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Microbial Nitrogen Cycling

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Transmission electron micrograph of Nitrosoarchaeum limnia SFB1
Transmission electron micrograph of Nitrosarchaeum limnium SFB1, a novel ammonia-oxidizing archaeon isolated from low-salinity sediments in the San Francisco Bay estuary (see Blainey/Mosier et al., 2011; Mosier et al., 2012; Tolar et al., 2019)

The oxidation of NH3 to NO2- and ultimately NO3- by chemoautotrophic ammonia- and nitrite-oxidizing microorganisms is a critical branch of the nitrogen cycle in marine, estuarine, freshwater, and terrestrial environments, where this process provides the key link between the mineralization of organic nitrogen and the subsequent loss of fixed nitrogen via denitrification and anammox. Much of our research is focused on exploring the diversity and structure of ammonia-oxidizing microbial communities, based on amoA genes encoding the alpha-subunit of the key nitrification enzyme, ammonia monooxygenase (AMO). Our work has revealed the widespread occurrence of the previously unrecognized group of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. We are currently using molecular and biogeochemical approaches to explore the diversity, abundance, and activity of AOA and AOB in a number of ecosystems, including San Francisco Bay, Monterey Bay, Elkhorn Slough, Stinson Beach, and Riverton, WY, among others. Finally, we are using cultivation as well as metagenomic and metatranscriptomic approaches (see CSP Projects through the DOE Joint Genome Institute) to gain novel insights into AOA within both aquatic and terrestrial environments.


Sampling sites for our microbial N cycling research in San Francisco Bay (left) and Monterey Bay (right)



Diagram of the marine microbial nitrogen cycle
Diagram of the marine microbial nitrogen cycle, with key processes and functional genes studied in the Francis Laboratory highlighted in bold or yellow, respectively (modified from a figure that appeared in Francis et al., 2007).

The dissimilatory reduction of nitrate and nitrite to gaseous products (NO, N2O, N2) under suboxic conditions, denitrification, is a major loss term for fixed nitrogen from ecosystems. This process removes up to 50% of external N inputs from estuarine and coastal sediments, and also leads to the production of potent greenhouse gases, NO and N2O. We are currently involved in a collaborative research project  with the San Francisco Estuary Institute (SFEI) focused on measuring benthic denitrification rates throughout South San Francisco Bay.

Despite the global importance of denitrifiers, the "key players" in most environments are simply not known. Functional genes encoding key metalloenzymes in the denitrification pathway have proven to be useful molecular markers for studying denitrifying communities. Our work has focused on characterizing the distribution, diversity, abundance, and activity of denitrifiers across physical/chemical gradients in many of the environments where we are also studying ammonia-oxidizers (e.g., San Francisco Bay, Elkhorn Slough, Riverton, etc.). By simultaneously examining these two key branches of the microbial N cycle, we hope to gain new insights into the relationships between functional diversity, environmental gradients, and biogeochemical function.