Unearthing an Unseen World Through Root Imaging

“It’s like a CT scan—for plants.”

That’s how Warren Shafer, Ph.D. Vice President of Global R&D and Regulatory Affairs at Valent BioSciences (VBC) describes the cutting-edge imaging research that is being conducted at the Donald Danforth Plant Science Center in St. Louis, in collaboration with VBC and parent company Sumitomo Chemical Company. 

Why a CT scan for plants? The answer for using medical imaging technology is right under our feet. 

Just Below the Surface

For years, the study of soil has largely encompassed its physical properties (soil structure) and chemistry (the chemical compounds within the soil). Only in recent years has attention started to turn to the biology of soil.  

Below the soil surface, in close proximity to plant roots, is an area called the rhizosphere (rhizo means root). It’s the area of the soil that is influenced by plant roots and the other organisms such as bacteria and fungus all interacting with one another. 

Dr. Chris Topp, one of the Principle Researchers at the Danforth Center, explains that the evolutionary partnership among these organisms has to do with the exchange of nutrients, such as phosphorus (P), nitrogen (N) and carbon. 

“Plants literally suck carbon out of the air to make sugar through photosynthesis. Whereas diazatrophs, specifically rhizobacteria that can colonize the roots of plants, can suck N out of the atmosphere,” Topp says. “Plants really need N, but N is the most limited resource for plants on earth because it’s in a form that is difficult to use. Similarly, diazatrophs can’t do photosynthesis, so they get N out of the air, make it into a form that plants can use, and trade it for carbon with plants. Arbuscular mycorrhizal fungi (AMF) have a similar problem as diazotrophs in that they can’t easily get carbon, so they mine the soil for P and use that to trade with plants.”

AMF. That’s what inspired the beginning of the VBC and Danforth Center research partnership in 2016. The year prior, VBC acquired Mycorrhizal Applications, a company with a unique portfolio of products that contain multiple species of AMF that are used to enhance root growth and nutrient uptake in crops. The project with the Danforth Center would focus on better understanding plant root growth and development, and thus the symbiotic relationships of organisms within the rhizosphere, without disturbing the soil or plant roots.

A Picture is Worth 1,000 Aggregates

In the past, to study roots of plants, scientists would have to dig up a plant in order to see the entire root system, and in the process destroy the soil aggregates around it and usually the roots themselves.

“To understand how the organisms in the rhizosphere interact with a plant, we need to be able to see the roots and have a way to measure,” Topp says. “My lab specializes in root and rhizosphere imaging and functional aspects of the root systems.” 

The partnership with the Danforth Center is creating a new non-destructive and non-disruptive way to examine and investigate the dynamics of living roots through 3D imagery. 

“The technology is based on x-rays,” just like a human CT scan says VBC’s Shafer. “Inside an x-ray tomography (XRT) booth, a plant growing in a pot is placed on a platform that slowly rotates.  Thousands of 2D x-rays are taken and then assembled to create a 3D image. The use of artificial intelligence allows for a detailed look at the rhizosphere and inside the roots without cutting into or disturbing the plant. In a further new development, virtual reality technology can be used to interact and experience the roots in ways that people never have been able to do before.”

Shafer says it has taken three years to develop these techniques for the XRT, but now the technology methods and machine learning capabilities are in a place where scientists, like Topp and his team, can see plant roots growing in soil and understand the effects of cold, heat, drought, insect pressures and other stress conditions, and how crop protection products could mitigate those pressures. 

Topp says it could also lead to the discovery of new fungal and/or bacterial consortiums that enhance existing plant and rhizosphere relationships or new application sites to optimize nutrient uptake and plant growth.

Partnerships Make it Possible

Shafer says the benefit of working with the Danforth Center is access to a world class plant science research facility directed towards the advancement of scientific knowledge and ultimately the creation of better solutions for growers. 

“Working with partners within our Biorational Research Network (BRN), such as the Danforth Center, allows us to collaborate and make greater progress than on our own,” Shafer says. “An open innovation platform, like the BRN, recognizes that an organization is more effective when it strategically reaches out and works with third parties to meet a set of shared goals.”