Article Summary
• Most soil science research focuses on topsoil (up to 10 inches deep).
• Researchers are beginning to look at soils that are thousands of years old that could shed new light on carbon storage, nutrient cycling, and beneficial microbial life.
• The new Deep Soil Ecotron (DSE), at the University of Idaho, is the world’s first research facility dedicated to deep soils.
• The DSE facility allows researchers to simulate various climatic events like wet years or droughts, which may help farmers respond to extreme weather, manage soil, and improve yields.
At the Sandpoint Organic Agriculture Center in Northern Idaho, a hydraulic press pushes a massive, hollow stainless steel cylinder, 4 feet across and 10 feet long, deep into the ground. An excavation crew constantly removes surrounding soil so the cylinder can continue to its slow descent. Four feet down it goes, then 6 feet, then 7, enclosing soils that are thousands of years old, dating to epochs of volcanic eruption and glacial retreat.
Michael Strickland is no stranger to such unearthings. A microbial ecologist, he often goes into the field to collect soil samples, or cores, to study in the lab. Usually, he’s probing to a depth of about a foot. This dig will go 10 times deeper.
As the press nears the 8-foot mark, the soil layer, which is likely near 10,000 years old, is heavily compacted and does not budge. Watching nearby, Strickland catches his breath as the machine grinds to a halt. “I’m thinking, ‘Is it going to happen? Are we going to get this core out of here?’” he says. The work slows to a creep, but with some coaxing, the land opens up centimeter by labored centimeter.
This new research facility provides a rare chance to study deep soils, largely uncharted domains that are at once remnants of the past and potential harbingers of the future.
Over the course of three weeks, the process continues until finally, six soil-filled cylinders are ready to be capped, strapped onto a truck, and driven to their new home: The University of Idaho’s Deep Soil Ecotron, where Strickland is the director.
This new research facility, opened in May 2025, provides a rare chance to study deep soils—largely uncharted domains that are at once remnants of the past and potential harbingers of the future for agriculture and climate science.
At the Deep Soil Ecotron excavation site, a hydraulic press pushes a lysimeter deeper into the ground. The crew constantly clears soil from the base of the column as it descends. (Photo courtesy of University of Idaho)
Why Study Deep Soils?
Most soil research focuses on topsoils, which reach an average depth of 27 centimeters (about 10 inches). This surface-level focus is partially a matter of logistics: Taking intact soil cores from deep underground is time-consuming, challenging work that requires special machinery.
Scientists have paid less attention to deep soils for another reason: They’re relatively stable. Deep soils start roughly 30 centimeters (about a foot) below the surface and are lower in oxygen than topsoil, limiting their microbial turnover, gas exchange, and plant activity. Topsoils, which are constantly shifting in response to environmental conditions, offer a more dynamic field of study.
In the last few years, however, emerging research has suggested that the hidden realms of deep soils are worth exploring. Deep soils, for example, could play an important role in climate change mitigation by storing carbon deep underground. While carbon sequestered in topsoil—once hailed as a solution to the climate crisis—is anything but permanent, carbon at deeper depths appears to be more stable and protected. Beyond their carbon-sequestering capacity, the way that deep soils cycle and store other compounds, like nitrogen and water, could prove relevant to farmers looking to maximize yields.
Deep soil has been compared to outer space and the depths of the ocean: a “dark forest” that is mysterious and relatively unchartered.
Deep soil also seems to be teeming with novel bacteria that don’t exist anywhere else, and could be just as rich in microbial life as surface soil. The intact soil cores collected here will give Strickland and his team a glimpse into what types of organisms have adapted to these dark, dense, low-oxygen environments, and how they impact the wider ecosystem.
“The interaction between roots, minerals, and microbes going beyond the topsoil is really fascinating and can help us better understand the soil, our climate, and how changing conditions above ground are driving dynamics below ground,” says Ashley Keiser, a DSE science advisor and soil ecologist at UMass Amherst.
Deep soil has been compared to outer space and the depths of the ocean: a “dark forest” that is mysterious and relatively unchartered. The new Idaho facility offers a look into an otherwise unseen world—and the possibilities that come with it.
A New Type of Laboratory
Ecotrons exist all over the world, but are relatively new. They realistically simulate natural ecosystems in a controlled environment and allow researchers to monitor how atmosphere, soil, and plants interact as the conditions around them change.
A soil pit at Sandpoint Organic Agriculture Center after a Deep Soil Ecotron excavation exposes the levels of deep soil. (Photo credit: Michael Strickland)
Since the first ecotron facility opened at Imperial College London in the early 1990s, about a dozen others have been built, mostly in Europe. Many of these facilities research how climate changes affect the functioning of different ecosystems, from heathlands to freshwater ponds.
Idaho’s Deep Soil Ecotron (DSE) is the first in the world dedicated to deep soils. The DSE, mostly funded by a $18.95 million grant from the U.S. National Science Foundation, houses 24 of the gigantic columns. Six are filled; the remainder will house soil from Idaho and beyond.
These “ecounits” are notable not only for their size and depth, but also for their scientific controls. They are equipped with heat exchangers for adjusting soil temperature and ceramic suction cups for modifying water content. Scientists can also tinker with the light, humidity, and greenhouse gas (methane, carbon dioxide, and nitrous oxide) concentrations at the surface of each unit. “We can essentially mimic almost any climate conditions, barring extreme cold,” says Strickland. At the top of each soil column rests a “grow chamber” where researchers can interact with the topsoil, growing crops or applying soil amendments depending on what they’re studying.
