Nathan Cude pulls open the top of a white Tupperware container labeled Q8R, which holds one of the hundreds of samples of American farmland he’ll handle in a year. The dark brown soil inside looks lifeless, but the microbiologist at Novozymes smiles as he utters one of his favorite lines: A spoonful of soil contains about 50 billion microbes, representing up to 10,000 different species. The number of organisms in the container surpasses the number of people who have ever lived on Earth.

Communities of soil-dwelling bacteria and fungi are crucial to plants. They help plants take up nutrients and minerals from the dirt and can even extend root systems, providing more access to food and water. They also help plants grow, cope with stress, bolster immune responses and ward off pests and diseases.

Now scientists at agricultural companies are digging through the dirt, like prospectors panning for gold, to find the exact microbes that make specific crops grow better. Agribusiness firms Novozymes and Monsanto are leading the way by coating seeds with microbes, planting them on farms across the U.S. and harvesting the crops to see how they fared. The two companies, through their BioAg Alliance, have just concluded the world’s biggest field-test program of seeds laced with promising microbes. This past autumn they harvested a variety of crops, planted using seeds with more than 2,000 different microbial coatings, grown in some 500,000 test plots from Louisiana to Minnesota, and they have been busily analyzing the outcomes. They will announce early results today. But they gave Scientific American a peek at their operations, and their aspirations, prior to releasing any findings.

In 2015 Monsanto and Novozymes planted seeds coated with one of more than 2,000 different microbes on some 500,000 test plots across the central U.S. to see if any of the organisms helped crops grow bigger or stronger.
Map courtesy of The BioAg Alliance

Ultimately, such microbial agricultural products could significantly reduce fertilizer and pesticide use, easing the burden farming imposes on the environment and potentially helping a farmer’s bottom line by reducing costs or increasing crop yields. The research is the beginning of an ambitious movement to replace chemistry in agriculture with microbiology.

Field trials are the key. “There is nothing that translates a greenhouse result to a field result,” says Thomas Schäfer, vice president of bio-ag research at Novozymes, and Cude’s boss. “Because the field is so complex, we have to test [seeds] in the field directly.”

A growing need
The world’s population is predicted to reach nine billion by 2050. With more mouths to feed, agricultural yields will have to nearly double. Climate change isn’t helping: droughts, floods, rising salinity and soil erosion are creating harsher growing conditions. Many pests and pathogens are developing resistance to pesticides. Chemical fertilizers only partly address the problem, and some studies show they contaminate groundwater, possibly contributing to human illnesses, and amplify harmful algae blooms in rivers and oceans. Scientists are hoping microbes can provide a viable alternative.

That solution could also alter the economics of big ag companies. Today the market for agricultural biologicals, such as natural pest controls, plant extracts and beneficial insects, is about $2.9 billion a year [updated Jan. 7, 2016]—a mere fraction of the $240 billion brought in by traditional fertilizers and pesticides, according to the alliance. Monsanto thinks the microbial market could grow substantially. Microbials have faster development cycles and fewer regulatory hurdles than other agricultural products, which can take 10 to 14 years to move from idea to market. And if widespread use lessens dependence on fertilizers and pesticides, that could ease public wariness of industrial farming.

The notion of bio-agriculture isn’t new. In 1888 the Dutch microbiologist Martinus Beijerinck discovered that the roots of leguminous plants were inhabited by a bacterium called rhizobium, which could take nitrogen from the air and convert it into a form the plants could use. Farmers and gardeners have been sprinkling packets of powdered rhizobiaon their peas and beans ever since. One by one, other microbes have been transformed into products, like biofungicides and biopesticides. But it wasn’t until recently that new DNA-sequencing tools allowed researchers to see the vast, complex microbiome, known as the rhizosphere, living in, on and around plant roots. A 2012 report written by the American Academy of Microbiology, titled How Microbes Can Help Feed the World, argued that tapping into this resource could generate products that “increase the productivity of any crop, in any environment, in an economically viable and ecologically responsible manner.”

The tricky part is figuring out which of the billions of members of the rhizosphere to go after first. Novozymes sends out teams of researchers to collect soil samples from private farms, which they bring back to the company’s labs in Research Triangle Park, N.C., where scientists like Cude process them. Although each sample might contain billions to trillions of microorganisms, only about 1 percent of will grow in the lab. Those that do often materialize in petri dishes in a dazzling array of shapes and colors: thin streaks of indigo blue, droplets of mustard yellow, a fuzzy asterisk of charcoal gray, a giant glob of blood red. Each microbe’s genome is sequenced (decoded) and checked against a database of known pathogens; any matches are discarded whereas the rest move on to the next phase.

The researchers test the remaining contenders to see if they could be used as one of two things: inoculants, which help plants take up nutrients, or bio-control products that help protect against disease and pests. One test checks if the microbes help plant roots better absorb nutrients such as nitrogen or break down inorganic soil phosphates so plants can use them. Another test assesses whether the finalists could offer protection against plant diseases or pests. For example, parasitic nematodes cause more than $120 billion in damage to plants worldwide. Jennifer Petitte, a zoologist at Novozymes, shows me a dish writhing with these tiny worms, which are barely visible to the naked eye. She adds promising batches of microbes to the dishes to determine if any can paralyze or kill the nasty pests.

