Denitrifier abundance and activity across the San Francisco Bay estuary

Summary Over 50% of external dissolved inorganic nitrogen inputs to estuaries are removed by denitrification – the microbial conversion of nitrate to nitrogen gas under anaerobic conditions. In this study, denitrifier abundance, potential rates and community structure were examined in sediments from the San Francisco Bay estuary. Abundance of nirK genes (encoding Cu‐containing nitrite reductase) ranged from 9.7 × 103 to 4.4 × 106 copies per gram of sediment, while the abundance of nirS genes (encoding cytochrome cd1 nitrite reductase) ranged from 5.4 × 105 to 5.4 × 107 copies per gram of sediment. nirK gene abundance was highest in the riverine North Bay, whereas nirS gene abundance was highest in the more marine Central and South Bays. Denitrification potential (DNP) rate measurements were highest in the San Pablo and Central Bays and lowest in the North Bay. nirS‐type denitrifiers may be more biogeochemically important than nirK‐type denitrifiers in this estuary, because DNP rates were positively correlated with nirS abundance, nirS abundance was higher than nirK abundance at every site and time point, and nirS richness was higher than nirK richness at every site. Statistical analyses demonstrated that salinity, organic carbon, nitrogen and several metals were key factors influencing denitrification rates, nir abundance and community structure. Overall, this study provides valuable new insights into the abundance, diversity and biogeochemical activity of estuarine denitrifying communities and suggests that nirS‐type denitrifiers likely play an important role in nitrogen removal in San Francisco Bay, particularly at high‐salinity sites.