Pacific staghorn sculpins (Leptocottus armatus) are recognized generalist predators that feed on ghost shrimp (Neotrypaea californiensis) in estuaries along the US West coast where these burrowing shrimp cause substantial losses to oyster aquaculture. Ghost shrimp have been shown to harbor the third larval stage of a nematode parasite Ascarophis sp. but adult nematodes have not been described nor have the final hosts been identified. We designed surveys to discover whether staghorn sculpins serve as final hosts and whether this nematode and host regulate burrowing shrimp abundance on oyster aquaculture beds. Larval nematodes identified as Ascarophis (Ascarophis) sp. A were found in several populations of ghost shrimp in four US West coast estuaries. Mean nematode abundance varied by sampling site, but not season, and was 29

The ghost shrimp Neotrypaea californiensis is a species of burrowing shrimp that negatively affects Pacific oysters Magallana gigas, by burying and suffocating these shellfish, and is considered a pest by shellfish aquaculture workers. The present study was undertaken to better understand the transmission and lifecycle of a larval spirurid nematode, Ascarophis sp., and determine whether this nematode could enhance biocontrol of ghost shrimp on shellfish aquaculture beds. We examined the relationship between mean larval Ascarophis sp. abundance in estuarine N. californiensis populations on the US West Coast and the feeding activity of migrating sturgeon Sinosturio spp., which feed on benthic organisms including N. californiensis and are potentially the definitive hosts of this nematode. Mean Ascarophis sp. abundance in N. californiensis populations was positively correlated with sturgeon feeding pit density, and parasite abundance was higher in larger N. californiensis (carapace length >= 12.5 mm). While nematode abundance in N. californiensis populations was positively related to sturgeon feeding activity, there was no evidence that nematode presence in the shrimp influenced this relationship. A laboratory experiment revealed that while N. californiensis size affected their burrowing speed, Ascarophis sp. infection did not. Our results do not support the idea that the presence of Ascarophis sp. enhances N. californiensis predation or would be useful for biocontrol. However, our findings improve understanding of the relationship between Ascarophis sp., their intermediate host, N. californiensis, and their potential final hosts, migrating sturgeon species.

Bivalve aquaculture benefits from non-chemical, operational-scale pest management tools to sustain or increase production. Mechanical methods to control a bioturbating pest (burrowing shrimp Neotrypaea californiensis) have been tested in Washington State (USA), providing a roadmap for other regions affected by native or widespread pests. These shrimp smother and bury ground-cultured oysters on tidal flats even when the shrimp are at low densities. Therefore, control methods with high efficacy are required, also considering non-target effects and costs to implement. From 2002 to 2023, 55 mechanical control trials were carried out, plus two shell-addition trials from earlier research. Methods included: 1) surface barriers, 2) shrimp removal, 3) sediment disruption, and 4) physical conditions intended to cause direct mortality (e.g. electricity, heat). Data were compiled through a meta-analysis framework, in which effect size was calculated as the log response ratio of treated relative to reference plots. Most surface barriers were not effective because they were penetrated by shrimp or insufficiently anchored; an exception was application of five inches (12.7 cm) of gravel. Shrimp removal was effective with a water-jet technique developed to collect shrimp for bait at low tide, but efforts to deploy multiple jets with a towed mechanized device were unsuccessful. Sediment disruption through surface compaction was the most common farm-scale approach but insufficiently reduced shrimp densities, whereas consolidating sediment with vibration to 1 m depth had high efficacy but has been applied only in small plots. Effect sizes were not available for any field trials of direct mortality methods, but energy required to kill shrimp was calculated from laboratory studies (1-50 kW-hr m(-3) in water, and higher energy required in saturated sediment). Across all field methods, efficacy improved with effort (person-hours per area). Sediment showed reduced penetrability and increased muddiness following treatment. Non-target effects on infauna included both positive and negative effect sizes, consistent with a community change following a reduction in shrimp density. In the six studies measuring epibenthic species, no overall positive response to control of shrimp occurred, even though the reason for control is to protect surface-dwelling species from bioturbation by shrimp. This outcome illustrates the importance of pairing efficacy in terms of reduction of shrimp and improvement of farming. The vertical position of N. californiensis below nearly a meter of water-saturated sediment, along with an innate tolerance to pressure and anoxia, has placed them out of reach of most attempted mechanical methods. Although progress has been made in recent years, mechanical control options remain limited that can be carried out without permits and that economically reduce shrimp to densities compatible with benthic shellfish aquaculture at a farm scale.

