Nitrification in a nutrient-rich urban estuary [electronic resource] : regional and temporal variations in the microbial ecology and biogeochemical activity of ammonia oxidizers in San Francisco Bay
Keywords: Earth System Science.

The global nitrogen (N) cycle has been profoundly affected by human activity. N enrichment has dramatically altered the water quality and ecological functioning of estuaries, including San Francisco Bay, which receives massive N inputs from sewage effluent and agricultural runoff. However, relatively little is known about the microbes responsible for the dominant N cycling pathways in estuaries. Nitrification, the microbial oxidation of ammonia to nitrate, is the only link between reduced and oxidized N in an ecosystem. The first step of nitrification, ammonia oxidation, is catalyzed by two clades of microbes: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This dissertation combines techniques from microbial ecology and N biogeochemistry to study the ecology of nitrification in San Francisco Bay. Previous work studying benthic ammonia oxidizers in San Francisco Bay documented distinct regional shifts in abundance and diversity. Chapter 2 extends these analyses to the freshwater delta at the head of the bay. Ammonia-oxidizing communities in the Sacramento River, the San Joaquin River, and the upper estuary were distinct, both in terms of abundance and diversity. Furthermore, these differences were reflected in potential nitrification rates, which were far greater in the Sacramento River than in the San Joaquin River or the upper estuary. The final three chapters focus on nitrification in the San Francisco Bay water column. Chapter 3 is an assessment of nitrification rates throughout the estuary, comparing rate measurements to environmental variables. Nitrification rates were related to temperature, ammonium, and suspended sediment concentrations, indicating high nitrification rates in turbid and ammonium-rich waters. Chapter 4 builds upon this by examining monthly measurements of nitrification rates and ammonia oxidizer community structure in the northern estuary over one year. Ammonia-oxidizing communities in freshwater, brackish, and marine regions of the northern bay had distinct seasonal patterns of ammonia oxidizer abundances, with AOA and AOB gene abundances correlated to different sets of environmental variables. Examinations of seasonal patterns between stations suggested mixing was an important factor affecting AOA and AOB abundances along the estuary. Chapter 5 presents data collected in the broad but shallow shoal waters fringing the estuary, providing a comparison between shallow and deep waters of the bay. Nitrification in shallow waters was extremely high at stations with high resuspended sediment concentrations. Bottom water nitrification in these regions was comparable to previously measured rates of benthic ammonium efflux. AOA and AOB in shallow waters appeared to be strongly affected by sediment resuspension, suggesting resuspended benthic communities are driving much of the nitrification in these waters. Comparisons of gene and transcript abundances of AOA and AOB also indicated different transcriptional behavior between these two clades. This dissertation advances our understanding of nitrogen cycling rates and the ecology of environmentally relevant microbes in estuaries, an important step toward understanding ecosystem function both today and as conditions change in the future.