Functional regimes define soil microbiome response to environmental change

Abstract

The metabolic activity of soil microbiomes has a central role in global nutrient cycles¹. Understanding how soil metabolic activity responds to climate-driven environmental perturbations is a key challenge^2,3. However, the ecological, spatial and chemical complexity of soils^4,5,6 impedes understanding how these communities respond to perturbations. Here we address this complexity by combining dynamic measurements of respiratory nitrate metabolism⁷ with modelling to reveal functional regimes that define soil responses to environmental change. Measurements across more than 1,500 soil microcosms subjected to pH perturbations^8,9 reveal regimes in which distinct mechanisms govern metabolite dynamics. A minimal model with two parameters, biomass activity and growth-limiting nutrient availability, predicts nitrate utilization dynamics across soils and pH perturbations. Parameter shifts under perturbation reveal three functional regimes, each linked to distinct mechanisms: (1) an acidic regime marked by cell death and suppressed metabolism; (2) a nutrient-limited regime in which dominant taxa exploit matrix-released nutrients; and (3) a resurgent growth regime driven by exponential growth of rare taxa in nutrient-rich conditions. We validated these model-derived mechanisms with nutrient measurements, amendment experiments, sequencing and isolate studies. Additional experiments and meta-analyses suggest that functional regimes are widespread in pH-perturbed soils.