Since 2019, outbreaks of an apicomplexan parasite caused catastrophic mortalities of adult northern bay scallops (Argopecten irradians irradians) in New York, USA. Anecdotal observations suggested different levels of mortality between different scallop stocks and mortality outbreaks appeared to occur in years displaying positive temperature anomalies. In this study, field and laboratory experiments were designed to evaluate the effect of environmental conditions and host (scallop) background on disease susceptibility and mortality. Wild and aquacultured scallops originally sourced from the same area were deployed in lantern nets (suspended in the water column) or oyster culture bags (on bottom) at two different enzootic sites showing contrasting environmental conditions. Subsets of wild and aquacultured stocks were also used in laboratory experiments exposing scallops to different temperatures and dissolved oxygen levels, mimicking different environmental scenarios. Results showed higher mortality in aquacultured scallops compared to wild scallops, especially in the more stressful conditions. Laboratory experiments showed that the trajectories of disease development and mortality were significantly affected by initial disease levels and environmental factors. For instance, high temperature and low dissolved oxygen were shown to favor disease development when initial disease levels were low (wild scallops) but also appear to lead to an overall reduction in disease via culling of the most heavily infected scallops when initial disease levels and mortality during the experiment were high (aquacultured scallops). Altogether, these findings underline the impact of environmental conditions, in particular temperature, on host-parasite interactions and suggest the potential existence of more resilient scallop stocks.

BACKGROUND:Understanding the genetic basis of resilience in marine organisms is critical for conservation and management, particularly in the face of escalating environmental stress and disease outbreaks. The bay scallop Argopecten irradians is a commercially and recreationally important shellfish species found in estuarine and coastal environments of the United States from New England to the Gulf of Mexico. In New York, adult bay scallop populations have been decimated every summer since 2019 leading to the collapse of their fishery. These mortality events were associated with annual outbreaks of an undescribed apicomplexan parasite recently named Bay Scallop Marosporida (BSM) that disrupts scallop kidneys. RESULTS:This study investigates host-pathogen interactions and assesses changes in population structure during BSM-associated mortality events. The research compared wild and aquacultured scallops used for stock enhancement in New York, revealing significant change in population structures throughout the mortality outbreak. The results underscore the selective pressures exerted by BSM infection and environmental stressors, as evidenced by shifts in genetic divergence and allele frequencies particularly in genes associated with kidney function, stress and infection response. Through a detailed genomic and population genetic approach, this research represents a unique case study highlighting the impact of disease on marine biodiversity and advances our understanding of the impact of summer mortality events on the scallop population in NY. CONCLUSIONS:This study highlights changes in the genomic structure of bay scallops during a BSM-associated mortality event. Identified mutations (such as the one in the nephrocystin-3-like gene) represent prime candidates for specific targeted investigations to link genotypes to phenotypes. By integrating genomic and epidemiological data, the research provides a basis for understanding the impact of disease on scallop biodiversity. These findings may help guide conservation strategies for sustainable fisheries in the face of environmental change and disease outbreaks.

Spatial refugia offered by structurally complex habitats mitigate high rates of predation for many aquatic and terrestrial prey species. These refuges are particularly important for small juvenile marine invertebrates, for which predation often represents the greatest cause of mortality. When the availability or quality of habitat landscapes and refugia are diminished by natural or anthropogenic forces, prey populations face further risk. In this study, we examined the utilization of alternative types of submerged aquatic vegetation (SAV) by juvenile bay scallops, Argopecten irradians , in a system where their historical habitat of eelgrass, Zostera marina , has largely disappeared. We found that scallops settled on and remained attached, above the bottom, to 9 species of macroalgae, 6 of which were fine filamentous or fleshy red algae. Macroalgae thus serve as suitable substrates for scallop larval settlement and early juvenile life, clearly important to successful population rebuilding that occurred following commencement of our restoration efforts. However, the much smaller maximum observed size (2–9 mm) and calculated duration of attachment (5–27 days) of scallops in the canopy of red macroalgae were considerably lower than those previously reported for eelgrass and the green macroalgae Codium fragile . With scallops dropping sooner to the bottom from red macroalgae, at smaller sizes, they are accessible to greater numbers of predator species/sizes and higher rates of predation (as shown in supporting laboratory experiments). Furthermore, this transition occurs well before scallops have undergone an ontogenetic shift to evasive swimming or have grown to reach a refuge in larger size. Fine filamentous red macroalgae, in which juvenile scallops demonstrated the highest frequency of attachment in this study and among the shortest duration in the canopy, now predominate in many areas of the Peconic Bays, New York, where eelgrass was formerly widespread. This apparent habitat degradation/replacement is thus acting to compress the length of time scallops are able to utilize a spatial refuge from predation at a critical life history stage, with potential cascading ontogenetic impacts on the use of a subsequent behavioral refuge and possible negative demographic consequences. Few prior studies have revealed such clear impacts of this kind resulting from habitat loss.

