Farmers Are Manipulating Microbiomes to Help Crops Grow

In the back of Indigos Boston headquarters—past the gleaming new desks, past empty rooms awaiting new employees after a $100 million fundraising round—is a giant elevator. The elevator has one main purpose: to haul dirt up by the pallet load.

Indigo is an agriculture company. But it doesnt sell seeds or fertilizer or pesticides or any of the typical products agriculture companies have made billions selling in the past century. It sells bacteria, as a coating sprayed onto seeds—bacteria that could replace the chemical fertilizers modern agriculture has come to rely on. And this fall, farmers are harvesting 50,000 acres of the cotton planted with Indigos first product, designed to help the crop grow in low-water conditions.

Just as the human microbiome has opened up new frontiers in human medicine, scientists think that the plant microbiome could change modern ag. Indigo is not the first to take notice. Big ag companies like Monsanto, Bayer, and DuPont are all racing ahead into so-called microbials, with smaller startups maneuvering their way in too. What makes Indigo stand out is its singular focus on bacteria that live inside plants, called endophytes, rather than those that live on or around it.

Thousands of types of bacteria may live on plants; only dozens or maybe hundreds live inside. But the very fact that bacteria live inside plants is surprising. It catches almost everybody off guard, says Indigo CEO David Perry. And these bacteria that plants allow inside their roots, leaves, and stems can be beneficial, allowing them to, for example, capture nutrients from the air. Plants even pass along their endophytes via seeds, packaging their beneficial bacteria up into a convenient packet for their offspring. Because fewer bacteria live inside the plant than outside, endophytes also face less competition, meaning they’re more likely to be effective as a product for farmers.

But endophytes were initially slow to gain recognition. Joseph Kloepper, now a plant biologist at Auburn who works with several plant microbiome companies, remembers that most of the early work was down in the Soviet Union, which didnt have access to the chemical fertilizers and pesticides that dominated in the west. For many years, it was looked down upon as not very good science, he says.

But the falling cost of DNA sequencing has made it possible to easily sequence and sample plant microbiomes. Were all of a sudden having tools to study entire communities rather than single microbes, says Maggie Wagner, a plant biologist at North Carolina State University. Cheap sequencing means its much easier to go out prospecting and cataloguing microbes.

Thats exactly what Indigo has spent the past several years doing. With its network of collaborators, the company has collected microbes from plants all around the world. What the companys scientists have noticed, says Perry, is that modern monoagriculture seems to have wiped out the diversity of endophytes—just as it has with the genetic diversity of the plants themselves. So Indigo set out to sample wild and non-commercial plants, too. “I think we have one the largest collections of endophytes now,” says Perry, “and were just getting started.”

Indigo first tests its endophytes in a grow room in its Boston office—hence the dirt elevator. If those bacteria prove to increase yields indoors, it goes to greenhouse and farms across the country. This falls cotton crop, sprayed with Indigos first commercial bacteria product, will be the true test of how much bacteria can improve a harvest in a world challenged by drought. If it works, great. If not, Indigo has hundreds of bacteria it can keep testing.

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