Research: Archaea

Archaea are the third domain of life, as evolutionarily distinct from other microbes in the bacteria as they are from animals or plants.  Two decades ago, surprising research found that these organisms are the dominant microbial group in the deep sea and one of the most abundant groups of microbes on the planet—however, the role of these microbes in ocean chemistry and biology was unknown.  Over the past decade, my work helped define them as ammonia-oxidizing Archaea (AOA) (FRANCIS05_PNAS; Francis et al. 2007 ISME Journal), and I’ve used them as a model for understanding linkages among microorganisms and biogeochemical processes in reefs, estuaries, and the ocean (Beman and Francis 2006, AEM; Beman et al. 2007, AEM; BEMAN08_ISMEJ; Beman et al. 2010, EM; Beman et al. 2012, Frontiers in Microbiology).  

Our work in the eastern tropical North Pacific (ETNP) and Gulf of California (GOC) examined archaeal ammonia oxidation in a broader biogeochemical context by studying a critically important region of the ocean, the ocean’s largest (natural) oxygen minimum zone (OMZ).  OMZs are expanding as a consequence of climate change with significant and poorly understood effects.  This work was funded by NSF Chemical Oceanography (  

Using molecular and biogeochemical techniques, we quantified ammonia oxidation rates and the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in tandem in the ETNP and GOC.  Our findings indicate that AOA are the dominant ammonia-oxidizers in this region, and that ammonia oxidation occurs rapidly (Beman et al. 2012, L&O).  We also measured rates of a coupled process, nitrite oxidation, about which much less is known.  These rates were also high, and Nitrospina bacteria appeared to be quantitatively important (BEMAN13_ISMEJ).  For both processes we observed substantial variation with depth and between sampling stations, and analyzed the environmental factors that may cause this variation.

We continue to work on the archaea just about everywhere, including recent work in soils and in freshwater lakes in Yosemite.

Image above was taken by Jesse Wilson during fieldwork in Palau in 2011