(Chronicle photos by Tricia Fulks) Atlantic salmon, weighing about 10 to 12 pounds, swim in their controlled environment at the Freshwater Institute. Once the research is finished, the fish are harvested and donated to area food banks or the Maryland Department of Natural Resources.

The Conservation Fund’s Freshwater Institute in Shepherdstown is at risk of losing funding from a key partner due to President Obama’s budget cuts, which could result in a loss of a 20-year research program.

Director Joe Hankins said the federal budget cuts mean the institute’s “consistent funder,” the USDA-Agricultural Research Service, might have to end its partnership with the institute, where researchers developed an aquaculture research and development program.

“The notion that they would support fish farming was a novel idea 20 years ago,” Hankins said.

But, he said, in this budget climate, this is where the government decided to make the cuts.

“In order to meet the president’s proposed budget for fiscal year ’12, a large part of ARS’ research capacity across the board has been reduced,” he said.

Aquaculture Research Director Steve Summerfelt opens the drawers to the incubator where just last month fish eggs were stored. The Freshwater Institute has researched efficient aquaculture technologies for the past 20 years in Shepherdstown.

Hankins said earmarks, redundant programs, physical facility and maintenance funds and special programs – like the institute’s aquaculture project – were reduced or eliminated.

“It’s very difficult financial times,” said USDA-ARS National Program Leader Jeffrey Silverstein.

He said the Freshwater Institute’s aquaculture research was “visionary” and would be “hard to replace.”

Hankins said it was about a month ago he received word about the budget cuts, which would mean termination of the institute’s aquaculture program, in fiscal year 2012.

“That was a wake-up call,” he said.

He said the same weekend the U.S. House of Representatives passed House Bill 1, a $60 billion budget cut bill. Hankins said this piece of legislation could make the project’s termination date even sooner.

“We’ll get through this,” he said. “But in my career, this is an upheaval that is pretty unusual.”

At this point, Hankins knows his program’s fate is up to Congress.

“Congress determines the final numbers,” he said. “It’s not a sure thing, but it doesn’t look real good for us.”

With two possible budget cut options he said his staff remains hard at work – even the division that could be up for termination.

Steve Summerfelt, director Aquaculture Research system at the Freshwater Institute, said the program in Shepherdstown is one of the highest rated in the nation.

What the program does, he said, is develop new technologies that are environmentally friendly and economically viable for fish farming. Clean water means healthy fish for a healthy environment, Summerfelt said.

“We want to do our research to help fish farmers,” not compete with them, he said.

The institute’s latest research has been with Atlantic salmon, which are usually raised in net pins in the ocean. But at the institute’s campus in Shepherdstown, researchers are raising the fish in a controlled environment, resulting in a healthy product.

“When we have a controlled environment, we’re excluding fish pathogens,” Summerfelt said.

Summerfelt leads a team of engineers, researchers, biologists, veterinarians and maintenance workers.

“All of us are a good team,” he said. “We’re the best at what we do.”

Of the 22 full-time staffers at the institute, 15 positions are at risk of termination.

Summerfelt said while he understands it is important for the government to be fiscally responsible, his team’s research is also important. He said while the USDA values their work, cuts are still happening – which means some of the research may not see an end and his team might be out of a job soon.

John Davidson, senior research associate, took a job at the Freshwater Institute upon graduation from Shepherd College 13 years ago.

Since then, he has worked in the program’s aquaculture division.

“I love my job here. For a lot of people here, we have a lot of specialized careers,” Davidson said. “There’s a lot of dedication here to what we’re doing.”

And to Hankins, that dedication shows through the numerous letters received so far since word has gotten out about the possible funding cuts.

One read “I can’t emphasize enough the importance of the Freshwater Institute’s efforts. I hope the Agricultural Research Service can continue to support Freshwater Institute’s research,” while another called Obama’s choice an “ill-conceived financial cut.” Another writer wrote, “I believe the quality of their work will stand up to scrutiny at any level it would be a tragedy to lose this resource at such a critical time.”

If termination does happen, Hankins said it will be sad to watch his talented staff look for jobs again.

But it could also mean reassessing part of the Freshwater Institute’s mission. With ARS funding the aquaculture research for 20 years, Hankins said the program would have to reinvent itself.

“This is not a red or blue issue,” he said. “This is a food issue. This is a science issue. This is a conservation issue.”

He said the institute, whatever the next big project is, will remain to do the best work possible.

“I’ve always taken the approach that if you do really good work, the rest will take care of itself,” Hankins said. “Well, in today’s budget climate, that’s not sufficient.”

That’s why Hankins is currently exploring funding and investment options from production and farming companies interested in aquaculture – that way the program won’t have to be cut.

Right now, one-third of the institute’s aquaculture research budget is fee-based work.

“It’s great leverage for our federal investments,” Hankins said.

But he isn’t certain that private funding can carry the program alone.

If reinvention is in the institute’s future, natural resources and sustainability will remain the institute’s mission.

And even though the possibility of the loss of the aquaculture research program looms on the horizon, morale remains positive.

“We’re going to ride this out, and hopefully try to sustain ourselves,” Davidson said.