Picture a plant—your favorite flower, an herb from an outdoor garden or a stately tree. As you visualize the elements of the flora, did you remember to include the roots? If you didn’t, you’re in good company.

“Roots definitely are central to plant systems, but when it comes to attention and studies in plant biology, the focus has mainly been on above-ground shoots, leaf tissues and photosynthesis,” says Amir Ahkami, a biologist at the Department of Energy’s Pacific Northwest National Laboratory.

Roots are typically at least half of a plant’s biomass, but you wouldn’t know it given how little scientific research has been devoted to these critical tendrils. Only recently have scientists given plant roots their day in the sun—in fields like collections research, climate science and microbiology. Historically, the reasons for this discrepancy were laughably simple: Studying something you have to dig up isn’t that easy.

Still, scientists hundreds of years ago managed to study these elusive subjects with ingenious methods. As early as the 19th century, botanist Julius von Sachs grew plants in a glass-sided root box to study their root systems in situ. His contemporaries—biologists Edward Janczewski, Sydney Howard Vines and Wilhelm Pfeffer—all made important advances in our understanding of root growth, development and osmosis, respectively. Yet, specialization in the intervening centuries siloed root science from the rest of botany, prompting the authors of a major root textbook to subtitle their work “The Hidden Half.” But now a scientific renaissance for root systems has been fueled by a combination of technological advances and a striking realization: Roots, we now know, can help us track our changing world, shape food security and model our future.

Digging back into the history of root science

For centuries, collections specialists would have looked at the dirty roots of specimens and considered them to be, at best, contamination. To these specialists, in charge of herbarium collections containing anywhere from hundreds to hundreds of thousands of dried plant samples, plant roots were a nuisance to preservation for several reasons. A full root system could complicate the collection process and exceed the dimensions of a standard herbarium sheet (16.5 inches by 11.75 inches). Moreover, pests could be hiding in the soil attached to specimen roots, with the potential to destroy an entire collection if not treated promptly and aggressively The upshot of these complications was that roots were often not included in the samples at all. One 2019 study found that just a quarter of the specimens from four focal species studied at the herbarium included roots.

Botanist Mason Heberling, a co-author of that study, focused on 48 of the specimens that did contain roots, which were collected over a period of 127 years. Instead of fixating on the downsides of root systems, he set out to realize their potential as pristine, untapped time capsules.

“What got me excited and interested was that the specimens were kind of dirty,” he says. “I was awestruck that I was looking at a specimen that was collected over 100 years ago, and then by extension, I was also like, ‘Geez, there are pieces of dirt on the roots that are more than 100 years old.’”

Mason Heberling
Botanist Mason Heberling at work Carnegie Museum of Natural History

Heberling, the associate curator of botany at the Carnegie Museum of Natural History in Pittsburgh, looked into the existing body of literature on plant roots in herbarium collections. He came up empty-handed, writing in 2022 that no study to his knowledge had conducted studies of root traits (like length, diameter, mass or microbial composition) in herbariums’ samples. Herbariums “are untapped repositories” of these kinds of data, he writes.

Heberling decided to undertake some of the research he thought had been overlooked. After scrutinizing dried samples in his collection, he noticed that the plants’ roots preserved troves of fungal DNA long after they had died. Much as humans outsource crucial parts of digestion to the microbes inhabiting our guts, plants rely on a similar microbial network to produce hormones, process nutrients and fight off disease. These fungi can envelop the roots or even penetrate their outer layers, as is true with a type called arbuscular mycorrhizal fungi. And as with the human microbiome, the question of what constitutes “self” versus “other” is largely a philosophical one: Remove the microbes from either a plant or a person, and the organism fails to thrive.

Heberling reasoned that a dried plant’s roots would have a unique assortment of fungi, acting as a snapshot of a given place and time. With that kind of data, he’d be able to answer fundamental questions about plant species that have been well represented in museum collections over the past two centuries. Are the arbuscular mycorrhizal fungi that colonize a species consistent throughout its geographic range, or could different regions be associated with their own microbes? And has the makeup of these communities changed over time, in response to climate change, acid rain and invasive species?

“Even though there’s a lot of really fascinating studies and a lot of fundamental knowledge about [root biology], there’s a lot that we don't know,” he says.

His first effort, detailed in that 2019 study, confirmed his hunch that fungal DNA could be successfully isolated from the roots of 21 of the 48 preserved specimens, which represented four species of western Pennsylvania wildflowers collected between 1881 and 2008. Moreover, Heberling and ecologist David Burke of Holden Forests and Gardens added an ingenious control experiment to make sure that these fungi were not contaminants introduced after the specimen was collected. They tried and failed to isolate arbuscular mycorrhizal fungi DNA from the specimens’ leaves. Since those fungi only colonize plant roots, the presence of fungi on the leaves would have indicated contamination.

Now, Heberling’s postdoctoral researcher Ben Lee is using herbariums’ records to reconstruct the fungal communities of white trillium, a wildflower found across eastern North America. By charting these communities across space and time, this research will let scientists peer into the past in an unprecedented way, seeing how our actions could be shaping the trajectory of a striking flower.

“The big global change question is: Have these mycorrhizal communities changed over time? Because we really don’t know. It’s invisible,” Heberling says. Lee, he adds, is “looking at the visible effects of these invisible players.”

