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Root for Roots (and Microbes, Too)

Two Fortune 500 companies didn’t form the first successful alliance. Nor did two armies or nations. Ditto for an arranged power marriage between two royal families.

Instead, flash back 470 million years ago. “We know from fossil records that is when fungi and plants had already formed an ancient alliance,” says Chris Topp, who studies crop root dynamics as an associate member at the Donald Danforth Plant Science Center in St. Louis.  

Back then, plants had just migrated to land after residing in water. They grew roots to hold them in place and also to mine for resources like food, says Topp. Besides evolving roots, another way plants could do this was to team with fungi that were already adept food foragers. 

“This connected plants to resources that they could not capture on their own,”  Topp says. 

The same relationship between soil microbes like fungi and crop plants still exists today.  

“Plants capture carbon dioxide from the air and convert it to sugars,” says Topp. “Plants then decide what to do with those sugars. They may use them to form new roots or leaves. Or, they may swap them with a microbe in exchange for nitrogen (N) or phosphorus (P) that a microbe has ingested.”

Besides fungi, other microbes including bacteria and viruses turbulently churn through the soil. Many benefit plants. Some raise havoc and cause crop disease. Fortunately, Mother Nature can take care of them akin to a subterranean Silence of the Lambs movie.

“Some bacteria can turn cannibalistic, preying on their brethren,” says Mike Lehman, a soil microbiologist with the USDA-ARS North Central Agricultural Research Laboratory in Brookings, South Dakota.

Meanwhile, thousands of interconnected root tips per crop plant work in concert with microbes to seek out nutrients and water. Some soil microbes help broker the building block of soil – carbon – while others help fix atmospheric nitrogen. 

Roots also exude organic acids that can change pH in a localized soil environment. 

“This changes the chemical properties of the soil, which can free up nutrients like P that are bound to clay particles and make them available to the plant,” says Topp. 

“Multiplied many times over, these microbial and root processes can benefit farmers by cutting dependence on commercial fertilizer and boosting crop performance,” he adds. 

Demystifying a Mystery

Yet, there’s much to learn regarding this unseen world.  

“That’s exactly why I tell my grad students to work on roots, because no one else wants to. You will get a job,” deadpans Michelle Watt, who heads the Roots Dynamics Group at Forschungszentrum Juelich, a Helmholtz Research Center in Germany. “It’s quite complicated research.” 

Still, the rhizosphere – the area surrounding the roots where microbes reside and where chemical and biochemical processes also occur – is spurring research and product development on top of what nature already does. It’s the science behind BASF’s Poncho/Votivo 2.0. This product combines chemical insect control in the Poncho component with Votivo’s biological control of nematodes and a bacterium that BASF officials say enhances soil microbial activity. Other firms offer microbial products that tout benefits ranging from capturing atmospheric nitrogen to reducing plant stress. 

Here are three practices farmers can do to leverage existing soil microbes.

  • Less tillage. This enables soils and accompanying soil life to thrive undisturbed by building soil structure. “If you build soil structure, they (microbes) will come,” says Jodi DeJong-Hughes, a University of Minnesota Extension educator.
  • Diverse rotations with cover crops. Besides helping to nix erosion through year-round cover, a diverse cash crop mix laced with cover crops helps spark microbial numbers that benefit soils. “We always see improvement in soil properties when we have wheat in the rotation,” says Lehman. 
  • Livestock and accompanying manure applications.  “There is just something about manure that, along with a cover crop, helps build soil biology,” says Jeff Reints, a Shell Rock, Iowa, farmer. 

In the Beginning 

All this, though, starts with roots. 

“Roots are the dominant force in the soil,” says Topp. “Roots are what literally push carbon in the soil.” 

Soil carbon promotes:

  • Nutrient release for plants
  • Soil structure
  • Soil life

Yet, roots seldom come up in conversations that Lance Torochione has with farmers. Much is due to the culling process that seed companies use.

“Hybrids with root issues that lead to lodging get weeded out of seed lineups pretty quickly,” says the Illinois-based DeKalb and Asgrow agronomist. 

Roots haven’t been a direct focus of plant breeders, either, adds Watt. 

“The main argument that breeders and agronomists use is ‘If we’re selecting for better yields and performance, we select for better roots indirectly,’ ” says Watt. 

Roots do play a role in corn breeding, says Sean Evans, technology development manager with Bayer Crop Science. It’s just one of the many factors, though, that Bayer considers in its corn breeding program.  

