EASTPORT – Salmon farmers can begin reintroducing fish to Cobscook Bay within the month, but regulators say efforts to protect against future outbreaks of a deadly fish virus and increasing public scrutiny are going to change the way the industry does business.

“We never intend to depopulate a bay again,” Steve Ellis, U.S. Department of Agriculture veterinarian, said Thursday during the 10th Annual New England Farmed Fish Health Management Workshop. “We’re not going to let this situation get out of hand again.”

Those changes may be necessary, but they will increase operating costs, according to at least one industry representative.The USDA has been supervising the effort to clean all traces of infectious salmon anemia or ISA from Cobscook Bay since January. That is when the Maine Department of Marine Resources ordered fish farmers to kill the remaining 1.5 million farmed salmon in the waters off Eastport and Lubec.

Ellis and his USDA colleagues arrived in Eastport on Jan 7. By Jan. 19, the four companies that have leases in Cobscook Bay had emptied their pens, sending 95 percent of the fish to a rendering plant in New Brunswick and the remaining 5 percent to a compost site in Lubec, he said.

The next step was disinfecting, beginning with the removal of all 720 fish nets from the bay and their being transported in leakproof containers to be cleaned and sterilized. The next job was lifting cages out of the water, scraping off the organic debris and then steam-cleaning them, the federal veterinarian said.

Some cages were too heavy to lift, and workers had to go underwater to scrape and clean, a chore that Ellis described as “long and frustrating.”

Meanwhile, tests for ISA were conducted on gear, boat hulls, water, plankton, sediment and on sea lice removed from infected fish, he said. Sea lice is believed to carry the virus from one fish to another.

ISA was detected on the boat hulls, floats and in the water, but follow-up tests two to three days later failed to detect the virus, he said

Within two weeks of depopulation, the entire bay was dragged, but no sea lice were recovered, he said.

With no positive tests and only two sites left for final testing, the current concern is sea lice eggs that may have dropped to the bottom, Ellis said

“The fish weren’t treated for sea lice this fall because growers knew they were going to be destroyed,” Ellis said. “Our concern now is these [eggs], and we’re going to have to address this issue in the next six weeks.”

DMR’s kill order in January came after nine months of ISA outbreaks at various sites in Cobscook Bay. During those months, 1 million salmon had died or been harvested early as the disease, which is not harmful to humans, was detected at all but one of the 15 lease sites.

Ellis said the Jan. 7 DMR depopulation order did not apply to two lease sites in neighboring Passamaquoddy Bay. One company voluntarily removed its fish from one of those sites in January, and ISA was detected at the second site in February, he said.

The $7 million in federal funds that will reimburse fish farmers for salmon killed after Jan. 7 and cover the costs for disinfecting and cleaning has not yet been released, he said.

Ellis was one of 20 speakers who addressed the 160 people who attended Thursday’s workshop at Washington County Technical College’s Marine Trades Center in Eastport. The annual event is sponsored by University of Maine Cooperative Extension, Maine Sea Grant Program, the Maine Aquaculture Association and the Maine Aquaculture Innovation Center.

Topics ranged from the latest research on fish viruses and ISA vaccinations to farming alternative species, such as cod and haddock, to the technology behind the SuperSmolt, an Atlantic salmon developed by the Portland company MariCal LLC, which maintains that the fish can be transferred from fresh water to salt water three to four months earlier than normal.

An underlying theme of many presentations was the changes the industry will face in the aftermath of ISA and as a result of the increasing public questioning of the environmental impact of salmon farming.

Only half of Cobscook Bay will be restocked this spring, and once those fish are harvested 18 months later, those cage sites must lay fallow for a period of months before other fish can be restocked. The remaining half of Cobscook Bay will be restocked next spring under the same conditions, according to state and federal restocking plans.The changes will increase costs as lease sites sit empty for months at a time, according to Sebastian Belle, director of the Maine Aquaculture Association.

Belle said the industry is voluntarily moving to bay management agreements, in which all fish farmers in the same area develop plans on how they will work together to prevent the spread of disease. Protective restrictions on moving equipment and personnel – such as specialized harvest crews – from site to site are going to increase the cost of doing business, he said.

Reporting requirements also will increase beyond the current DMR required monitoring and diver surveys, according to Jon Lewis, aquaculture environmental coordinator for the Maine Department of Environmental Protection.

The DEP is in the process of developing a pollutant discharge permitting program for cage sites to bring them into compliance with federal requirements, he said.

Lewis said the new permit requirements will include increases in both the scope and frequency of monitoring for such environmental indicators as dissolved oxygen content in the water, and the diversity of marine life on the ocean floor beneath the cage sites.

Phrases such as “dead zones under pens” and sediments “filled with antibiotics” aren’t accurate, but there will have to be a clear definition of what is acceptable under the pens, he said.

The new permits may require off-site monitoring, including laboratory analysis of sediments, and the industry will have to submit timely and accurate reports, he said.

Lewis suggested to industry representatives that they had been almost paranoid in refusing to release information about their industry.

“We’re living in a real transparent environment and in the five years I’ve worked at this, I feel like you’ve hidden unnecessarily,” Lewis said. “Basically, I think you have a better operation than people realize.”

Steve Page, environmental compliance officer for Fjord Seafood USA – parent company of Atlantic Salmon of Maine and Ducktrap River Fish Farm – said his company is pursuing certification for its 14 cage sites, two processing plants and two hatcheries under the International Standards Organization 14000 program.

While such certification is standard practice in European aquaculture operations, Fjord Seafood USA is the first Maine salmon farmer to apply for the certification.

In order to be certified – a decision that is made by third-party auditors – a company must identify the environmental impact of all corporate activities and actively manage and reduce those impacts, he said.

Page said Fjord USA environmental policy includes sustainable fish farming and processing, the efficient use of natural resources, full compliance with all environmental regulations, limiting potential impact on wild salmon stocks, consideration of the aesthetic qualities of the coastal landscape and making information available to the general public, regulators and public interest groups.