Abstract: 

Denitrifying microbial communities are the invisible engines driving the global nitrogen cycle. Yet, how these microbial guilds adapt to environmental stressors—spanning long-term evolutionary timescales to rapid physiological responses—has long remained a major scientific enigma. While much of our understanding has focused on intracellular metabolism, extracellular vesicles (EVs) have recently emerged as critical, yet overlooked, mediators of intercellular communication and survival.
In this dissertation, I presented a comprehensive, multiscale framework that bridged the macroscopic genomic evolution of functional guilds with the microscopic, vesicle-mediated dynamics of individual cells. First, I conducted a genome-resolved metagenomic analysis of denitrifying communities—spanning natural ecosystem, Lake Donghu, to engineered nitrogen-removal bioreactors—to explore the divergent evolutionary trajectories of nirS- and nirK-type denitrifiers. The results revealed how horizontal gene transfer (HGT) and metabolic potentials shaped their genomic plasticity and ecological niche differentiation across these diverse habitats. Transitioning from community-level evolution to cellular physiology, I elucidated the dual, dose-dependent roles of EVs in the model denitrifier Pseudomonas aeruginosa. This study uncovered how these nanoscale structures acted as metabolic shuttles to enhance denitrification efficiency, yet could transition into cytotoxic agents under environmental stress. Finally, the research delved into the roles of EVs in marine oligotrophic ecosystems, establishing a novel dual-fluorescence flow cytometric framework to elucidate cyanobacteria-cyanophage interactions. I demonstrated how cyanobacterial EVs served as proactive, population-level "decoys," acting as an immune shield in the relentless host-phage arms race.
By integrating genome-resolved metagenomics with high-throughput single-cell analyses, this research redefined EVs not merely as cellular byproducts, but as indispensable ecological mediators. Ultimately, these findings unveiled previously hidden regulatory layers of microbial ecosystems, offering profound implications for global biogeochemical models and engineered microbiomes.