Probiotics for plants? Here’s how AI-optimized bacteria could accelerate agriculture

Indigo Agriculture cotton

Indigo Agriculture

The global population is rapidly rising. The rate is slowing, sure, but experts predict that two billion more people will inhabit the Earth by 2050. That’s equivalent to adding another India and a half, which will put the total global population at around 9.7 billion people. That’s a lot of mouths to feed and one huge task — especially considering our failure to do so at present.

Experts predict that two billion more people will inhabit the Earth by 2050.

If we’re going to feed all these extra people we won’t just need big ideas. We’ll need a bunch of microscopic microbes as well.

That’s the bet being made by a biotech startup called Indigo Agriculture whose plan is to pump plants with a bunch of beneficial microbes to make the crops grow faster, stronger, and more productively. It’s a long shot, but it could give farmers access to crops that not only grow better in current climates but are better prepared for the impacts of climate change around the world.

Microbes, Microbes Everywhere

At any given moment, you’re sitting in a sea of trillions of microbes that live on, in, and all around you. Though they’re invisible to the naked eye, they’re far from inert. A growing body of research is showing that microbes affect a wide range of factors, including our mood, our health, and even our ability to handle stress and fend off disease.

But our microbiome is in danger of being destabilized. Ever since we began swallowing antibiotics, the bacterial environment in our bodies has changed. Antibiotics work great for eliminating harmful bacteria but their indiscriminate nature means that they wipe out a lot of beneficial bacteria as well.

Indigo Agriculture

“Our microbes have evolved with us, enhancing our ability to maintain optimal health and fend off disease,” Lauren Moores, Vice President of Data Strategy and Data Sciences at Indigo, tells Digital Trends. “The mass adoption of antibiotics affected these beneficial microbes. So we’ve taken to consuming live and active cultures – probiotics – to repopulate our intestines with good bacteria.”

Much the same goes for plants. The widespread use of agricultural chemicals and fungicides have disrupted a nuanced plant microbiome that developed over millions of years. These chemicals kill disease causing bacteria, but they also eliminate specialized microbes that may help the plant better withstand stresses like drought, or grow more productively by trapping vital nutrients like nitrogen.

Indigo’s founders figured that if the human microbiome has such a massive effect on human health, shouldn’t a plant’s microbiome also be key to its survival? And, if so, how do we identify which microbes are beneficial and for what purpose? And how do we restore these thriving communities of bacteria in our crops?

Microscopes on the Microbiome

Most studies conducted on microbial life have centered on the ones most closely associated with humans — like those found on our skin and in our gut. And though there has been a fair amount of research into microbes found on other animals, plant microbes (and the roles they play) have been relatively neglected until recently.

“Our microbes have evolved with us, enhancing our ability to maintain optimal health and fend off disease.”

“A lot of papers have come out in the last five years, kind of as a follow up to what we’ve learned from the microbiome in other [biological] systems,” Harsh Bais, a plant and soil scientists at the University of Delaware, says. “But the whole functional significance of the microbiome association in plants is still not fully out in terms of the detailed mechanisms of why a plant needs them,”

For decades, researchers have known that bacteria on plants and in the soil help “fix” nitrogen, allowing the plants to better access this key nutrient. But in 2015, Sharon Doty, a plant microbiologist at the University of Washington, showed that entire communities of beneficial bacteria exist within plants and allow species like poplar and willow trees to grow tall and strong in rocky and otherwise nutrient-poor conditions. In her study, Doty was even able to transfer these nitrogen-fixing microbes to another plant — rice, in this case — which let the crop grow taller, with a fuller root system.

Indigo Agriculture

“Just as the human microbiome is important for our health, so too the plant microbiome is necessary for plant health, but perhaps more so,” Doty wrote in her book, Functional Importance of the Plant Endophytic Microbiome. “Since plants cannot move, they face more challenges in acquiring sufficient nutrients from a given site, defending against herbivores and pathogens, and tolerating abiotic stresses including drought, salinity, and pollutants. The plant microbiome may help plants overcome these challenges.”

Building on this knowledge, the folks at Indigo have sequenced the genes of tens of thousands of plant-based microbes: the largest database of plant microbe that exists today. With this data, they use machine learning algorithms to predict the microbial strains that have the greatest impact on important crops like cotton, corn, rice, and wheat.  The hope is that Indigo can restore — and even boost — the microbial environment to help these crops perform better out in the field.

“The real impact will come from combining this tool with other technologies we have that are rapidly evolving in the plant breeding space.”

“All in all, with machine learning, we can precisely identify microbes, map their functional capabilities, understand the communities they live in, and unite this information with laboratory and field data to rapidly develop and target new microbial products,” Moores said.

Ultimately, Indigo provide a microbial coating that’s applied to seeds before they are planted in the ground. And while there are other companies looking into beneficial bacteria for plants, they’re primarily focused on those found in the soil, while Indigo investigates those inside plants.

Indigo’s approach shows huge potential for agriculture and its funding rounds have reeled in over $400 million as a result. But there are plenty of question marks behind the company’s research. Indigo may be able to identify what microbes are present in plants, and they may even be able to pick out which ones are beneficial, but determining their role and the most effective combinations will prove challenging. It’s one thing to know which bacteria are present, and another thing entirely to know what they do and why.

For his part, Bais remains cautious but intrigued. “There are a lot of open-ended and unanswered questions that we have no clue about” he says. Not that these questions can’t be answered, but that it will take a lot of trial and error to do so. As Bais explains, scientists will have to “take a bug, take a plant, and see what the bacteria is doing to that plant. Then take the same bug and take multiple plants and see whether that can be translated to multiple plants.”

But as the science behind the plant microbiome progresses, Indigo has positioned itself to be a top contender, if not ahead of the game.

“The scientific community is still early in its study of the plant microbiome, particularly as compared to fields such as plant pathology and soil science,” Moores says. “That being said, our emerging understanding of the role that microbes play in humans has sparked a revolution in healthcare. We believe that we’re on the forefront of a similar revolution in agriculture. There is a tremendous opportunity here.”

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