Combining Molecular, Genomic, and Isotopic Techniques to Examine the Metabolism of Marine Thaumarchaeota in Monterey Bay and the California Current System

Thaumarchaeota are major players in the marine nitrogen cycle with a nearly ubiquitous distribution in the global ocean. These ammonia-oxidizing Archaea (AOA) are detected in the environment traditionally through molecular surveys of the 16S rRNA gene and the gene encoding the α subunit of ammonia monooxygenase (amoA) – the enzyme catalyzing the oxidation of ammonia. AOA are typically 10-1000 times more abundant than ammonia-oxidizing Bacteria in the ocean, yet, less is known about the metabolic activity and controls on archaeal ammonia oxidation. Within the broader phylum Thaumarchaeota, two AOA ecotypes have been described in marine environments – the ‘shallow’ water column A (WCA) and ‘deep’ water column B (WCB) clades, which are thought to have distinct physiological properties and can be distinguished based on the amoA gene sequence alone. We collected DNA and RNA samples from Monterey Bay and the California Current System, with simultaneous physicochemical and nitrification rate measurements, for metagenomic and metatranscriptomic sequencing. AOA 16S rRNA gene abundances correlated significantly with changes in nitrification rate with depth, while the relative abundance of genes and transcripts binned to a single AOA (Nitrosopumilus maritimus) was not significantly correlated to nitrification rate. We found a correlation between the relative abundance of Marine Group I (MGI) Thaumarchaeota 16S rRNA reads (as % of total) and the absolute abundance of AOA amoA genes (determined via qPCR). All sequenced metagenomes and metatranscriptomes contain genes relevant to nitrification and other portions of the nitrogen cycle. Further analysis of the sequenced AOA metagenomes and metatranscriptomes will allow us to determine whether nitrification rates correspond to a particular group of AOA, or if other metabolic genes (such as those involved in carbon fixation pathways) are correlated to nitrification.