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How new beneficial microbes are performing on the farm

Companies have bet big on the organisms, but growers are waiting to see real-world results

by Melody M. Bomgardner
September 16, 2018 | A version of this story appeared in Volume 96, Issue 37


Photo shows an Indigo researcher checking on cotton grown from seed coated with beneficial microbes.
Credit: Indigo Ag
An Indigo researcher checks on cotton plants grown from seeds coated in beneficial microbes.

In early fall, farmers walk their fields and look ahead to the harvest. They think about how decisions they made six months ago will affect their bottom lines. When the weather turns cold, they’ll review the data they collected during the growing season and decide what to buy for the next one.

Growers will consider if they got their money’s worth out of that new corn hybrid, how much fertilizer to add in the spring, and what weed control plan to follow. And many will consider trying something new: applying beneficial microbes.

It has long been known that healthy soils are teeming with microbes that help plants grow and make them more resilient to stress. Starting around 2014, firms such as Indigo Ag, Pivot Bio, and the BioAg Alliance (a partnership between Monsanto and Novozymes) took the concept a step further by cultivating useful organisms and turning them into products.

While many microbial products are still in development, results from some of the first out of the gate are coming in from field trials and farm partnerships. They look promising so far, but it will take more seasons and experience under diverse conditions to find out if microbes can consistently improve plant health and farm profits.

Already, microbes are powering the fast-growing ag biologicals industry, a category that also includes growth stimulators and biobased pesticides. Global sales of biologicals reached $4.8 billion in 2017 and are expected to hit $10.7 billion by 2025, a rate of 11.5% per year, according to the consulting firm Frost & Sullivan.

Frost says the growth is driven by consumer demand for food free of chemical fertilizers and pesticides. At the same time, retailers are rolling out policies to limit use of agrochemicals, and regulators are issuing strict maximum levels for chemical residues on food.

But it’s farmers who must ultimately decide whether to pay for a helping hand from symbiotic microbes. Some are happy to give microbes a try because they feel there’s nothing else to help them increase profits.

“The innovation stream has slowed way down,” says Benjamin Riensche, an Iowa corn and soybean grower. “There’s only been a few new herbicides in the past two decades—even those are not cutting edge.” Riensche says improvements in plant genetics and fungicides have also not kept pace with farmers’ needs.

While traditional farming inputs like pesticides and seeds are generally sold by big agriculture companies, many of the microbe purveyors are start-ups.

Of these, the largest is Indigo. It was launched in 2014 out of the labs of Flagship Pioneering, a technology venture firm that builds its own start-ups. Indigo has raised more than $350 million from investors and has 490 employees worldwide.

Riensche is in an Indigo program for farmers. The company supplies him with microbe-treated seeds, tests grain quality, and pays him a premium per bushel.

“The place to do your pioneering is microbes,” Riensche says. “It’s kind of exciting because they open the door to much more sustainable agriculture.”

Indigo specializes in discovering endosymbionts, symbiotic microbes that live inside plants and help them resist drought and other kinds of environmental stress. Plants evolved along with these microbes, the company says, but they were winnowed away by modern agriculture practices.

Indigo launched its first products, cotton and wheat seeds coated with microbes, in 2016. Last year, farmers planted Indigo cotton on 110,000 hectares across Texas and the southern Midwest.

Company data from 2017 field trials in Texas show cotton yields were 14% higher on average compared with control fields. The boost was worth an additional $168 per hectare. In West Texas, where many farmers grow cotton without irrigation, the so-called win rate, or percentage of fields that showed a benefit, was 91%. Indigo attributes the gain to improved water stress tolerance.

Meanwhile, in Texas, Oklahoma, and Kansas, Indigo wheat fields yielded 13% more than controls. The results varied depending on how stressed the plants were: In low-yielding conditions in Kansas, the boost was 16%, versus 8% across all conditions. The win rate across all states was 62.5%.

For new agriculture products, a win rate over 60% is a positive, says Geoffrey von Maltzahn, Indigo’s chief innovation officer.

A female scientist at Pivot Bio examines flasks of microbes and broth.
Credit: Indigo Ag.
An Indigo Ag researcher monitors growth of symbiotic microbes.

“The annual rate at which yield is improving in wheat is approximately 1% a year. That’s the sum of all tools—breeding, agronomic insights, tractors, and chemistry,” von Maltzahn says. Genetically modified wheat has not been commercialized, and more than 90% of wheat fields are not irrigated, he adds. “In that context, the yield increases we’re describing are enormous.”

