How Tiny Soil Organisms Could Help Farmers Adapt to Climate Change

In recent years, the global average temperature has climbed past one degree celsius warmer than pre-industrial times. And, like a raisin in the sun, the planet is drying out — or, at least, parts of it are.

In semi-arid areas around the world, drought conditions have worsened with intensified heat. Unfortunately, many of these places have something else in common: they are home to communities that are built around agriculture.  

The “dry corridor” that stretches inland of the pacific coast of Central America is one such place. Here, generations of farmers have subsisted off of small-scale, rain-fed agriculture. A prolonged period of drought coupled with hotter temperatures eradicated 700,000 acres of corn and beans there during the summer of 2018. While some farmers have found ways to adapt to the changing climate, it has forced others off their land. 

In the western U.S., where agriculture accounts for the majority of water used by people, most operations have long forgone a rain-fed approach. From Wyoming to Southern California, the verdant fields of alfalfa, wheat, leafy greens and everything in between are fed by the Colorado River watershed.

But this too is a dwindling resource, as the Western U.S. is currently in a period of “mega-drought.” Lake Mead, the largest reservoir along the Colorado River Watershed, dropped below 1,075 feet this spring, a level that triggered cutbacks in outflow to Arizona, Nevada and Mexico.

Farmers on semi-arid land throughout the world therefore must make a choice: They can either migrate, or try to adapt their crops to drier, hotter conditions.

Emerging Microbes

Since the green revolution of the mid-20th century, crop improvement has mostly focused on manipulating genes through breeding or genetic modification. But USDA research microbiologist Devin Coleman-Derr worries that this approach is beginning to show diminishing returns for staple commodities.

“We’ve seen, in recent decades, a plateauing from the amount of boost we can get. We’ve sort of tapped out genetic variability,” he says. “It looks like we’re gonna need something new.”

In search of a novel approach to adapt crops to a quickly changing climate, researchers and industrial giants alike have set their sights on the subterranean realm of soil microbiota — the vast symbiotic network of fungi and bacteria that coexist among the roots of all plants. Although researchers have studied microbiota extensively in certain natural ecosystems, it’s a newly understood concept within an agricultural context. “The crop isn’t just the plant,” says John Taylor, an evolutionary mycologist at the University of California, Berkeley. “It’s the plant and it’s microbes.”

Perhaps the best-known example of a symbiotic relationship between microbes and a crop occurs between nitrogen-fixing bacteria and legumes. These bacteria dwell in “nodules” on the roots of legumes like peas and alfalfa. In exchange for nutrients from the plant, they convert atmospheric nitrogen into the biologically useful compound ammonia. 

This is just one example from a complex web of interactions, which varies between plant species and locations. Since scientists want to unlock microbiota-based solutions to drought-induced stress, they must first understand how these communities living under the soil react to prolonged dryness.

Both Taylor and Coleman-Derr have focused their research on microbial communities that co-exist with sorghum, a cereal that was originally domesticated in Africa and is known for its drought tolerance. Their research has offered a more nuanced glimpse into how the crop reacts to drought.

It seems that actinobacteria, which decompose organic matter, dominate within the soil of a drought-stressed sorghum plant. This knowledge represents a step in the right direction, but why (and how) does this occur? “We have some evidence that there is a benefit, but we’re not exactly sure how it’s conferred,” he said.

In some studies, bacteria have been shown to modulate a plant’s response to its environment by promoting or producing certain hormones, which in turn can improve stress tolerance. Coleman-Derr says that these findings are especially promising when it comes to developing new technologies for boosting crop successes. “Then you have two strings you can pull,” he says.

Researchers can add the microbe to the system — or cut out the middleman and just add the hormone instead.

Sorghum isn’t the only crop species to benefit from these helpful microscopic communities. Strains of bacteria from semi-arid wheat and maize fields have been shown to improve drought tolerance, too.

Making It Stick

Identifying a beneficial microorganism is only half the battle. Since the climate, soil composition and pre-occurring microbes vary from site to site, transplanted microbes don’t always linger. “You introduce some new microbe, and its ability to sort of stick in that system has been our biggest challenge. Usually, you go back later to look for the thing, and it’s gone,” Coleman-Derr says. 

Still, particularly hardy or adaptable microbes can be transplanted via relatively simple methods. Most commonly, bacteria or fungal spores are included in a slurry of ingredients called a “seed coat” that’s adhered to the outside of a seed before planting. Then, ideally, the microbes colonize the soil as the seed germinates.

In the commercial seed industry, this practice has been used for years with well-known inoculants — like nitrogen-fixing bacteria on legume seeds.

“We started adding biologicals back in 2005. Now almost all of our coatings have some type in them,” says Bill Talley, the owner of a seed supplier called Summit Seed Coatings. “It’s a growing area. There’s a lot of investment from the big companies and startups, too.”

Researchers like Taylor and Coleman-Derr hope to keep identifying microbes and hormones that could be used in agricultural applications like seed coating. Although seed coating may be more useful in commercial agriculture within wealthier countries, Taylor points out that low-income nations may yield some benefit from microbes without needing technological intervention. 

“There are two strategies: You can either hope that fungi migrate, or they evolve,” he says. “We know that fungi can probably, over a short period of time, evolve to handle different temperatures.”

Beneficial microbes are by no means a cure-all for food insecurity or intensified drought. But, as we uncover more of their story, they may be the key to growing food in places teetering on the margins of viability — just a little too dry, just a little too hot.

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