DAMARISCOTTA, Maine — The calm waters of the Damariscotta River reflect rich autumn hues, the liquid stillness broken only by industry.

Close to the harbor town, an oyster farmer hauls up bags a diver had loaded with the shellfish, dumping the harvest on his boat deck. A bit downriver, Bill Mook and his workers progress down long strings of oyster floats, flipping each one to dry unwanted plant and animal growths.

Aboard the Oyster Girl boat, Jeff “Smokey” McKeen and Carter Newell sort through the oysters they’ve dragged from the bottom. And a bit further down the Damariscotta, three small draggers ply the bottom and haul their catch to a floating 40-by-30 raft, where six Muscongus Bay Aquaculture workers sort oysters nonstop — a mid-river processing operation.

On the Damariscotta, oysters are king. And oysters from the river represent about 75 percent of Maine’s yearly oyster harvest. The shellfish, generally eaten raw on the half-shell, are an important part of the area’s economy, not only for the aquaculturists who grow and harvest them, but for area restaurants and the local tourism businesses, too.

But Damariscotta River oyster farmers face a new challenge: MSX, a disease deadly to oysters that has wiped out beds elsewhere, but hasn’t been a concern in Maine before this year.

“We’re really worried — where’s this all going to go?” says Chris Davis, a partner with Pemaquid Oyster Co. “I would say there’s a very guarded optimism.

“It’s a wonderful industry, a wonderful way to make a living. We want to see it continue.”

The disease is caused by the parasite haplosporidium nelson, and doesn’t hurt humans or other sea life. The river’s oyster farmers are still harvesting their shellfish, bringing them to market. But the state has issued an emergency order, blocking any movement of the oysters from the river to other waters. The hope is the quaran-tine will prevent the spread of MSX to other oyster beds.

Out on the Damariscotta, Newell, one of Davis’ partners, takes a break from harvesting oysters he and his partners have carefully planted on the seafloor. There are different estimates on the impact of the disease, and results continue to develop. Newell, who like Davis has his doctorate in marine biology, thinks the disease has killed about half of the oysters in the beds, leaving them with gaping shells. Others suggest a 35 percent mortality rate.

MSX has been in the Damariscotta historically for at least 20 years, says Newell. But MSX has never been a prevalent problem — to such an extent that growers were never concerned about breeding disease-resistant brood stock, and seed oysters from the river were vaunted in other regions because of the lack of disease.

Pemaquid was seeing some small percentages of mortality in July and August, and then in early September. The company sent out some samples for testing, and learned of the presence of MSX. The partners told other growers, who sent in their own samples, confirming the widespread presence of the disease. The industry reported the problem to the state’s Department of Marine Resources, which quarantined the river earlier this month.

Newell and others think abnormal weather over the past few years is to blame. First came last winter, which was very mild. The river didn’t even freeze, says Newell. Then came a consistently warm summer, where the water hit 77 degrees, where the norm is 68, he said.

Newell speculates that the stretch of warm weather allowed MSX to flourish.

“We’re hoping for a good, cold, normal Maine winter,” says Newell.

Pemaquid and other growers plan to bring in brood oysters that are from disease-resistant lines. Most haven’t brought in out-of-state oysters previously, concerned about importing a disease. Circumstances have obviously changed.

And, says Newell, the hope is that Damariscotta growers will be able to use oysters that have survived the MSX outbreak as brood stock. The thinking, he said, is that they are genetically resistant to the disease, and their spawn may be, as well.

Newell says Pemaquid has increased production this year, planting more and larger oysters, with an eye toward getting them out of the water in a year and a half, rather than two years. With the increased production, the company’s customers shouldn’t see any impact from the MSX outbreak, he says. Davis notes, however, that 50 percent mortality is a “pretty big hit.”

The real test will come next summer, says Sebastian Belle, executive director of the Maine Aquaculture Association. That’s when it will be seen if the disease has hung on through what’s predicted to be a normal winter, and whether the 2011 harvest will be impacted.

MSX mortalities tend to decline in the fall, says Davis. Oysters with the disease won’t make it through the winter. Come spring, growers will see how prevalent the disease is.

Growers’ experiences vary on the river.

Mook, standing on a platform off his boat that puts him waist-deep in the water, flips the oyster floats that he bought this year. In the past, he grew and harvested his oysters from the seabed, like the other growers. This year, to fight an incursion of green crabs that were feeding on oysters, he raised his oysters to market in the new floats.

Mook says he’s not seeing the effect of MSX on his floating oysters.

“Right now, we are not being impacted,” he says.

But he doesn’t think the state is overreacting with its decision to quarantine the river. Growers and state officials met on Wednesday to figure out a plan. The growers support the continued quarantine of the river, beyond the Jan. 9 date on the emergency order. The growers plan to work together to develop a brood stock that’s resistant to disease. Industry and the state will work together to monitor the disease in the beds, and in other beds along the coast, says George LaPointe, commissioner of marine resources. The state and the farmers need to determine how often to sample, look at what’s been done elsewhere and adapt it for Maine, LaPointe explains.

“We’re all on this huge learning curve,” he says.

It’s important to treat the outbreak seriously, says Mook. He’s been farming oysters here since 1982, and the industry is beginning to flourish.

“It’s just hitting its own a little bit,” he says.

Maine’s overall shellfish industry — which includes clams, mussels, oysters and scallops — had sales of between $7 million and $9 million last year, according to Belle, executive director of the Maine Aquaculture As-sociation. Industry estimates put sales of oysters at $3 million to $4 million.

Maine oysters, particularly those out of the Damariscotta, are among the most expensive on the market, typically commanding a 10 to 15 percent premium. The oysters don’t tend to spawn due to the cold waters, preserving its resources. Their resulting high glycogen and lipid contents of the oysters add to the Maine oysters’ buttery and sweet taste, says Belle.

The market for Maine oysters runs from Atlanta north and Chicago east, says Belle. And the town of Damariscotta has become known as a destination for oysters, says Charlie Herrick, owner of the Schooner Landing restaurant. At the oyster festival in September, they went through 14,000 oysters, he says. On a typical week, the Schooner Landing will serve 1,500 to 2,000, he says — and there are several other restaurants in town that highlight oysters.

“I don’t think you can over-state the importance of the oyster,” he says. “It’s an essential industry — not just to the people it employs, but for the tourism it brings to the area. It’s critical.”

Mook notes that he buys building material from area businesses, banks with local banks and purchases diesel and heating fuel from area companies. And oyster hatcheries go through a lot of heating oil, to warm the buildings and water, as well.

Mook employs four right now, and another four or five in the summer. Pemaquid has four employees, and sells about 14,000 oysters a week, mostly to local restaurants and shops. Newell estimates his business alone represents a $50,000 weekly economic impact on the immediate area. The industry supports 40 to 50 jobs in the area directly, with another several hundred supported indirectly — from shipping to processing to restaurants.

With traditional fisheries squeezed by catch limits and other challenges, many whose families have fished the ocean have now looked to farming it, says Belle. The average age of commercial fishermen is 57, he notes. For those in aquaculture, it’s 32. And many of those who harvest oysters on the river have degrees in marine biology, with more than a few masters’ degrees and doctorates.

“They are the next generation of the working waterfront in this state,” he says.