Location: Pacific Shellfish Research Unit
2024 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 where the establishment (recruitment) of juvenile burrowing shrimp as pests to shellfish culture beds is compared with that of dense colonies of shrimp outside culture beds and follows shrimp survival over time to determine whether culture influences both shrimp recruitment and survival. A previous survey implemented in Willapa Bay, Washington, revealed that juvenile shrimp recruit to areas outside culture beds, but do not recruit to, or their survival is low, in these beds. ARS researchers continued to monitor the changing distribution of shrimp across broad tideflats adjacent to culture beds in 2023 and 2024. Adult shrimp populations have been shifting since 2019 and declining shrimp abundance has allowed oyster culture to again take place in some areas while in others shrimp have moved in and culture has been abandoned. ARS researchers determined that juvenile shrimp recruit to areas where dense shrimp beds have contracted, but they do not persist.
Sub-objective 1B focuses on juvenile oyster mortality and reduced growth due to ocean acidification (OA) and the oyster herpes virus (OsHV-1). Most documented effects of OA have been shown to occur for oyster larvae, but juvenile oysters may still be vulnerable when planted on beds in the estuary. Eelgrass, an estuarine plant, can modify water chemistry through photosynthesis and carbon dioxide uptake and thus co-planting oysters with eelgrass has been suggested as a strategy for adapting to OA. ARS researchers found that both water chemistry and the effect of eelgrass on oyster growth were site dependent within estuaries and oysters appeared to devote more energy to shell than tissue growth under stressful conditions. Further analysis of results from a second experiment suggested that density of eelgrass affected the quality of food available to juvenile oysters, and this could be responsible for observed site differences in juvenile oyster growth rather than the effect of eelgrass on seawater chemistry.
Addressing Sub-objective 1B, progress continued towards examining OsHV-1 as a source of juvenile oyster mortality in the field. This included further deployments and analysis of results from a “sentinel” monitoring program implemented in 2020 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 and a family selected for tolerance to OsHV-1 were planted in Tomales Bay and San Diego Bay, California, and the susceptible family planted at sites in Oregon and Washington. Oysters were counted every two weeks to determine survivorship and samples sent to partnering labs for analyses. Sentinel oysters planted at sites in Oregon and Washington demonstrated high survival and tested negative for OsHV-1. Both families of sentinel oysters planted in San Diego Bay experienced nearly 100 percent mortality in 2020, with all oysters testing positive for a more virulent strain of the virus (OsHV-1 microvariant). Results confirmed that selected stocks survived better and were tolerant, not resistant to the non-microvariant strain of OsHV-1 in Tomales Bay. Though occurrence and timing of mortality events differed in 2021-2023, oysters selectively bred for tolerance to the non-microvariant survived better than the susceptible family in Tomales Bay, whereas the opposite was true in San Diego Bay. Data is currently being analyzed, but this mortality is not yet linked to presence of either viral strain in oysters at either location. The crossed experimental design was implemented again in 2024 and is important because it enables continued monitoring of variation in the presence and pathogenesis of both variants of the OsHV-1 virus in the field.
Sub-objective 1C concerns quantification of intertidal estuarine habitats, including oyster aquaculture and use of these habitats by fish and invertebrates at landscape scales. Progress included using the completed geographic information system (GIS) layers for aquaculture and eelgrass created with 2020 ortho-imagery for Willapa Bay to quantify the interaction between eelgrass and oyster aquaculture at the estuarine seascape scale and compare results with previous estimates made using 2009 imagery. ARS researchers continued to quantify use of intertidal aquaculture and eelgrass habitat by fish and crab utilizing previous seine net data collected by project collaborators. Catch data was apportioned to estuary scale using estimates of available habitat focusing on the most frequently used areas close to subtidal channels. An accurate intertidal layer was created and eelgrass classification initiated for Grays Harbor, Washington, using 2021 imagery. This research will continue to be used for permitting decisions regarding both current and proposed expansion of aquaculture in estuaries and continues to be important since permits for existing aquaculture operations where eelgrass is present have been recently challenged.
Sub-objective 2A is a new effort to investigate the potential advantages of using genomic selection in a new ARS Pacific oyster genomic selection (POGS) breeding program for oysters on the West Coast. Non-lethal tissue sampling and animal tagging methods were refined and a high-throughput protocol developed. ARS researchers also evaluated whether non-lethal swab and tissue samples from the same individual returned the same genotype to ensure the protocol would be effective. The evaluation of genomic selection for improving selection accuracy is ongoing. Oysters from the Oregon State University (OSU) Molluscan Broodstock program (MBP) 2022 cohort had poor on-farm survival, so the experiment was repeated with oysters from the POGS 2023 year class (YC2023) to more robustly evaluate the hypothesis. In support of Subobjective 2A, ARS researchers in Newport, Oregon, contributed to the creation and publication of a novel genetic panel that enables lower cost relationship assignment. This panel will be used to assign oysters back to their parents, enabling common-garden experiments where families are grown together and later genotyped eliminating environmental variance and simplifying logistics associated with breeding program operations.
