Functional Phases Encode the Response of Soil Microbiome to Environmental Change

How does a complex ecological system maintain robust functions when facing environmental fluctuations? The ecological, spatial, and chemical complexity of soils makes understanding the metabolic response of microbial communities 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 consumer-resource 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. The model parameters reveal the existence of 3 functional phases in acidic/neutral/basic conditions, whose dynamical features and underlying mechanisms are qualitatively distinct. The model predictions are tested via amendment experiments, nutrient measurements, and sequencing. Together, we conclude that (1) within the range of small environmental perturbations, the denitrification function is dominated by the major component of the community but limited by hidden nutrients; (2) under extreme perturbations, the denitrification function can be preserved by rare taxa when access to newly released nutrients.