Fascinated by Fish:

URI Researchers Use Molecular Biology to Advance Aquaculture Techniques

By Arliss Ryan

ß How do you vaccinate a fish?
ß How do you outwit an oyster parasite?
ß How do you relieve stress in salmon?

These aren’t the kind of questions that spring to most people’s minds when they sit down to a delicious dinner of pan-seared sea bass or grilled salmon. But for Marta Gómez-Chiarri, associate professor, and Terence Bradley, professor, both of the University of Rhode Island (URI) department of fisheries, animal and veterinary science in the College of the Environment and Life Sciences, such questions are fascinating. They’re also vital to ensuring that fish and shellfish continue to be a major food source for the world’s ever-growing population. By using both traditional science and cutting-edge molecular biology to study the environmental conditions and diseases that affect the health of fish, the researchers are beginning to discover the answers to their questions. Their results could one day mean the difference between sitting down to a nutritious fish dinner and an empty plate.

Gómez-Chiarri and Bradley, who work independently on a variety of projects, often find their scientific investigations begin as a mystery that requires detective work to solve. Take the case of an aquaculture farm that opened at Quonset Point in North Kingstown, R.I., with a stock of summer flounder and high expectations. Two weeks later, the fish started dying. Within eight weeks, 30 percent of the stock was lost and the brand-new farm was forced to close. Using both traditional methods and molecular tools such as gene sequencing, Gómez-Chiarri and her team, with funding from Rhode Island Sea Grant, began a process of isolating bacteria to determine which one was causing the disease. They discovered the culprit was Vibrio carchariae, a bacterium first isolated in sharks in the Chesapeake. It has also caused disease in grouper in Taiwan, sea bass in the Mediterranean, and is very similar to one that affects shrimp. The bacterium especially likes warm water and fish in stressed conditions, both typical conditions in aquaculture farms.

"When disease strikes fish in the wild, there is little you can do about it," says Gómez-Chiarri, whose interest in fish pathology was partly fueled by a crisis in the fishing industry in her native Spain. "But in aquaculture, although the stress and close quarters are conducive to the spread of disease, there’s also the opportunity to prevent and treat it."

Gómez-Chiarri is continuing her research to learn more about the disease and the possibility of combating it by a vaccine. Vaccinating fish can be done either by giving each individual fish an old-fashioned inoculation, a very labor-intensive process, or by immersing the fish in a solution, which is easier and less costly but also less effective. Each disease must be approached differently, but if a vaccine can be proven to work and has wide applications, there will be an economic impetus to produce it. Future aquaculture farms may then be able to immunize their stock for infectious diseases and prevent the kind of outbreak that devastated the Quonset Point operation.

Gómez-Chiarri also tracks the health of shellfish in Rhode Island by collecting and examining samples both from farms and the wild population. Her research shows that disease is on the rise overall; and for oysters, the situation is particularly worrisome. An infectious disease called Dermo, caused by the parasite Perkinsus marinus, has decimated oyster populations on the East Coast. First discovered in the Gulf of Mexico in the 1950s, the parasite traveled to the Chesapeake, then up to Delaware Bay. In the 1990s, it began affecting Rhode Island, with currents and warmer weather possibly aiding and abetting its northward spread. Treating afflicted oysters presents a different set of challenges than in the case of the summer flounder.

"Because shellfish lack an antibody immune response, they can’t be vaccinated," explains Gómez-Chiarri. "So different strategies must be used to prevent and treat infectious diseases. One solution is to genetically breed oysters that are more disease resistant."

In the case of Dermo, the parasite progresses slowly and usually doesn’t kill the oysters until they mature at about two years. Armed with this knowledge, researchers can use breeding to try to create oysters that can be harvested in 18 months. Meanwhile, back in the Gulf of Mexico, some strains of oysters have become resistant to the parasite. Exactly how did these oysters respond to the parasite to achieve that? And Pacific oysters are also resistant—why? Is it possible to select and breed from them?

"Before, it was a shot in the dark," says Gómez-Chiarri. "You didn’t really know what was making the oysters resistant. Now we can infect oysters with the parasite in our lab and compare them to healthy oysters to determine which genes turn on or off in those oysters that are infected. We can then catalog genes in a library, and we can use genomics and biotechnology to identify and develop disease-resistant stocks."

Despite the setback with the summer flounder farm and the Dermo in oysters, Gómez-Chiarri believes these two, as well as quahogs, are well suited to aquaculture in Rhode Island, which is, at present, a $300,000 annual industry. She notes that in Connecticut, that figure is in the $1 million range, so there is potential for growth. She also acknowledges the challenges. Due to the heavy recreational use of Narragansett Bay, erecting netpens in certain areas would pose user conflicts. Land-based aquaculture farms resolve that issue but are very expensive, requiring facilities with tanks and equipment to pump, filter, and treat water from the Bay, not to mention the price of waterfront property.

