Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Role of Nitrogen Oxides in a High Nitrate and Heavy Metal Contaminated Field Site: What Has Been Observed and What Researchers Aim to Understand


K. A. Hunt1,2* (, A. V. Carr1,2, A. E. Otwell1, J. J. Valenzuela2, K. F. Walker3,4, E. R. Dixon3,4, L. M. Lui5, T. N. Nielsen5, S. Bowman6, F. von Netzer1, J-W. Moon3, C. W. Schadt3, M. Rodriguez Jr.3, K. Lowe3, D. C. Joyner3,4, K. J. Davis7, X. Wu5, R. Chakraborty5, M. W. Fields7, J-Z. Zhou8, T. C. Hazen3,4, S. D. Wankel6, N. Baliga1,2, D. A. Stahl1, A. P. Arkin5,9, P. D. Adams5,9


1University of Washington; 2Institute for Systems Biology, Seattle, WA; 3Oak Ridge National Laboratory; 4University of Tennessee–Knoxville; 5Lawrence Berkeley National Laboratory; 6Woods Hole Oceanographic Institution, MA; 7Montana State University, Bozeman; 8University of Oklahoma–Norman; 9University of California–Berkeley.



ENIGMA-Ecosystems and Networks Integrated with Genes and Molecular Assemblies use a systems biology approach to understand the interaction between microbial communities and the ecosystems that they inhabit. To link genetic, ecological, and environmental factors to the structure and function of microbial communities, ENIGMA integrates and develops laboratory, field, and computational methods.


Increasing atmospheric nitrous oxide, a greenhouse gas with 300 times greater radiative trapping than carbon dioxide (CO2), is primarily attributed to intensive agriculture and the impact of climate change on soil conditions, estimated to contribute 73% of all U.S. nitrous oxide emissions. Prior studies revealed extremely high fluxes of nitrous oxide from the saturated subsurface and groundwater within the Field Research Center (FRC) at Oak Ridge National Laboratory, but the virtual absence of surface emissions. Ongoing characterization of system microbiota suggested a source derived from the activities of a subsurface community dominated by Rhodanobacter (see Carlson et al poster) species active in the low pH, high nitrate groundwater whereas the microbiota expressing the nitrous oxide reductase in the less contaminated upper soil column functioned as a major sink. These features suggested the utility of this system to better resolve environmental factors controlling nitrous oxide flux, both of its production and consumption. Ongoing studies, using stable isotope analyses and geochemical monitoring, demonstrated active nitrous oxide reduction at pH of 4, well below the observed limit for described industrial and environmental systems. Isotopic compositional studies of nitrogen species suggested that denitrification and chemodenitrification were both major sources of nitrous oxide, with a minor contribution by nitrification in shallower regions supported by the recovery of 16S sequences affiliated with known nitrifiers. A depth-resolved metagenomic analysis of the soil column showed a strong correlation between nitrous oxide depletion in the upper soil and the enrichment of microorganisms encoding the Clade II nitrous oxide reductase, whereas Clade I populations were more abundant near the variably saturated zone in proximity to groundwater. Researchers are now developing instrumentation, isotopic methods, and sampling strategies to confirm the role of the Clade II nitrous oxide variant in suppressing surface nitrous oxide emissions, combining isotopic, geochemical, and molecular measures to identify environmental variables controlling this critical function. Researchers are also quantifying isotopic fractionation and affinity for nitrous oxide of isolates encoding Clade I and II NosZ to inform the ecological role of these variants at the site. These studies will be based at the newly installed ENIGMA SubSurface Observatory (SSO; see Newcomer et al poster) at the FRC, providing the opportunity for continuous monitoring of nitrous oxide flux from wells screened at different depths coupled with geochemical, isotopic, and biological characterization. The goal is to develop a predictive understanding of biological and environmental factors controlling the emission of this critical greenhouse gas.

Funding Information

This material by ENIGMA-Ecosystems and Networks Integrated with Genes and Molecular Assemblies a Science Focus Area Program at Lawrence Berkeley National Laboratory is based upon work supported by the U.S. DOE, Office of Science, Office of BER under contract number DE-AC02-05CH11231.