Native freshwater mussels of the Upper Mississippi River filter over 14 billion gallons of water and transfer tons of nitrogen into surrounding sediment each day. My research aims to determine how mussels influence nitrogen-cycling microorganisms using next-generation sequencing and bioinformatic techniques. Results suggest sediment microbiomes with mussels have greater potential for ammonia and nitrite oxidation, decreased potential for nitrous oxide production, and ultimately enhances the ecosystem services of nitrogen cycling and greenhouse gas mitigation.