Jon Kiel, left, and Verlyn Sneller of the agriculture company Verity with a corn stalk produced without a glyphosate-based herbicide.

ALTON, Iowa — The puny, yellow corn stalks stand like weary sentries on one boundary of Dennis Von Arb’s field here.

On a windy day this spring, his neighbor sprayed glyphosate on his fields, and some of the herbicide blew onto Mr. Von Arb’s conventionally grown corn, killing the first few rows.

He’s more concerned, though, about the soil. During heavy rains in the summer, the runoff from his neighbor’s farm soaked his fields with glyphosate-laden water.

“Anything you put on the land affects the chemistry and biology of the land, and that’s a powerful pesticide,” Mr. Von Arb said.

But 20 miles down the road, Brad Vermeer brushes aside such concerns.

He grows “traited,” or biotech, corn and soy on some 1,500 acres and estimates that his yield would fall by 20 percent if he switched to conventional crops and stopped using glyphosate, known by brand names like Roundup and Buccaneer.

In short, it is just too profitable to give up.

“Local agronomists are starting to say we have to get away from Roundup,” Mr. Vermeer said. “But they’re going to have to show me that conventional genetics can produce the same income.”

The local differences over glyphosate are feeding the long-running debate over biotech crops, which currently account for roughly 90 percent of the corn, soybeans and sugar beets grown in the United States.

While regulators and many scientists say biotech crops are no different from their conventional cousins, others worry that they are damaging the environment and human health. The battle is being waged at the polls, with ballot initiatives to require labeling ofgenetically modified foods; in courtrooms, where lawyers want to undo patents on biotech seeds; and on supermarket shelves containing products promoting conventionally grown ingredients.

Now, some farmers are taking a closer look at their soil.

First patented by Monsanto as a herbicide in 1974, glyphosate has helped revolutionize farming by making it easier and cheaper to grow crops. The use of the herbicide has grown exponentially, along with biotech crops.

The pervasive use, though, is prompting some concerns.

Critics point, in part, to the rise of so-called superweeds, which are more resistant to the herbicide. To fight them, farmers sometimes have to spray the toxic herbicide two to three times during the growing season.

Then there is the feel of the soil.

Dirt in two fields around Alton where biotech corn was being grown was hard and compact. Prying corn stalks from the soil with a shovel was difficult, and when the plants finally came up, their roots were trapped in a chunk of dirt. Once freed, the roots spread out flat like a fan and were studded with only a few nodules, which are critical to the exchange of nutrients.

In comparison, conventional corn in adjacent fields could be tugged from the ground by hand, and dirt with the consistency of wet coffee grounds fell off the corn plants’ knobby roots.

“Because glyphosate moves into the soil from the plant, it seems to affect the rhizosphere, the ecology around the root zone, which in turn can affect plant health,” said Robert Kremer, a scientist at the United States Agriculture Department, who has studied the impact of glyphosate on soybeans for more than a decade and has warned of the herbicide’s impact on soil health.

Like the human microbiome, the plants’ roots systems rely on a complex system of bacteria, fungi and minerals in the soil. The combination, in the right balance, helps protect the crops from diseases and improves photosynthesis.

In some studies, scientists have found that a big selling point for the pesticide — that it binds tightly to minerals in the soil, like calcium, boron and manganese, thus preventing runoff — also means it competes with plants for those nutrients. Other research indicates that glyphosate can alter the mix of bacteria and fungi that interact with plant root systems, making them more susceptible to parasites and pathogens.

“Antibiotics kill bacteria or reduce their growth, but some of those bacteria are useful,” said Verlyn Sneller, president of Verity, a small company that sells sugar-based fertilizers and water systems and works to persuade farmers like Mr. Vermeer to switch to conventional crops.

But research detailing the adverse effects with glyphosate is limited, and other studies counter such findings.

Monsanto, which sells Roundup and seeds resistant to glyphosate, says “there is no credible evidence” that the herbicide “causes extended adverse effects to microbial processes in soil.” A team of scientists from the Agriculture Department similarly reviewedmuch of the research and found the herbicide to be fairly benign. In response to a request from Monsanto, the Environmental Protection Agency recently increased the amount of glyphosate that is allowed on food and feed crops.

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“Another factor that weighed on our minds quite a bit was that when you look at the yields of the three major glyphosate-resistant crops — corn, soybeans and cotton — there’s generally been a trend upwards that hasn’t changed since they were adopted,” said Stephen O. Duke, one of the U.S.D.A. scientists who worked on the review. “If there was a significant problem, I don’t think you’d see that.”