INSIDE THE BLACK BOX: ILLUMINATING THE SOIL MICROBIOME FROM AGRICULTURAL FIELDS TO URBAN ROOFTOPS

Abstract

Soil processes are central to agricultural productivity and sustainability, however conventional assessments tend to emphasize bulk physicochemical measures and often fail to capture the full complexity of microbial processes driving nutrient cycling, phytohormone production, carbon stabilization, and ecosystem resilience. Multi-omics approaches, which integrate genome-resolved metagenomics, metatranscriptomics, and amplicon sequencing with geochemical and enzymatic measurements, offer a more holistic means of linking microbial community diversity, composition, functional potential, and activity to critical soil processes and outcomes across diverse agroecosystems. This dissertation applies high-resolution microbiome tools to both production-scale field soils and engineered rooftop agrivoltaic systems, providing the first glimpse into how microbial community structure, assembly, and function respond to contrasting environmental and management contexts, in ways that modulate soil processes. In production scale maize cropping systems, metatranscriptomic and amplicon data in Chapter 2 revealed that the soil conservation management practice of strip tillage promoted microbial strategies favoring carbon cycling and reduced nitrogen loss, whereas conventional tillage enhanced nitrogen turnover and potential gaseous losses. These functional differences were not apparent in standard soil health metrics, highlighting the value of microbial gene expression as a more sensitive indicator of functional change. By coupling multi-omics with the Soil Management Assessment Framework (SMAF), this research provided one of the first field-scale demonstrations that molecular-level data can expose management effects not yet captured in conventional soil health assessments. In contrast to the established field system, incipient rooftop agrivoltaic systems offered a unique window into early microbial community diversity, assembly and ecological filtering in an engineered urban agroecosystem. Chapter 3 used amplicon sequencing to reveal that rooftop substrate microbial communities diverged rapidly from their initial greenhouse inocula but gradually converged toward the structure of mature rooftop soils over three years. Photovoltaic shading acted as an ecological filter on community composition rather than richness: alpha diversity increased uniformly across shaded and full-sun plots, whereas beta diversity remained distinct over time, indicating persistent compositional divergence between treatments. Pairing genome-resolved metagenomics with geochemical and enzyme activities in Chapter 4 revealed that photovoltaic rooftop shading influenced both functional potential and realized activity over time. Carbohydrate-active enzyme genes were enriched under shaded conditions, and β-glucosidase activity, which was initially lower than in full-sun plots, increased over time in the most extreme shading and ultimately surpassed full-sun activity in the second year, indicating delayed but amplified carbon cycling under moderated moisture and temperature regimes. In contrast, full-sun substrates exhibited lower moisture, and heat stress–adapted and potentially pathogenic taxa were detected. Together, these findings indicate that photovoltaic rooftop microclimates exert strong selective pressures on microbial assembly and function, with direct implications for engineered substrate resilience. By integrating multi-omics with soil health frameworks, this dissertation reveals how microbial communities function as both indicators and agents of ecological processes across conventional and novel agroecosystems. Field-based tillage experiments highlight the sensitivity of microbial functional responses to management, while rooftop agrivoltaic systems demonstrate how environmental design and microclimate shape microbial succession and activity. Together, these findings provide a framework for incorporating microbial ecology into soil health assessments and guiding resilient agroecosystem design. These advances pave the way for scalable monitoring and management of soil function in a changing world.