In estuaries where native eelgrass ( Zostera marina ) and Pacific oyster ( Magallana gigas ) aquaculture co-occur along the US Pacific Coast, contemporary landscape-scale distributions are essential to properly assess the interaction between these habitats and balance priorities of eelgrass conservation and sustainable aquaculture. We classified eelgrass distribution and delineated active oyster aquaculture throughout Willapa Bay, WA, using orthoimagery to examine eelgrass coverage among aquaculture practices and compare current and historical estimates. Eelgrass covered an estimated 5550 ha (or 25.7%) of the intertidal area and had not substantially changed from that of 2009. Active oyster aquaculture encompassed approximately 3096 ha of intertidal area, wherein eelgrass coverage differed among aquaculture management practices ( p < 0.001), exhibiting the highest proportional coverage (0.60) within off-bottom culture beds. Bottom-culture beds that were harvested mechanically contained lower proportional eelgrass coverage (0.27) than those harvested by hand (0.44, p < 0.001). We further demonstrated the utility of these landscape-scale datasets by integrating nekton data to develop novel abundance estimates for two managed nekton species within channel-fringing habitats. Estimated seasonal densities of juvenile Dungeness crab ( Metacarcinus magister ) and English sole ( Parophrys vetulus ) differed among aquaculture methods ( p ≤ 0.03, except for P. vetulus in spring ( p = 0.05)), with bottom culture generally containing the highest densities of both species. Species densities did not differ between areas of eelgrass presence and absence. Collectively, channel-fringing habitat composed 9% of the estuary’s expansive lower intertidal area and was estimated to support just 1.3–2.1% of the juvenile M. magister but a relatively high 13.6–23.5% of the juvenile P. vetulus throughout the same intertidal zone. These landscape-scale methodologies, datasets, and findings provide valuable information on the spatiotemporal dynamics of eelgrass and oyster aquaculture that can support stakeholder efforts to navigate the dual challenges of preserving eelgrass and supporting sustainable aquaculture.

Ostreid herpesvirus-1 (OsHV-1) is a threat to the global production of Pacific oysters Crassostrea gigas, often resulting in nearly complete mortality in affected stocks. A sentinel monitoring program was conducted between June and October 2020, to characterize OsHV-1 outbreaks in Pacific oysters along the west coast of the USA. Deployment of sentinel oysters at 5 commercial growing locations, coupled with frequent sampling, allowed measurement of the spatial and temporal occurrence of OsHV-1 outbreaks as well as the viral load and pathogenesis of OsHV-1 during C. gigas mortality events. In addition, 2 divergent oyster families were deployed at sites that have historically tested positive for OsHV-1 to measure the effect of oyster genotype on the severity of OsHV-1-induced mortality in the field. Mortality events at California test sites were associated with elevated levels of OsHV-1 in oyster tissue. OsHV-1 was not detected in oysters at Oregon and Washington test sites. In Tomales Bay, California, high variation among replicate culture units was observed in cumulative field survival and peak viral load. A negative relationship was observed between peak OsHV-1 load in oyster tissues and shell height at the time of peak viral load, suggesting larger seed may be less vulnerable during periods of OsHV-1 infection risk. Cumulative survival over the duration of the growing season in Tomales Bay was related to peak viral load and differed by family. These results corroborate previous findings suggesting selective breeding may effectively increase survival of oyster families during OsHV-1 outbreaks along the US west coast.

Species persist through resistance and recovery traits induced by natural stressors. Whether human activities exacerbate or moderate the effects of natural stressors is an open question. Because eelgrass (Zostera marina) creates coastal habitat, its response to natural stressors and human activities is of particular management importance. In this study, traits of intertidal eelgrass were examined across cumulative stressors of emersion and oyster culture, including two culture types: oysters grown directly on sediment (ground culture) or supported by gear above the sediment (off-bottom culture). Summer eelgrass was larger above- and below-ground and branched less than in spring, while density and cover were similar seasonally but declined at higher elevation and in ground culture. Eelgrass traits were divided into those related to resistance (larger above-ground size and below-ground storage) and recovery (increased flowering, branching, and rhizome extension). Resistance traits responded additively to intertidal elevation and oyster culture, with above- and below-ground size reduced in all conditions except that rhizome mass was maintained in ground culture. Smaller above-ground size may confer resistance to emersion stress, as a departure from expectations for other stressors. For resilience traits, flowering increased and internode length declined at higher elevation, whereas these traits did not change in ground culture, and off-bottom culture was associated with shorter internodes (additive cumulative stressor) and tended to moderate the enhanced flowering at higher elevations (non-additive, P=0.058). Transitory disturbance in ground culture may reduce eelgrass density with few effects on resilience, whereas off-bottom culture involves longer-term gear placement and trait responses by eelgrass.

