Robustness of Microbiome Function to Environmental Change

Microbial communities drive essential ecosystem processes and promote human and environmental health through their metabolic activities. This dissertation investigates how these communities sustain functional robustness in the face of constant environmental perturbations, with a focus on soil microbiomes. First, drawing on insights from other complex biological systems in the literature, I propose a perspective for understanding and predicting microbiome robustness. Next, through dynamic measurements of respiratory nitrate metabolism across over 1,500 soil microcosms, I identify three functional regimes in response to pH perturbations: an acidic regime marked by cell death, a nutrient-limited regime driven by dominant taxa using soil matrix-released nutrients, and a resurgent growth regime characterized by rare taxa exponentially growing under nutrient surplus. A minimal mathematical model explains and predicts the functional dynamics with just two mechanistic parameters: indigenous microbial activity and nutrient availability, which are further validated by experiments and meta-analyses. This work deepens our understanding of the principles underlying microbial functional robustness, offering strategies to predict and engineer microbiome functions in varying environments.