Research Project: Improving the Sustainability and Productivity of Shellfish Culture in Pacific Estuaries

Location: Pacific Shellfish Research Unit

2022 Annual Report

Objectives
The long-term goal of this project is to develop an improved understanding of the ecology of bivalve shellfish aquaculture in the estuarine environment in order to increase production by reducing mortality while ensuring that culture practices are sustainable and environmentally acceptable. Bivalves are reared on privately owned or leased tidelands in US West Coast (USWC) estuaries. This project addresses several sources of juvenile mortality and quantifies them at the estuarine landscape scale. Sub-objective 1A advances previous work on annual recruitment of larval and juvenile burrowing shrimp pests by determining whether management practices on aquaculture beds influence shrimp recruitment and subsequent survival. Juvenile shellfish are also subject to emerging pathogens like ostreid herpes virus that have the potential to severely impact oyster farming and to changing water chemistry which is known to cause problems with shell formation and growth of larvae in the hatchery, but has largely unknown effects on juveniles thereafter. Subobjective 1B aims to monitor juvenile oyster growth and mortality along estuarine gradients and determine whether planting practices can improve oyster growth and survival. Finally, USWC shellfish production is also constrained by regulatory actions regarding siting shellfish farms in the estuarine environment. Subobjectives 1C and 1D seek to model the interaction between shellfish culture production, burrowing shrimp and aquatic vegetation at the estuarine seascape scale and describe the function of these habitats for managed species of estuarine fish and invertebrates. Objective 1: Develop management practices for shellfish aquaculture that reduce juvenile mortality and optimize estuarine habitat function. Subobjective 1A: Quantify and model burrowing shrimp recruitment patterns to shellfish beds in West Coast estuaries to determine whether various bed management practices influence shrimp recruitment and survival at the landscape scale. (Dumbauld) Subobjective 1B: Quantify juvenile oyster growth and mortality at the landscape scale comparing habitats and locations as potential factors that reduce effects of stressors including reduced carbonate saturation states and disease vectors. (Dumbauld) Subobjective 1C: Quantify the effects of oyster aquaculture and burrowing shrimp on aquatic vegetation and verify models developed to examine this interaction at the estuarine landscape scale using new tools. (Dumbauld) Subobjective 1D: Quantify the function of intertidal habitats including oyster aquaculture for managed species of fish and invertebrates at the landscape scale.(Dumbauld) Objective 2: Advance and implement genome-enabled improvement technologies for the Pacific oyster. Subobjective 2A: Investigate advantages of using genome-enabled selection (GS) and develop methods for selection candidate screening to implement GS in oyster aquaculture. Subobjective 2B: Identify standing genetic variation and architecture of resistance to OsHV-1 microvariant and develop GS methods to increase resistance in the Pacific Shellfish Breeding Center population.

Approach
Conduct research to understand the ecology of bivalve shellfish aquaculture in the estuarine environment and the advantages of an enhanced breeding program that uses genome enabled selection to reduce mortality and increase production while ensuring that culture practices are sustainable and environmentally acceptable. Evaluate several sources of juvenile oyster mortality and quantify effects at the estuarine landscape scale by: 1) examining annual recruitment of larval and juvenile burrowing shrimp pests to determine whether management practices on aquaculture beds influence shrimp recruitment and survival, and 2) monitoring juvenile oyster growth and mortality along estuarine gradients and determining whether planting practices can improve oyster growth and survival in the face of emerging threats like altered seawater water chemistry but especially the ostreid herpes virus (OsHv-1) that have the potential to severely impact oyster production. Investigate the advantages of using genome enabled selection versus a selective pedigree approach and develop tools for implementing this method in oyster aquaculture. Identify the genetic architecture of resistance to OsHv-1 and its microvariants and determine the standing genetic variation for this resistance in US west coast oyster stocks. Use a multidisciplinary approach in collaboration with Oregon State University, University of California, USDA-APHIS, University of Washington, and other scientists to: 1) model the interaction between shellfish culture production, burrowing shrimp and aquatic vegetation at the estuarine seascape scale and describe the function of these estuarine habitats for managed species of estuarine fish and invertebrates and 2) lay the foundation for producing improved, disease resilient stocks in an enhanced Pacific oyster breeding program. Work with outreach and extension personnel to transfer technology to managers and shellfish industry.

