity to modify coastal and estuarine habitats and the highly degraded status of their habitats worldwide. However, models to predict dynamics of ecosystem engineers have not previously included the effects of exploitation. We developed a linked population and habitat model for autogenic ecosystem engineers undergoing exploitation. We parameterized the model to represent eastern oyster (Crassostrea virginica) in upper Chesapeake Bay by selecting sets of parameter values that matched observed rates of change in abundance and habitat. We used the model to evaluate the effects of a range of management and restoration options including sustainability of historical fishing pressure, effectiveness of a newly enacted sanctuary program, and relative performance of two restoration approaches. In general, autogenic ecosystem engineers are expected to be substantially less resilient to fishing than an equivalent species that does not rely on itself for habitat. Historical fishing mortality rates in upper Chesapeake Bay for oysters were above the levels that would lead to extirpation. Reductions in fishing or closure of the fishery were projected to lead to long-term increases in abundance and habitat. For fisheries to become sustainable outside of sanctuaries, a substantial larval subsidy would be required from oysters within sanctuaries. Restoration efforts using high-relief reefs were predicted to allow recovery within a shorter period of time than low-relief reefs. Models such as ours, that allow for feedbacks between population and habitat dynamics, can be effective tools for guiding management and restoration of autogenic ecosystem engineers.

Nonlinear threshold responses to biotic or abiotic forcing may produce multiple population trajectories dependent upon initial conditions, which can reinforce population recovery or drive local extinction, yet experimental tests of this phenomenon are lacking in marine ecosystems. In field experiments at 4 sites in 2 tributaries of lower Chesapeake Bay, we examined demographic responses (density and survival) of eastern oyster Crassostrea virginica populations to reef height and associated gradients in sediment deposition and habitat complexity. After 2 yr, oyster reefs exhibited diverging trajectories toward either degradation or persistence, dependent upon initial reef height. Reefs higher than 0.3 m supported greater oyster density, survival, and reef complexity, whereas sediment deposition was reduced. Reefs lower than 0.3 m experienced heavy sediment deposition and were eventually buried. These observations (1) provide experimental evidence for threshold dynamics in marine species, (2) suggest that the collapse of oyster populations was largely due to anthropogenic habitat degradation that eliminated positive feedbacks and which may have created an alternative reef trajectory towards local extinction, and (3) indicate an avenue by which oyster restoration is achievable.

Following a planktonic dispersal period of days to months, the larvae of benthic marine organisms must locate suitable seafloor habitat in which to settle and metamorphose. For animals that are sessile or sedentary as adults, settlement onto substrates that are adequate for survival and reproduction is particularly critical, yet represents a challenge since patchily distributed settlement sites may be difficult to find along a coast or within an estuary. Recent studies have demonstrated that the underwater soundscape, the distinct sounds that emanate from habitats and contain information about their biological and physical characteristics, may serve as broad-scale environmental cue for marine larvae to find satisfactory settlement sites. Here, we contrast the acoustic characteristics of oyster reef and off-reef soft bottoms, and investigate the effect of habitat-associated estuarine sound on the settlement patterns of an economically and ecologically important reef-building bivalve, the Eastern oyster (Crassostrea virginica). Subtidal oyster reefs in coastal North Carolina, USA show distinct acoustic signatures compared to adjacent off-reef soft bottom habitats, characterized by consistently higher levels of sound in the 1.5-20 kHz range. Manipulative laboratory playback experiments found increased settlement in larval oyster cultures exposed to oyster reef sound compared to unstructured soft bottom sound or no sound treatments. In field experiments, ambient reef sound produced higher levels of oyster settlement in larval cultures than did off-reef sound treatments. The results suggest that oyster larvae have the ability to respond to sounds indicative of optimal settlement sites, and this is the first evidence that habitat-related differences in estuarine sounds influence the settlement of a mollusk. Habitat-specific sound characteristics may represent an important settlement and habitat selection cue for estuarine invertebrates and could play a role in driving settlement and recruitment patterns in marine communities.

Estuarine organisms are exposed to periodic strong fluctuations in seawater pH driven by biological carbon dioxide (CO sub(2)) production, which may in the future be further exacerbated by the ocean acidification associated with the global rise in CO sub(2). Calcium carbonate-producing marine species such as mollusks are expected to be vulnerable to acidification of estuarine waters, since elevated CO sub(2) concentration and lower pH lead to a decrease in the degree of saturation of water with respect to calcium carbonate, potentially affecting biomineralization. Our study demonstrates that the increase in CO sub(2) partial pressure (pCO sub(2)) in seawater and associated decrease in pH within the environmentally relevant range for estuaries have negative effects on physiology, rates of shell deposition and mechanical properties of the shells of eastern oysters Crassostrea virginica (Gmelin). High CO sub(2) levels (pH ~7.5, pCO sub(2) ~3500 mu atm) caused significant increases in juvenile mortality rates and inhibited both shell and soft-body growth compared to the control conditions (pH ~8.2, pCO sub(2) ~380 mu atm). Furthermore, elevated CO sub(2) concentrations resulted in higher standard metabolic rates in oyster juveniles, likely due to the higher energy cost of homeostasis. The high CO sub(2) conditions also led to changes in the ultrastructure and mechanical properties of shells, including increased thickness of the calcite laths within the hypostracum and reduced hardness and fracture toughness of the shells, indicating that elevated CO sub(2) levels have negative effects on the biomineralization process. These data strongly suggest that the rise in CO sub(2) can impact physiology and biomineralization in marine calcifiers such as eastern oysters, threatening their survival and potentially leading to profound ecological and economic impacts in estuarine ecosystems.

Understanding the genetic architecture of economically important traits is essential for the design and implementation of efficient breeding programs. Here, we analysed 3,653 Eastern oysters ( Crassostrea virginica ) from 62 crossing groups and 307 full-sib families, all genotyped with a 200 K SNP array, to (i) estimate heritability and genetic correlations for six growth-related traits, (ii) detect quantitative trait loci (QTL) and candidate genes, and (iii) compare the accuracy of pedigree- (PBLUP) versus genomic-based (GBLUP) predictions across marker densities, selection strategies (physical distance (PD) versus linkage disequilibrium (LD) and phenotype-based genotyping strategies. SNP-based Heritabilities ranged from 0.33 to 0.56, and genetic correlations among traits exceeded 0.61, indicating strong pleiotropy. GWAS revealed a polygenic architecture with a shared QTL on chromosome 2; the top SNP explained ≤ 1.1% of phenotypic variance. Except for the 0.5 K LD panel—where PBLUP was more accurate—and the 1 K LD panel—where both methods performed similarly—GBLUP outperformed PBLUP in all scenarios, with the greatest advantage observed for physically spaced (PD) panels. The highest accuracy (0.80) was achieved with the full 100 K SNP set. GBLUP models required panels containing ≥ 0.5 K PD (accuracy ≥ 0.55) or ≥ 2 K LD (accuracy ≥ 0.56) to significatively surpass PBLUP predictions. Training sets built from extreme phenotypes boosted accuracy in small to intermediate sample sizes (e.g., 0.74 at n  = 1,500 with 5 K PD SNPs versus 0.53 under random sampling). These results provide novel insights into not only the genomic regions controlling growth in this species but also about the utility of PD-based SNP panels and balanced sampling designs for enhancing GS accuracy in C. virginica .