Functional regimes define soil microbiome response to environmental change

Authors: LEE, KISEOK - University Of Chicago; LIU, SIQI - University Of Chicago; CROCKER, KYLE - Northwestern University; WANG, JOCELYN - University Of Chicago; Huggins, David; TIKHONOV, MIKHAIL - Washington State University; MANI, MADHAV - Northwestern University; KUEHN, SEPPE - University Of Chicago

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/10/2025
Publication Date: 6/10/2025
Citation: Lee, K.K., Liu, S., Crocker, K., Wang, J., Huggins, D.R., Tikhonov, M., Mani, M., Kuehn, S. 2025. Functional regimes define soil microbiome response to environmental change. Nature. https://doi.org/10.1038/s41586-025-09264-9.
DOI: https://doi.org/10.1038/s41586-025-09264-9

Interpretive Summary: How soil biology, particularly microbes respond to changes in their environment is extremely challenging. Here, using data generated from the USDA Long-term Agroecosystem Site at the Cook Agronomy Farm, a simple mathematical model was developed that quantifies nitrate use across field scale differences in soil pH . Here, the model was useful in describing three important phases of nitrate use in response to short and long-term changes in soil pH. The results unify decades of previous studies on nitrogen utilization and pH in soils under a single quantitative framework where a simple mathematical model captures both the mechanisms and dynamics of a community responding to environmental change. The research will be of interest to soil microbiologists and others interested in how soil pH influences soil N cycling.

Technical Abstract: A major challenge in microbiome research is how natural communities respond to environmental change. The ecological, spatial, and chemical complexity of soils makes understanding how these communities respond metabolically to perturbations particularly challenging. Here we measure the dynamics of respiratory nitrate utilization in >1,500 soil microcosms from 20 soil samples subjected to pH perturbations. Despite the complexity of the soil microbiome a minimal mathematical model with two parameters, the quantity of active biomass and the availability of a limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. This model reveals in the data the existence of three distinct functional phases of nitrate utilization that encodes its low dimensional responses to short and long-term pH perturbations: a phase where acidic perturbations induce cell death that limits metabolic activity, a nutrient limiting phase where nitrate utilization is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth phase in extreme basic conditions, where nutrients are in excess and rare taxa rapidly out grow dominant populations. The underlying functional mechanism of each phase is revealed by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. The long-term pH of the soil determines the size of pH changes necessary to drive transitions between functional phases. Our results unify decades of previous studies on nitrogen utilization and pH in soils under a single quantitative framework. A simple mathematical formalism reveals the existence of a few qualitative phases that capture the mechanisms and dynamics of a community responding to environmental change.