Sensors are installed throughout each column to deliver continuous information about how the soil is responding to the changes happening below and above the surface.
All six of the filled columns contain soil from the Sandpoint site. Three have intact soil cores that were extracted with the hydraulic press and represent natural, untouched soil environments. The other three have “disturbed” soils that were filled manually and exposed to oxygen, likely affecting their structure and function. These different sample types are now undergoing data collection and proof-of-concept work before the facility opens up to the broader scientific community in the next six to 12 months.
Deep Soil’s Potential for Farmers
Robert Blair is a farmer and University of Idaho alum who grows wheat, barley, lentils, chickpeas, and alfalfa on 800 acres in Kendrick, Idaho. Like many producers across the country, he is struggling to maintain profits amid increasingly high production costs and volatile tariffs on commodity crops. He grows without irrigation, which also leaves him at the mercy of often unpredictable rain and snowfall.
At the Deep Soil Ecotron, a soil cylinder equipped with sensors that monitor soil conditions like temperature and moisture content. (Photo credit: Michael Strickland)
Once he learned about the DSE through his role on a university advisory board, he started digging into ways it could help him prepare for and respond to unpredictable weather events like drought so they wouldn’t hurt his yields and margins as much.
“This [facility] can allow us to simulate different climatic events—from a really wet year to a drought year—not only in the top at the grow chamber, where the crop is, but throughout that soil profile,” Blair says. “Once we know what the moisture levels are 2 feet, 3 feet, 10 feet down, we as farmers may be able to better manage our crops based upon those findings.”
Beyond providing information on deep soil moisture, Stickland and DSE co-director Zachary Kayler say the facility could help predict how soils will respond to temperature extremes like heat waves, which can be simulated in each column.
Using the data constantly collected from the ecotron sensors, the DSE team may even be able to develop hyperrealistic computer models of each soil system, which Kayler refers to as “digital twins,” and run tests on these ahead of forecasted weather events to predict how soils might be affected in real life.
Data from the DSE could help farmers better manage soil nutrients to maximize yield—and reduce fertilizer costs, too, Strickland says. Nitrate, for example, is a highly mobile compound that can easily move through the soil profile and become stored in deeper layers. “Rather than applying more nitrogen, you might be able to [one day] mine the deeper nitrogen pools within ecosystems,” he says.
The facility could also assist farmers in pest detection and management. Since each soil unit is contained, researchers will be able to introduce pests without worrying about contaminating nearby environments. This would allow them to run experiments that would be difficult in the field and potentially identify early signs of a pest problem so farmers can stop infestations before they begin. The units could also serve as a testing ground for new agricultural products like GMO crops and microbial inoculants—soil amendments made with bacteria—to help ensure they work as intended before being released into the field.
Earlier this month, Kayler hosted a conference with local growers, producers, and farm industry affiliates to unveil the new facility, discuss how it could best meet their needs, and get the word out about its potential.
“Until the University of Idaho started this project, I had no clue what an ecotron was,” says Blair. “I think it’s a hidden secret that needs more publicity in agriculture circles.”
An active grow chamber on top of an ecounit at the Deep Soil Ecotron facility. (Photo credit: Kris Faulkner)
Digging Deeper on Carbon
More organic carbon is stored in our soil than in our atmosphere and terrestrial plants combined. A large proportion of it extends into deep soils and even down into bedrock. Globally, anywhere from 30 to 60 percent of soil organic carbon is located below the 30-centimeter mark.
Soil organic carbon, formed by decaying plant and animal material, gets pulled deeper underground through precipitation, root transfer, animal activity, and certain microbial processes. The deeper the soil organic carbon (SOC), the less likely it is to be released into the environment due to a variety of factors, including reduced microbial disruption. But research suggests that it can still be unearthed under certain conditions.
“Some of this deeper soil carbon is more stable, but we don’t necessarily know what could change that,” says Gabrielle Feber, a third-year Ph.D. candidate at the University of Idaho who is part of a DSE student research team.
The DSE could help demystify deep soil carbon cycling and storage in a few ways. First, it allows researchers to manipulate different environmental conditions like temperature and precipitation to get a better idea of how deep soils might retain or release carbon as climate conditions change. Researchers will also be able to manipulate the surface of each ecotron column and could study how different land management practices, like planting perennials, impact the carbon activity of deeper soils below. Findings from the facility could help inform future strategies to keep stored carbon deep underground and out of the atmosphere as climate conditions change.
“Deeper soils have the potential to be our ally or foe when it comes to mitigating climate change.”
This information will be just as relevant to farmers, who rely on soil organic carbon as an essential nutrient for crop growth, as it will be to environmental scientists, who cite uncertainties about soil carbon storage as one of the main barriers to accurate climate modeling.
“Deeper soils have the potential to be our ally or foe when it comes to mitigating climate change, depending on whether they can be managed to actively sequester SOC or whether global changes increase the decomposition of deep SOC, causing it to be respired to the atmosphere as CO2,” according to a 2023 paper in the Annual Review of Ecology, Evolution, and Systematics.
Now that major construction on the DSE facility is complete, funding must be secured to keep it up and running. This will likely come from a mix of federal funding, grants, and scientific partners who pay to conduct their research there.
The ultimate vision is to fill the remaining columns with soils from around the country and potentially the world—a sprawling tapestry of the Earth and an arena for diverse science.
“This is not a University of Idaho-only facility,” says Strickland. “It’s something anyone who has ideas can come in and potentially utilize.”
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