Progress Report
Sub-objective 1A includes a study that compares the establishment, known as recruitment, of juvenile burrowing shrimp as pests to shellfish culture beds with that to dense colonies of shrimp outside these culture areas, and follows shrimp survival over time to determine whether culture practices (planting, harvesting by hand or dredge) influence both shrimp recruitment and survival. Progress included implementing a survey at two locations in Willapa Bay, Washington, during the period when ghost shrimp actively settle and recruit as postlarvae to this estuary and then following survival by conducting a second survey in spring 2022. Juvenile shrimp were found in dense shrimp colonies outside culture beds, but no juvenile shrimp were present inside the surveyed beds. Since some larger shrimp are present on these beds, settlement and survival will continue to be followed to determine whether larger juveniles move into the beds. A field predation and movement experiment is also expected to begin in fall 2022. In a related study, ARS researchers and collaborators in Newport, Oregon, completed an examination of larval nematode parasites found in burrowing shrimp populations along the U.S. West Coast. These larval nematodes are transmitted to a final host, usually a fish, by predation and develop to adults. Consequently, the goal of this study was to determine the final host and whether biocontrol could be achieved on shellfish beds by enhancing the abundance of larval nematodes in shrimp by a pathway that increased abundance of these fish. Having determined that the final host for these nematodes were not Pacific staghorn sculpins, progress in 2022 included collecting additional data that suggests green sturgeon might instead be the final host. This suggests that biocontrol may be less practical since sturgeon are rarely found to forage in aquaculture beds. Sub-objective 1B focuses on juvenile oyster mortality and reduced growth due to ocean acidification (OA) and the oyster herpes virus (OsHV-1). Progress was made towards examining both of these factors in 2022. Most documented effects of OA have been shown to occur for oyster larvae during initial shell formation or at metamorphosis when these larvae settle to become juveniles, referred to as “seed” commercially. The U.S. West Coast aquaculture industry has adapted to this problem by buffering water in shellfish hatcheries, but seed may still be vulnerable when planted on the shellfish grower beds in the estuary. Researchers have shown that eelgrass, an estuarine plant, can modify water chemistry through photosynthesis and carbon dioxide (C02) uptake. Data collected by ARS researchers suggested this effect might differ along the estuarine gradient and that factors other than water chemistry might be equally or more important. Progress in 2022 included completing analyses of data from an experiment confirming that this estuarine gradient in water chemistry was present but differed in two estuaries and that other factors were equally important. Initial data analyses were also completed for a more comprehensive second experiment conducted in Tillamook Bay, Oregon, in 2021 that examines these additional factors, especially food supply, which have also been shown to be influenced by eelgrass. Progress was made towards examining OsHV-1 as a source of juvenile oyster (spat) mortality, which also addresses Sub-objective 1B. This included analyzing results from a “sentinel” program implemented to track the presence of and mortality due to this virus in juvenile oysters deployed at five locations from San Diego Bay, California, to Totten Inlet, Washington. A susceptible family of genetically uniform hybrid oysters was planted at each of these sites and a second family of oysters selected to be tolerant to the reference strain of OsHV-1 were planted in Tomales Bay and San Diego Bay, California, in 2020 and 2021. Industry partners counted spat every two weeks to determine survivorship and sent samples to one of three partnering labs for analyses. Sentinel oyster spat planted at sites in Oregon and Washington demonstrated high survival in both years and tested negative for OsHV-1 in 2020. Both families of sentinel oysters planted in San Diego Bay experienced nearly 100% mortality over a two to four-week period in 2020 with all samples testing positive for a more virulent strain of the virus. The less virulent reference strain of OsHV-1 was detected in Tomales Bay where spat survival was higher for the OsHV-1 tolerant family than for the OsHV-1 susceptible family. Overall, higher survival was observed in both San Diego and Tomales Bay in 2021 with mortality occurring more gradually over the trial period compared to distinct and rapid mortality events the previous year. Sentinel oyster families were created again in 2022, but due to low growth and survival of oysters in the hatchery, these sentinel families were only planted at test sites in San Diego Bay and Tomales Bay, California. This