Date Awarded


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Virginia Institute of Marine Science


Bong Keun Song


Estuaries and coastal areas are highly diverse and productive ecosystems that serve as critical habitats for many marine organisms. Anthropogenic activities and changes in coastal land use have resulted in nutrient over-enrichment, posing a threat to the ecological integrity of estuaries. Nitrogen is often the limiting nutrient and its dynamics are central in determining coastal ecosystem health. The cycling and removal of nitrogen is primarily microbially mediated and the structure of these microbial communities is tightly interlaced with ecosystem function. Recycling processes nitrification and dissimilatory nitrate reduction to ammonium (DNRA) serve as a conduit for loss when coupled to the removal processes of denitrification and anaerobic ammonium oxidation (anammox). These processes occur simultaneously in estuarine sediments and are influenced by a suite of environmental factors. Understanding these interactions within the complex microbial communities, how microbial community structure responds to environmental changes, and how this relates to ecosystem function is a challenging but important goal in microbial ecology and particularly relevant in today's changing world, as climate change and sea level rise are eminent threats to coastal ecosystems. This study identified geomorphological, hydrological, and biogeochemical features, including water residence time, sediment %organics, nutrient availability, salinity, and hydrogen sulfide, that are important in controlling the community structures of nitrogen cycling microbes and their activities. Quantitative criteria were established to identify and assess the role of nitrogen removal hotspots in estuarine sediments. Specific groups of denitrifying and anammox bacteria with a higher nitrogen removal capacity were identified, suggesting the community composition is important in ecosystem function. Additionally, niche differentiation of nitrifying microbes was unveiled by linking their physiology to specific environmental parameters. Examination of microbial community structure and its response to environmental conditions combined with measurements of biogeochemical rates enabled the linkage of nitrogen cycling members with particular functions, a theme addressed throughout this dissertation.



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