Doctoral Defense | Danyang Duan

Long-term fertilization can leave lasting legacies on soil microbial communities and their functions, with important implications for biogeochemical cycling and plant-microbe interactions. This dissertation investigates how fertilization history shapes soil microbial ecology across multiple levels of biological organization, drawing on long-term agricultural experiments in Miscanthus grasslands and the historic Morrow Plots. By integrating measurements of soil GHG emissions with microbial enzyme activities, community profiling with amplicon and metagenomic sequencing, and comparative genomics, this research explores how fertilization legacies extend from ecosystem processes to microbial functions, community, and population-level variation. Particular attention is given to microbial processes involved in carbon and nitrogen cycling, as well as the symbiotic performance of rhizobia associated with legumes. Together, these studies provide a multi-scale perspective on the persistent effects of long-term nutrient fertilization, advancing our understanding of the connections between microbial communities, ecosystem functions, and plant-microbe interactions.