We stroll past wheat, clover, and grass and see only the green half of the story. The other half – the roots – do the heavy lifting: anchoring plants, pulling up water and nutrients, and locking away carbon in the soil.
Yet because roots are hidden, scientists have spent decades using muddy, labor-intensive methods to guess their size and spread, often missing the finest, most active threads. According to a team of researchers at Aarhus University, that guesswork can finally stop.
A high-tech root census
“It’s a bit like studying marine ecosystems without ever being able to dive,” said senior author Henrik Brinch-Pedersen, a professor in the Department of Agroecology.
Until now, the standard approach was to carve out big blocks of soil, wash away the dirt, sort and dry what remained, and weigh the roots. It’s slow, destructive, and misses the fine roots that absorb nutrients and release carbon to the soil.
The new approach swaps spades for droplet digital PCR (ddPCR), a DNA technology that partitions a teaspoon of soil into tens of thousands of microscopic droplets. Each droplet then answers a yes/no question: Does it contain plant DNA with a specific genetic signature?
The team uses a marker called ITS2 – think of it as a barcode that differs among species – so a single run can reveal not just that roots are present, but whose roots they are. Crucially, it also shows how much underground biomass each species contributes.
“It’s a bit like giving the soil a DNA test,” Brinch-Pedersen said. “We can suddenly see the hidden distribution of species and biomass without digging up the whole field.”
Mapping roots with precision
Because ddPCR counts DNA molecules across thousands of droplets, it can quantify roots that would otherwise be pulverized or rinsed away.
That makes it possible to map root communities at high resolution in living fields, pastures, and mixed-species grasslands and to repeat measurements over time without disturbing the site.
The payoff spans several fronts. For climate research, it lets scientists measure how much carbon different crops actually push belowground – data that’s been frustratingly hard to pin down but is essential for credible climate accounting in agriculture.
For plant breeding, the digital DNA method creates a path to select varieties that invest more in roots without sacrificing grain or forage aboveground.
And for biodiversity science, the technology finally illuminates the underground dynamics in species mixes – who’s competing, who’s complementing – insights that were “almost impossible before,” Brinch-Pedersen noted.
Roots matter for the climate
We tend to picture wind turbines and EVs when we think of climate solutions, but roots are a vast, quiet carbon pump.
As plants photosynthesize, some of the captured carbon flows belowground into roots and the surrounding soil. Depending on the crop, soil type, and management, a fraction of that carbon can persist for decades or even centuries.
Farmers and policymakers talk about “soil carbon sequestration,” but without precise measurement tools it’s been hard to document gains in ways that stand up to scrutiny. A rapid, species-resolved root assay changes that equation.
DNA test in soil
In practice, researchers collect small soil cores, extract DNA, and run ddPCR with species-specific probes keyed to the ITS2 barcode. The number of positive droplets scales with root biomass for that species in that sample.
Because the test targets DNA directly in soil, it captures fine roots and root fragments as well as thicker roots that are tough to wash and weigh.
There are, however, limits. Close relatives can be tricky to tell apart when their barcodes are nearly identical – ryegrass and Italian ryegrass hybrids, for instance, can blur the signal.
And the method recognizes only what it’s trained to find. Researchers must validate a probe for each species, so expanding the “DNA library” is both the hurdle and the goal.
“For us, the most important thing is that we have shown it can be done,” Brinch-Pedersen said. “Our vision is to expand the library so we can measure many more species directly in soil samples.”
Rapid answers from soil
Speed is the other advantage. Traditional root studies hinge on days to weeks of field and lab work per site. The ddPCR method turns around results in hours, making it practical to scale from a few experimental plots to entire farms, seasons, and regions.
That opens the door to experiments that were previously unrealistic. Researchers can compare cover crops for their belowground carbon contributions across soil types.
They can track how drought shifts root allocation among species in a pasture. They can also screen hundreds of breeding lines for deeper, denser root systems.
Plants that work smarter
Brinch-Pedersen sees a straight line from measurement to design. If breeders can quantify underground investment as easily as they count kernels or measure protein, they can begin to select for crops that are not only high-yielding but also high-sequestering. These are plants that do more of the climate work for us.
The same logic applies to mixtures. With species-level root data, agronomists can compose plant communities that pack more carbon belowground while maintaining forage or grain output above.
The bigger picture is simple: half a plant lives out of sight, and that half shapes soil health, farm resilience, and the climate. With a “DNA test for dirt,” researchers can finally watch that hidden half at work – no shovels required.
The study is published in the journal Plant Physiology.
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