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ARS Home Pacific West Area Newport, Oregon Pacific Shellfish Research Unit Research





- Dumbauld, Brett
- Thompson, Neil
- Calla, Bernarda
- 2023
- 2022
- 2021
- 2020
- Publications
- Aquaculture (106)

Research Project: Improving the Sustainability and Productivity of Shellfish Culture in Pacific Estuaries **Location:
                            Pacific Shellfish Research Unit** 2023 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 these culture areas and follows shrimp survival over time to determine whether culture practices influence both shrimp recruitment and survival. A survey implemented in Willapa Bay, Washington, revealed that juvenile shrimp recruited to areas outside culture beds, but few juveniles were found inside culture beds. Juvenile densities declined over time, but small shrimp were only present outside the culture beds when a follow-up survey was conducted, suggesting that shrimp either do not recruit to or abundance is relatively quickly reduced in culture beds. Progress in 2023 included analysis of additional data for larger shrimp, which were present both inside and outside these beds but increased over time suggesting that larger shrimp had moved in. ARS researchers have been monitoring the changing distribution of shrimp across tideflats adjacent to culture beds in Willapa Bay. Progress included collecting additional spatial data to track contracting areas of high shrimp density and sampling shrimp in both areas to contrast with data collected at established monitoring locations. Declining shrimp abundance has allowed oyster culture to again take place in once abandoned areas, but if larger shrimp move into adjacent aquaculture beds, this must also be evaluated.

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 in examining both these factors. Most documented effects of OA have been shown to occur for oyster larvae and the West Coast aquaculture industry has adapted to this problem by buffering acidic water in shellfish hatcheries, 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 suggested as a strategy for adapting to OA. Data collected by ARS researchers showed that eelgrass presence did not influence average pH in the field but reduced available food. Site dependent effects on oyster growth suggested that factors other than OA might be equally or more important. Progress included a re-analysis of data from this experiment suggesting that shell size may not represent growth, since oysters appeared to devote more energy to shell than tissue under stressful conditions. Analysis of results from a second experiment conducted in Tillamook Bay, Oregon, was also completed suggesting that the density of eelgrass and the quality of food available may also be responsible for site dependent effects.
  
Progress was also made towards examining OsHV-1 as a source of juvenile oyster mortality, which addresses Sub-objective 1B. This included 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 to be tolerant to OsHV-1 were planted in Tomales Bay and San Diego Bay, California, in 2020 and 2021. Oysters were counted every two weeks to determine survivorship and samples were 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 from Tomales Bay showed that peak viral load was correlated with survival and confirmed that selected stocks were tolerant and not resistant to the reference strain of the virus. Due to differences in growth and survival of oysters in the hatchery, the sentinel program only utilized two separate families at test sites in San Diego Bay and Tomales Bay in 2022 and 2023, but this design 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 and will be adapted and used to evaluate OsHV-1 and other stressors in the new USDA-ARS breeding program.

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 capture of new bay-wide aerial imagery of Tillamook Bay and Netarts Bay, Oregon, completing the spatial geographic information system (GIS) layer for aquaculture using 2020 imagery for Willapa Bay and classifying eelgrass habitat for Grays Harbor, Washington, using 2021 imagery. ARS researchers continued to quantify use of intertidal habitat by fish and invertebrates in several West Coast estuaries. Progress in 2023 included finalizing analysis of data from underwater video surveys using new cameras in Tillamook Bay and obtaining data collected by collaborators to expand analyses to the landscape scale using new GIS layers for habitat in Willapa Bay. This research will be used for permitting decisions regarding both current and proposed expansion of aquaculture in these 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 breeding program for oysters on the West Coast. The USDA-ARS Pacific Oyster Genomic Selection (POGS) breeding program was officially announced in January 2023, and has conducted two spawns producing a total of 167 families in 2023. Pacific oyster families are being used to evaluate whether genomic selection improves prediction accuracy for wet weight. Animals produced in collaboration with Oregon State University’s Molluscan Broodstock Program (MBP) and deployed at a farm site in Tomales Bay in 2022 are expected to be harvested in December 2023. Progress was made on non-lethal tagging and DNA collection methods, but mortality rates associated with sampling procedures have not been acceptable for large scale deployment of animals younger than one year of age. The experiment has been modified to use larger, older animals that are potentially more robust to tagging and DNA sampling stress and animal tagging will occur in 2023.

