Scientists Want to Replace Pesticides With Bacteria

Fresh snow coats the sidewalks outside Indigo Ag Inc.’s Boston offices, but inside the temperature is calibrated to mimic spring in the Midwest. Hundreds of almost identical soy seedlings sit beneath high-intensity arc lamps, basking in the artificially sunny 60F weather.

The plants aren’t destined to stay identical for long. “We haven’t imposed the stress yet,” says Geoffrey von Maltzahn, the company’s lanky 37-year-old co-founder. The MIT-trained microbiologist gestures toward photos showing what happens when you apply Indigo’s signature product—a coating of carefully chosen microbes—to some seeds but not others before planting, then dial back the water supply: One shows a tall, flourishing stalk; the other, what looks like a tangle of shriveled leaves.

In humans, a healthy microbiome—the universe of bacteria, fungi, and viruses that lives inside all of us—is increasingly recognized as critical to overall health. The same is true of the plant world, and Indigo is among the dozen or so agricultural technology startups trying to take advantage of the growing scientific consensus. Their work is enabled by advances in machine learning and a steep reduction in the cost of genetic sequencing, used by companies to determine which microbes are present. Approaches vary: AgBiome LLC, with funding from the Bill & Melinda Gates Foundation, is studying how microbes can help control sweet potato weevils in Africa, while Ginkgo Bioworks Inc. announced a $100 million joint venture with Bayer AG to explore how microbes can encourage plants to produce their own nitrogen.

Indigo is the best-funded of the bunch, having raised more than $400 million. To develop its microbial cocktails, Indigo agronomists comb through normal fields in dry conditions to see which plants seem healthier than average. They take samples of the thriving plants and “fingerprint” their micro­biomes using genetic sequencing; once they’ve done this with thousands of samples, they use statistical methods to pick out which microbes occur most often in the healthiest plants. These proceed to testing, then large-scale field trials.

The company’s first commercial products are focused on improving drought tolerance, one of the most difficult traits to address through genetic modification. “It’s like a symphony,” founder von Maltzahn says of a plant’s reaction to water stress, “and GMOs are like slamming down on one note on one instrument.” Drought conditions are likely to become a greater threat to agriculture because of global warming. Indigo is also investing heavily in research and development efforts to see how microbes influence factors such as nitrogen use and pest resistance, aiming to reduce or even eliminate the use of synthetic pesticides and fertilizers as well as genetically modified seeds. With the general public rejecting chemical treatments and GMOs in favor of “natural” foods, Indigo is counting on a potentially multibillion-­dollar market. So far, its microbe coatings have boosted cotton yields by an average of 14 percent in full-scale commercial trials in Texas and wheat yields by as much as 15 percent in Kansas.

Indigo Chief Executive Officer David Perry doesn’t want to just market a suite of seed treatments, however. He wants to reshape the structure of the agriculture industry completely, competing not only with chemical companies such as Monsanto and Dow Chemical, but also with agricultural distributors like Cargill and Archer Daniels Midland. Perry, a biochemist who grew up on a small farm in rural Arkansas, founded two pharma-related companies, a drugmaker he eventually sold for multiple billions of dollars and an online marketplace for research supplies that went public in 1999. After joining Indigo in 2015, Perry quickly zeroed in on a fundamental business challenge: Most farmers have no choice but to sell their harvest at commodity prices. Without the opportunity to earn more for using environmentally sustainable methods, they have little incentive to alter their ways.

For farmers to adopt Indigo technology, they’d need a buyer willing to pay a premium for non-GMO, pesticide-free products. So, Perry reasoned, Indigo would facilitate the sale. Today the company contracts upfront with hundreds of farmers to buy their entire harvest of, say, Indigo Wheat, at a hefty premium. “Now you’re growing a value-added product, and that starts to go directly to farm profitability,” he says. Indigo then sells the wheat to end users such as breweries, flour mills, and food companies, which have become more interested in transparency and control when it comes to the origin of their grains. Perry says he’s betting on a long-term shift away from commodity agriculture and toward specialty markets, as the coffee and cocoa industries are seeing.

While the science behind microbiome treatments is promising, Indigo has a long road ahead. Its success depends on proving that microbes can meaningfully influence more than just drought tolerance while at the same time scaling up to the kind of sprawling, complex operation that can buy and sell millions of bushels of grain from tens of thousands of farms.

Michael Dean, chief investment officer for the venture capital investment platform AgFunder Inc., sees Indigo’s technologies as potentially disruptive but suggests that one of the biggest challenges the company will face is persuading farmers to turn their back on comfortable relationships with Big Ag. “Farmers have tended to buy seed from the guy their dad bought from, and sold it to the same grain elevator,” Dean says. “This is going to make waves, and not everyone will be happy about it.”


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Scientists Want to Replace Pesticides With Bacteria

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