Soil microbes are mostly bacteria and fungi. Scientists and farmers have known for a long time that some disease-causing microbes can wreak havoc on crops. So they paid close attention to those detrimental soil inhabitants.

"We focused over the last century-plus on the bad microbes, the microbes that cause diseases," explained Kinkel. "And we've asked one pretty straightforward question, which is, 'How do we kill those bad guys?'"

The answer, typically, has been: Pesticide, which kills both the bad and the good microbes.

"And this is the funny thing. It's like everything we do in agriculture to produce a crop is going to have an effect on our microbiome, but we've been working blind, for hundreds of years we had no perception of what we're doing to our microbiomes," she said.

But what if, instead of killing the disease-causing microbes, farmers focused on the good ones? What if they tried feeding and supporting the beneficial microbes that can help prevent disease or help plants absorb more nutrients from the soil?

Some plants have a mutually beneficial relationship with microbes. Legumes provide food for microbes on their roots and the microbes produce nitrogen the plants can use to grow.

Those relationships are what Kinkel and her colleagues are exploring.

"As scientists, what we really want to do is shift that balance for the good microbes and not let those aggressive bad ones win," said Kinkel.

The theory is that, if good microbes are strengthened, there will be less need to find ways to eradicate the bad ones. And that could have a significant impact on the way farmers think about pesticides and fertilizer use.

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