Meta-omic and Biogeochemical Signatures of Ammonia-Oxidizing Archaea Blooms in South San Francisco Bay

San Francisco Bay (SFB) is a highly nitrogen (N) polluted estuary containing two distinct ecosystems: North Bay and South Bay, a tidal lagoon with high ammonia inputs from wastewater treatment plants. Despite the importance of nitrification for conversion of ammonia to nitrate, rate measurements are limited in South Bay. Generally, nitrification is carried out by two functional guilds: ammonia-oxidizing archaea (and bacteria) and nitrite-oxidizing bacteria. Sequence data from South Bay indicates that ammonia-oxidizing archaea (AOA) were highly abundant in autumn 2012 and 2013, accounting for >20% of 16S rRNA amplicon reads in some samples. High AOA abundances coincide with high nitrite concentrations (up to 10 μM) in the oxic water column, indicating ammonia and nitrite oxidation may have become decoupled. Metagenomes from October 2013 samples also reveal high abundances of amoA sequences and have resulted in high quality (>95% complete) AOA metagenome-assembled genomes. While both genomic and geochemical data suggest that AOA may have bloomed in South Bay, corresponding nitrification rates during these apparent bloom periods are lacking. From November 2018 to July 2019, nitrification rates were measured at four South Bay stations on roughly quarterly cruises via ¹⁵N-based stable isotope incubations. In autumn 2018, ambient nitrite concentrations reached up to 12 μM, suggesting high rates of ammonia oxidation. Water samples for measuring ambient N₂O concentrations were collected at this time. In addition, pelagic microbial biomass was collected for nucleic acid extraction and subsequent qPCR analyses to measure ammonia oxidizer abundances and expressional activity. Based on historic biogeochemical and DNA based assessments, we anticipate high nitrification rates and abundances of AOA in autumn 2018 samples. Potentially recurrent seasonal AOA blooms could have important implications for water quality modeling and assessing N₂O production in SFB.