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Bountiful harvests of corn and other major crops rely on a mysterious phenomenon known as hybrid vigor. When highly inbred varieties are crossed, their offspring are taller, hardier, and bear more grain. Now, researchers report that this vigor is somehow influenced by microbes in the soil, perhaps via a plant’s immune system.

“This is a really interesting finding,” says Giles Oldroyd, a plant geneticist at the University of Cambridge who was not involved in the research. “I am surprised it has taken until now to be studied.”

Charles Darwin was one of the first researchers to describe hybrid vigor. In the early 20th century, biologists began to apply this effect to agriculture by creating inbred parent lines that yielded hybrid seed. By the 1940s, almost every farmer in the United States was planting hybrid corn, and the harvests multiplied.

Geneticists have proposed several theories about the cause of hybrid vigor, but no definitive explanation has emerged.

Maggie Wagner, a plant geneticist at the University of Kansas, Lawrence, and her colleagues wondered whether microbes might be involved. The tiny organisms can have a large impact on plants. For example, leaves and roots are often colonized by communities of beneficial bacteria and fungi that help protect the plant against disease-causing microbes. Some crops, like soybeans and other legumes, host microbes that feed them nitrogen—an essential plant nutrient, which farmers must otherwise deliver with fertilizer.

Last year, Wagner and colleagues found an interesting clue in a field study. They discovered that the leaves and roots of hybrid corn had microbial communities that differed from those living on inbred varieties of corn.

When winter came and the fields were fallow, Wagner tried to replicate the finding with a laboratory experiment. The researchers planted seeds in bags of a soillike substance that had been sterilized to kill all microbes. Then they added a simple community of soil bacteria—seven strains that are known to colonize corn roots—to some of the bags while leaving others sterile. When the microbes were present, the hybrids grew better than an inbred variety, as expected, with roots weighing 20% more. To their surprise, however, the hybrid and inbred corn plants grew about the same in the sterile soil, they report this month in the Proceedings of the National Academy of Sciences. The weight of their roots and shoots hardly differed.

The finding held up when the scientists repeated the experiment by adding a full set of microbes, taken from soil, to some of the sterilized bags. “The results look convincing,” Oldroyd says.

The takeaway? “Something about being a hybrid makes a plant interact differently with microbes,” Wagner says. Based on some of the results, the team thinks microbes retarded the growth of inbreds, rather than giving the hybrids a special boost.

It could be that the inbreds’ immune systems overreact to benign microbes, compromising their growth. (The experiment did not include any pathogens.) Alternatively, hybrid plants may be better able to defend against weak pathogens in the soil. “We have a lot of work planned to follow up on that idea,” Wagner says.

Oldroyd says the results highlight the need for plant breeders to match the genetics of crops to the microbial communities with which they live. The findings drive home the importance of understanding the role of soil microbes in making agriculture more productive and sustainable, adds Corné Pieterse, a plant biologist at Utrecht University. “This holds great promise.”