The relationship between ammonia-oxidizing bacteria (AOB) and potential nitrification rates was examined along a salinity gradient in a New England estuary in spring and late summer over 3 years. Ammonia-oxidizing bacteria abundance was estimated by measuring gene copies of the ammonia monooxygenase catalytic subunit (amoA) using real-time polymerase chain reaction. Ammonia-oxidizing bacteria abundance ranged from below detection to 6.0 x 10(7)amoA copies (gdw sediment)(-1). Mean potential nitrification rates ranged from 0.5 to 186.5 nmol N (gdw sediment)(-1) day(-1). Both AOB abundance and potential rates were significantly higher in spring than late summer. Correlations between rates and abundance varied significantly among sites, but showed site-specific ammonia oxidation kinetics related to AOB community structure. The effect of salinity on potential nitrification rates was evaluated by incubating sediment from each site under four salinity conditions (0, 5, 10 and 30 psu). At all sites, rates were generally highest in the intermediate salinity treatments, but rates at the upstream site were inhibited at high salinity, while rates at the two downstream sites were inhibited at the lowest salinity. Although salinity appears to be an important factor in determining AOB distribution, it may not be the primary factor as AOB exhibited a broad range of salinity tolerance in our experiments. Our results indicate that there are significant differences in abundance and community composition of AOB along the salinity gradient, and the differences are reflected in community function.

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Benthic respiration, sediment-water nutrient fluxes, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in the upper section of the Parker River Estuary from 1993 to 2006. This site experiences large changes in salinity over both short and long time scales. Sediment respiration ranged from 6 to 52 mmol m −2 day −1 and was largely controlled by temperature. Nutrient fluxes were dominated by ammonium fluxes, which ranged from a small uptake of −0.3 to an efflux of over 8.2 mmol N m −2 day −1 . Ammonium fluxes were most highly correlated with salinity and laboratory experiments demonstrated that ammonium fluxes increased when salinity increased. The seasonal pattern of DNRA closely followed salinity. DNRA rates were extremely low in March, less than 0.1 mmol m −2 day −1 , but increased to 2.0 mmol m −2 day −1 in August. In contrast, denitrification rates were inversely related to salinity, ranging from 1 mmol m −2 day −1 during the spring and fall to less than 0.2 mmol m −2 day −1 in late summer. Salinity appears to exert a major control on the nitrogen cycle at this site, and partially decouples sediment ammonium fluxes from organic matter decomposition.

These data indicate that radiant energy is most effectively utilized as a source of photoreducing power in the presence of elevated cellular carotenoid : chlorophyll a ratios of surface populations.It is concluded that enhanced cellular carotenoid synthesis increases light utilization in the low and middle regions of the photosynthetically active radiation (PAR) spectrum and provides protection from UV damage. This is shown to have a positive effect on photosynthetic CO, fixation and bloom persistence in surface waters.

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