Unlocking the hidden half of plants with DNA

When we walk across farmland, we see only the parts of plants above ground. Below the surface, roots provide stability, take up water and nutrients, and store carbon in the soil. Yet despite their importance, researchers have had no precise way to measure roots.

“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,” noted Henrik Brinch-Pedersen from Aarhus University.

Old ways failed to measure roots

The usual way meant digging up soil, rinsing roots, drying them, and weighing them. It took hours and destroyed many of the fine roots that matter most.

Scientists also tried methods like rhizotrons or tracer studies. These helped but often underestimated root biomass.

Fine roots – the ones that take up nutrients and release carbon – were especially easy to lose. Without them, much of the underground story stayed invisible.

DNA reveals hidden root systems

Now comes droplet digital PCR, or ddPCR. Instead of tearing apart the soil, scientists divide a tiny sample into thousands of droplets and test each for DNA. They use a genetic marker called ITS2, which acts like a barcode.

This doesn’t just show that roots exist in the soil. It shows which species they belong to and how much they contribute.

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

Reliable root measurements

Earlier approaches like qPCR struggled with soil contaminants and inconsistent reactions. The ddPCR method avoids these problems by turning each droplet into a tiny reaction chamber.

The technology counts DNA molecules directly, using statistics to link those counts to root biomass. The result is a reliable measurement, even in complex soils with multiple plant species.

The method also works across a wide range of concentrations. Whether the sample contains lots of roots or very few, ddPCR maintains accuracy. That flexibility makes it suitable for both small experimental plots and large, diverse fields.

DNA method works in mixed roots

To test it, researchers mixed soils containing ryegrass, white clover, and yarrow. They found that ddPCR identified each plant and measured its share of the underground biomass.

Hybrids like ryegrass crosses sometimes confused the system, but overall, the accuracy remained high.

Even when species grew together, the method could still tease apart their contributions. That is something old root washing methods could never do with confidence.

Why it matters

The new digital DNA method has the potential to transform how we study crops. Climate researchers can now calculate how much carbon plants actually store underground.

Breeders can choose crop varieties that send more growth into roots without hurting yields. Ecologists can finally see how plants compete or cooperate beneath the surface.

“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,” noted Brinch-Pedersen.

Roots play a role in storing carbon

Roots are more than anchors. They could be powerful allies in slowing climate change. Plants pull in carbon dioxide and send some of it underground, where it can stay locked away for decades. But without precise tools, proving this has been difficult. The ddPCR technology gives scientists that missing tool.

Imagine grasslands where certain species funnel extra carbon into deep roots. Or croplands where breeders select varieties with stronger underground storage potential. With the right choices, agriculture could shift from being a major emitter to a carbon sink.

Challenges still remain

The method isn’t perfect. Hybrids remain tricky, since their DNA overlaps with parent species. Each plant type needs its own probe, which takes effort to design and test.

Probe development requires careful validation, because even small genetic changes can throw results off. Still, once a probe library expands, the technology becomes faster and easier to apply.

“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,” noted Brinch-Pedersen.

Studying roots with DNA tools

Droplet digital PCR already works in medicine for spotting rare mutations and pathogens. Applying it to roots is a natural next step.

Once established, the method is simple, scalable, and powerful. It could help create crops that store more carbon belowground while keeping food production steady.

Beyond crops, the technology could also reshape how we manage ecosystems. Grasslands, forests, and mixed farmlands all depend on root systems we rarely measure well. Now, we finally have a way to look underground without tearing everything apart.

For the first time, researchers can explore the hidden world beneath our feet – and measure it with confidence.

The study is published in the journal Plant Physiology.

—–

Like what you read? Subscribe to our newsletter for engaging articles, exclusive content, and the latest updates. 

Check us out on EarthSnap, a free app brought to you by Eric Ralls and Earth.com.

—–