"In Rhode Island, we are way behind the rest of the United States in aquaculture, and the United States is behind most of the world," says Gómez-Chiarri. Nevertheless, she’s encouraged by changing attitudes toward aquaculture. "Before, fishermen seemed to be very opposed to it, but now that wild fish stocks are decreasing, they see it as complementary."

Bradley also sees a future for aquaculture in Rhode Island, especially with a focus on research and development. Like Gómez-Chiarri, he combines detective work with molecular biology to investigate how fish adapt and survive. One project examines the genes involved in the adaptation of salmon. In the wild, salmon start life in freshwater streams, migrate to the sea as juveniles, then return to fresh water to spawn as sexually mature adults. In routine aquaculture practice, juveniles are transferred directly from freshwater hatcheries, which is a hydrating environment, to net pens in full-salinity seawater, which is dehydrating, so they must develop a whole series of mechanisms to adapt. This scenario is complicated by the fact that, in the wild, the juveniles migrate to the sea during a four to five week period in the spring following parr-smolt transformation, a developmental process that encompasses numerous physiological and biochemical changes that prepare the fish for life in the marine environment. If the salmon are exposed to seawater outside the parr-smolt window, the fish can become stunted and die and an aquaculture farm may lose up to 50 percent of its stock.

"In our lab research, we’re trying to study the genes that enable salmon to make a successful transition to sea- water," says Bradley, whose early work was funded by Rhode Island Sea Grant. "If we over-express certain genes or cause them to turn on early, can we develop fish that will better tolerate the stress of transfer and continue to grow?"

Bradley and his team also use molecular biology to study bacteria in the gastrointestinal (GI) tract of salmon. From fecal material, they can develop a complete picture of which bacteria inhabit the GI tract based on the DNA that is present. The next step is to determine which populations of bacteria provide the best conditions for growth during various conditions of stress, a change in temperature and/or diet, and in a salt- versus freshwater environment. With this information, they hope to develop certain strains of "good" bacteria with which the fish can be seeded to protect them from pathogenic bacteria that could otherwise colonize the GI tract and cause illness. A related area of Bradley’s research involves a growth and differentiation factor called myostatin, which may enable fish to grow faster.

"The problem with a lot of finfish like halibut is that they take so long to grow that aquaculture of these species is not economically feasible," says Bradley. "If you can reduce the production period for halibut from two years down to 18 months, you improve the economic viability."

Eighteen months, however, is still a long time to get fish to market compared to chickens or vegetables, and during that time there are opportunities for disaster with disease and water quality problems. And once again, the recreational value of Narragansett Bay makes it difficult to erect net pens. But this is precisely where Bradley feels research and development can reap economic benefits for Rhode Island.

"All the research at URI holds the promise for making Rhode Island an area where techniques are developed, patents are issued, and the university and the state stand to gain from intellectual property," says Bradley. "We could breed fish and supply eggs with specific characteristics. Selling stock and intellectual property is a very clean, high-tech industry that won’t affect the Bay."

In addition to Atlantic salmon, Bradley and his colleagues work with black sea bass, rainbow trout, cod, haddock, and summer flounder. He’s seen aquaculture at URI grow from a small program in the early 1970s of simply trying to raise fish to using molecular manipulations to enhance the product in the 1990s. Bradley himself grew up working on fishing boats, and he notes that much of the research in their field is ultimately market driven; quite simply, it comes down to what people want on their plate. If consumers are introduced to a new fish and discover they like it, they want to be able to purchase it year round. Aquaculture can produce fish out of season, thus complementing the wild stock. It can also fulfill the demand for a fish like black sea bass, where the traditional fishery has plummeted. Bradley and his team were the first to develop techniques to culture black sea bass, and they use DNA fingerprinting and the insertion of microchips to identify and study individual fish.

For Bradley, Gómez-Chiarri, and other URI researchers, it’s an exciting time to be fascinated by fish. They’d like to see Rhode Island and the United States take a leadership role in investing in new research and technology that can bring about a thriving and profitable aquaculture industry.

"With the help of biotechnology, we can produce healthy fish to meet the growing demand for seafood," says Gómez-Chiarri. "That, in turn, will relieve enormous pressure on marine fisheries and help preserve biodiversity in our oceans."

"The molecular biology of fish is still a relatively new field with lots of promise," adds Bradley. "With over 24,000 species of fish, that should keep us busy for quite a while." 

—Arliss Ryan is a Freelance Writer who worked with the URI College of the Environment and Life Sciences to develop this article. 

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