design will nonetheless enable continued monitoring of variation in the presence and pathogenesis of both variants of the OsHV-1 virus. Sub-objective 1C concerns the use of intertidal estuarine habitats including oyster aquaculture by fish and invertebrates. New bay-wide aerial photography was captured for Willapa Bay, Washington, in 2020 and Grays Harbor, Washington, in 2021. Progress in 2022 included completing the classification of eelgrass and delineating and creating a new shellfish aquaculture layer for Willapa Bay using this imagery. This is important because regulations developed by management agencies to protect eelgrass as essential nursery habitat for commercially valuable fish, like English sole and salmon, restrict expansion of new shellfish culture in areas where eelgrass is present, and permits for existing aquaculture operations where eelgrass is present in Washington have been recently challenged. These regulations do not currently consider aquaculture as habitat and instead are designed to minimize its potential effect on eelgrass. A new effort to quantify use of intertidal habitat by fish and invertebrates was initiated in Tillamook Bay, Oregon, in 2021 as part of a broader study being conducted in several U.S. West Coast estuaries. Some of the data from this survey were analyzed in 2022 but capture of aerial imagery of Tillamook Bay was postponed until 2023 due to poor weather. This research will be immediately useful for permitting decisions regarding both current and proposed expansion of aquaculture in these estuaries. Sub-objective 2A is a new effort implemented in 2022 to investigate the potential advantages of using genomic selection in a breeding program for Pacific oysters on the U.S. West Coast. Oysters were spawned in March 2022, producing 75 bi-parental families. Unfortunately, due to poor growth after setting, low survival occurred in approximately half of the families. This required modification of the original experimental design, but research was still initiated using 28 families. Spat from each family were mixed together in common garden replicates and deployed on a farm in Tomales Bay, California. These animals will be harvested approximately 18 months after farm deployment. A set of juvenile oysters were also reared to approximately 3-4 cm shell length and used to test non-lethal DNA sampling and animal tagging protocols. These protocols will be especially useful for identifying and sampling individual juvenile oysters (under one year) as selection candidates so that a genome-enabled selection program can be used to produce the next generation of animals within an oyster breeding program. Sub-objective 2B is part of the same oyster breeding program effort implemented in 2022 to start developing oysters and germplasm that are resilient to infection by the more virulent OsHV-1 microvariant in San Diego Bay, California. The families produced in the oyster spawn described in Sub-objective 2A above were delivered to USDA-APHIS collaborators in Ames, Iowa, who obtained a sample of the microvariant from a collaborator in Davis, California, which made the deployment of juveniles to San Diego Bay unnecessary. Oysters in multiple size ranges were delivered and these collaborators are continuing to work on replicating the virus under laboratory conditions. In addition to this research, an additional collaboration was established to conduct an experiment to challenge individual breeding program families to the San Diego Bay OsHV-1 microvariant under laboratory conditions. This will provide data on how a common garden disease challenge design performs compared to this widely used pedigree challenge (single family) model. Data collection is ongoing and genetic data production and statistical analyses will occur after this fiscal year. Heritability of survival to OsHV-1 microvariant challenge and survival differences among families will be compared as well as mean survival rankings among the two challenge protocols (common garden versus single family pedigree method). Siblings of the animals tested will be deployed in Tomales Bay as part of Sub-objective 2A. This will enable a comparison of survival ranking by family to determine whether survival among oysters exposed to the Tomales OsHV-1 strain and San Diego microvariant is correlated.

Accomplishments

Review Publications
Divilov, K., Schoolfield, B., Cortez, D.M., Wang, X., Fleener, G.B., Jin, L., Dumbauld, B.R., Langdon, C. 2021. Genetic improvement of survival in Pacific oysters to the Tomales Bay strain of OsHV-1 over two cycles of selection. Aquaculture. 543. Article 737020. https://doi.org/10.1016/j.aquaculture.2021.737020.
Dumbauld, B.R., Graham, E.R., McCoy, L.M., Lewis, N. 2022. Predicted changes in seagrass cover and distribution in the face of sea level rise: Implications for bivalve aquaculture in a US West Coast estuary. Estuaries and Coasts - Journal of the Estuarine Research Federation. https://doi.org/10.1007/s12237-022-01060-2 .