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

Location: Forage Seed and Cereal Research Unit

2021 Annual Report

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.

Conduct research to understand the ecology of bivalve shellfish aquaculture in the estuarine environment in order 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 pathogens like ostreid herpes virus and altered seawater water chemistry that have the potential to severely impact oyster farming. Develop a multidisciplinary approach in collaboration with Oregon State University, University of Washington, and other scientists to 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. 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 to shellfish culture beds with that to dense colonies of shrimp outside these culture areas and follow shrimp survival over time to determine whether culture practices themselves might influence both recruitment and survival. Progress included re-evaluating our initial choice of sites for conducting and implementing this survey after discussion with a working group and project collaborators who initiated a project to monitor shrimp populations on shellfish beds in Willapa Bay, Washington, in Fall 2020 and Spring 2021. We monitored shrimp recruitment to our long-term monitoring locations in dense shrimp colonies at different time points to make initial comparisons. We revisited some of the adjacent shellfish beds and will use the data collected to design and implement a complete survey beginning Fall 2021. We established sites and monitored shrimp recruitment across various estuarine gradients, such as tide height and distance to channel, in Yaquina Bay, Oregon. We also completed some laboratory predation experiments with staghorn sculpins. A field predation/movement experiment is expected to be initiated in Fall 2021. In a related study with collaborators at Oregon State University (OSU), we completed an examination of larval nematode parasites found in burrowing shrimp populations along the U.S. West Coast and determined that the final host for these nematodes does not appear to be staghorn sculpins, though they do prey on the shrimp. These larval nematodes are suspected of indirectly causing shrimp mortality by affecting shrimp behavior. The goal of this study was in part to see whether abundance of these nematodes in shrimp, and therefore their final host, could perhaps be enhanced on shellfish beds. This was a significant result because it indicates that sculpins may benefit from nematode presence in shrimp, but some other vector is necessary for larval nematode spread. Sub-objective 1B focuses on juvenile oyster mortality and/or reduced growth due to ocean acidification (OA) and the oyster herpes virus (OsHv-1). Progress was made on examining both of these factors in 2021. Most documented effects of OA have been shown to affect oyster larvae during initial shell formation or at metamorphosis when these larvae settle to become juveniles, when they are 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 via photosynthesis and carbon dioxide (C02) uptake. Data collected by ARS researchers suggested that this effect might differ along the estuarine gradient and that factors other than water chemistry might be important. Progress in 2021 included completing analyses of most of the data from an experiment conducted in 2019 to examine the effect of eelgrass on oyster survival and growth in two estuaries with expected differences in estuarine water chemistry gradients and designing and implementing a new experiment to examine food supply alongside water chemistry variables. Progress was made towards examining OsHV-1 as a source of juvenile oyster mortality, which also addresses Sub-objective 1B. This included analyzing the 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 deployed at all of these sites in June 2020 and a second family of oysters selected to be tolerant to OsHV-1 (over two generations in Tomales Bay, California) were planted in San Diego Bay and Tomales Bay. Sentinel oyster spat at sites in Oregon and Washington all demonstrated high survival and tested negative for OsHV-1. The virus was detected at both California test sites (San Diego Bay and Tomales Bay). Sentinel oysters from both families planted in San Diego Bay experienced nearly 100% mortality over a two to four-week period and all samples tested positive for an OsHV-1 µvar that was found to be genetically identical to a microvariant strain of this virus detected in San Diego in 2018. The less virulent reference strain of OsHV-1 was also detected in Tomales Bay, where spat survival was higher for the OsHV-1 tolerant family than for the OsHV-1 susceptible family. Oysters planted in June had higher survival than those planted later in July. Peaks in mortality were associated with warm temperature events. Oysters were saved, and analysis and quantification of the bacterial species present is ongoing. This analysis will pay particular attention to target species, such as those in the genus Vibrio, that have been previously associated with oyster deaths after OsHV-1 infection. Sub-objective 1C concerns the use of intertidal estuarine habitats, including oyster aquaculture by fish and invertebrates. New bay-wide aerial photography for Willapa Bay was captured in 2020, and progress in 2021 included completing a new analysis for eelgrass using this imagery. This is important because regulations developed by management agencies to protect eelgrass as essential nursery habitats 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 a habitat and instead simply 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. This research will be immediately useful for permitting decisions regarding both the current and proposed expansion of aquaculture in these estuaries. Research continued, and progress was made on developing OsHV-1 disease-resistant oysters. A third generation of resistant oyster families was selected, paired matings made in the hatchery, and juvenile oysters planted in Tomales Bay and Willapa Bay. Crosses to produce about 100 oyster families were carried out in March 2021 among parents with the highest predicted survival breeding values for the Tomales Bay OsHV-1 strain, based on data from all three past cohorts planted in Tomales Bay. In addition, a subset of crosses was made between individual oysters that carried several genetic DNA markers identified to be associated with tolerance to OsHV-1. This experimental planting included two types of control families for comparison: a) “wild control” crosses made among naturalized oysters collected from southern Willapa Bay and b) crosses between several highly inbred lines maintained by the breeding program. Oysters were planted in San Diego Bay, where an OsHV-1 microvariant was found in the 2020 sentinel oyster plantings described above. Survival will be evaluated and compared among families to determine if survival against the OsHV-1 Tomales Bay strain and the San Diego OsHV-1 microvariant strain are correlated. Progress was also made with the completion of a new high-quality genome for the Pacific oyster that is being compared with similar genomes constructed by scientists in the United Kingdom and China.

