Nitrification from the Pacific Ocean to the Sacramento River: Do Distinct Microbial Communities Affect Biogeochemical Nitrogen Cycling in the Waters of a Large Urban Estuary?

Nitrification provides the only path between reduced and oxidized nitrogen. Ammonia-oxidizing microorganisms catalyze the rate-limiting step of ammonia oxidation and thus are key players in estuarine nutrient cycling. Few studies, however, have measured nitrification rates in tandem with ammonia oxidizer expression, abundance, and diversity in estuary waters. We present data on the microbial ecology and biogeochemistry of nitrification in the San Francisco Bay-Delta collected along the salinity gradient from summer 2013 to spring 2014. Microbial communities were assessed using functional gene-based PCR assays to determine the diversity, abundance, and mRNA expression of ammonia oxidizers, and nitrification rates were measuring using stable isotope tracer incubations. Ammonia-oxidizing archaea (AOA) typically outnumbered ammonia-oxidizing bacteria (AOB) throughout the sampled gradient, though the relative abundance of AOB was often greater in brackish regions and following periods of higher freshwater flow. mRNA expression of amoA appeared to largely track DNA abundance, but suggested only a fraction of the community was typically active. Average nitrification rates were highest in the lower Sacramento River, which was mostly dominated by AOA, suggesting the AOA communities here are responsible for a constant nitrification hotspot. Additionally, depth profiles suggested high biogeochemical activity near the sediment-water interface in samples with high turbidity, particularly in shallow lateral bays. These embayments appear to be transient nitrification hotspots during periods of sediment resuspension. Marine regions and the oligotrophic upper river were also dominated by AOA but had low nitrification rates. Overall, nitrification rates and microbial communities appear to respond to changes in freshwater flow and suspended sediment dynamics. This work increases our knowledge of the ecology of ammonia oxidizers in anthropogenically-impacted estuaries and rivers.