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

Reactive Transport Modeling for Prediction of Nitrous Oxide Emission from the Subsurface Observatory at a Nitrate-Contaminated Site in Response to Rainfall Events


Michelle E. Newcomer1* (, Jinwoo Im1, Dipankar Dwivedi1, Andrew D. Putt2, Kathleen F. Walker2, James Marquis3, Lauren M. Lui1, Alex V. Carr4, Yupeng Fan5, Jennifer L. Goff6, Kristopher A. Hunt7, Jonathan P. Michael5, Farris L. Poole6, Yajiao Wang5, D. Williams2, Michael W. Adams6, Nitin S. Baliga4, David A. Stahl7, Jizhong Zhou5, Matthew W. Fields3, Terry C. Hazen2,8, Adam P. Arkin1,9; Paul D. Adams1,9


1Lawrence Berkeley National Laboratory; 2University of Tennessee–Knoxville; 3Montana State University–Bozeman; 4Institute for Systems Biology; 5University of Oklahoma–Norman; 6University of Georgia–Athens; 7University of Washington–Seattle; 8Oak Ridge National Laboratory; 9University of California–Berkeley



Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) 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.


The subsurface environment is one of the major sources of global nitrous oxide (N2O) emissions. However, the estimation of N2O from biotic/abiotic pathways in subsurface systems is still poorly understood. Researchers estimated N2O production by building a field-scale reactive transport model via PFLOTRAN that integrates potential pathways of N-cycling at Area 3, which exhibits high concentrations of nitrate and low pH levels. The Subsurface Observatory (SSO) is located at Area 3 and is an intensive sampling site (5 x 5 x 8 m3). The SSO was designed and established by the ENIGMA Science Focus Area to provide high-temporal resolution datasets of groundwater flow, chemistry, and microbial communities with a highly instrumented set of continuously monitored nine multiport groundwater wells. The heterogeneous permeability field of the SSO site is reconstructed on the basis of the high-resolution data of soil types from Cone Penetration Testing (CPT), with fine grid blocks (0.3 x 0.3 x 0.004 m3 for a variably saturated zone (302.5 to 304.5 m depth) and or 0.3 x 0.3 x 0.1 m3 for the rest of the domain). The flow model has been initially calibrated and validated from the dataset of rainfall events and groundwater table elevation, collected for a dry season from September to December 2023.

Regarding reactive transport, the reaction network of the model includes many biogeochemical

reactions for and sulfate reduction. Based on this wide range of biogeochemical reactions, N2O emission can be estimated by various biotic/abiotic pathways and calibrated by the measurements (e.g,. pH, DO, and nitrate concentration) from the SSO wells. As a result, researchers show the emergence of hot spots and hot moments of N2O emission at the SSO site under a series of rainfall events.


Lui, L. M., et al. 2021. “Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology,” Frontiers in Microbiology 12, 642422. DOI:10.3389/fmicb.2021.642422.

Funding Information

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