Pacific oysters (Crassostrea gigas) were introduced to the US west coast in the early 1900's, but only regularly spawned in several discrete estuarine locations like Willapa Bay where conditions allowed for adult oyster gametogenesis as well as larval survival, retention, and settlement. Oyster industry participants have long recognized that the condition of marketable oysters was related to proximity of their growing areas to the ocean. This prompted resource managers to routinely collect data and identify trends in oyster condition index (CI) in this estuary. An analysis of this almost seven-decade long CI record revealed consistent trends across four sampling locations in Willapa Bay where 50-70% of the variability in CI was explained by a single component. This component of variability in CI was related most strongly to variability in the upwelling index (UI) which was positively correlated with CI during the summer upwelling season. A relationship with the Pacific Decadal Oscillation (PDO), a broader basin-scale index of temperature was also significant, but weaker and PDO was negatively correlated with CI. Shifts or breaks in the long-term CI record occurred in 1977/78 and 1999/2000 with another shift related to the second component of variation in CI that occurred in 1988/1989. The change in 1977/78 has previously been shown to correspond with a shift in the basin scale PDO, but more recent shifts appear to be correlated with local fluctuations in both temperature and upwelling intensity. Further investigation into shifts in the seasonal timing of temperature and phytoplankton as variables that control the oyster game-togenic cycle seem warranted.

Ocean acidification threatens many marine organisms, including oysters. Seagrass habitat has been suggested as a potential refuge for oysters because it may ameliorate stressful carbonate chemistry and augment food availability. We conducted an in situ study to investigate whether eelgrass Zostera marina habitat affects the growth of juvenile Pacific oysters Crassostrea gigas and influences local carbonate chemistry or food quantity at sites where we expected contrasting conditions in two US west coast estuaries. Juvenile oysters were out-planted in typical intertidal on-bottom (just above sediment) and off-bottom (45 cm above sediment) culture positions and in adjacent eelgrass and unvegetated habitats from June to September 2019. Water quality was measured with sondes for 24 h periods each month, and discrete water samples were collected in conjuncture. Results show that eelgrass habitat did not alter average local carbonate chemistry (pH, p CO2, Ωcalcite), but consistently reduced available food (relative chlorophyll a) . Eelgrass habitat had little to no effect on the shell or tissue growth of juvenile oysters but may have influenced their energy allocation; oysters displayed a 16% higher ratio of shell to tissue growth in eelgrass compared to unvegetated habitat when cultured on-bottom. At the seascape scale, average site-level pH was negatively correlated with shell to tissue growth but not with shell growth alone. Overall, these findings suggest that juvenile oysters may display a compensatory response and allocate more energy to shell than tissue growth under stressful conditions like acidic water and/or altered food supply due to reduced immersion or eelgrass presence.

Sea level rise (SLR) is changing coastal habitats that support valuable ecological and economic resources. A rise in global mean sea level (GMSL) will lead to changes in water depth in coastal bays and estuaries, affecting the distribution of seagrasses, which provide numerous ecosystem services, but are declining globally. In estuaries along the west coast of the USA, seagrasses often co-occur with shellfish aquaculture and some aquaculture practices negatively influence seagrass. Understanding this interaction and future shifts in seagrass distribution has therefore become a concern for both natural resource managers and aquaculturists. In this study, a model is developed to establish relationships between seagrass presence and seven predictor variables (bathymetric elevation, salinity, distance to estuary mouth, distance to nearest channel, cumulative wave stress, sediment composition and burrowing shrimp density) and then used to predict the distribution of eelgrass (Zostera marina) in aquaculture habitats of Willapa Bay, Washington, for the years 2030, 2050 and 2100 under conservative and high rates of SLR. The model predicts Z. marina will increase throughout the intertidal for all SLR scenarios and years, resulting in as much as 34% more eelgrass in Willapa Bay by 2100 and a 40% increase within aquaculture beds. By 2100, Z. marina could increase in as many as 333 of the 458 aquaculture beds examined and the majority of aquaculture beds could experience over 50% Z. marina coverage. Such increases in Z. marina will likely result in future management challenges for aquaculture operations.

