Climate change poses a severe threat to agricultural productivity globally. Unpredictable weather patterns, such as more frequent floods and droughts, disrupt crop production and growth. Ensuring sustainable and reliable food production in the future requires climate-resilient crops.

Engineering plant root ecosystems is one approach that could improve crop resilience to climate change. Plants use roots to find water and nutrients, interact with soil microbes, and withstand environmental stresses. Building upon these functions could make roots and, thus, plants more resilient to environmental stresses while improving nutrient uptake.

Root development involves complex regulatory pathways involving multiple genes and hormonal regulation. Their interactions with soil microbes are far knottier than previously understood. Now, synthetic biology researchers and companies are using gene editing to tweak root morphology and activity.

Manipulating Root Architecture

When roots grow, they forage in response to the environment and seek water and nutrient patches to exploit. Conversely, root development is suppressed in areas where water and nutrients are scarce. Manipulating root architecture could allow plants to utilize available resources more efficiently. However, little is understood about how roots develop despite their central role in how plants use nutrients.

That’s because crop improvement has historically focused on above-ground traits with an eye on increasing yields. Even when researchers wanted to investigate what’s happening at the roots, they couldn’t, as it’s difficult to look under the ground. Also, “we knew very little about the role of roots in soil health and the nature of roots and soils as a composite material,” said Claire Grierson, a plant biologist at the University of Bristol.

That’s changed over the last decade. Researchers have developed assays to visualize and measure roots’ growth and interactions with the soil. Gene editing tools for plants lagged behind those for microbes or animals, but plant synthetic biologists have caught up in recent years. “Whether it's prime editing or CRISPR-Cas9 editing, these are robust technologies now in plants," said Todd Michael, co-founder of US-based biotech startup Cquesta. “Coupling that with artificial intelligence, we can more robustly predict which changes in the genome will lead to the things that we're interested in,” Michael added. 

This allows researchers to identify and leverage genetic mechanisms underlying root architecture. For instance, Cquesta is developing gene-edited plants with deeper roots that are more tolerant to inconsistent weather. Researchers, such as Stanford University plant biologist Jose Dinneny, are investigating how roots perceive and respond to water availability and salinity in their environments. “As we discover pathways involved in this response, we want to test how those pathways might be engineered to change the structure of the root system and potentially improve it under environmental stress conditions like drought,” said Dinneny.

In a 2022 paper published in Science, Dinneny and colleagues implemented synthetic gene circuits to modify the density of root branches in Arabidopsis, a standard model plant. As genome design and editing improve, bioengineers will be able to make thousands or millions of genome edits rather than a few at a time. This will facilitate the rewiring of entire metabolic pathways in a programmable manner.

Researchers are also exploring ways to increase the number of lateral roots within a root system. “That would be particularly useful when dealing with nutrient deficiency," said Dinneny. “An increase in branching and the overall surface area of the root system would improve the ability of the plant to take up limited resources within the soil.” 

Root phenotyping captures how roots grow in a lab or a greenhouse which isn't always physiologically relevant. “The real obstacle in making deeper, bigger root systems in plants is the ability to look at how those roots are functioning in the field,” said Michael.

A relatively neglected aspect of root physiology, particularly relevant to climate resilience, is erosion resistance. Plants that anchor more tightly to soils have greater resistance to strong winds, floods, and other climate events. Reducing erosion slows the loss of soil nutrients and reduces emissions related to fertilizers. 

For example, phosphate content is depleting in topsoil around the world as it gets washed away into waterways, silting them and causing algal blooms before eventually being lost to the ocean. In the short term, farmers could switch to crops that tolerate poor soil. “But in the long run, if we want to grow a full range of nutritious and tasty food, we'll need better crops that don't promote soil erosion,” said Grierson.

Engineering Soil Microbes

Although modern agriculture relies heavily on nitrogen fertilizer, using more of it to compensate for falling crop productivity isn’t sustainable. “It’s made through the Haber process, which is unbelievably energy-costly, and you have to ship all that nitrogen around,” said Grierson. Fixing nitrogen from the air locally with microbes, she added, would be massively better. 

Many legumes can fix nitrogen at the roots, thanks to symbiotic bacteria. If other crops, say cereals, could also fix nitrogen, that’d considerably reduce agriculture’s reliance on nitrogen fertilizer. This is why engineering microbes to improve the uptake of nitrogen and other nutrients is another attractive approach to making crops more climate resilient. 

Typically, nitrogen-fixing bacteria added to replenish soil nitrogen die as they are alien to the root microbiome. As with plant genome editing, microbiome editing has improved significantly in recent years. “Now we can work with microbes that are naturally part of a crop’s microbiome,” said Karsten Temme, chief innovation officer at Pivot Bio. Unlike non-native bacteria, gene-edited native bacteria can thrive and grow throughout the growing season.

Pivot Bio is engineering these microbes to make nitrogenase, the enzyme that fixes nitrogen. When nitrogen fertilizers are added to soil, native microbes stop producing the enzyme. “We use gene editing to break that feedback loop and allow the microbes to produce nitrogenase even though the farmers are still using fertilizers,” said Temme. Additionally, these gene-edited bacteria do not contain foreign DNA and, therefore, don’t have the regulatory challenges that come with transgenic organisms.

Temme believes plants could be modified to become better hosts for soil microbes. Imagine a plant that supplies a more robust and higher amount of sugars and organic acids to microbes or alters the signaling between plants and microbes. Further, while still early, with cross-kingdom regulatory circuits, researchers could simultaneously tweak both sides of the plant-microbiome equation.

Boosting Carbon Sequestration

Plants, including those not grown for food and wild varieties of common crops, display diverse root morphologies adapted to different environments. Large-scale phenotyping of this diversity will yield insights into what makes certain plants more climate-resilient than others. Intensive agriculture increased yields at the cost of environmental resilience. Gene-edited plants could reverse this tradeoff, combining the high yields of modern crops with the hardiness of their wild varieties.

Moreover, they are better for the climate: Increased crop productivity translates to reduced agricultural carbon emissions. However, engineered roots can do more, as agricultural soil has a massive potential for carbon sinks. “If you can increase the amount of roots on a global scale, they would be drawing down more carbon into the soil,” said Michael. Likewise, deeper roots also increase carbon sequestration as the deep-buried carbon is less likely to escape. In addition to pulling more carbon out of the atmosphere, voluminous and deeper roots would enhance soil quality.

Along with engineered plants, gene-edited microbes could boost agricultural carbon sequestration. “We can engineer plants to deliver more carbon below ground and use bacteria to convert that carbon into a stable form unlikely to enter back into the atmosphere under short-term conditions,” said Dinneny.

However, companies will need to demonstrate that carbon captured by engineered plants stays in the soil for a long time. Michael added, “This will be important if companies are to make money with these plants as they need to be able to get credits for the stored carbon.”