The bay scallop, Argopecten irradians, is a species of major commercial, cultural, and ecological importance. It is endemic to the eastern coast of the United States, but has also been introduced to China, where it supports a significant aquaculture industry. Here, we provide an annotated chromosome-level reference genome assembly for the bay scallop, assembled using PacBio and Hi-C data. The total genome size is 845.9 Mb, distributed over 1,503 scaffolds with a scaffold N50 of 44.3 Mb. The majority (92.9%) of the assembled genome is contained within the 16 largest scaffolds, corresponding to the 16 chromosomes confirmed by Hi-C analysis. The assembly also includes the complete mitochondrial genome. Approximately 36.2% of the genome consists of repetitive elements. The BUSCO analysis showed a completeness of 96.2%. We identified 33,772 protein-coding genes. This genome assembly will be a valuable resource for future research on evolutionary dynamics, adaptive mechanisms, and will support genome-assisted breeding, contributing to the conservation and management of this iconic species in the face of environmental and pathogenic challenges.

Warming temperatures and diminishing dissolved oxygen (DO) concentrations are among the most pervasive drivers of global coastal change. While regions of the Northwest Atlantic Ocean are experiencing greater than average warming, the combined effects of thermal and hypoxic stress on marine life in this region are poorly understood. Populations of the northern bay scallop, Argopecten irradians irradians across the northeast United States have experienced severe declines in recent decades. This study used a combination of high-resolution (similar to 1 km) satellite-based temperature records, long-term temperature and DO records, field and laboratory experiments, and high-frequency measures of scallop cardiac activity in an ecosystem setting to quantify decadal summer warming and assess the vulnerability of northern bay scallops to thermal and hypoxic stress across their geographic distribution. From 2003 to 2020, significant summer warming (up to similar to 0.2 degrees C year(-1)) occurred across most of the bay scallop range. At a New York field site in 2020, all individuals perished during an 8-day estuarine heatwave that coincided with severe diel-cycling hypoxia. Yet at a Massachusetts site with comparable DO levels but lower daily mean temperatures, mortality was not observed. A 96-h laboratory experiment recreating observed daily temperatures of 25 or 29 degrees C, and normoxia or hypoxia (22.2% air saturation), revealed a 120-fold increased likelihood of mortality in the 29 degrees C-hypoxic treatment compared with control conditions, with scallop clearance rates also reduced by 97%. Cardiac activity measurements during a field deployment indicated that low DO and elevated daily temperatures modulate oxygen consumption rates and likely impact aerobic scope. Collectively, these findings suggest that concomitant thermal and hypoxic stress can have detrimental effects on scallop physiology and survival and potentially disrupt entire fisheries. Recovery of hypoxic systems may benefit vulnerable fisheries under continued warming.