Yearly mass mortalities of Pacific oysters in a major oyster-growing estuary on the West Coast of the United States (Tomales Bay, California) present a constraint to shellfish aquaculture. These mortalities have been associated with the presence of Ostreid herpesvirus 1 (OsHV-1; Tomales Bay strain) and increased seawater temperature in the estuary. In order to develop oyster families that are more tolerant to OsHV-1 than current oyster stocks, one cohort was planted in Tomales Bay per year over a three-year period, two of which were selected based on survival data collected from previous cohorts. Analyzing survival data from 23,590 oysters from 191 biparental families planted in Tomales Bay over three years, we estimated the heritability of survival on the observed and underlying liability scales to be 0.30 and 0.47, respectively. Survival breeding values increased 10.3 and 21.2 percentage points after one and two cycles of selection, respectively, suggesting that genetic selection was highly effective at producing oysters that were more tolerant of OsHV-1. The oyster families developed in this breeding program are the first in the United States specifically bred to be tolerant to OsHV-1 under elevated temperatures and will be valuable to oyster growers as well as researchers studying the genetic basis of OsHV-1 tolerance in Pacific oysters.

Temporal variation in the density and distribution of the burrowing shrimps, Neotrypaea californiensis and Upogebia pugettensis, were compared in two estuaries along the West coast of the United States (USA) where they are recognized as important ecosystem engineers. Since these shrimp construct deep burrows in the sediment, we quantified the relationship between burrow openings and shrimp density (1.5 and 1.7 burrow openings per shrimp for N. californiensis and U. pugettensis, respectively) to permit population abundance estimates to be made over broad landscape scales. Neotrypaea californiensis populations estimated from burrow counts collected using a gridded survey design across representative tide flats declined by 25% between 2008 and 2010 in Yaquina Bay, Oregon and by 67% in Willapa Bay, Washington from 2006 to 2011, but increased again in Willapa Bay by 2014. Upogebia pugettensis had mostly disappeared from Willapa Bay by 2006 and declines were observed in Yaquina Bay, but the magnitude and long-term trajectory of U. pugettensis in this estuary was less clear. These species population fluctuations mirrored those observed in density collected at discrete sampling locations over the same period, equate to large changes in secondary production, and have likely resulted in substantial changes to estuarine habitat and food webs.

Oysters and seagrasses provide structurally complex estuarine habitat for fish and invertebrate species. On the U.S. West Coast, complex oyster habitat was historically provided by the native Olympia oyster Ostrea lurida but is now provided by the commercially cultured oyster Crassostrea gigas. Ostrea lurida is found in subtidal and low intertidal areas, whereas C. gigas is predominantly cultured at higher intertidal elevations, resulting in a potential shift in available habitat for other fish and invertebrates that use this intertidal habitat. This change in the available habitat and its use was examined for the juvenile Dungeness crab Metacarcinus magister, and results showed the following: (1) comparable crab densities in remnant and restored populations of O. lurida and cultured C. gigas in two estuaries, (2) generally higher crab densities in both of these shell habitats than those observed in eelgrass Zostera marina or open mud habitat, (3) contemporary juvenile crab density in intertidal areas of Willapa Bay was most influenced by distance from the estuary mouth (declining with increasing distance) but also declined with increasing tidal elevation, and (4) when extrapolated to the estuarine ecosystem scale using areal estimates of habitat coverage, historical habitat provided by O. lurida potentially produced three times more juvenile crabs than those currently produced in cultured C. gigas. Nonetheless, both intertidal oyster habitats contribute more to juvenile crab production than eelgrass or open unstructured mud, and the ecosystem services associated with the placement of native and commercial oyster beds should be considered when defining goals for and permitting both aquaculture and native oyster restoration in Willapa Bay and other U.S. West Coast estuaries. Managers should consider this shifting temporal baseline in intertidal habitat provision, but also conducting similar evaluations at this broader estuary scale when evaluating habitat value for other resources that use these habitats differently.

