Urea use drives niche separation between dominant marine ammonia oxidizing archaea

Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms in the ocean and play a critical role in marine nitrogen cycling. Recently, urea has been shown to serve as an additional substrate for marine AOA, with substantial urea use in the ammonium-depleted open-ocean. Yet, the mechanisms that control urea use and potentially maintain high AOA abundances remain unclear. Here, we investigate urea and ammonia use by AOA in three contrasting marine environments, from coastal, ammonium-rich to open-ocean, ammonium-poor waters. Our combined results indicate that distinct substrate utilization strategies of Nitrosopumilus and Nitrosopelagicus control their environmental distribution. The more coastal AOA genus, Nitrosopumilus, primarily uses ammonium. In contrast, enhanced urea utilization in ammonium-limited waters is linked to the activity and growth of Nitrosopelagicus. Thus, the use of urea, and potentially other organic-N compounds by Nitrosopelagicus plays a major role in fueling open-ocean nitrification and sustaining primary productivity in these vast regions.