Mass mortality events, due to a variety of natural and anthropogenic causes, usually result in population (and associated fishery) crashes. Recovery from such events may not occur for many years, if at all. We have witnessed a mass die-off of adult (1+ yr) bay scallops Argopecten irradians irradians in the Peconic Bays, New York, USA, from 2019-2022, with declines in population density from spring to fall of 90-99%. Similar declines in commercial landings have occurred since 2018, with severe economic consequences for fishermen. Observed mortality levels are well above those seen prior to 2019. However, since die-offs of adult scallops have been occurring after the first seasonal spawning cycle, larval and benthic juvenile (0+ yr) recruitment have remained robust through 2021. Nevertheless, with lower numbers of adults surviving to spawn in September-October, resulting in fewer fall recruits, potential buffering of marked annual fluctuations in abundance is now less likely for this short-lived species. Peconic bay scallops are again in a precarious state as these recurring die-offs, likely driven by changing environmental conditions, present further challenges to the persistence of robust populations and the likelihood of successful restoration efforts.

The bay scallop, Argopecten irradians, represents a commercially, culturally and ecologically important species found along the United States' Atlantic and Gulf coasts. Since 2019, scallop populations in New York have been suffering large-scale summer mortalities resulting in 90-99% reduction in biomass of adult scallops. Preliminary investigations of these mortality events showed 100% prevalence of an apicomplexan parasite infecting kidney tissues. This study was designed to provide histological, ultrastructural and molecular characteristics of a non-described parasite, member of the newly established Marosporida clade (Apicomplexa) and provisionally named BSM (Bay Scallop Marosporida). Molecular diagnostics tools (quantitative PCR, in situ hybridization) were developed and used to monitor disease development. Results showed that BSM disrupts multiple scallop tissues including kidney, adductor muscle, gill, and gonad. Microscopy observations allowed the identification of both intracellular and extracellular stages of the parasite. Field surveys demonstrated a strong seasonal signature in disease prevalence and intensity, as severe cases and mortality increase as summer progresses. These results strongly suggest that BSM infection plays a major role in the collapse of bay scallop populations in New York. In this framework, BSM may synergistically interact with stressful environmental conditions to impair the host and lead to mortality.

Quantifying predator–prey interactions and gaining insights into predator behavior are crucial for optimizing restoration strategies. However, such knowledge is often lacking for marine invertebrates. We examined potential impacts of predation by channeled Busycotypus canaliculatus and knobbed whelks Busycon carica on natural and planted populations of bay scallops in the Peconic Bays, New York, through laboratory and field investigations. In lab experiments, mean predation rates exhibited by small channeled whelks were low: 0.06 and 0.005 scallops d−1 for adult and juvenile scallops, respectively. Predation rates of small knobbed whelks on juvenile scallops were 22 × higher. Eighty-six percent (86%) of scallops consumed by channeled whelks had undamaged shells, while 73% eaten by knobbed whelks had notched ventral margins. In field plots where scallop densities were manipulated via removals/plantings, whelks consumed ~ 2% of ~ 19,100 planted juveniles, whereas crabs and presumably finfish consumed > 40% overall. Acoustic telemetry revealed that tagged channeled whelks moved shorter distances and spent more time in plots planted with scallops versus those without scallops. Whelks spent more time in low versus high-density plots, but consumed far more scallops in the latter. In trials without scallops, whelk movement rates were 5 × higher, presumably due to increased exploratory behavior. Overall, whelks were most active during crepuscular hours and during periods of increasing wind speeds. Our results, combined with population abundance data, suggest that whelks (especially B. carica) are drawn to planted bay scallop aggregations, but probably contribute to relatively low overall mortality in the context of restoration efforts.

While predation impacts the abundance and distribution of prey species, the overall impact of predation varies with predator identity, predator density, and habitat complexity, among other factors. Numerous commercially and recreationally important prey species, such as bivalves, face intense predation that may affect management and restoration efforts. Therefore, predicting sites with elevated predation risk can be critical for successful restoration, although making predictions based on lab feeding assays may provide challenges. This study used bay scallops Argopecten irradians as a model organism to examine scallop abundance and survival in relation to predator density, habitat complexity, and predicted consumption, across multiple sites within the same estuary. Published predator-specific relationships between scallop consumption and habitat complexity were combined with field survey data to predict consumption potential at six sites in Shinnecock Bay, NY, USA. Using a series of Pearson correlations, the relationships between scallop abundance and tethered survival and site characteristics (habitat complexity, predator density, estimated consumption, scallop recruitment) were explored. Seagrass cover and recruitment of new individuals both strongly influenced scallop abundance, although tethered survival was not strongly correlated to any site metric (predator density, seagrass complexity, or estimated consumption). This study demonstrates potential issues when trying to link mesocosm studies to the field environment, such as sites with no seagrass but potentially confounding habitat complexity (i.e., Crepidula fornicata) and overestimates of consumption due to lack of realism in mesocosm studies. Overall, our study highlights the necessity of conducting field experiments to test mesocosm results, but also provides several valuable conclusions for shellfish restoration.

