SIOUX FALLS, S.D.  — Pheasants once drew hundreds of weekend hunters to Fairbury, Neb., each fall, filling the 45 rooms at Randy Brown’s Capri Motel with sportsmen eager to bag their limits.

But times have changed. The native grasslands and milo crops that used to dot surrounding Jefferson County have been overtaken by corn and soy crops. Neither provides the shelter that wildlife once enjoyed. This year’s opener drew just two rooms of out-of-state hunters to the Capri, one of many businesses indirectly affected as farmers move to meet the nation’s demand for biofuel.

“We don’t have the habitat we had 20 years ago,” said Brown, owner of the motel near the Nebraska-Kansas border. “Everything’s against the pheasants right now.”

The U.S. Conservation Reserve Program, which pays landowners not to farm their property, has been a boon to wildlife. Since its creation in 1985, it has boosted populations of ducks, ring-necked pheasants, prairie chickens, Columbian sharp-tailed grouse and other wildlife by providing areas where they can feed and reproduce. The birds bring money.

Pheasant hunting has long been a pastime in the region, especially in South Dakota. Its reputation for stocked fields has made it a national draw, credited with pulling $170 million into the state economy last year. Each fall, thousands of out-of-staters arrive at the state’s airports with dogs, shotguns and plenty of blaze orange for their trip afield.

But fees paid to landowners under the Conservation Reserve Program haven’t kept pace with crop prices. Farmers found that it makes economic sense plowing into native prairies and putting land once considered marginal for farming back into production. The result throughout the nation’s Corn Belt has been fewer birds.

Since the government began requiring oil companies to add billions of gallons of ethaol to their gasoline each year, the states of Iowa, Kansas, Minnesota, North Dakota, South Dakota and Nebraska have lost 2.8 million acres from the conservation reserve program, as farmers planted nearly 10 million more acres of corn, the main feedstock used to produce ethanol. About 5 million other acres are now included in other conservation programs, but nearly all that land is being actively farmed.

Over the same period, pheasant harvests in those six states dropped by 44 percent, a reflection of the downward population trend, according to data collected from state biologists.

“That is one of the reasons we are seeing such a substantial loss of wildlife,” said Dave Nomsen, of Pheasants Forever, which works with farmers to encourage practices that are good for birds. “Few programs put grass on the landscape the way the way the Conservation Reserve Program has done.”

Before the 2007 ethanol requirement, the conservation program had grown every year for nearly a decade. Farmers began leaving the program almost immediately after the mandate. Meanwhile, Congress cut money for the program, reducing the amount of farmland that could be placed in conservation.

More than 5 million acres have disappeared from the program since 2008.

Meanwhile, the U.S. Fish and Wildlife Service, along with non-profit groups, spent tens of millions of dollars to buy land to permanently protect bird habitat.

Even those programs have been hurt by the high prices for corn in recent years. With farm property values and rental rates increasing, the cost of protecting land has gone up. The average inflation-adjusted cost of buying grassland increased 300 percent from $195 per acre in 1998 to $778 per acre in 2012 in the prairie pothole region of South Dakota and North Dakota.

Agriculture Secretary Tom Vilsack, speaking recently to ethanol producers and lobbyists in Washington, said that despite the loss of conservation reserve lands, a record number of farmers and record number of acres are enrolled in conservation. In fact, the number of acres in those other programs, which occur mostly on active farmland, has nearly doubled, to 301 million acres since the ethanol mandate was passed.

“There is some great work beyond CRP being done,” he said.

A close look at the Corn Belt reveals a more complicated picture. Agriculture Department data obtained by the Associated Press show that the amount of land enrolled in the grassland reserve program has declined in every state and in Iowa by more than 50 percent. That program keeps property in grass that can be grazed by livestock. In Kansas and Nebraska, total lands enrolled in these other conservation lands have dropped.

A different program that protects wetlands permanently has increased by only 45,000 acres since 2006 with most of that land — 30,000 acres — in North Dakota.

Steve Bublitz, a guide with Fair Chase Pheasants, said he and his groups have noticed a significant drop in bird numbers this year in the fields around the Huron area.

“I’d say we’ve got about half the birds we had last year,” he said.

Bublitz, who’s been hunting birds for more than a half century, said months of persistent drought followed by a cold and wet spring have contributed to the drop, but the loss of adequate nesting cover also had a huge impact, leading to more predators.

“The skunks, raccoons and possums, they eat the eggs,” Bublitz said. “Foxes and coyotes eat the pheasants.”

South Dakota brood counts have shown significant declines the past two years alongside the pheasants’ loss of habitat. Minnesota, North Dakota, Iowa, Kansas and Nebraska saw smaller drops, and hunters there are having to work harder to reach their limits.

“As long as you’re willing to walk a bit, you’ll find some,” said Josh Divan, a northwestern Iowa wildlife biologist for Pheasants Forever. “But it’s not like it was.”

Divan said his part of Iowa has seen a dramatic loss in cover since 2008 as farmers have converted more acres to corn and soybeans. Growers can help provide habitat by integrating some grassland on the outskirts of the fields, hills or wetlands, but he said most of what he sees are fields planted fence row to fence row.

“If you’re in a corn-bean rotation, you’re doing little to no good for wildlife,” he said.

Divan said he sees hope for a turnaround, with the settling of corn prices and the government offering higher contract prices for conservation acres, which vary by state.

“I think the stage is set for a pretty big CRP signup again here,” he said.

Brown hopes so. A dozen or so years ago, his hotel would be full the first two or three weeks of hunting season and for weekends afterward. Now it’s only the occasional hunter hoping to relive golden memories of past shoots with their grandfathers or uncles.

“It’s tough,” he said.