Collaborative Research:(PRISM) - Predicting Resilience in Soil Microbiomes through multi-scale analysis of monsoon-driven adaptations

About This Grant

Changing environmental conditions are dramatically transforming Earth’s drylands, which cover nearly half of the planet and support the livelihoods of 3 billion people through farming and food production. As these regions face increasing drought and more extreme weather, it is crucial to understand how the tiniest organisms in soil—microbes—cope with stress. These microbes are responsible for recycling nutrients like nitrogen, which plants need to grow. This project focuses on how microbial communities in desert soils continue performing these essential roles, even as their environment becomes more difficult to survive in. The research will examine soils in the Sonoran Desert over several years to explore how microbes adapt and reorganize in response to environmental stress. The team will use advanced genetic tools to study these tiny organisms—revealing who they are, what they do, and how they respond to environmental stress—alongside carefully designed laboratory experiments to detect early warning signs that soil ecosystems may be approaching collapse. In addition to advancing understanding of how life persists in extreme environments, the project will deliver practical tools for monitoring soil health. These tools aim to support decision-making for land managers, farmers, and environmental agencies working in dry regions. Educational resources will be developed, including an interactive public art installation that invites people to explore the hidden world of soil microbes through gameplay. The project will also provide research training opportunities for students and foster collaboration with agricultural extension professionals, ensuring the work benefits both scientific progress and real-world land stewardship. This project investigates molecular mechanisms underlying microbial community resilience in arid ecosystems using Thermoproteota as a model system for understanding organism-mediated stability. The research combines five years of temporal multi-omics analysis (2021-2025) with controlled mesocosm experiments to test three nested hypotheses spanning community, population, and molecular scales. The team will integrate metagenomics, metatranscriptomics, and metabolomics with Bio-orthogonal Non-Canonical Amino Acid Tagging (BONCAT) to distinguish active from dormant populations and track protein synthesis during stress responses. Controlled manipulation experiments will simulate intensified monsoon cycles to identify critical thresholds where adaptation mechanisms fail, particularly focusing on Thermoproteota’s unique stress tolerance strategies including manganese-based catalases and protein repair systems. Advanced statistical modeling using Structural Equation Models and Mixed Effects Models will connect molecular adaptations to ecosystem-level nitrogen cycling stability. The research will develop a hierarchical framework of resilience indicators spanning rapid molecular responses to slower community restructuring patterns. Key innovations include dual amino acid BONCAT protocols for soil systems, integration of activity measurements with genome-resolved multi-omics, and development of predictive models linking individual adaptations to community stability. The experimental design employs 272 archived samples and 243 controlled mesocosm samples to validate indicators across temporal scales and stress intensities, ultimately producing quantitative tools for monitoring ecosystem resilience and predicting critical transition points in arid systems. 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.