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.