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Diverse Ammonia-Oxidizing Archaea Dominate Subsurface Nitrifying Communities in Semi-Arid Floodplains

Ammonia oxidation may be driven by archaea rather than bacteria within the riparian subsurface

The Science

Subsurface microbial communities mediate key biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen (N). By linking the most reduced and oxidized pools of N in the biosphere, nitrification plays a critical role in the global N cycle. Ammonia oxidation is the first and rate-limiting step of nitrification and also represents a major biological source of the potent greenhouse gas, N2O.  While ammonia-oxidizing bacteria (AOB) have been well-studied for over a century, the capacity for ammonia oxidation was only recently discovered within the domain Archaea (<15 years ago). Ammonia-oxidizing archaea (AOA) are now recognized as one of the most abundant microbial groups on the planet — often comprising over 20% of single-celled life in the deep ocean — and have also been studied extensively in topsoils (<30 cm) worldwide. However, their presence in the continental riparian subsurface beyond a meter belowground has been largely unexplored. To fill this knowledge gap, in this study, we examined the microbial ecology of ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900 km N-S transect within and surrounding the upper Colorado River Basin. Overall, our study identified ammonia oxidizer diversity and community composition trends through depth and at a regional-scale. The data suggest that the AOA and AOB ‘ecotypes’ within these terrestrial subsurface soils are primarily associated with conditions influenced by water table position, the location of reducing zones, or both. Furthermore, our study revealed that AOA outnumber their bacterial counterparts by several orders of magnitude at sites we sampled across this region.

The Impact

Due to their tremendous biogeochemical importance, ammonia-oxidizing microbial communities have been previously characterized in a wide variety of natural and engineered environments, including oceans, lakes, rivers/streams, estuaries, soils, sediments, caves, aquaria, and wastewater treatment plants, among others. However, until now, no study has ever systematically examined these key N-cycling communities within the riparian subsurface. By examining multiple sediment cores/depths and across five geographically-distinct DOE legacy sites within the intermountain west, we were able to gain unprecedented insights into the environmental factors potentially driving the distribution and diversity of subsurface AOA and AOB communities, including depth, salinity, and total N. Our results also suggest that archaeal ammonia oxidation may predominate within the terrestrial subsurface beyond a meter belowground. 


Nitrification is a critical branch of the subsurface N cycle within semi-arid floodplain environments, but the underlying microbial communities have not been thoroughly characterized to date. Both AOA and AOB use a multi-subunit ammonia monooxygenase (AMO) enzyme for ammonia oxidation. Although AOA and AOB can be detected using 16S rRNA-based approaches, the amoA gene (encoding the a-subunit of AMO) is the most commonly used genetic marker for specifically analyzing AOA and AOB populations in the environment. In this study, the diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry and hydrology by applying a combination of amoA gene sequencing, quantitative PCR, and geochemical techniques. Analysis of ~900 amoA sequences from AOA and AOB revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with key depths and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Interestingly, the most abundant and cosmopolitan archaeal amoA sequence type in our dataset (representing ~25% of all amoA sequences, from all five sites) was closely related to AOA from marine/estuarine ecosystems. The widespread presence of ‘aquatic’ AOA potentially adapted to high-salinities within the terrestrial subsurface is intriguing and suggests that hydrological and geochemical variability proximal to the water table likely exerts a strong influence over the community membership found in the surrounding sediment.  The key finding that AOA outnumber AOB by 2- to 5000-fold within these sediments highlights the future need to employ a combination of meta-omic and biogeochemical approaches to examine both the detailed ecophysiology and activity of subsurface AOA communities in this region.  


Contacts (BER PM)

Amy Swain
DOE Office of Biological and Environmental Research, Climate and Environmental Sciences Division

(PI contact)

Christopher Francis
Earth System Science, Stanford University


Funding was provided by the DOE Office of Biological and Environmental Research, Subsurface Biogeochemistry Research (SBR) activity to the SLAC SFA program (Bargar, lead PI) under contract DE-AC02-76SF00515 to SLAC, as well as contract DE-SC0019119 to C.F. The US DOE, Office of Legacy Management provided access and logistical support to the Riverton, WY, Shiprock, NM, Naturita, CO, and Grand Junction, CO field sites.


Cardarelli, E. L., Bargar, J.R., Francis, C.A. Diverse Thaumarchaeota dominate subsurface ammonia-oxidizing communities in semi-arid floodplains in the Western United States. Microbial Ecology (in press)

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