When we think about the Amazon rainforest, our attention naturally rises toward the enormous trees, dense vegetation and extraordinary wildlife. But beneath this spectacular green world lies another living system – one that quietly works with the atmosphere above it. The rainforest soil.
Far from being an inactive layer beneath our feet, rainforest soil is alive with microorganisms and chemical processes. It absorbs gases from the atmosphere, breaks down organic compounds and participates in the continuous exchange of materials between the land, vegetation and air.
Now, new research suggests that extreme drought can interfere with one of these hidden processes. Scientists studying the Amazon have found that severe drought and heat can dramatically reduce the ability of rainforest soil to absorb isoprene, a gas naturally released by plants.
During the extreme drought of 2023, the soil’s capacity to take up isoprene fell by more than four times compared with normal conditions. The discovery offers a remarkable glimpse into how climate extremes can disrupt the invisible connections between soil and atmosphere.
When Rainforest Soil Stops Breathing: Soil is more than the ground beneath the forest
We often think of soil as the place where trees grow. But healthy soil is much more than a physical foundation for vegetation. It is a living ecosystem containing enormous communities of bacteria, fungi and other microorganisms. These organisms break down organic matter, recycle nutrients and participate in countless chemical reactions. Some of these processes also affect the atmosphere.
One example involves isoprene, a volatile organic compound produced naturally by plants. Tropical forests are major sources of this gas, releasing enormous quantities into the atmosphere. Yet some of the isoprene released by vegetation does not remain in the air.
Rainforest soils can absorb it. Microorganisms living in the soil help break down the compound, creating a natural biological pathway through which the forest floor influences atmospheric chemistry. This means that the Amazon’s climate influence is not confined to its trees. It extends beneath them.
What happens when the soil dries?
Researchers from the Max Planck Institute for Chemistry measured isoprene exchange between the atmosphere and Amazonian soils across several seasons. Their measurements included the exceptionally dry conditions of 2023, when a strong El Niño contributed to severe drought, record-low river levels and widespread vegetation stress in parts of the Amazon. The researchers found a striking change.
As the soil became extremely dry, its ability to absorb isoprene declined sharply – by more than fourfold compared with normal conditions. The researchers associate this decline with soil moisture falling below roughly 20%. At such low moisture levels, the microorganisms responsible for breaking down isoprene appear to become physiologically constrained. The soil, in effect, loses part of its ability to perform one of its atmospheric functions.
The hidden connection between trees and soil
The finding becomes even more interesting when we look at what happens above the ground. Plants can release more isoprene when exposed to high temperatures and oxidative stress. Scientists believe that isoprene can help plants cope with thermal stress and other environmental pressures.
During extreme drought and heat, therefore, two processes can occur simultaneously. Stressed vegetation can increase isoprene emissions, while dry soil becomes less capable of absorbing the gas. That creates a stronger connection between drought, vegetation and atmospheric chemistry.
The forest canopy is releasing isoprene, while the soil sink beneath it is weakening. This can leave more isoprene in the atmosphere.
Why should we care about a soil gas?
Isoprene may be invisible, but its atmospheric chemistry matters. It reacts with hydroxyl radicals and, to a lesser extent, ozone—important atmospheric oxidants that help determine how long certain gases remain in the atmosphere. Changes in isoprene concentrations can therefore influence atmospheric oxidation processes.
One important consequence concerns methane, a powerful greenhouse gas. Increased isoprene levels can reduce atmospheric oxidation capacity and potentially extend methane’s lifetime during drought conditions. Isoprene chemistry also contributes to the formation of secondary organic aerosols, which can influence atmospheric particles and cloud processes. So a change occurring only centimetres beneath the rainforest floor can eventually affect chemistry much higher in the atmosphere.
When drought changes the role of soil
This research reveals something profound about extreme drought. Drought does not simply deprive trees of water. It can alter the biological activity of the soil itself. As moisture disappears, microorganisms can become less active or physiologically constrained. Chemical processes change. Gas exchange changes. And the relationship between the soil and atmosphere can weaken.
Previous research in an artificial rainforest had already indicated that when soil moisture falls below roughly 19%, the soil’s ability to absorb certain volatile organic compounds can decline substantially. Under very dry conditions, soil can even become a source of some of these compounds. The new Amazon measurements provide important evidence from a natural rainforest environment.
The climate system beneath our feet
The Amazon is usually discussed in terms of trees, carbon storage and rainfall.
But this study adds another dimension: the climate system beneath the forest floor.
The microorganisms living in rainforest soil are part of a vast biological network connecting plants, soil and atmosphere.
When climate extremes disturb one part of that network, other parts can respond.
A drought dries the soil.
Dry soil constrains microbial activity.
Reduced microbial activity weakens isoprene uptake.
Meanwhile, heat-stressed vegetation can release more isoprene.
The atmosphere then receives a different chemical mixture than it would under normal conditions.
This is a powerful reminder that Earth’s climate system is not made up of isolated parts. What happens underground can influence what happens in the air.
A warning written into the soil
The researchers say more work is needed to determine whether soil microorganisms will adapt if extreme drought and heat become increasingly common.
That question is particularly important as climate change alters temperature and rainfall patterns across tropical regions.
If severe droughts become more frequent, the relationship between rainforest soil and the atmosphere could change as well.
Climate models therefore need to account for processes that have traditionally received less attention—including the gases exchanged between soil and atmosphere.
The Amazon’s future may depend not only on the trees standing above the ground, but also on the microscopic life beneath them.
The rainforest beneath the rainforest
Walk through a rainforest and the soil may appear silent.
But beneath the fallen leaves, roots and damp earth, billions of microorganisms are constantly working.
They decompose organic matter, recycle nutrients and participate in chemical exchanges that connect the forest floor with the atmosphere.
The new research shows how vulnerable some of these hidden processes can be when drought becomes extreme.
Perhaps that is one of the most important lessons from the Amazon:
The rainforest is not only above the soil. Much of its invisible life—and some of its influence on the atmosphere—begins below it.
As the climate becomes hotter and droughts intensify, protecting forests may therefore mean understanding and protecting the living soil beneath them too.