Sub-objective 2B is part of the POGS project to begin developing germplasm that is tolerant to infection by more virulent microvariant strains of OsHV-1. POGS families are currently being assayed for OsHV-1 tolerance by a collaborating lab. Seventy-two families were tested in June 2023, and an additional set of 72 families will be tested in September 2023. All POGS families tested in the laboratory will be deployed at a farm site in Tomales Bay, where the less virulent non-microvariant form of OsHV-1 occurs to assay if laboratory tolerance to microvariant infection is correlated with field survival. A separate experiment was conducted using a subset of 2023 POGS families. This experiment seeks to evaluate tolerance to three OsHv-1 microvariant strains using two Pacific oyster populations. Laboratory processing of these samples began in Summer 2023. Prior samples from an experiment with an OsHV-1 microvariant found in San Diego Bay conducted in June 2022 were processed and genetic data produced. Analysis comparing common-garden vs. petri dish methods, estimating heritability of survival, and assaying standing genetic variation is being finalized. This is the first experimental evaluation of Pacific oyster response to an OsHV-1 microvariant found on the Pacific coast of the United States. Siblings of the experimentally tested oysters were deployed in Tomales Bay and will be harvested in December 2023. 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. Oysters from two genetic backgrounds were tested against three strains of the OsHV-1 microvariant to examine gene expression. Samples for RNA-seq are being processed for sequencing and data analyses will be conducted during the second half of 2023. ARS scientists continued to collaborate with Oregon State University researchers to develop selectively bred oyster stocks exhibiting tolerance to the less virulent reference strain of OsHV-1. This research has identified candidate genes associated with field survival and was published to further marker assisted selection as a tool for breeding programs.
  
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 to further identify available genetic variation in Pacific oyster populations. Preliminary analyses show that these populations can be genetically differentiated. The 2021 cohort population, which has undergone selective breeding for desirable traits since the 1990s, was most genetically distinct, while a founder population for the MBP breeding program was more similar to naturalized populations from Willapa Bay. A population collected from southern Japan, but not used in the MBP, was also genetically distinguishable. Further analysis to obtain estimates of population differentiation and nucleotide diversity are ongoing. Collectively, this suggests that existing populations of oysters along the Pacific Coast can support a robust breeding program. This data will also be used to examine regions of the genome that may have been naturally selected and conferred adaptation in naturalized populations. **Accomplishments**
                                

1. New breeding program established to provide tolerance to OsHV-1 virus in oysters. Utilizing modern genetic and genomic methods, ARS scientists in Newport, Oregon, and collaborators at Oregon State University, made significant advances in developing an oyster breeding program to address the threat of oyster herpesvirus (OsHV-1), a threat to oyster production in the United States and abroad. This research included identifying markers associated with field survival in Tomales Bay which enables marker assisted selection efforts and successfully challenging oysters with the more virulent strain of OsHV-1 from San Diego. ARS scientists in Providence, Rhode Island, and Newport, Oregon, also developed a novel genomic selection workflow that is the foundation for the new ARS Pacific Oyster Genomic Selection project. This has positioned this project to address the immediate disease threat and produce an OsHV-1 tolerant population of oysters for commercial propagation. **Review Publications**
                            *Tsvetkov, N., Bahia, S., Calla, B., Berenbaum, M.R., Zayed, A. 2023. Genetics of tolerance in honeybees to the neonicotinoid clothianidin. iScience. 26(3). Article 106084. https://doi.org/10.1016/j.isci.2023.106084.*
                                *Ngumbi, E., Dady, E., Calla, B. 2022. Flooding and herbivory: The effect of concurrent stress factors on plant volatile emissions and gene expression in two heirloom tomato varieties. BMC Plant Biology. 22. Article 536. https://doi.org/10.1186/s12870-022-03911-3.*
                                *Delomas, T.A., Hollenbeck, C.M., Matt, J.L., Thompson, N. 2023. Evaluating cost-effective genotyping strategies for genomic selection in oysters. Aquaculture. 562:738844. https://doi.org/10.1016/j.aquaculture.2022.738844.*
                                *Dumbauld, B.R., Du, X., Hunsicker, M., Forster, Z. 2023. Multi-decade changes in the condition index of adult Pacific oysters (Crassostrea gigas) in response to climate in a US west coast estuary. Journal of Sea Research. 193. Article 102383. https://doi.org/10.1016/j.seares.2023.102383.*


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