Vials containing the best microbial candidates travel down the street to another Novozymes laboratory, where they are grown in large flasks filled with various formulations of rich broth, ranging from pale yellow to amber to almost black. Bill Throndset, a microbial physiologist at Novozymes, tells me the flasks’ exact contents are a trade secret, “like the recipe for Coca-Cola.” None of the microorganisms are genetically modified or engineered; instead, they are derived and cultured from soil samples. After each batch is cultured in its favorite media, it is cryopreserved and stockpiled, much the same way eggs or sperm are stored in banks. They’ll need to be alive and healthy when spring arrives and they are applied to seeds, so when the seeds germinate they can become part of the rhizosphere as soon as the plant takes root. “We essentially only have one experiment a year, so we have to get it right,” Throndset says.

Shortly before the growing season, the microbes are shipped a Monsanto facility in Saint Louis, where they are sprayed on seeds in big stainless steel bowls, like giant popcorn holders. In 2014 Monsanto planted seeds coated with hundreds of different microbial strains on around 170,000 plots, ranging from three by three to three by 10 feet in size. In 2015 the company greatly expanded the trial to more than 2,000 types of microbes on some 500,000 plots. Beside each test plot, the company planted a control plot with no microbe-laden seeds, creating a checkerboard effect across portions of the U.S. South and Midwest.

More bushels per acre
In October and November 2015 researchers harvested the crops and began crunching the numbers to determine which if any microbes made a difference. Many of the 2,000 coatings turned out to have no effect. But the top five increased corn yields by an average of four to five bushels per acre and soy yields by an average of 1.5 bushels per acre. The early results “look great,” says Jeff Dangl, a scientist at the University of North Carolina at Chapel Hill who studies the plant microbiome and is not involved with the experiments. “However, typically field trials have to run for seven years before anybody believes them. So the jury is still out. After we see several years’ worth of data, then we will have a more complete picture of which microbes are doing what.”

Nevertheless, the alliance says it plans to launch one of the five microbes as a product in 2017—an inoculant based on fungus found in cornfield soil. Novozymes’ Schäfer admits that even with all of the laboratory testing, he and his colleagues are still making educated guesses when choosing which microbes to send into the field. He hopes after multiple rounds of field testing, with top performers returning year after year, that patterns will emerge to help them predict which strains of microbes will benefit specific crops. The alliance will again field-test thousands of strains in 2016.

Unleashing microorganisms into new environments—particularly when the end product is destined for our kitchen tables—can raise concerns, some more valid than others. For example, Dangl says it is possible that messing with the microbial milieu might affect the taste of a particular crop, much like the composition of soil is known to influence the flavor of wine. There is also a risk that seed coatings, like many agents applied to a field, could slough off one crop and contaminate another. Some proponents don’t see a downside to sharing these “plant probiotics,” however, saying they would at best be beneficial to other crops and at worst have no effect.

Gwyn Beattie, a professor of biology at Iowa State University in Ames and one of the contributors to the American Academy of Microbiology report, has been following Novozymes’ efforts for years. She thinks the biggest concern is not necessarily that newly introduced microbes will grow and spread to other crops but rather that they won’t stick around long enough to do their job in the first place. “My analogy is if you throw one person [at a time] into New York City, the vast majority of people you throw in there do not change New York City. Every now and then there is one that will change the world, but it is not very likely to happen,” Beattie says. “It is like that in a microbial community. Introducing organisms rarely has an impact at all, and that’s actually the biggest frustration.” As a result, she argues, there will always be a need for chemical pesticides and fertilizers, but perhaps in smaller amounts as microbes are added to the mix.

The transient nature of the microbiome is one of the reasons Novozymes and Monsanto are currently field-testing microbes coated on seeds, rather than using other applications like sprays or root soaks. Hitting plants when they are germinating and sprouting, even if the effects are fleeting, could put them on track to be healthier as they grow. Although Schäfer would love to find a single blockbuster microbe, his scientists are also beginning to realize that bigger benefits may come from sets of microbes working together. With thousands of species in one gram of soil, the possible combinations are endless. Right now they are testing the species one by one, and they will wait until they have strong enough data on the singletons before testing combos.

Despite the challenges, Schäfer maintains microbes are poised to make a lasting impact on modern agriculture. Existing microbial products such as Novozymes’ Met52, a fungus that limits vine weevils, are already used on millions of acres; if seed coatings take off, that number could jump. The two firms think bio-ag products will be used on up to 500 million acres, or 50 percent of U.S. farmland, by 2025. “Companies like Monsanto, Bayer, Syngenta and BASF are working on microbes because they believe [the technology] has the potential to reduce chemistry and allow us to live more sustainably,” Schäfer says.

Marla Broadfoot is a freelance writer in Wendell, N.C., and has a PhD in genetics.