Microbially-mediated nitrogen transformations were examined at two intertidal and three subtidal locations in Tomales Bay, California. Intertidal sediments were inhabited by productive microbial mat communities and served as net sources of combined nitrogen since nitrogen fixation rates exceeded denitrification rates. Though potential denitrification rates were positively correlated with nitrogen fixation rates over diel cycles, the two processes were comparable in magnitude only at night throughout most of the year.

Both nitrogen fixation and denitrification were inhibited by photosynthetic oxygen production, but denitrification was more strongly inhibited than nitrogen fixation. This inhibition of denitrification served to limit losses of combined nitrogen from microbial mat communities and resulted in a net input of combined nitrogen to intertidal environments during most of the year.

However, during winter, a different pattern was observed with denitrification rates exceeding nitrogen fixation rates. At this time, low rates of photosynthesis reduced oxygen inhibition of denitrification and high water column concentrations of dissolved inorganic nitrogen depressed nitrogen fixation. Both of these factors led to a domination of the net nitrogen budget by denitrification during winter.

In subtidal sediments, denitrification rates exceeded nitrogen fixation rates and these regions served as net sinks for combined nitrogen. Nitrogen fixation was present throughout the upper 50 cm of sediment and showed no apparent seasonal pattern. Rates of nitrogen fixation amouted to at most 30% and on average 10% of denitrification rates. Denitrification rates were highest in the upper 3 cm of sediment and activity extended to significant depth (40 cm) in these sediments throughout the year. High rates of denitrification were fueled by nitrate derived from both in situ nitrification and by the diffusive flux from the overlying water column to the sediment. Seasonally, maximum denitrification rates were observed during summer and fall with lower rates observed during winter. Denitrification showed a strong positive correlation with bottom water temperature and nitrification.

Both denitrification and nitrification were higher in vegetated compared to unvegetated subtidal sediments in the inner portions of the Bay. However, no significant spatial trend in denitrification was observed along a horizontal transect running from the headwaters to the mouth of the Bay. An interesting dichotomy exists between the intertidal and subtidal sediments of Tomales Bay. Intertidal sediments were net autotrophic, with production exceeding respiration. These regions served as net sources of combined nitrogen, due primarily to the activity of autotrophic, nitrogen- fixing cyanobacteria. In contrast, heterotrophic subtidal sediments served as net sinks for combined nitrogen. Because the area of subtidal sediments exceeds that of intertidal sediments (28 versus 3 km^2), the Bay as a whole functions as a sink for combined nitrogen with denitrification exceeding nitrogen fixation rates by 5 to 15 times.