The impact of urbanization on the tree-associated microbiome
Embargo Date
2028-01-14
OA Version
Citation
Abstract
Urbanization profoundly reshapes ecosystems, altering both abiotic conditions and the interactions between organisms, yet its effects on tree-associated microbial communities and their implications for urban forest health remain poorly understood. This dissertation examines how urbanization influences soil- and tree-associated microbiomes and microbial functional potential across urban-to-rural gradients, with the goal of linking microbial ecology to tree growth and mortality outcomes. I first demonstrate that urbanization increases overall soil microbial connectivity while simultaneously disrupting key ecological interactions, notably reducing connectivity among ectomycorrhizal fungi that form mutualistic relationships with tree roots. Urbanization also shifts the structure and composition of oak tree microbiomes, decreasing mutualistic symbionts and increasing decomposers and pathogens, with consequences for biogeochemical cycling, including higher nitrogen loss potential and reduced methane consumption. These microbiome shifts correlate with urban stressors such as heat, drought, and inorganic nutrient deposition. Integrating microbial and environmental data, I show that urban tree growth and survival are shaped by microbial composition: growth is positively associated with microbial functional groups such as saprotrophs and C-fixing bacteria, while mortality is linked to pathogenic and wood-decomposing taxa. These findings highlight the central role of the tree holobiont (i.e., the tree and its associated microbes) in determining urban tree performance. To better predict functional outcomes from microbial surveys, I developed Fun2FITS, a computational pipeline that links fungal ITS amplicon data to predicted gene content, enabling scalable inference of fungal functional potential across ecosystems. Validation demonstrates that Fun2FITS captures ecologically meaningful patterns, particularly for ectomycorrhizal fungi. Finally, I translate these insights into applied urban forestry strategies through GIS-based analyses that identify optimal front-yard planting locations in Boston to maximize ecological and social benefits. Collectively, this work provides a mechanistic understanding of how urbanization reshapes tree-microbe interactions, microbial functional potential, and urban forest health, offering tools for evidence-based management of resilient, sustainable urban tree populations.
Description
2026
License
Attribution-NonCommercial 4.0 International