The Impact of Salinity on the Diversity of Microbial Sediment Communities

The nitrogen cycle is a global process, largely mediated by microorganisms, that exchanges nitrogen between its biologically available forms (NH₄⁺, NO₃^-) and its inert (N₂) form. This cycle enables the biological uptake of nitrogen for the formation of DNA, amino acids, and other biological compounds critical to life. Several processes are responsible for facilitating the cycling of nitrogen through eight different oxidation states. Two nitrogen removal processes include anaerobic ammonium oxidation (anammox), in which N₂ is produced directly from ammonia and nitrite, and denitrification, the sequential oxidation of NO₃ to N₂. Together, these two processes play a large role in determining the biological availability of nitrogen in estuarine ecosystems.

To better understand how microbial communities conducting these processes change under varying environmental conditions, a manipulation experiment was developed to simulate an environmental site salinity shift. Sediment cores were collected from north San Francisco Bay in the Carquinez Strait, a site of seasonally varying salinity. These cores from the Carquinez Strait were incubated in two treatments: one with local brackish water and one with freshwater from Suisun Bay. Using Sanger sequencing, we examined shifts in the microbial communities containing the functional genes hzsA (anammox) and nirS (denitrification). Geochemical characteristics such as NO₃^- and NH₄⁺ concentrations in the water and the C:N ratio of the sediment were measured to determine subsequent changes these communities had on the sediment chemistry. This study provides insight into how changes in salinity affect microbial sediment community composition in San Francisco Bay.