CAREER: Mechanisms of functional robustness in soil microbiomes

This project aims to connect detailed microbial processes to broader ecological and environmental outcomes such as soil fertility and greenhouse gas emissions, with critical implications from climate change to agriculture. The project includes a robust outreach mechanism that will support hands-on educational activities that integrate mathematical and biological thinking for K-8 students, secondary school teachers, and undergraduates, fostering a well-prepared STEM workforce equipped with cutting edge mathematical and experimental tools.

The research objective of the project is to understand the mechanistic basis of functional robustness in the soil microbiome. The project will reveal how environmental variation impacts ecological processes within the microbiome giving rise to variation in denitrifying metabolic activity in soils. The approach leverages massively parallel experiments on soil microcosms, precise quantification of metabolite dynamics, and mathematical models to connect metagenomic, transcriptomic, and population dynamics to the emergent functional properties of these complex microbial communities.

The project is structured around three main objectives. The first is to elucidate the mechanisms through which soil microbiomes respond to pH changes and how these responses impact the rate of anaerobic nitrate reduction in soils, a key process in nitrogen cycling. In this objective the researchers will combine transcriptomic and metagenomic measurements with mathematical modeling to predict how pH perturbations impact the metabolism of soil microbiomes.

The second objective is to identify specific microbial taxa that drive observed changes in soil functions under different environmental conditions. This objective will involve identifying the key groups of bacterial taxa that are responsible for the metabolism identified in the first objective. The goal is to define the set of bacterial taxa that are responsible for the transcriptional and metagenomic responses to environmental perturbations described in the first objective.

The third objective focuses on isolating and characterizing key microbial taxa identified in earlier phases of the study. The goal is to perform isolations and quantitative phenotyping of individual strains in the microbiome with the objective of linking individual bacterial traits to higher level microbiome metabolic function again via quantitative modeling.

The goal will be to understand the metabolic response of the nitrate reduction rate to changes in pH in terms of the underlying traits of members of the microbiome. Collectively, this research will provide new insights into the soil microbiome's resilience and adaptability, offering strategies for enhancing soil health and agricultural productivity in the face of global environmental changes.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.