In our ongoing bay scallop restoration efforts in eastern Long Island, NY, United States, we have planted millions of hatchery‐reared juveniles to serve as broodstock when they mature. These plantings have driven the resurgence of larval recruitment, benthic population sizes, and commercial fishery landings over a 12‐year period. In this article, we detail an attempt to track the contribution of our restoration efforts to population rebuilding using planted “skunks,” an uncommon color morph, by looking for increased skunk frequencies in subsequent wild cohorts. Although we saw higher skunk frequencies among large juveniles in natural populations in the first 3 years after extensive skunk plantings, supporting use of uncommon color morphs as a passive tracer, this conclusion was not supported when examined over a 12‐year period, as no strong correlations were seen between skunk frequencies at different life stages (adult broodstock, small and large F1 juveniles, F1 adults) for respective cohorts. Potential reasons for poor correlation between skunk frequencies and restoration efforts include lower than expected production of skunk offspring, dilution of out‐planted contribution to growing natural populations, interannual variability in skunk frequencies that may have obscured the expected skunk signal, and/or differentially higher mortality of skunks at postset and larger juvenile stages. In the latter case, skunks experienced higher overwinter mortality, most likely due to predation, in 9 of 11 years. This led us to suspend skunk plantings after 3 years. Nevertheless, commercial fishermen perceived skunks to be “our” scallops, helping raise the profile of and support for our restoration efforts.

Experimental exposure of early life stage bivalves has documented negative effects of elevated pCO2 on survival and growth, but the population consequences of these effects are unknown. Following standard practices from population viability analysis and wildlife risk assessment, we substituted laboratory-derived stress-response relationships into baseline population models of Mercenaria mercenaria and Argopecten irradians. The models were constructed using inverse demographic analyses with time series of size-structured field data in NY, USA, whereas the stress-response relationships were developed using data from a series of previously published laboratory studies. We used stochastic projection methods and diffusion approximations of extinction probability to estimate cumulative risk of 50% population decline during ten-year population projections at 1, 1.5 and 2 times ambient pCO2 levels. Although the A. irradians population exhibited higher growth in the field data (12% per year) than the declining M. mercenaria population (-8% per year), cumulative risk was high for A. irradians in the first ten years due to high variance in the stochastic growth rate estimate (log λs = -0.02, σ2 = 0.24). This ten-year cumulative risk increased from 69% to 94% and >99% at 1.5 and 2 times ambient scenarios. For M. mercenaria (log λs = -0.09, σ2 = 0.01), ten-year risk was 81%, 96% and >99% at 1, 1.5 and 2 times ambient pCO2, respectively. These estimates of risk could be improved with detailed consideration of harvest effects, disease, restocking, compensatory responses, other ecological complexities, and the nature of interactions between these and other effects that are beyond the scope of available data. However, results clearly indicate that early life stage responses to plausible levels of pCO2 enrichment have the potential to cause significant increases in risk to these marine bivalve populations.

The Northern Star Coral (Astrangia poculata) is an understudied temperate scleractinian coral that inhabits hard bottom ecosystems from the northwestern Atlantic to the Gulf of Mexico and therefore can withstand significant annual shifts in temperature, salinity, and light. A. poculata is facultatively symbiotic, meaning that it can exist in both symbiotic (brown) and aposymbiotic (white) states. Here, brown and white colonies of A. poculata were collected from Virginia (VA) and Rhode Island (RI), USA and will be exposed to heat (18-30C) and cold (18-6C) acute temperature ramps during which photosynthesis (P), respiration (R), and variable fluorescence (Fv/Fm) will be measured. Thermal response curves of P, R, and Fv/Fm for A. poculata will be produced from experiments conducted in February and March 2017. Additionally, Q10 of the metabolic rates (a measure of thermal sensitivity) will be calculated for brown and white colonies of both populations and compared to look for evidence of local adaptation. This study will examine A. poculata’s response to heat and cold stress across symbiotic states and geography and provide insight into effects of future temperature increases on valuable hard bottom communities of VA and RI.

