Electron micrographs of ‘N. maritimus’. a, Scanning electron micrograph of Au/Pd sputtered cells. b, Transmission electron micrograph of negative stained cells. Scale bars represent 0.1 μm.

For over a century, studies of aerobic ammonia-oxidizing microorganisms have been limited to two narrow clades within the domain Bacteria [34, 1, 18, 26]. Despite the application of molecular techniques to the characterization of natural microbial communities and improved methodologies for cultivating microorganisms, general understanding of the microbiota sustaining nitrification in soil and marine environments has not been significantly modified until now. Our recent discovery of an autotrophic ammonia-oxidizing archaeon [28], the first documentation of this physiology within the domain Archaea, necessitates a reassessment of nitrifying diversity and of the potential contribution of Archaea to global nitrogen and carbon cycles [28]. The isolate (‘Nitrosopumilus maritimus’) belongs to the Crenarchaeota, one of the recognized kingdoms in the domain Archaea. The general physiology of this isolate is similar to that of characterized bacterial ammonia oxidizers, growing autotrophically via the oxidation of ammonia to nitrite. It is the first representative of the planktonic marine Crenarchaeota in pure culture. The marine Crenarchaeota, first discovered in cultivation-independent molecular surveys over a decade ago [13, 20], may represent some of the most abundant organisms on our planet. Estimated to number approximately 1028 cells in the world’s oceans [23], they almost certainly play important roles in global biogeochemical cycles.

The discovery of ‘N. maritimus’, by revealing significant gaps in our knowledge of microbial ammonia oxidation, now raises a variety of critical questions about the diversity, ecology, and evolutionary origins of ammonia oxidation-based metabolism. We anticipate that the availability of a genome sequence will greatly accelerate studies of the physiology of this novel isolate, offer an important perspective on the origin(s) and diversification of ammonia-oxidizing microorganisms, and provide an essential framework for interpreting partial genome sequence recovered from past and ongoing environmental surveys of environments inhabited by low-temperature Crenarchaeota. More generally, it should contribute to a better understanding of the biogeochemical cycling of nitrogen and carbon.

References

1. Aakra, A., Utaker, J.B., Pommerening-Roser, A., Koops, H.P., and Nes, I.F. (2001). Detailed phylogeny of ammonia-oxidizing bacteria determined by rDNA sequences and DNA homology values. International Journal of Systematic and Evolutionary Microbiology 51, 2021-30.

13. DeLong, E.F. (1992). Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89, 5685-9.

18. Egli, K., Langer, C., Siegrist, H.R., Zehnder, A.J.B., Wagner, M., and van der Meer, J.R. (2003). Community analysis of ammonia and nitrite oxidizers during start-up of nitritation reactors. Applied and Environmental Microbiology 69, 3213-22.

20. Fuhrman, J.A., McCallum, K., and Davis, A.A. (1992). Novel major archaebacterial group from marine plankton. Nature 356, 148-9.

23. Karner, M.B., DeLong, E.F., and Karl, D.M. (2001). Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409, 507-10.

26. Koops, H.P., Purkhold, U., Pommerening-R?ser, A., Timmermann, G., and Wagner, M. (2003). The lithotrophic ammonia-oxidizing bacteria, In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, M. Dworkin, S. Falkow, E. Rosenberg, K.H. Schleifer, and E. Stackebrandt, eds. (New York: Springer-Verlag), pp. http://link.springer- ny.com/link/service/books/10125/.

28. K?nneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B., and Stahl, D.A. (in press). Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature.

34. Purkhold, U., Pommerening-Roser, A., Juretschko, S., Schmid, M.C., Koops, H.P., and Wagner, M. (2000). Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveyss. Appl Environ Microbiol 66, 5368- 82.