A Simple Model Describes How the Soil Microbiome Responds to Environmental Change

 A deceptively simple mathematical model can describe how the soil responds to environmental change, our recent research has shown. Using just two variables, the model shows that changes in pH levels consistently result in three distinct metabolic states of the microbial community. The multi-institutional study, spearheaded by myself (Dr. Kiseok Lee) and Dr. Siqi Liu at The University of Chicago and Northwestern University respectively, was published in Nature.

Understanding how soil microbes adapt to change

Understanding how communities of microbes living in the soil respond to changes in the environment – such as temperature, moisture, acidity – is critical if we want to understand how these microbiomes adapt to the demands of climate change. Soil microbiomes play a central role in regulating global nitrogen and carbon cycles, and their activity can be sensitive to changing environmental conditions. Rising temperatures or increasing soil acidity, for instance, can disrupt microbial metabolism, potentially destabilizing biogeochemical processes essential for soil fertility, greenhouse gas regulation and overall planetary health. Despite their importance, it remains unclear how microbial communities maintain functional stability, or fail to, under such environmental perturbations. To address this knowledge gap, we sought to find generalizable principles governing how microbial functions respond to environmental gradients.

Changes produce three consistent results

I sampled 20 natural soils from Cook Agronomy Farm in Pullman, Washington that has large natural variations in pH. I then prepared over 1,500 soil slurry samples, experimentally manipulated pH levels and tracked microbial responses over time using time-series measurements of nitrate concentration. We analyzed these responses across a wide pH gradient to identify distinct functional regimes, classifications of soil behavior in the face of pH perturbations. We then looked to create a simple consumer-resource model to describe the resulting dynamics.

The key findings of the paper were:

• Depending on how the pH was changed we saw three consistent results:
  - Regime I, or the “acidic death regime”: Large changes toward acidity caused the death of functional biomass.
  - Regime II, “nutrient-limiting regime”: During moderate changes, acidic or basic, the nitrate metabolism was limited by the availability of a limiting nutrient (carbon), resulting in linear nitrate dynamics.
  - Regime III, “resurgent growth regime”: Large changes toward basic conditions caused dominant groups of microbes to become less active, while rare groups rapidly grew and metabolized nitrate exponentially.
• A simple model was able to describe and predict how the soil metabolism responded to environmental perturbations.

Putting the model to use in ecological planning

Remarkably, our model was able to describe and predict the responses seen in our samples to the environmental changes we initiated – a surprising outcome given that soils are typically considered too complex to model. The success of the model highlights how describing the collective behavior of complex systems mathematically can cut through the complexity, enabling predictions of how the soil and its metabolism will respond to change. Ultimately, this will help scientists design interventions for improving agriculture or restoring ecosystems. For example, if nitrogen fertilizer runoff from farms contaminates nearby waterways, officials could take measures to increase pH and remove excess nitrate to prevent algal blooms.

We also think the same modeling approach can be applied to other environmental factors, applying it to elucidate functional responses in other microbial systems against different environmental changes, whether it be from temperature, pH, salinity or something else.

One limitation of our study is that we used soil slurries – soils mixed with water in the lab – to facilitate measurements. However, real soils experience daily changes in moisture and oxygen levels and there exists a mix of aerated and anaerobic pockets due to the physical structure of soil particles. These natural conditions and structures can significantly affect microbial behavior, so our experimental setup may not fully capture the environmental factors that influence nitrate utilization in real soils.

Towards a deeper understanding of how microbial communities function in nature

This framework links microbial traits to ecosystem metabolism, enabling predictions of community responses to environmental change. Future research may use it to design functionally resilient microbiomes to environmental change. Ultimately, this work paves the way for ecosystem function predictions and management strategies in a world of climate change.

Reference: Lee KK, Liu S, Crocker K, et al. Functional regimes define soil microbiome response to environmental change. Nature. 2025:1-11. doi:10.1038/s41586-025-09264-9 

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