Current Research at Milford Laboratory

NOAA Fisheries' primary mandates are to use sound science to manage and conserve the nation's ocean resources and habitats, and to ensure their renewability for the future. Although our techniques have advanced over the years, the Milford Laboratory has always made strong positive contributions to meeting these objectives.

Current research at the Milford Laboratory emphasizes shellfish aquaculture and ecosystem-related work. Our well-integrated aquaculture research program evaluates current and proposed marine aquaculture practices for technical effectiveness, environmental compatibility, and sustained commercial success. Working closely with industry partners, we provide shellfish aquaculture science and develop new methods and technologies to enhance production. In addition, we study the interactions between aquaculture practices and coastal marine habitats and species. Our research supports the sustainable expansion of domestic aquaculture.

Our scientists are trained in a wide variety of disciplines, including chemistry, ecology, physiology, biochemistry, genetics, immunology, bacteriology, algology, and pathology. The versatility of both the facility and our staff at the Milford Lab make this unique blend of research possible.

Shellfish Aquaculture

Probiotic Bacteria for Use in Shellfish Hatcheries

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Bacterial disease can be a major cause of death among shellfish larvae in commercial hatcheries. In the United States, hatcheries do not use antibiotics to control these diseases. While some bacteria can cause lethal disease, other strains of bacteria can actually protect larvae from it, improving hatchery production and reducing costs. These “good” bacteria are called “probiotics,” the Latin for “promote life.”

The Milford Lab discovered and developed a probiotic bacterial strain labeled OY15, a benign strain of Vibrio alginolyticus isolated from the digestive glands of oysters, as an environmentally-friendly way to manage bacterial shellfish pathogens in hatcheries. This naturally-occurring bacterium provides disease resistance to Eastern oyster larvae, improving survival by 20 to 35 percent when challenged with the known larval shellfish pathogen Vibrio corallilyticus. Our research confirmed that probiotic strain OY15 works by stimulating the defense abilities of oyster hemocytes (similar to white blood cells) to respond to and eliminate harmful bacteria.

The Milford Lab is collaborating with public and private industry partners to commercialize OY15 for use as a feed supplement in commercial hatcheries. Prospective Research, a private biotech firm in Massachusetts, has manufactured a freeze-dried powder formulation of OY15, and provided it to the Milford Lab. With funding from the NOAA Office of Aquaculture, we have successfully beta-tested this new formulation of OY15 on Eastern oyster larvae in collaboration with public and private shellfish production hatcheries.

Preliminary data from a trial on Pacific oyster larvae performed at Hawaiian Shellfish Oyster Hatchery suggest that growth and performance of OY15-treated larvae were markedly better than for larvae not treated with OY15. To confirm OY15’s probiotic effects on Pacific oyster larvae, three commercial Pacific oyster hatcheries will perform hatchery-scale trials during the 2021 season—two in the U.S. Pacific Northwest and one in Ireland.

If we confirm that OY15 effectively improves performance and survival of two different species of oyster larvae in hatchery-scale trials, that may be an indication that the benefits of OY15 are more widely applicable. Success with Pacific oysters will likely increase the market for OY15, as this species is the most widely cultured oyster worldwide. Prospective Research plans to make this probiotic strain commercially available. This transfer of natural and environmentally-friendly methods of controlling disease from the lab to commercial oyster aquaculture facilities will help increase sustainable aquaculture production.

Learn more about the NOAA Technology Transfer Program

• An Irish Oyster Farmer and a CEO of an Aquaculture Research Company Discuss the Future of Probiotics

For more information, contact Diane Kapareiko.

Shellfish Genetics

A major focus of the Genetics research program is to investigate the application of genetics and breeding technology for improving growth and survival of economically and ecologically valuable shellfish, which have declined, such as bay scallops. Results could contribute to increased commercial production, recreational harvesting, and reduced imports. Three major approaches are being explored for culture, enhancement and restoration: breeding, population or molecular genetics, and field evaluations. Responses to selective breeding, inbreeding and hybridization are being determined by developing lines for increased growth and survival, with positive results previously with oysters and currently with scallops. In addition, genetic diversity of various stocks and populations is being ascertained with molecular technology to support or complement breeding and broodstock management. Molecular (e.g., DNA) analyses are investigated for genotypic markers and expression in stock identification, with innovative biotechnology methods applicable to other shellfish species and different marine organisms from bacteria to fish. Habitat and environmental suitability and field performance evaluations also are being conducted with phenotypic markers such as striped shells credited to us. Observations are made on differences in growth and survival of shellfish under various conditions, comprising laboratory and field components. There are collaboration, outreach, resource and technology transfer activities.

