Metabolic regimes and low-dimensional dynamics in soil microbiomes

Soil microbial communities drive the chemical fluxes that sustain life on Earth, yet we lack a quantitative understanding of how their collective metabolism responds to environmental change. The challenge is complexity: these communities are massively diverse, spatially disordered, and chemically complex. We approach this problem empirically by measuring the dynamic utilization of resources (nitrate) by intact soil microbiomes in the lab. A model that describes the community as a single effective biomass captures metabolite dynamics across a range of pH-perturbed conditions. Just two parameters in the model, biomass activity and nutrient availability, vary to predict nitrate consumption dynamics across a wide range of soils and perturbations. We find that soil microbiomes organize into a small number of functional regimes, distinct dynamical states governed by different mechanisms. Shifts in these parameters reveal transitions between three regimes: an acidic collapse dominated by cell death, a nutrient-limited state maintained by a constant rate of resource consumption, and a resurgent growth regime driven by the rapid expansion of rare taxa. Despite their complexity, soil microbiomes exhibit low-dimensional dynamical structure. This structure offers a route toward predictive, physics-like laws of ecosystem metabolism discovered phenomenologically.