Grounding models in the capabilities of roots

Plants play a key role in climate models due to their role as carbon sinks. They sequester carbon as well as other elements while they are alive by removing carbon dioxide from the air and converting it into sugars. Some of these sugars go into creating the roots; roots also burn sugar and release carbon back into the atmosphere. And variation in root forms and efficiencies change the amount of carbon and other nutrients taken up and recirculated by a given plant. But climate models historically have not incorporated the diversity of root systems into their calculations.

“A lot of the models that are trying to predict the climate of the Earth and carbon cycling are all focused on above-ground plant traits,” says Stephanie Kivlin, an ecologist and evolutionary biologist at the University of Tennessee, Knoxville. “Most of them don’t even include roots at all—they just assume roots are all the same.”

Red Trillium
Preserved leaves and roots of red trillium Carnegie Museum of Natural History

Kivlin realizes the need for truer root representation in these models, but she acknowledges that tweaking a large climate model isn’t as easy as inserting a line of code. Computers model the climate by solving a handful of complex equations about the movement and cycling of air, water and energy. Introducing variables, like information about root systems, can make the computer’s solution to these equations more accurate, but they also become much more difficult to solve. And the harder these equations become, the more time, computing power and resources they require.

Working within these constraints, Kivlin and her collaborators adjusted a global climate model to include arbuscular mycorrhizal fungi and ectomycorrhizal fungi, which do not penetrate the roots. These two types of fungi induce plants to cycle water, nitrogen and other elements in very different ways. She and her co-authors found that a climate model accounting for arbuscular mycorrhizal fungi and ectomycorrhizal fungi was 80 percent more accurate in predicting nitrogen cycling. When there is less nitrogen in the soil, plants cannot accumulate carbon as efficiently, limiting their potential as sinks. By accounting for the dichotomy between the two root fungi, Kivlin found an efficient way to improve a climate model while only introducing a single variable.

Bolstering crops with a greater understanding of their roots

One of the most important roles that microbes play for plants is upping the roots’ intake of vital nutrients like water, phosphorus, copper and zinc. The balance of these compounds determines a plant’s growth as well as its resilience in the face of extreme weather events. By understanding what an ideal root system looks like for a given plant species, farmers can breed two naturally robust plants together and create hardier varieties of crops.

Harnessing this vast potential to improve crops is why Jonathan Lynch, a recently retired Penn State biologist, devoted his career to studying roots.

“I didn’t go into science thinking I’d be a root biologist. I went into science thinking I was going to do something about world hunger,” he says. “But my work showed me clearly that the real thing going on here is with the roots.”

Global hunger soared to an all-time high in 2023, due to a combination of conflict and the effects of climate change. In January, the authors of a United Nations report estimated that nearly a quarter of the global population is drought-stricken. Lynch realized early on in his career that the differences between higher- and lower-yield crops were only exacerbated in poor conditions.

And in “bad soil,” as he terms it, “the difference between a good plant and a bad plant is the roots.” When the resources in soil are limited, resilient root systems can penetrate deeper and make the most of their environment.

But 40 years ago, the characteristics of a promising root system were ill-defined. So Lynch and his colleagues invented a protocol for assessing the roots of a plant that they termed “shovelomics.” The subdiscipline basically denotes the study of everything that can be uprooted with a shovel.

Shovelomics swaps out cutting-edge lab technology for that popular metal tool available at any hardware store. Lynch’s protocol for the subdiscipline involves identifying and digging up samples and then creating metrics by which multiple plants’ root systems can be judged. The number of the roots and the rate at which they branch; their length; their diameter; and the angles at which they emerge from the shoots of the plant can all make for rich comparisons.

When Lynch first submitted his paper on shovelomics in 2010, he says a journal editor threatened to bury it because of how silly the name sounded. Despite the early misgivings, “a lot of people have picked up shovelomics,” he says. A search for shovelomics on the research engine Google Scholar turned up over 1,200 academic papers.

But requiring that researchers resort to shoveling up entire plants to monitor their roots is still a barrier to discoveries, says Ahkami. “Unless it is at the end of the season or your experiment and you don’t need those plants anymore, you may not want to dig the whole plants up,” he says.

What if there were noninvasive ways of quantifying root systems? Some researchers are testing methods and technologies to study the roots while they remain in the ground. One Washington-based company, CID Bio-Science, creates minirhizotrons, which are transparent tubes and cameras installed in the ground to capture root growth in real time. For his part, Lynch recently co-wrote a new study that uses measurements of the element strontium in plant leaves to estimate the root lengths. An above-ground monitoring device may soon follow from this work, he says.

“You could even imagine a [device with a] light, so whenever you’re zapping the leaf of a deeper plant it displays a little green light, and a shallower one has a red light,” Lynch says.

Devices like these could help farmers and plant breeders select for hardier crop varieties—with thicker, longer or more dense roots that can absorb scarce nutrients—a marked shift from previous agricultural revolutions, according to Lynch. In the past, farmers applied innovations like chemical fertilizers and automated irrigation to maximize available nutrients for crops. As humans run up against limited resources, though, this strategy is no longer tenable.

“We can’t just fertilize and irrigate our way out of everything,” he says. “This is the second Green Revolution, and I think these roots are going to be key.”

Editor's note, March 21, 2024: This story has been updated to reflect the affiliation of ecologist David Burke. He is with Holden Forests and Gardens.

Get the latest Science stories in your inbox.