Aerial view of the Shumate impoundment filled with 2-plus billion gallons of coal waste slurry at the massive Massey Energy Edwight MTR site near Marsh Fork, WV. (Harrison Shull/Aurora Photos)

In West Virginia’s Appalachian mountains, fish are vanishing. The number of species has fallen, the populations of those that remain are down, and some individual fish look a little skinny.

A new government study traces the decline in abundance to mountaintop removal, the controversial coal mining practice of clear cutting trees from mountains before blowing off their tops with explosives.

When the resulting rain of shattered rock hits the rivers and streams that snake along the base of the mountains, minerals released from within the stone are changing the water’s chemistry, the study said, lowering its quality and causing tiny prey such as insects, worms and invertebrates to die.

“We’re seeing significant reductions in the number of fish species and total abundance of fish downstream from mining operations,” said Nathaniel Hitt, a research fish biologist for the U.S. Geological Survey’s office in Kearneysville, W.Va., and one of the study’s two authors.

Hitt and his co-author, Doug Chambers, a biologist and water quality specialist in the Charleston, W.Va., office of the USGS, took a 1999 study of the Guyandotte River basin’s fish populations by Pennsylvania State University researchers to compare them over time.

For two years starting in 2010, they sampled the populations in waters downstream from an active mountaintop coal mining operation. In one of the sample areas, the Mud River watershed, which contains the largest tributary of the Guyandotte River, at least “100 point source pollution discharge permits associated with surface mining have been issued,” the study said.

North America’s central Appalachian mountains, where the basin lies, are considered a global hot spot of freshwater fish biodiversity, but few researchers have investigated the impact of mountain strip mining on stream fish, and the effects “are poorly understood,” the study said.

Hitt and Chambers found that the number of species was cut in half and the abundance of fish fell by a third. The silverjaw minnow, fosyface shiner, silver shiner, bluntnose minnow, spotted bass and largemouth bass, along with at least two other species detected before their study, were no longer there.

Another fish species, the small and worm-like least brook lamprey, never before detected, had moved in. In areas of the river basin where there was no mountaintop mining, fish flourished. In addition to species that were in those waters previously, seven new ones were found, including the spotfin shiner, the spottail shiner and the golden redhorse.

The confluence of the Guyandotte and the Slab Fork rivers in South Mullens, W.Va. (JON C. HANCOCK/AP)

“I think if we only focus on the fact that it’s fish . . . some people will say, ‘So what?’ ” Chambers said. But fish and invertebrates they eat are canaries in a coal mine for researchers, “indicators of the water quality,” he said.

The USGS looks “at the nation’s water resources . . . their significance to the nation, and [tries] to understand processes that are degrading water quality. [Tainted] water may not be suitable for additional uses.”

Research such as the USGS’s mountaintop mining study, published online early this month by the Society for Freshwater Science, is viewed with suspicion in coal country, where mining operations provide thousands of jobs.

“The people opposed to the coal industry are trying to pile on with more studies,” said Bill Raney, president of the West Virginia Coal Association. “It sounds like this is one of those studies that sets out to show there’s harm done. It sounds like perhaps more of the same.”

Raney said he has not seen the USGS study and cannot strongly criticize its methods or conclusions, but people “don’t just wake up in the morning and decide they are going to do mountaintop mining,” he said. “It takes three to four years to get a permit. Every aspect of the operation is analyzed.”

Mountaintop removal as a way of extracting coal has been in practice since the 1960s, but its use has expanded in the past two decades and it now takes place in the Appalachian regions of Ohio, Kentucky and Virginia, in addition to West Virginia.

The coal the process produces provides power to hundreds of thousands of homes, industry advocates say, and creates about 14,000 jobs that pay middle-income salaries in regions where work is hard to find.

“The average mining wage is more than $66,000 per year . . . 57 percent higher than the average for industrial jobs,” according to the National Mining Association. “Mountaintop mining accounts for approximately 45 percent of the entire state’s coal production in West Virginia.”

Raney’s association disputed claims that mining destroys streams and mountains, saying state permits and government regulations require the land to be restored after use.

But the Sierra Club Eastern Missouri Group called the practice “quite possibly the worst environmental assault yet” because of the amount of landscape it removes and the impacts to people and animals.

Homeowners in one West Virginia community, Lindytown, were bought out by a company before the town essentially disappeared following mountaintop removal. Homes and a grave site were left behind. Cascading debris has buried streams, impacting a diversity of wildlife, a major concern raised by the Environmental Protection Agency.

Often, companies are granted exemptions that ease requirements to restore land. Conservationists call the practice a plunder, and protesters, including Quakers in Appalachia and demonstrators at the White House, have called on the government to end it and banks to stop funding it.

“Mountaintop removal mining is one of the fastest-changing land use forms in the region,” Hitt said. “One of the main questions for our research lab is how biological communities respond to land use changes.”

In the case of the fish, they seemingly do not respond well, Chambers said. “To sum up, 10 fish species were apparently extirpated from the mined sites,” meaning they were rooted out, completely destroyed, he said.

Fish with a more diverse diet appeared to fare well, but those that relied primarily on invertebrates, such as small aquatic insects, tended to fare poorly.

“It’s telling us that the water quality is changing,” Chambers said. Water in that area is not used for drinking, he said, but “if you look at it from a regulatory perspective, you have to determine if the water is fishable, swimmable, drinkable, all of these are benchmarks.”