Different Microorganisms Have a Taste for Different Flavors of Ammonia

Research on ammonia-oxidizing microorganisms reshapes scientists’ perspective on those microbes’ physiology and ecological niche.

Researchers determined the nitrogen source preference of different ammonia-oxidizing microorganisms by growing cells in an ammonia-urea mixture with nitrogen-15 labeled urea or ammonia and imaging labeled cells with NanoSIMS.
Image courtesy of Wei Qin, Britt Abrahamson, and Lawrence Livermore National Laboratory.
Researchers determined the nitrogen source preference of different ammonia-oxidizing microorganisms by growing cells in an ammonia-urea mixture with nitrogen-15 labeled urea or ammonia and imaging labeled cells with NanoSIMS.

The Science

Ammonia-oxidizing microorganisms (AOMs) use ammonia as an energy source while converting it to nitrite. They play a pivotal role in the global nitrogen cycle. Scientists have long sought to understand how multiple species of AOMs can coexist in the same environment. This work explored whether different AOM species preferred to use urea, a widely available organic chemical that contains nitrogen and carbon, over ammonia. Surprisingly, some AOMs preferred urea, despite the need to break it down before it could be used, while others used ammonia and urea simultaneously. These preferences may provide distinct niches for different AOMs in the same environment.

The Impact

AOMs account for the oxidation of approximately 2.3 trillion kilograms of nitrogen per year in marine, soil, freshwater, subsurface, and human-made ecosystems. This process is connected to nitrate leaching, which causes eutrophication. This is the process where nutrients in a body of water lead to the increased growth of microorganisms that can use up all the oxygen in the water. AOMs’ oxidation of nitrogen also produces nitrous oxide, a potent greenhouse gas. AOMs’ use of urea is especially important because urea accounts for about 40% of the nitrogen in fertilizers. This research provides new insight into how AOMs use nitrogen in the environment. The results may help scientists mitigate nitrogen pollution. The results also show that AOMs are an important part of the link between the global carbon and nitrogen cycles.


Researchers conducted experiments with four evolutionarily distinct AOM lineages: ammonia-oxidizing archaea, beta- and gamma-proteobacterial ammonia-oxidizing bacteria, and Nitrospira complete ammonia-oxidizing (comammox) bacteria. The researchers grew cultures in a mixed ammonia-urea media containing either nitrogen-15-labeled urea or nitrogen-15-labeled ammonia. The researchers used the cultures to track substrate preference across catabolism with stable isotope tracing and anabolism with NanoSIMS conducted at Lawrence Livermore National Laboratory. Distinct patterns emerged across the tested AOM lineages with archaea and comammox preferring ammonia, beta-proteobacteria preferring urea, and gamma-proteobacteria using both substrates simultaneously. The kinetics of ammonia and urea oxidation reflected substrate preference with each AOM lineage having a higher specific affinity for their preferred substrate. Finally, the researchers used RNA sequencing to elucidate the regulatory mechanisms behind the observed preferences. 

The results suggested that PII nitrogen regulatory proteins are involved in repressing ammonia utilization in the tested beta-proteobacteria when urea is present. In contrast, the tested archaea and comammox regulated the expression of their ammonia and urea transporters to modulate the intake of their preferred substrate. Taken together, this study expands our understanding of AOM niche differentiation and displays convergence of the nitrogen and carbon cycles.


Mari Winkler
University of Washington


This research was supported by grants from the Department of Energy Office of Science, Division of Biological and Environmental Research, the National Science Foundation, the Defense Advanced Research Projects Agency, the Simons Foundation, the University of Oklahoma, the Florida Agricultural Experiment Station, a University of Florida IFAS Early Career Award, a USDA NIFA award, and a National Natural Science Foundation of China award to Yue Zheng.


Qin W., et al., Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nature Microbiology 9, 524–536 (2024). [DOI: 10.1038/s41564-023-01593-7]

Related Links

Microbial Research Unravels a Global Nitrogen Mystery, University of Oklahoma news release

Microbial research unravels a global nitrogen mystery, Lawrence Livermore National Laboratory news release

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