Designing Soil Microbiome Function Robust to Environmental Perturbations

The objective of this project is to quantitatively understand how the genomic structure enables soil microbiomes to retain or change emergent metabolic processes in the face of environmental fluctuations. Microbes seldom exist in isolation and live in complex communities, making their genomic, proteomic, and metabolomic composition highly intricate. Concurrently, these microbial communities experience a barrage of environmental perturbations, such as changes in temperature, pH, moisture, and nutrients. Yet, these communities perform metabolic functions that sustain life in the biosphere, such as global carbon and nitrogen cycling. This raises the question of how these complex systems perform ecosystem functions in the face of environmental perturbations. To address this question, we densely sampled topsoils of pH ranging from 4 to 8 (0.2 increments) from Cook Agronomy Farm (Pullman, WA) and perturbed each soil sample from different native pH to pH of 4 to 8 (13 varying pH levels) in the lab. With both long-term natural pH variation and short-term lab-controlled pH perturbation experiments, we mapped community structure to denitrification activity, a crucial nitrogen cycle process. With simplified consumer-resource models, we observed two modes of functional robustness. In moderate pH perturbations, the community adjusted its dominant species' abundance to adapt to new pH levels. However, in the extreme pH perturbation regimes, the metabolic activity of the community was sustained and even increased due to the emergence of rare native species. Our findings shed light on designing microbial communities with functions robust against environmental perturbations, impacting fields like agriculture and climate change.