Locomotion of infaunal bivalve mollusks primarily consists of vertical movements related to burrowing; horizontal movements have only been reported for a few species. Here, we characterize hard clam walking: active horizontal locomotion of adults (up to 118 mm shell length, SL) of the commercially important species, Mercenaria mercenaria, at the sediment surface—a behavior only briefly noted in the literature. We opportunistically observed walking over a 10-yr period, at 9 different sites in the Peconic Bays, New York, USA, and tested several hypotheses for the underlying cause of this behavior through quantitative field sampling and reproductive analyses. Hard clam walking was exhibited by males and females at equal frequency, predominantly during June/July and October, when clams were in peak spawning condition. Extensive walking behavior appears to be cued by a minimum population density; we suggest it may be mediated by unidentified pheromone(s), infaunal pressure waves and/or other unidentified factors. There was no directionality exhibited by walking clams, but individuals in an area of extensive walking were highly aggregated and walking clams were significantly more likely to move toward a member of the opposite sex. Thus, we conclude that hard clam walking serves to aggregate mature individuals prior to spawning, thereby facilitating greater fertilization success. In the process of investigating this behavior, however, we apparently oversampled one population and reduced clam densities below the estimated minimum threshold density and, in so doing, suppressed extensive walking for a period of >3 years running. This not only reinforces the importance of detailed field investigations of species biology and ecology, even for those that are considered to be well studied, but also highlights the need for greater awareness of the potential for research activities to affect focal species behavior.

Intensive efforts to restore bay scallop Argopecten irradians irradians populations and fisheries in the Peconic Bays of eastern Long Island, New York, USA, were begun in 2006, following a 12 yr period during which commercial fishery landings averaged 1 to 2% of historical levels seen prior to 1985 to 1995 brown tide algal blooms. Compared to 2005 to 2006, natural population densities of 0+ yr scallops in fall increased 16x by 2007 in Orient Harbor (OH), the focus of our restoration efforts; by 2009, densities in OH and other, unplanted, embayments had increased by 110x and up to 331x, respectively. Spatial and temporal patterns paralleled those documented for larval recruitment; highly significant correlations between commercial harvest levels and both baywide larval settlement and juvenile benthic densities were revealed. Official fishery landings were 13x those of pre-restoration levels by 2010 and have remained relatively stable through 2013. Following commencement of restoration, dockside revenues and economic benefit to the regional economy have increased by similar to US$2 million and $20 million, respectively; our calculations suggest that these figures are 40% of actual numbers. Population resurgence is not correlated to temporal changes in predator populations or submerged aquatic vegetation cover. We conclude that rebuilding of Peconic bay scallop populations and fisheries has been driven by dramatic increases in bay scallop larval supply emanating from our intensive restoration efforts. By definition, we cannot say that Peconic bay scallops have attained an alternate stable state, but it is clear that dramatic increases in populations, fishery landings, and economic value are possible in just a few years.

Netminder((R)), a water-based silicone barrier release coating, was highly effective in reducing biofouling of lantern nets during grow-out/overwintering of bay scallops, Argopecten irradians irradians, in a large-scale restoration programme in New York, USA. Compared with untreated nets, scallops held in Netminder((R))-coated nets experienced reduced survival after 8months, probably due to higher loads of epibionts on their shells. However, this was countered by higher reproductive and overall condition of scallops in treated vs. untreated nets; there were no consistent differences in shell growth in different net treatments. Although further testing is recommended under a wider range of conditions, we conclude that for the purposes of our scallop restoration work, coating nets with Netminder((R)) would eliminate the need for a gear change in spring, thus reducing labour costs; the coating process should be refined so that Velcro closures of nets do not become sealed shut.