Winkler, Mari K. H.Flinkstrom, Zachary2025-08-012025-08-012025-08-012025Flinkstrom_washington_0250E_28226.pdfhttps://hdl.handle.net/1773/53478Thesis (Ph.D.)--University of Washington, 2025Microbial communities drive essential nutrient fluxes in diverse ecosystems, and their activity is strongly influenced by oxygen availability, which governs the balance between aerobic respiration and anaerobic metabolisms such as denitrification, sulfate-reduction, fermentation and methanogenesis. This dissertation explores how oxygen gradients shape microbial community structure and function across three systems: a global metagenomic dataset, a freshwater wetland, and twin aerobic and anaerobic chemostat bioreactors. Clustering of thousands of metagenomic functional gene profiles revealed oxygen as a major axis of differentiation, alongside light, with distinct traits such as antibiotic production and archaeal abundance. In the wetland study, microbial communities were structured primarily by soil depth rather than seasonal variation, reflecting the persistent influence of vertical oxygen gradients despite shifts in porewater chemistry and greenhouse gas fluxes. In bioreactors fed with N-acetylglucosamine—a model compound for microbial necromass—both aerobic and anaerobic communities mineralized the substrate, but with divergent metabolic byproducts and community trajectories. The aerobic system exhibited strong coupling of carbon and nitrogen cycles, including nitrification and denitrification, while the anaerobic system became increasingly methanogenic and resilient to oxygen perturbations. Metagenomic and transcriptomic analyses revealed distinct pathways of compound utilization between treatments. Overall, this work integrates field data, laboratory experiments, and bioinformatics to deepen our understanding of how oxygen availability governs microbial community dynamics and ecosystem-scale biogeochemical processes.application/pdfen-USCC BY-SABiogeochemistryBioinformaticsMetagenomicsMicrobiologyWetlandsMicrobiologyBiogeochemistryBioinformaticsCivil engineeringThesis