Shellfish Immune Status

Hemocytes, essentially blood cells, in bivalves such as oysters, clams, scallops, and mussels, are responsible for various physiological functions including immune defense, nutrition, and waste disposal. By understanding the functions and responses of these cells to environmental conditions, we are able to gain insight into the ability of hemocytes to maintain health when exposed to environmental stresses. We are able to achieve this understanding with the use of physiological probes, coupled with microscopy and flow cytometric applications in both laboratory and field settings. Eastern oysters, northern quahogs, bay scallops, blue mussels, and soft-shell clams, all species of economic or ecological importance in coastal habitats, are being studied. Ultimately, an improved understanding of the effects of changing environmental conditions on the health of farmed and wild-harvest shellfish will aid in local and national decision making.

For more information, contact Gary Wikfors.

Modeling to Predict the Spread of Oyster Disease

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Oyster herpes virus OsHV-1 μvar has caused major die-offs of juvenile oysters in Europe, Australia, and New Zealand. The virus is a potential threat to U.S. oyster populations, as infected Pacific oysters have been detected in California. To evaluate the risk of spread and transmission of the virus in Pacific oyster populations along the West Coast, we are adapting a mathematical disease simulation model. The model incorporates oceanography, ecology, and epidemiology, and we are developing it in collaboration with our partners at the National Centers for Coastal Ocean Science, IFREMER, and Oregon State University.

Understanding and anticipating the risks this virus poses to U.S. oysters is important to protect both cultured and natural populations. The model will serve as a framework for disease management in aquaculture, informing practices and policies that promote aquatic animal health.

For more information, contact Gary Wikfors.

Aquaculture and Environmental Interactions

Measuring the Ecosystem Benefits Provided by Shellfish Farms

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Shellfish feed by filtering algae and other organic material out of their local environment. They use the nutrients in this organic material, including nitrogen and phosphorus, to grow their tissues and shell. Filter-feeding shellfish can improve water quality in coastal areas that have excess nutrients and overabundant phytoplankton. Too much phytoplankton can lead to environmental problems including low oxygen concentrations and loss of marine life. Shellfish farms are included in nutrient management programs to help achieve water quality goals in some areas, including in the Chesapeake Bay.

Aquaculture Nutrient Removal Calculator

We recently developed the Aquaculture Nutrient Removal Calculator. This science-based tool is designed for oyster growers and resource managers to estimate how much nitrogen an oyster farm removes from the water. It is supported by a peer-reviewed publication synthesizing data on sizes and nitrogen concentration of farmed oysters from Maine to North Carolina. The calculator generates a report that can be included in permit applications for new or expanding oyster farms, specifically during the Army Corps Public Interest Review process. We are working to expand the calculator to estimate phosphorus removal for a more comprehensive estimate of nutrient removal. We are also expanding the geographic range to include the Gulf of America (formerly Gulf of Mexico). Additionally, we are synthesizing data from the GoPro Aquaculture Project and partner projects across the Northeast to develop a calculator that will estimate the habitat services that oyster farms provide.

Economic Value of Nutrient Removal

We calculated the value of nitrogen removal provided by farmed clams and eastern oysters in the Greenwich, Connecticut, watershed, in collaboration with NOAA National Centers for Coastal Ocean Science and Stony Brook University. Working with economist partners, we estimated the value of this service at $2.8–5.8 million per year. This estimate is based on the cost to replace this ecosystem service with traditional nutrient reduction approaches. The transferable approach we used in this study can be applied to other coastal communities wishing to reduce nutrients and improve water quality.

Improving the Accuracy of Nutrient Removal Estimates

We recently expanded the functionality of the Farm Aquaculture Resource Management model, an existing shellfish aquaculture model. It can now predict nitrogen removal by eastern oyster farms using local data from Long Island Sound, Connecticut. This is the first time the model was validated for nitrogen removal with local data. Nutrient managers and spatial planners can now use the model outputs to predict the benefits that new or expanding farms could achieve in areas that suffer from excess nutrients.

We partnered with two oyster farms in the Chesapeake Bay, and researchers from NOAA’s Chesapeake Bay Office and the Virginia Institute of Marine Science. We measured nitrogen and phosphorus concentration in farmed diploid (two sets of chromosomes) and triploid (three sets of chromosomes) oysters over the course of 1 year. This research greatly expanded available data on phosphorus removal by farmed oysters. We determined that the oysters’ nutrient concentration was stable over time. We also found no difference in nutrient removal between diploid and triploid farmed oysters. This suggests a need to revisit the current practice of crediting triploid farmed oysters with higher nutrient removal.