“We spend less time characterizing below-ground attributes and more time studying overall performance,” he says. 

Still, focusing on roots as well as yield during breeding paid dividends during the Green Revolution of the 1960s, says Watt. 

“Norman Borlaug wanted to reduce the height of wheat, especially in India,” she says. “They needed to apply more fertilizer, but when they did, the wheat grew too tall and fell over. So, he had to go outside the normal breeding gene pool in order to find a shorter dwarf wheat to make a cross that didn’t fall over.

“Another reason the dwarfing was so successful was that he didn’t compromise anything in terms of root system depth in order to capture nitrogen,” Watt says. “All this wouldn’t have come along by just screening for yield.”


Joining forces with roots are microbes. “Microbes are the ecosystem’s service providers,” says Lehman. “Their intimate relationships with every living being on earth enable life itself.”

They’re also team players that closely work together, says Lehman. 

“Microbes are committed to communal living, and it’s not by choice,” he says. “One of them cannot conduct a reaction unless another one is there sucking up the waste that comes out.”

One microbe group that’s particularly beneficial is arbuscular mycorrhiza fungi (AMF). AMF can extend the reach of roots by capturing nutrients roots could not get on their own. 

“They are embedded in the cells of roots and extend out from the surface and form a branched network similar to roots,” says Topp. 

Lehman adds that studies show AMF can acquire relatively immobile elements like P and improve soil structure. This aids water infiltration and helps nix erosion. 

AMF thrives in native grass prairies, where an undisturbed network results. Cropping systems? Not so much. Tillage shatters the complex networks AMF builds. 

Scientific trials have shown microbe loss in soils correlates to:

  • More leaching of N
  • Increased P loss
  • An increase in nitrous oxide (a greenhouse gas)
  • Less carbon retention

There’s a catch to all this, though. Most trials have shown this occurs in greenhouse trials. In field trials, it’s been harder to prove. 

“We’re learning huge amounts continually, but there’s still a lot to learn,” Lehman says.

In the meantime, though, he advises farmers to continue to implement steps like less tillage, more cover crops, or adding livestock and/or manure to encourage microbial numbers and diversity. 

“If you’re doing these things, I have no doubt you are encouraging microbial diversity,” he says.

More to Come

The relationship between roots and microbes has historically been difficult to study. Trials typically entail physically digging up roots and analyzing them. Not only is this labor intensive, but also shatters the fragile networks roots and microbes have formed.

That’s changing. The Danforth Plant Science Center and Valent BioSciences formed a multiyear agreement in 2016 to use large-scale X-ray computed tomography imaging for noninvasive root measurements. This system – the first in the U.S. for plant science – records unseen processes without disturbing plant development, says Topp. 

“We can now see fungi infecting the cells of maize (corn) that access carbon from the plant and trade that for P and N and other nutrients,” says Topp.

“These are old alliances that have withstood the test of time,” he adds. “Now, we can begin to understand the mechanisms that are involved and get answers to  what we don’t know.”

Jennifer Hahn in a soil pit with farmers at a soil health field day
Photo credit: Gil Gullickson

Roots Tell a Story

Worried about soil compaction? A shovel and some elbow grease to dig up roots can reveal if you’re on the right track, says Jennifer Hahn, coalition coordinator of the Minnesota Soil Health Coalition. (Hahn, shown right, speaks to farmers at a field day.)

“We want the roots growing vertically,” she says. “If you find some roots growing horizontally, it’s hitting some kind of hardpan compaction.

“The thing about looking at roots is that it also tells you a story,” she adds. “If it was plowed 20 years ago, there will be remnants of that. It takes a while for it to break up.”

Soil health experts examine a pair of shredded briefs as part of a soil health demonstration
Photo Credit: Gil Gullickson

Soil Your Undies

Luke Ressler, a former North Dakota State University (NDSU) soil technician who now farms near Hillsboro, North Dakota, and Allie Marks-Slykerman, a Centrol crop consultant in LaMoure, North Dakota, aren’t looking at the remnants of a wild party. 

Instead, the shredded briefs are a “Soil Your Undies” test farmers can use to assess soil health. Since cotton briefs are a carbon source, soil microbes will find them and feed. The more microbes present, the more the briefs will be shredded when they’re dug up a few weeks later. 

“I’m not sure how scientific it is, but it’s visual and it gets farmers out in their fields looking at soils,” says Abbey Wick, NDSU Extension soil specialist. “I like this approach because it helps build relationships when you’re laughing together over something so goofy.”

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