1. A multi-state oyster herpesvirus detection program was established. The Ostreid herpesvirus 1 (OsHV-1) has severely impacted Pacific oyster production around the globe. Though this disease was first detected in the United States in 1995 in Tomales Bay, California, a more virulent microvariant strain was detected in San Diego Bay, California, in 2018. Recognizing the risk of regional spread, a multi-state sentinel program was initiated by ARS researchers in Newport, Oregon, and collaborators to monitor the prevalence and disease development of OsHV-1 in naïve and genetically uniform hybrid oysters planted at commercial farms in California, Oregon, and Washington. A second family of oysters selected for OsHV-1 tolerance was planted for comparison in San Diego and Tomales Bay. Oyster mortalities were almost 100% for both families in San Diego Bay where the microvariant was again identified. Mortalities also occurred in Tomales Bay, but survival was higher for the tolerant family. Mortality events occurred during high seawater temperature spikes and followed peaks in the amount of virus present. This was important because it established a consistent protocol for a more extensive OsHV-1 monitoring and research program.

Review Publications
Dumbauld, B.R., McCoy, L.M., Dewitt, T.H., Chapman, J.W. 2021. Estimating long-term trends in population declines of two ecosystem engineering burrowing shrimps in Pacific Northwest (USA) estuaries. Hydrobiologia. 848. 993-1013.
Muething, K.A., Tomas, F., Waldbusser, G., Dumbauld, B.R. 2020. On the edge: assessing fish habitat use across the boundary between Pacific oyster aquaculture and eelgrass in Willapa Bay, WA. Aquaculture Environment Interactions. 12:541-557.
Agnew, M., Friedman, C.S., Langdon, C., Konstantin, D., Schoofield, B., Morga, B., Degremont, L., Dhar, A.K., Kirkland, P., Dumbauld, B.R., Burge, C.A. 2020. Differential mortality and high viral load in naive Pacific oyster families exposed to OsHV-1 suggests tolerance rather than resistance to infection. Journal of Pathogens. 9(12):1057.
Dumbauld, B.R., Murphy, J., McCoy, L., Lewis, N. 2021. A comparison of juvenile Dungeness crab (Metacarcinus magister) produced in current oyster aquaculture versus historical native oyster habitat in a U.S. West Coast estuary. Journal of Shellfish Research. 40(1):161-175.