WASHINGTON -- A federal judge has ordered Patriot Coal Corp. to spend millions of dollars to clean up selenium pollution at two surface coal mines in West Virginia.

Environmental groups said it was the first time a court had demanded restrictions on selenium, a trace mineral commonly discharged from Appalachian surface mines, where the tops of mountains are blown away to expose coal.

Too much selenium in streams kills or deforms fish and other aquatic life, and in high doses, it can damage human health. Selenium is one of a number of contaminants -- including arsenic, cadmium and lead -- that are discharged from mining operations and also are found in coal ash and other wastes from coal-fired power plants.

The ruling, made Tuesday and filed Wednesday, applied to only two mines. But environmental groups fighting the spread of mountaintop mining said that if it became a precedent, it might make some mines too expensive to operate.

U.S. District Judge Robert Chambers of the Southern District of West Virginia gave Patriot about two years to get its selenium discharges down to the limits specified in its mining permits. He also ordered the company to post a $45 million letter of credit to ensure that it installs the equipment at the two mines.

Patriot said in a statement that it would have to spend $50 million on the cleanup system and $3 million a year to run it. The company said its subsidiary Apogee was ordered to install a type of treatment called a fluidized bed reactor, or FBR, system to treat selenium discharges at its Ruffner mine. Another subsidiary, Hobet, was required to submit a treatment plan for its Hobet 22 mine.

"While Patriot believes that FBR has promise, it is important to understand that this technology has never before been used in commercial applications for the removal of selenium in any context, including coal mining," the company statement said.

The judge previously had ruled that the selenium discharges at the mines exceeded what was authorized by their permits under the Clean Water Act. The order found Patriot in contempt of court and specified what its subsidiaries must do about the permit violations.

"We are particularly disappointed with the contempt ruling," Patriot's president and chief executive officer, Richard M. Whiting, said in the company statement. He said Patriot had "dedicated significant resources over the last several years to take an industry-leading position in identifying viable treatment technology to address selenium discharges."

Patriot and other mining companies have been lobbying for looser federal selenium standards. In its statement, the company said it was waiting to see the written court case before deciding what to do.

Environmentalists said the ruling could have a wider impact. "This sets the precedent that coal companies can and must treat their discharges of selenium and other toxic pollutants, and state regulators must do more than continually grant compliance extensions," Ed Hopkins, the Sierra Club's senior Washington director, said in a statement.

Sierra Club spokesman Oliver Bernstein said that although the judge's decision wasn't binding on other mines, it would weaken the ability of other companies to claim that there was no way to treat selenium, or that it would be unfair for a judge to force them to do so.

"This ruling should make clear to the coal industry and the regulatory agencies that mining coal in high-selenium seams is not economically viable ...," said Dianne Bady, a co-director of the Ohio Valley Environmental Coalition.

Washington correspondent Daniel Malloy writes the "Pittsburgh On The Potomac" blog exclusively at PG+, a members-only web site of the Pittsburgh Post-Gazette. Our introduction to PG+ gives you all the details.