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

Estuaries are subject to diverse anthropogenic stressors, such as shellfish aquaculture, which involve extensive use of estuarine tidelands. Pacific oyster Crassostrea gigas aquaculture is a century-old practice in US West Coast estuaries that contributes significantly to the regional culture and economy. Native eelgrass Zostera marina also commonly occurs in intertidal areas where oyster aquaculture is practiced. Eelgrass is federally protected in the USA as ‘essential fish habitat’, restricting aquaculture activities within or near eelgrass. To contribute scientific information useful for management decisions, we sought to compare fish habitat use of oyster aquaculture and eelgrass, as well as the edges between these 2 habitats, in Willapa Bay, Washington, USA. Furthermore, given a recent shift towards off-bottom culture methods, in part to protect seagrasses, long-line and on-bottom oyster aquaculture habitats were compared. A combination of direct (underwater video, minnow traps) and indirect (predation tethering units, eelgrass surveys) methods were employed to characterize differences in fish habitat use. Eelgrass density declined within both aquaculture habitats but less so within long-line aquaculture. Most fish species in our study used long-line oyster aquaculture and eelgrass habitats similarly with minimal edge effects, and on-bottom aquaculture was used less than either of the other 2 habitat types. These results are consistent with previously observed positive relationships between fish abundance and vertical habitat structure, but also reveal species-specific behavior; larger mesopredators like Pacific staghorn sculpins were sighted more often in aquaculture than in interior eelgrass habitats.

Abstract Background Variants of the Ostreid herpesvirus 1 (OsHV-1) cause high losses of Pacific oysters globally, including in Tomales Bay, California, USA. A suite of new variants, the OsHV-1 microvariants (μvars), cause very high mortalities of Pacific oysters in major oyster-growing regions outside of the United States. There are currently no known Pacific oysters in the United States that are resistant to OsHV-1 as resistance has yet to be evaluated in these oysters. As part of an effort to begin genetic selection for resistance to OsHV-1, 71 families from the Molluscan Broodstock Program, a US West Coast Pacific oyster breeding program, were screened for survival after exposure to OsHV-1 in Tomales Bay. They were also tested in a quarantine laboratory in France where they were exposed to a French OsHV-1 microvariant using a plate assay, with survival recorded from three to seven days post-infection. Results Significant heritability for survival were found for all time points in the plate assay and in the survival phenotype from a single mortality count in Tomales Bay. Genetic correlations between survival against the French OsHV-1 μvar in the plate assay and the Tomales Bay variant in the field trait were weak or non-significant. Conclusions Future breeding efforts will seek to validate the potential of genetic improvement for survival to OsHV-1 through selection using the Molluscan Broodstock Program oysters. The lack of a strong correlation in survival between OsHV-1 variants under this study’s exposure conditions may require independent selection pressure for survival to each variant in order to make simultaneous genetic gains in resistance.

Lack of robust aging methods for crustaceans has inhibited the use of age-structured population models. Individuals are often classified based on body size, but differences in growth can bias parameter estimates. Our study applied the lipofuscin aging method combined with catch-curve analysis to estimate mortality rate for the burrowing shrimp, Neotrypaea californiensis. This species is an important member of the estuarine community with an impact on oyster production along the US West Coast. Randomized surveys were conducted from 2011 to 2014 to estimate population abundance, average density, and age structure in Yaquina Bay, Oregon. Mortality rate was estimated to be 0.719 yr−1 (95% CI; 0.633–0.793 yr−1) and did not vary significantly across cohorts. The spatial extent of the survey revealed spatial patterns in shrimp density that could be explained by variation in mortality and recruitment rates. This is the first study to apply lipofuscin aging to estimate population parameters of an estuarine crustacean and the methods we present can inform managers seeking to incorporate population ecology into management plans for N. californiensis and other crustacean species worldwide.

AbstractThe burrowing shrimp Neotrypaea californiensis is an important ecosystem engineer that inhabits estuaries along the US Pacific Northwest coast. This species plays an important role in the estuarine ecosystem but negatively impacts oyster aquaculture through its burrowing activities. Development of population models for burrowing shrimp management requires more detailed life history information and accurate estimates of age. Ageing studies have been limited for crustaceans because it is generally believed that they do not retain structures with annual deposits commonly used to age other marine organisms, when they moult their exoskeletons. A mesocosm growth experiment and field surveys were combined to compare the performance of two ageing techniques, quantification of autofluorescent lipofuscin and gastric mill ossicular lamellae, for estimating age in N. californiensis. Animals of known age were grown in outdoor mesocosms and sampled regularly to correlate age metrics with body size and true age. Lipofuscin concentration increased with time across multiple cohorts at the rate of 1.430 ± 0.060 ng µg−1 year−1. Lamellae counts also increased with time (4.922 ± 0.337 lamellae year−1). While age estimates based on lipofuscin concentration and lamellae counts generally agreed, carapace size did not correlate to either age metric. Lamellae counts from field collections suggest they are added sequentially with age but the relationship can vary by location. When used together, the application of both techniques may provide robust estimates of crustacean age especially when size-based measurements are imprecise.