More Info

• How Much Is A Clam Worth To A Coastal Community?
• Global Study Sheds Light on the Valuable Benefits of Shellfish and Seaweed Aquaculture

For more information please contact es.tools@noaa.gov or Julie Rose.

Engineering for Offshore Aquaculture

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NOAA Fisheries aims to bolster sustainable shellfish aquaculture in the United States. Engineering can help accomplish this goal by developing science and systems to support the emerging offshore aquaculture industry.

Offshore Aquaculture Engineering Guidance

We are developing offshore aquaculture engineering guidance to support the domestic aquaculture industry and make the permitting process more efficient. We performed a case study to show how offshore aquaculture engineering guidelines can be applied to measure the structural integrity of a commercial mussel farm in New England.

On-Demand Gear for Aquaculture

While marine aquaculture can increase domestic seafood production, some gear uses lines that could potentially risk entangling marine mammals and sea turtles. This limits where aquaculture can take place. Although aquaculture does not have a history of entangling protected species in the United States, we are committed to engineering gear that is safer for these animals. We are learning from challenges and innovation in the fixed gear commercial fishing industry, such as “ropeless” or on-demand lobster gear currently in development. This gear reduces the number of lines in the water and the amount of time that the lines are present, lessening the risk of entanglement. 

We conducted field experiments with on-demand gear and collected operational and biological data. We used the experiments to refine our techno-economic model and identify potential improvements to aquaculture methods with cages on the seabed. We tested on-demand gear for mussel, oyster, and sea scallop aquaculture at three sites in the Gulf of Maine at depths ranging from 32 to 120 feet. We determined that sea scallops are the most economically viable species to grow with on-demand gear.

Project partners include the University of New Hampshire, New Hampshire Sea Grant, and the shellfish aquaculture industry. 

Visit the Engineering to Support the U.S. Aquaculture Industry project page

For more information, contact Matt Bowden or Lisa Milke.

Oyster Cages as Fish Habitat

Milford Lab scientists are using GoPro action cameras to document habitat services provided by aquaculture gear to fish in Long Island Sound. Off-bottom oyster cages are an increasingly common method for culturing oysters. These cages are complex three dimensional structures that may provide habitat for fish and other animals. Shellfish growers routinely observe fish of various life stages interacting with aquaculture gear on their farms. Oyster farms with large numbers of cages may act as artificial reefs, attracting a variety of fish species.

Researchers at Milford are conducting field trials to:

• Understand how fish interactions with oyster cages compare with fish activity at natural habitats such as a rock reef.
• Analyze how oyster cage density influences fish abundance and behavior.
• Determine whether different styles of oyster aquaculture cages provide different habitat services to the local fish community.
• Understand the relative importance of oyster cages and boulders as habitat for different life stages of fish.

To record video of fish activity in and around oyster cages, we equipped the cages with GoPro cameras. We also collected video on natural rock reef habitats for comparison.

We have collected over 1,600 hours of underwater video and analyzed it for fish abundance and community composition. To date, we've observed 21 species of fish associating and interacting with oyster cages. Observations of fish behavior suggest that fish use oyster cages in a variety of ways, including foraging, station keeping, and during courtship. We are working with regulators and fishery managers who make decisions about sites for shellfish farms and protecting habitat for recreationally and commercially important fish species. Our data will help inform their decision-making process.

To learn more visit the GoPro Aquaculture Project page, read the NOAA Fisheries feature story, check out our story map, and view a video about the project.

For more information, contact Renee Mercaldo-Allen, Julie Rose, or Lisa Milke

Understanding the Health of Long Island Sound's Oyster Beds

Whether wild, restored, or grown in aquaculture, oysters can improve water quality and provide habitat for fish. Because of this, oyster restoration efforts are increasing in Long Island Sound. We are collecting baseline data that will help promote the sustainable growth of oyster populations in Connecticut and Long Island, New York.

Working with local partners, we are taking a comprehensive look at oyster population health in natural and restored oyster populations. Our evaluation includes collecting data on:

• Population size and age distribution
• Survival and reproductive success
• Presence and severity of oyster diseases

We are monitoring levels of three diseases that have previously caused oyster die-offs in the region: Dermo, MSX and SSO. We are sampling oysters at four sites monthly for 2 years. We are also collecting environmental data. The results from our study will allow us to develop guidance for effective oyster restoration.

This project is supported by the U.S. Environmental Protection Agency Long Island Sound Study.

Visit the Understanding the Health Of Long Island Sound's Oyster Beds project page

For more information, please contact Lisa Milke.