Sub-objective 2B is part of the POGS breeding program designed to begin developing germplasm with high survival when exposed to microvariant strains of OsHV-1. POGS YC2023 families were evaluated for survival in multiple experimental challenges. A petri dish challenge model was used to quickly evaluate survival differences among populations and families. Results from that study indicate that a Midori population imported from southern Japan has higher survival to laboratory exposure of OsHV-1 microvariant than the Miyagi population, which has been the focus of OSU MBP selection efforts. All POGS YC2023 families were deployed in Tomales Bay to assess field performance where the non-microvariant OsHV-1 occurs and will be harvested in Fall 2024 to assess if laboratory and field survival are correlated. A separate experiment using a subset of 2023 POGS Midori and Miyagi families was conducted to evaluate survival to three OsHV-1 microvariant strains. Laboratory processing of these samples began in Summer 2023 and genotyping continues. The first experimental evaluation of Pacific oyster response to the OsHV-1 microvariant in San Diego Bay was conducted to examine two challenge methods and the heritability and opportunity to improve survival in the Miyagi population. Determining which Pacific oyster genes respond to OsHV-1 and the genetic backgrounds in which these genes are expressed to confer tolerance can inform genetic selection. Total RNA was extracted from 42 Midori and Miyagi samples (challenged with OsHV-1 microvariant and controls) and sequenced. Data is being analyzed to evaluate transcript and small-RNA abundance in infected vs. control samples from both populations. ARS scientists continued to collaborate with OSU researchers to develop selectively bred oyster stocks exhibiting tolerance to the non-microvariant strain of OsHV-1 in Tomales Bay. This research identified candidate genes associated with field survival to the non-microvariant to further marker assisted selection as a tool for breeding programs.
Experimental evaluation of POGS YC2024 cohorts is underway with 59 families challenged in July 2024 and 80 families expected to be challenged in September 2024. Given laboratory results from YC2023, an emphasis was placed on expanding the Midori population to create a suitable breeding population and 126 Midori families created in YC2024. If results from lab challenges continue to support higher survival for Midori than Miyagi families when exposed to OsHV-1, the POGS project will focus future selection efforts on the Midori population.
ARS scientists conducted whole genome re-sequencing of 100 individual oysters from five potentially segregated populations, including individuals that were part of the MBP and naturalized oysters from San Diego Bay and Willapa Bay. Results suggest that these populations can be genetically differentiated and that the MBP Cohort 30 (YC 2021) population, which has undergone selective breeding for desirable traits since the 1990s, was most distinct, while a founder population for MBP was more similar to naturalized populations from Willapa Bay. The Midori population from southern Japan was also distinguishable and nucleotide diversity tests within each of the five populations show that naturalized and founder groups have more DNA diversity than MBP Cohort 30. Collectively, this suggests that existing populations of oysters can support a robust breeding program, but MBP cohorts alone might lack enough diversity. This data will also be used to examine regions of the genome that may have conferred adaptation in naturalized populations.
Accomplishments
1. New genetic panel reduces cost for relationship assignment in Pacific oyster breeding program populations. Genotyping is a significant cost that often limits aquaculture breeding programs from developing genomic selection programs and utilizing common-garden evaluations where families are co-mingled and experience the same conditions. Popular genotyping methods for breeding include array technologies which rely on economies of scale and require expensive equipment and expertise to operate. ARS researchers in Newport, Oregon, developed a novel genetic panel that can be generated with standard laboratory equipment and is scalable depending on program size. This panel can be effectively utilized in multiple breeding programs on the Pacific Coast and advances Pacific oyster breeding enabling common-garden evaluations and relationship assignments necessary for imputation based genomic selection programs.
Review Publications
Thompson, N., Agnew, M.V., Calla, B., Burge, C.A. 2024. Assessing selection potential for Pacific oyster (Crassostrea gigas) to a North American OsHV-1 µvar: Comparing two experimental assay methods. Aquaculture. 590. Article 741076. https://doi.org/10.1016/j.aquaculture.2024.741076.
Dumbauld, B.R., Mc Intyre, B.A. 2023. Influence of seagrass on juvenile Pacific oyster growth in two US west coast estuaries with different environmental gradients. Aquaculture Environment Interactions. 15:287-306. https://doi.org/10.3354/aei00466.
Sutherland, B.J., Thompson, N., Surry, L.B., Gujjula, K., Carrasco, C.D., Chadaram, S., Lunda, S.L., Langdon, C.J., Chan, A.M., Suttle, C.A., Green, T.J. 2024. An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. G3, Genes/Genomes/Genetics. Article jkae125. https://doi.org/10.1093/g3journal/jkae125.