Tackling Food Insecurity with Plant Fungus, Microbes, and AI Microscopy

How to tackle food insecurity: it’s the urgent question on the mind of research scientist Keith Duncan. He zones in on plants and crops – finding methods to help them sustain climate change in some of the world’s hardest hit areas. Using X-ray microscopy, Duncan captures images that no one else on the planet has ever seen before.

Keith Duncan’s love of microscopy started at an early. age But what was the moment that piqued his curiosity? The hundreds of dead elm trees surrounding his childhood home. “A fungal disease killed all of them. They were simply removed and cut down” he remembers – it was the first time he realized that trees get sick and die. As the son of a medical researcher, Duncan knew he had his first samples: a stack of cut wood with chipped off bark and intricate patterns underneath. When peering at them through the microscope, Duncan says he saw a fluffy white material – the deadly fungus that had wiped out the trees. The image imprinted on his mind. It was the first time he understood “the enormous impact of microbes on the world around us” he says. From that moment onwards, plant science became his fascination.

For the past five years, Duncan has focused on introducing X-ray microscopy to the plant science research community through his work at The Danforth Center – the largest independent nonprofit plant science institute in the world. He uses this technology to investigate a multitude of samples where “every day I come into work and see something that no one else on the planet has ever seen before” he says. Most imaging technologies have high magnification which requires the use of small samples. Though this approach can be limiting when trying to understand the sample in a wider context. “You can have beautiful, highly detailed structures, but where does it sit in the larger picture?“ he asks.

Working at a global scale, Duncan collaborates with scientists in parts of the world where food security is an urgent problem. Through his work at the Danforth Center, he studies both major economic and food security crops.

His work considers how drought impacts the normal developmental stages of a crop and its nutrition value. Whether it’s the extreme heat, the salinity of the soil, or the impact of expensive chemical fertilizers on low-income countries. He wants to know how plant grain production can be supported as the Earth continues to be faced with greater environmental challenges. X-ray microscopy is key to understanding how to support crops, as it provides a more detailed and accurate 3D map of the structure.

When developing sustainable plant and crop structures, the computer must also be trained to identify only the structure that I want to see and ignore everything else. "I need computational science to pull biology out of that volume” says Duncan. Luckily, AI is now teaching computers how to recognize the features that support scientists. Once trained, Duncan explains that the AI can accurately feedback “exactly how much fungal biomass is inside the root and exchanging carbon for water and nutrients.”

The natural physics of projecting X-rays through these relatively large, dense samples causes some artifacts. “With the sophisticated, deep learning software that ZEISS has developed, we can automatically remove that noise from my scan data,” says Duncan, “so before I even sit down to teach a computer what to find, the ZEISS software has already cleaned it up and made the process much easier.”

Now, when Duncan images complicated, delicate structures with the X-ray microscope, he says he can see precisely how the seeds would attach to the crop. This has bridged the imaging gap between some existing technologies such as light, laser, and electron microscopy with the latest AI advancement. “This has improved a crop that directly benefits people: putting it in the ground and harvesting protein for food security,” he says. His passion for his job is evident from the first word to the last: “plant science is crucial for everybody on the planet. If you want to eat, drink, wear clothes, have medicine or breathe – because plants produce oxygen.” It’s a tough point to argue. Clearly plant science is of great interest to everyone.