Few of us ever think about what happens beneath our feet when we walk through a field of wheat or clover. We see the stalks, leaves, and flowers, but in practice we have no direct access to the roots.

Roots, however, are central. They anchor plants in the soil, supply them with water and nutrients, and contribute to carbon storage in the ground.
But because roots are hidden, researchers have for decades struggled to measure how much biomass lies below and how it is distributed among species.

“We have always known that roots are important, but we have lacked a precise tool to measure them. It’s a bit like studying marine ecosystems without ever being able to dive beneath the surface of the water,” says Henrik Brinch-Pedersen, professor at the Department of Agroecology, Aarhus University.

From Muddy Boots to Genetic Fingerprints

Until now, researchers typically measured roots by digging up large soil samples, washing the roots free, drying, and weighing them. This is a lengthy process, and the finest roots are often destroyed along the way. That is a major problem, since fine roots are the most active in absorbing nutrients and releasing carbon to the soil environment.

The new method is instead based on droplet digital PCR (ddPCR), a DNA technology in which a soil sample is divided into tens of thousands of microscopic droplets, each of which is analyzed for the presence of DNA.

The researchers use a genetic marker called ITS2, which works like a fingerprint for each species. In this way, they can not only see that roots are present but also identify which species they belong to and how much biomass they represent.

“It’s a bit like giving the soil a DNA test,” says Henrik Brinch-Pedersen. “We can suddenly see the hidden distribution of species and biomass without digging up the whole field.”

International Recognition

The method was developed by a research team consisting of Nurbanu Shynggyskyzy, Claus Krogh Madsen, Per L. Gregersen, Jim Rasmussen, Uffe Jørgensen, and Henrik Brinch-Pedersen. It has been published in the renowned journal Plant Physiology and has already received special attention in an accompanying News & Views article, where international experts highlight it as a breakthrough.

What Can It Be Used For?

The new technology opens up a wide range of applications:

• Climate research: Accurately measuring how much carbon different crops store in the soil is crucial for documenting and improving agriculture’s climate contribution.

• Plant breeding: The method enables researchers to select varieties that send more biomass belowground without reducing aboveground yields.

• Biodiversity: In grasslands and mixed crops, it is now possible to see how species compete or cooperate underground, something that was almost impossible before.

“We see great potential in using this method to develop varieties that store more carbon in the soil. It could become an important tool in future agriculture,” says Henrik Brinch-Pedersen.

Roots as a Climate Solution

It is no coincidence that researchers are focusing on roots. While we usually think of wind turbines and electric cars as climate solutions, plant root systems also hold great potential in the form of biological carbon storage.

When plants grow, they draw CO₂ from the atmosphere and send part of the carbon into their roots. There, it can remain stored in the soil for decades, or even centuries, if we can develop cropping systems that maximize this potential.

Without precise measurement tools, however, it has been difficult to document the effect. This is where the new DNA technology could become a gamechanger.

Limitations and Next Steps

The method is not without challenges. For example, genetic hybrids such as ryegrass and Italian ryegrass can be difficult to distinguish because their DNA is so similar. And the method requires developing specific DNA probes for each species researchers wish to measure.

“For us, the most important thing is that we have shown it can be done. That is the foundation we can build upon. Our vision is to expand the DNA library so that in the future we can measure many more species directly in soil samples,” says Henrik Brinch-Pedersen.

Where researchers previously depended on time-consuming fieldwork, the new method allows root analysis to be carried out quickly, precisely, and on a much larger scale.

That means researchers can now take a precise look into the underground world that has so far remained hidden.

More Information

Partners: Department of Agroecology, Aarhus University
Funding: The study was funded by Innovation Fund Denmark (project number 0224-00091B GrassTools)
Conflict of interest: None

Read more: The article “Digital PCR enables direct root biomass quantification and species profiling in soil samples” was published in Plant Physiology. Authors: Nurbanu Shynggyskyzy, Claus Krogh Madsen, Per L. Gregersen, Jim Rasmussen, Uffe Jørgensen, and Henrik Brinch-Pedersen.

Contact: Professor Henrik Brinch-Pedersen, Department of Agroecology, Aarhus University. Tel: +45 51239017 or email: hbp@agro.au.dk