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

Three-Dimensional High Spatial Resolution Simulation for Groundwater Flow and Nitrogen Transport Under Rainfall Perturbations in the Subsurface of Area 3


Jinwoo Im1* (, Andrew Putt2, Kathleen F. Walker2, Dominique C. Joyner2, James Marquis3, Lauren M. Lui1, Dipankar Dwivedi1, Alex Carr4, Yupeng Fan5, Jennifer Goff6, Kristopher Hunt7, Jonathan Michael5, Farris Poole6, Yajiao Wang5, Michael W. W. Adams 6, Nitin S. Baliga4, David A. Stahl7, Jizhong Zhou5, Matthew W. Fields3, Terry C. Hazen2,8, Michelle E. Newcomer1, Adam P. Arkin 1,9, and Paul D. Adams1,9


1Lawrence Berkeley National Laboratory (LBNL); 2University of Tennessee–Knoxville; 3Montana State University; 4Institute for Systems Biology; 5University of Oklahoma; 6University of Georgia; 7University of Washington; 8Oak Ridge National Laboratory (ORNL); and 9University of California–Berkeley



The Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Science Focus Area (SFA) uses 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.


Uranium and nitrate contaminant transport in Area 3 near the S3 ponds at ORNL are investigated through 3D field-scale modeling and simulation. This project leverages a recently acquired Cone Penetration Testing (CPT) dataset which provides the hydraulic conductivity field of Area 3 with a high spatial resolution as input data to the numerical subsurface model. The CPT data shed light on local heterogeneity of subsurface materials, significantly decreasing the uncertainty due to limited sampling points. By further using 27 well survey data collected by the ENIGMA SFA (e.g., meteorological, hydrological, microbial, and geochemical datasets), a hydrogeological model is built on PFLOTRAN and run on the high-performance computing system, National Energy Research Scientific Computing Center. Generalized stoichiometries are used for biogeochemical reactions related to nitrogen cycling. Computational results of the 3D field-scale simulation show: (1) different flow and transport regimes depending on subsurface materials, (2) impacts of rainfall events on nitrous oxide emission, (3) influential controls of flow conditions through sensitivity analysis enabling a full treatment of the ModEx approach to designing and implementing the Subsurface Observatory (SSO). The results help researchers understand nitrogen cycling in Area 3 and determine the location of the ENIGMA SSO site. Furthermore, the results will be compared to omics-informed modeling and simulation as planned in the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (Lui et al. 2021).


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 ENIGMA SFA Program at Lawrence Berkeley National Laboratory is based upon work supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research (BER) Program under contract number DE-AC02-05CH11231.