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\subsection{Background}  Submerged aquatic vegetation (SAV) are plants that are rooted in sediment and fully submerged most of the time. Their evolutionary history includes a transition from aquatic to terrestrial and back to aquatic, resulting in many adaptations for coping with varied salinity and osmotic conditions. The Potomac River provides the opportunity to sample the microbial leaf and root communities of multiple SAV species across a salinity gradient as the river empties into the Chesapeake Bay. The goal was to find a link between the microbial communities on different SAV species and the changing salinity across the river.  \subsection{Results}  One of the four successfully sampled sites was very different from the rest in terms of microbial community and water/sediment chemistry, clustering separately from the other sites on PCoA plots. Within this one site, samples were differentiated by host species and sample type. Alpha diversity graphs revealed that Methylotenera, Planctomyces, Rhodobacter, \textit{Methylotenera}, \textit{Planctomyces}, \textit{Rhodobacter},  and Providencia \textit{Providencia}  are commonly found amongst most SAV species across all sites, and that sulfur oxidizing bacteria were present in high relative abundance in the roots of Redhead Grass \textit{Potamogeton perfoliatus}  at one site. \subsection{Conclusions}  Water/sediment chemistry, Site location,  which was unique at each site, had distinct water and sediment chemistries,  was a main driver of the microbial community structure. Different Host  species of SAV and sample types (leaves or roots) also  have different microbial communities. Due to the small sample size in this study, it is difficult to draw robust conclusions about the impact of salinity on microbial community structure. Therefore, future efforts will sample more thoroughly along the Potomac river, as well as along the length of the James River, which provides a nearby, parallel salinity gradient.