Biogeochemical processes in a small California estuary. 2. Nitrification activity, community structure and role in nitrogen budgets

Nitrification rates, bacterial abundance and productivity, and the diversity of ammonia-oxidizing bacteria were measured at 5 sites in Elkhorn Slough, a small estuary in central California, between 1997 and 1999. Of the sampling sites, 2 received high nutrient runoff from agricultural fields and other non-point sources, and 3 received runoff from grasslands and woodlands. The diversity of ammonia-oxidizing bacteria in terms of DNA sequences was investigated at 3 of the sites in August 1998. Both 16S and amoA sequences from sediment samples were more closely related to those of Nitrosomonas marina than to any other cultured nitrifier, but there was considerable diversity within the group, and site-specific patterns were not detected. Potential nitrification was seasonally and spatially variable, with the highest rates occurring at the head of Elkhorn Slough in late winter and fall. Bacterial productivity was highest during the summer and generally higher at a site adjacent to grasslands compared to the 2 agricultural sites. The variability in nitrification rates was not directly correlated with hydrographic and environmental variables, Physical factors may affect nitrification rates indirectly by controlling salinity and bottom-water oxygen concentrations. Potential nitrification rates were positively correlated with pore water NH₄⁺ concentrations under well flushed conditions but were negligible in the presence of high NH₄⁺ concentrations under poorly flushed conditions, due to low oxygen availability, hypersaline conditions or both. Sediment nitrogen budgets for 3 of the sites suggested that denitrification removed about 25% of the mineralized nitrogen at the poorly flushed site, but 50% or more at well flushed sites. Poorly flushed systems appear to be less efficient at removing high nitrogen inputs than well flushed systems because of the low rates of coupled nitrification-denitrification in the former, implying that physical factors such as the flushing regime or residence time can significantly affect nitrogen removal by denitrification.