biostudies-literatureStuehrenberg JDeutsche ForschungsgemeinschaftState Key Laboratory of Marine Environmental Science (State Key Laboratory of Marine Environmental ScienceDeutsche Forschungsgemeinschaft (German Research Foundation)Max-Planck-Gesellschaft10946https://www.ebi.ac.uk/biostudies/studies/S-EPMC12686405biostudies-literatureUnknown16(1)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 uNature communicationsUrea use drives niche separation between dominant marine ammonia oxidizing archaea.PMC12686405EXC-2077-390741603Littmann SStuehrenberg JMilucka JMarchant HKLavik GOrsi WDGraf JSSchorn SSpeth DRWu SKitzinger KVuillemin AKuypers MMMvon Arx JNfalseUrea 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 u2025-01-01T00:00:00Z2025 Dec2026-06-06T00:32:17.434Z2026-05-24T03:11:54.886ZS-EPMC126864054135327910.1038/s41467-025-67048-1