Stick a shovel in the ground and you’ll dig up some soil, maybe a few little rocks and, of course, some roots.

Now — take those roots inside for a closer look and you’ll see something else as well.

“When you hold this thing up to the light, what you can see is little tiny filaments,” says geneticist Ian Sanders, holding up a root in his lab at the University of Lausanne in Switzerland.

The filaments look like tiny strands of cotton..

“That’s the fungus,” says Sanders.

Sanders is obsessed with fungi, because he thinks they can play a big role in solving the world’s big food challenges in a time of rapid climate change and population growth.

In particular, Sanders is obsessed with a type of fungi that live on the roots of about 80 percent of the plants on the planet. Their tiny filaments help plants grow by drawing water and nutrients to the plant. In return, the plants feed sugars to the fungi.

It’s a symbiotic relationship that Sanders says is incredibly important.

“Almost all our food plants naturally form this association with these fungi,” he says.

And these species of fungi aren’t alone. There are thousands, maybe millions of kinds of fungi, bacteria and other microbes that help plants in a variety of ways.

But their role has been almost invisible to people. In fact, critics say, modern agriculture actively works against them.

“What we’ve done over the last hundred years in agriculture, is to try to take microorganisms out of the picture,” says Seattle microbiologist Rusty Rodriguez.

“And by doing that, by disrupting the soil with tillage, by using chemical pesticides, we have greatly altered the agricultural microbiome.”

Rodriguez is also obsessed with fungi. And like Sanders, he wants to re-alter the agricultural mircobiome. Both are part of a growing field of researchers and entrepreneurs working to bring microorganisms like fungi back into the agricultural mix, but in a new and targeted way. Sanders is breeding new varieties in the lab, while Rodriguez’s company gathers fungi from extreme environments all over the US and cultivates them in their lab and greenhouse in Seattle.

Right now, Rodriguez is using the fungi to help grow tomatoes, soybeans and corn. His hope is that the microbes will help crops like these survive growing climate stresses like droughts and floods and extreme heat and cold.

Rodriguez is working with different kinds of fungi than Sanders. His grow throughout the plant, not just on roots. But his goal is the same — to find and develop fungi that make agriculture both more productive and more sustainable. And, he says, his first two products using these microbes are just about ready for prime time, with a possible launch later this year.

Sanders’s work isn’t quite there yet. He and his colleagues are still conducting field tests in places like Colombia. But he says the results so far have been very promising.

Columbia is home to cassava, a root crop that feeds more than a billion people around the world. Sanders and a group of Colombian researchers set up experimental plots there to grow cassava using a new fungal gel that they hoped would significant increase yields while significantly reducing fertilizer use.

When they harvested their first crop a year later, Sanders says, they were “delighted” by the results — the plants had grown up to 20 percent more roots.

Sanders says the result actually surprised him, but that it was just the beginning. The research team has since grown cassava with different varieties of lab-bred fungi, and so far, he says, the impact has been even more dramatic.

Rodriguez, in Seattle, shares Sanders’s bullish view of the future of agricultural fungi and bacteria.

“Biologics,” he believes, “are the next paradigm for agriculture.”

Of course we’ve heard talk like that before. Think chemical pesticides, synthetic fertilizers and GMOs, all of which brought big initial benefits, but also big environmental problems, or at least big concerns.

So far, there hasn’t been much push-back on biologics from environmentalists, but just because something’s natural doesn’t mean it’s safe. Which is why both Sanders and Rodriguez say they’re working to make sure the fungi they’re developing won’t bring any unwanted impacts.

“You have to know the organism is safe,” Rodriquez says. “I never want to be in a situation where I stand up in front of an audience and they ask me that question and I say ‘I don't know.’”

What Rodriguez does know is that lots of tools will be needed to help produce more food, more sustainably.

And Sanders says we’ve been standing on some of those tools all along.

“Sometimes people think you have to go to unexplored wilderness to find something completely new,” Sanders says. “But we just have to look in the soil that’s beneath our feet.”