On Riensche’s corn and soybean farm, the challenge this year has been excessive moisture. “We lose more yield to too much water than not enough,” he says. “Wet soil brings rots, molds, and bacterial invasions.”

This is Riensche’s first season using Indigo’s microbes. While harvest won’t start until next month, he says he’s seeing clear signs of plant health in the fields and in the data gathered by his sensing equipment.

Riensche says farmers today are tracking more than just yield with such equipment. He measures the nutrient availability and composition of soils and conducts in-season testing of plant tissues to anticipate needs, such as for more fertilizer.

With the Indigo partnership, the data flow has become intense. The information has shown Riensche how widely his conditions vary even in the same field.

Indigo can even measure plant health from space. “With satellite-based observation you can see the difference between Indigo field performance relative to county and neighbor fields that didn’t use Indigo,” von Maltzahn says.

All that information goes back to Indigo’s R&D team to help it develop products for different geographies and crop stresses. “We’ve got hundreds of thousands of dollars in sensing equipment to make the data sandwich of what puts together a good crop,” Riensche says. In the longer term, Indigo wants to help farmers cut pesticide use by 90% and fertilizers by half, von Maltzahn says.

The start-up Pivot Bio also aims to reduce the need for fertilizer. Pivot Bio is targeting corn, which unlike soybeans and other legumes doesn’t attract nitrogen-fixing soil organisms. The firm’s researchers have turned up gene regulatory pathways to trigger microbes’ latent genetic ability to fix nitrogen from the air and make it available to corn plants.

After five seasons of tests, Pivot Bio is trying out its microbes across a swath of the U.S. corn belt in preparation for commercial introduction next year. So far, the company reports, its product has hit key milestones in the field.

Pivot Bio’s microbes are applied at planting time and colonize the root zone. They live on sugars and aromatic organic acids exuded by the roots.

“We do a lot of shovel-omics,” Pivot Bio CEO Karsten Temme says. “We dig up a phenomenal amount of roots. We can ask questions about how environmental or geographic variability influences the root-microbe relationship at a molecular level.”

The colony of microbes delivers something akin to time-release nitrogen, which saves money and labor normally used to apply synthetic fertilizer, according to Temme. Nitrogen-fixing microbes stick around, whereas nitrogen-containing fertilizers can be lost to evaporation or heavy rains.

The stress that rain and other weather conditions can cause plants is the number one concern for Zeb Winslow, a sixth-generation corn, soy, and cotton grower in northeast North Carolina. “In our area, weather patterns seem to have changed a lot in the last five years. We’ve had wetter springs and excess moisture during planting, a dry run during the grain season, and then excess moisture during harvesting.”

Winslow is also concerned about how to control weeds and insects that over the years have developed resistance to chemical pesticides.

He’s invested in a long-term plan, heavy on biology, to manage moisture and beat back pest pressure. The plan includes growing a multispecies cover crop during the off-season and a no-till planting system to keep weeds from gaining a foothold and to add organic matter to the soil.

“What we’re seeing is the living roots aggregate carbon in the soil, building it back from when it was destroyed when it was tilled,” Winslow says. “It rejuvenates the soil and increases water filtration and the water-holding capacity for dry times.”

Winslow says he leans heavily on pest-controlling seed coatings, particularly for cotton. Last year, the BioAg Alliance asked him to try out QuickRoots, a microbial seed coating. The product became part of Bayer after its acquisition of Monsanto.

QuickRoots contains the microbes Bacillus amyloliquefaciens and Trichoderma virens, which help release bound soil nutrients in the root zone.

Winslow says it’s hard to draw strong conclusions after one year. “It really did pay for itself in cotton and didn’t really pay for itself in corn. The benefits I’m looking for is any additional root growth. If it helps with overall plant health, that’s a definite advantage.”

Next year, Bayer will introduce a new microbial product for corn. Taking a page from the way legumes attract nutrient-fixing soil fungi, the product harnesses the signaling molecule lipo-chitooligosaccharide.


According to Kelli Brown, the lead for Bayer’s North American seed treatment portfolio, microbes can be an inexpensive way to support consistent yields and improve sustainability even in the face of unpredictable weather conditions. “We want to make clear what they are getting so they know where they want to take a risk,” she says of growers.

Riensche says he is looking forward to seeing the results from his first year with Indigo. “As a grain farmer, this is pretty cool stuff.” He suggests microbes can solve problems on the farm without the need to modify plants genetically and could reduce reliance on chemicals. “We can raise more grain with a smaller carbon footprint.”


This story was updated on Sept. 19, 2018, to correct the credit and caption. The photo was provided by Indigo Ag, not Pivot Bio.


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