Fungicides were routinely applied on up to 30 percent of the nation's 220 million acres of corn, soybean and wheat, according to a 2009 estimate.

University of Kentucky plant pathologist Paul Vincelli estimates that 10 to 15 percent of all U.S. crops are treated with fungicide.

But experts acknowledge that without mandatory reporting, the amounts used are merely a best guess. "We don't have anything close to real data on the acreage being treated," Vincelli said.

In 2006, four fungicides were approved for combating Asian Soybean Rust, plus five more were allowed only for emergency uses. In 2009, it swelled to 14, according to data from the U.S. Environmental Protection Agency and the West Virginia Department of Agriculture.

"In the past 10 years there's been a huge change in the fungicides available," said Kuivila.

In 2008, farmers had a new incentive to use the chemicals. Studies from Iowa State University and the University of Missouri [PDF] found that so-called preventive use of fungicides increased soybean yields by as much as 20 percent. For corn, it increased yields by 5 percent, according to industry research. Disagreement between industry research and university studies over the efficacy of these kinds of treatments is ongoing, Vincelli said. A 2011 study that he was involved with found that farmers had a low likelihood of recovering the costs of applying fungicides when there was no disease.

Some scientists and agricultural experts are concerned about this rise in fungicide use. In a 2009 letter [PDF] to the EPA, 40 university scientists expressed their concern over the relabeling of pyraclostrobin, sold by BASF under the name Headline and used on a variety of crops including corn, cotton and wheat.

According to the letter, Headline was relabeled to say its “benefits may include improved host plant tolerance to yield-robbing environmental stresses, such as drought, heat, cold temperatures, and ozone damage” as well as bacterial and viral infections. “These benefits often translate to healthier plants producing greater yields at harvest, especially under stressful conditions.”

The idea of an all-purpose fungicide did not sit well with many scientists, who wrote that it “invites increased, widespread use of this product...The environmental and biological impact of these uses in the absence of a disease threat may be considerable."

The EPA allowed the new label for Headline, and several other strobilurin fungicides have since been relabeled, leading to their popularity.

"The ones that have been increasing rapidly, especially within the Corn Belt, are the strobilurins," Belden said. The biggest strobilurin fungicides include Headline, Stratego, made by Bayer Crop Science, and Quilt, made by Syngenta.

CropLife America, which represents pesticide manufacturers, said in a statement to EHN that the EPA’s review of fungicides is "rigorous" and that "new application technologies by farmers will serve to further minimize any potential environmental impacts of crop protection products."

Those technologies include applying fungicides directly to the seed, using low-drift applications and preserving marginal lands near water bodies to prevent runoff.

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