Ocean Acidification

Laboratory and Modeling Studies with Shellfish

About a quarter of the carbon dioxide released into the atmosphere is absorbed by the ocean. This causes changes to water chemistry (such as pH) that may impact marine life. Current research focuses on how ocean acidification may affect economically-important bivalve species including: eastern oysters, blue mussels, bay scallops, surfclams, and sea scallops.

Scientists at the Milford Lab are partnering with Rutgers University and Massachusetts Maritime Academy to conduct experiments measuring feeding, excretion, and respiration of eastern oysters, surfclams, and Atlantic sea scallops in differing pH scenarios. Pousse et al (2020) recently described the physiological response of surfclams to decreased pH. We will use these data in models to better understand metabolism and growth responses for each of these species under different environmental conditions. This project is expected to yield insight into how aquaculture and wild fisheries' performance may be impacted by changing ocean chemistry.

Milford Lab researchers are also partnering with scientists and students from Stony Brook University to determine whether blue mussels and bay scallops can overcome the effects of ocean acidification through acclimation and/or adaptation. Research focuses on investigating whether bivalves can adapt to ocean acidification conditions across multiple generations, and whether tradeoffs to growth and development occur when grown in lower pH conditions.

Visit the Understanding Atlantic sea scallops and ocean acidification project page

More Info

• New Study Finds Ocean Acidification and Warming Hinder Juvenile Atlantic Sea Scallop Growth
• Investigating the Effects of Ocean Acidification on Atlantic Sea Scallops
• How Will Changing Ocean Chemistry Affect the Shellfish We Eat?

NOAA at Mass Maritime Academy: Sea Scallop Growth Study video

For more information, contact Shannon Meseck.

Multigenerational Study to Understand Adaptive Capacity of Scallops

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Experiments with bivalve shellfish provide evidence that short-term exposure to ocean acidification conditions hinders growth, increases mortality, and disrupts larval shell formation. However, ocean chemistry is changing on the time scale of multiple generations. Scientists know less about bivalves’ ability to acclimate when exposed to these conditions throughout their lifespan, and/or to genetically adapt across multiple generations. 

Atlantic sea scallops support one of the most valuable commercial fisheries in the United States and we are interested in how they will respond to climate change. We are using bay scallops in our experiments, because they are genetically similar to sea scallops but mature and reproduce more quickly, and have a sequenced genome. To understand the capacity for scallops to adapt, we are continuously exposing three generations of bay scallops to three levels of carbon dioxide, from present day conditions to those expected in 2100. 

We are measuring survival, growth, development time, and physiological processes, including feeding, respiration, and excretion rates, across three generations of scallops to:

• Understand the effects across generations 
• Assess the effects of multiple environmental stressors, including ocean acidification, temperature, and food availability, on the sensitivity of scallops to changing ocean chemistry
• Investigate genetic changes in the second and third generations of scallops for signs of adaptation
• Map those genetic changes to responses we can observe, to identify genes related to ocean acidification resilience

This study will help scientists understand how resilient scallops can be as ocean conditions change. It will provide information needed to anticipate how the population will respond to ocean acidification, and identify the most vulnerable populations and regions. This information is needed for models that are used to manage scallop fisheries. 

For more information, contact Katie McFarland or Shannon Meseck.

Field Studies with Atlantic Surfclams

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Atlantic surfclams, one of the largest bivalves on the East Coast, support an economically important commercial fishery in the Northeast U.S., with landings valued at nearly $41.7 million in 2022. Massachusetts also has an active recreational harvest of nearshore surfclams, and young surfclams are an emerging aquaculture product often referred to as “butter clams.” 

We are conducting field studies on Atlantic surfclams in coastal Massachusetts habitats to better understand how site-specific environmental conditions and genetic variability affect survival and growth. By transplanting surfclams between sites with different populations, we can study environmental controls on subspecies growth, survival, and recruitment. During these experiments, we measure the survival, size, and growth rate of transplanted and local clams. We also study their genetics and monitor their environment with a focus on temperature, carbonate chemistry, and food availability. We hope to find out which local conditions affect surfclam growth rate, as well as whether they can adapt to changing pH conditions. 

Both laboratory studies and modeling predictions from our Milford Laboratory indicate that this species is especially vulnerable to ocean acidification. Previous research suggests that lower pH conditions could cause surfclams to grow more slowly. We will determine whether the results of lab experiments and model predictions match real-world results for this species. We will also spawn Massachusetts surfclams to determine the effects of ocean acidification on larval growth and survival. This information may help the commercial fishery, recreational fishermen, and the emerging surfclam aquaculture industry adapt to environmental change.

Visit the Atlantic Surfclams’ Response to a Changing Environment project page

For more information, please contact Matt Poach