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One startup’s plan to grow more crops: put the germs back in

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Indigo claims it can dramatically boost yields by restoring plant's microbiome

Indigo greenhouse
Indigo greenhouse

A startup launched this week with a radical plan for helping to feed the earth’s growing population — while also cutting back on farming practices that harm the environment. The company, Indigo, says it plans to replenish the microbiome of crops, adding back in microbes that have been killed over years of heavy use of herbicides, pesticides, and fungicides. It aims to do this by selling a probiotic seed coating for crops like corn, cotton, wheat, and soybeans.

Over the last decade the study of the human microbiome, the symbiotic bacteria and fungus that live in our bodies, has boomed. Scientific research has found that the biota in our guts, our mouths, and our skin can have an enormous impact on our physical and even mental health. Antibiotics, which have saved countless lives, also impact on the health and diversity of our microbiome. This has led people to experiment with new techniques for replenishing the bacteria in their bodies. Scientists actually know more about the microbiome in plants; Indigo is exploiting the new popular interest in friendly microbes to market itself.

The Indigo team spent two years building a database on the microbiome of the most popular row crops. It compared what it found in heritage plants, and those raised through traditional agriculture, to those raised with modern tools like pesticides, fungicides, and herbicides. Ultimately, the company says it collected data on over 40,000 symbiotic microbes from 36,000 samples of more than 700 plant species. It then used machine learning techniques to identify important microbes that are less common in modern agriculture. The company claims to have grown crops within these "renewed" microbiomes over four plantings and achieved yields 10 percent higher than comparable seeds.

comparison Indigo plants

A comparison of plants grow with Indigo's treatment (right) versus those without (left)

Indigo won’t say microbes it replaced, or how the seed coating works.. The company says it is going to keep the details of its trials and techniques private for now, while it works on filing hundreds of patents. It plans to share data from the trials for peer review in the future, but won’t offer any concrete timing.

For plants, the web of bacteria, fungi, and viruses that make up the microbiome is far more essential than it is for us. Plants can’t move to escape a predator or perilous environment, to find a better source of nutrients or a suitable mate. That most essential function of plants, turning sunlight into sustenance, was made possible by piggybacking on the working of cyanobacteria. And while the recent enthusiasm for our own microbiome has brought the subject into the popular consciousness, the study of how it impacts plants has actually been going on for centuries. Martinus Beijerinck, an influential Dutch botanist, described the way microbes known as Rhizobia helped provide usable nitrogen to roots of leguminous plants like peanuts and alfalfa way back in 1888.

Farmers often tried to tap into these benefits, developing techniques for rotating crops and transplanting soil in a way that encouraged a healthy microbiome to thrive. Unfortunately, just as often, they treated microbes as a threat to be suppressed, killing off helpful bacteria in equal number. Indigo says the work it did with plants was inspired by the recent strides made in understanding the human biome. But some experts say that’s actually a bit backwards.

"It’s actually the plant scientists who have been looking at the microbiome for years. It has a much longer history in the field than it does in human biology," says Vincent Young, a microbiologist at the University of Michigan who studies the role of bacteria in our gastrointestinal tract. "People on the plant side were more open to this a long time ago, because they were ecologists, and understood that there were things in the environment you couldn’t see that were just as important as what you could see, and that everything existed in a sort of mutually beneficial web." Indigo’s approach, and more specifically its messaging, is less revolutionary science than smart marketing. "They are framing it as coming from the study of humans because there is so much fuss and hype around the human microbiome," says Young. "Their approach seems comprehensive and modern, but nothing necessarily new."

Along with announcing its test results, Indigo says it raised $56 million in venture capital funding. Tech investors are clearly convinced of its promise, and two scientists, Young and another microbiologist who spoke with The Verge for this piece, agreed that Indigo’s approach seems sensible. In fact, the notion that finding ways to replenish the microbiome of plants could increase crop yields was endorsed by the American Society for Microbiology back in December of 2012:

Theoretically, if that gap could be closed — if all farmers could achieve the highest attainable yield — worldwide crop production would rise by 45-70%. Yield gaps can often be explained by inadequate fertilizer or water, or by losses to pests or disease, but vast increases in use of fertilizers, water, and pesticides are not only economically impractical, but would have many negative environmental consequences. Scaling up current high-input agricultural systems is simply not feasible….Producing more food with fewer resources may seem too good to be true, but the world’s farmers have trillions of potential partners that can help achieve that ambitious goal. Those partners are microbes.

As the global population grows, the microbiome offers one of the most promising avenues for increasing yields without harming the planet. Of course, the founders and their investors have economic motives as well. Taken together, just four of Indigo’s initial focus crops — corn, soy, wheat, and cotton — amount for hundreds of billions of dollars in annual sales. A 10 percent increase would have a massive impact on both the availability of food and on farmers’ pocketbooks, potentially positioning Indigo as a massive business.