COLLABORATIVE RESEARCH: The role of marine Crenarchaeota in nitrification and links among biogeochemical processes in the eastern tropical North Pacific and Gulf of California

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Nitrification, the two-step oxidation of ammonia to nitrate via nitrite, plays a critical role in the global nitrogen (N) cycle by changing the form in which N occurs, and consequently influencing the accessibility and availability of N to different groups of organisms and biogeochemical processes, indeed, the processes responsible for the fixation and removal of N from the ocean may ultimately be connected by nitrification. It has long been assumed that the first and rate-limiting step of nitrification, ammonia oxidation, is restricted to a few groups within the domain Bacteria. However, the recent discovery of ammonia-oxidizing Archaea (AOA) has seriously challenged our understanding of the microbial ecology and biogeochemistry of nitrification in the ocean. In this project, researchers at Stanford University and the University of Hawaii at Manoa will attempt to constrain quantitatively the contribution of marine Crenarchaeota to oceanic nitrification and investigate connections to other forms of nitrogen metabolism in the Gulf of California (GOC) and the eastern tropical North Pacific (ETNP). The specific objectives are to: (1) quantify 15N-ammonium oxidation rates, and bacterial and archaeal amoA genes and transcripts, at seven stations in the upper water column (0-100m) of the GOC and ETNP; (2) determine if Crenarchaeota are actively fixing inorganic carbon (i.e., autotrophic) based on uptake of 13C--labeled bicarbonate into archaeal membrane lipids; (3) quantify nitrite oxidation rates and nitrite-oxidizer abundances at the same depths and stations; (4) extend these measurements to multiple depths within the oxygen minimum zone (OMZ); (5) examine potential coupling between ammonia-oxidizing archaea and nitrogen loss processes in the OMZ of the GOC and ETNP, and (6) place our results in a broader oceanographic perspective by tying into NSF-funded work examining nitrogen fixation in N-deficient waters ultimately generated in OMZs. The researchers predict that marine Crenarchaeota will play a dominant role in ammonia oxidation-based on amoA abundance, gene expression, active fixation of isotopically-labeled inorganic carbon, and correlation to measured rates?in both the upper water column and OMZ. They also expect that metabolic coupling between AOA and both oxidative (nitrite oxidation) and reductive N metabolisms (e.g., anammox) will be apparent.With regard to broader impacts, nitrification plays a pivotal role in linking organic matter mineralization to anaerobic nitrogen removal, and this project will provide critical information regarding how nitrification and the underlying microbial communities are influenced by key environmental gradients, as well as their connections to other N-cycling processes. Ultimately, this multi-disciplinary study should provide insights into the ecology and regulation of this biogeochemically-important process in all marine systems. The proposed research has excellent educational opportunities, and the PIs have a history of successfully mentoring and graduating Masters and/or Ph.D. students and fostering student publications and presentations at national meetings. Undergraduate, graduate, and postdoctoral education will be furthered through active participation in the cruise and post-cruise analyses, where students will work collaboratively with experts in molecular microbial ecology and stable isotope biogeochemistry, and learn a spectrum of state-of-the-art experimental and analytical methods.