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

ENIGMA Environmental Simulations and Modeling: Predictive Modeling and Mechanistic Understanding of Field Observations


M. de Raad1* (, J. J. Valenzuela2, J. Wilson2, A. V. Carr2, S. Altenburg3, U. Strautmanis3, J. Rosenleaf3, H. J. Smith3, K. A. Hunt4, J. Goff5, F. L. Poole5, Y. Wang1, Y. Chen1, Z. Cooper2, T. Zhao1, J. V. Kuehl1, H. P. Lesea1, C. J. Petzold1, M. W. W. Adams5, R. Chakraborty1, M. W. Fields3, D. A. Stahl4, N. S. Baliga2, T. R. Northen1, A. P. Arkin1,6, P. D. Adams1,6


1Lawrence Berkeley National Laboratory; 2Institute for Systems Biology; 3Montana State University–Bozeman; 4University of Washington–Seattle; 5University of Tennessee–Knoxville; 6University of California–Berkeley



The goal of ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies) is to develop theoretical, technological, and scientific approaches to gain a predictive and mechanistic understanding of the biotic and abiotic factors that constrain microbial communities’ assembly and activity in dynamic environments. To link genetic, ecological, and environmental factors to the structure and function of microbial communities, ENIGMA uses a systems biology approach to integrate and develop laboratory, field, and computational methods.


To achieve its project goals, ENIGMA has been organized into several campaigns involving multiple institutes with varying expertise. The overarching goal of the Environmental Simulations and Modeling campaign is to simulate, model, and predict the mechanistic foundations of phenomena observed at a field site, the Oak Ridge Reservation Field Research Center.

Through field surveys and the recently installed SubSurface Observatory, the team collects high temporal–resolution datasets of environmental parameters [e.g., pH, dioxygen (O2), nitrate, metabolites] and has generated an insightful view of the dynamic nature of the field site subsurface. By monitoring rainfall events, researchers observed that such events can be followed by a sudden decline in both pH and dissolved O2, and this transition from a neutral to an acidic pH increases the emissions of nitrous oxide (N2O). To investigate this phenomenon in the laboratory, the team uses an established synthetic community of two field denitrifiers, Rhodanobacter sp. R12 and Acidovorax sp. 3H11, which together can perform complete denitrification but cannot independently. Through laboratory simulations utilizing time course experiments, researchers established that a change in pH from neutral to pH 6 can decouple the denitrification process within the synthetic community, leading to significant increases in N2O emissions. Additional abiotic controls have shown similar decoupling of denitrification partitioning at varying carbon/nitrogen ratios, oxygen levels, and increased metal concentrations such as nickel. These studies have generated a compendium of 306 transcriptomes that have been used to construct an R12/3H11 gene regulatory network that may help explain and predict how environmental fluctuations at the field site will impact emissions of N2O.

Given the observed field dynamics, the team has constructed customized drip-flow reactors to mimic ecologically relevant subsurface parameters. The reactors systems generate a vertical O2 gradient (aerobic to anoxic), mirroring observations from field wells. Additionally, reactors can contain sediment particles to allow for microbial surface attachment or to remain in suspension, reflecting different regimes in subsurface habitats. A five-member synthetic community comprising facultative anaerobes of varying physiological capabilities that respire nitrate is used to understand the interplay between attached and planktonic communities across the O2 gradient. Initial results show distinct stratification of microbial communities along the attached phase of the gradient suggesting structure-function relationships at the community level. Long-term experiments are underway to probe community stability and the effects of environmental perturbations that simulate field observations.

To further explore the abiotic factors that determine community composition and biogeochemistry at the field site, the project is constructing anaerobic microbiological enrichments under varying nitrate concentrations, carbon sources, and pH conditions. Long-read metagenomic analyses of these enrichments are used to construct community networks relating taxonomy, biogeochemistry, and functional abilities. This information will guide the development of next-generation synthetic communities that recapitulate the natural community assembly process for continued discovery of genetic mechanisms underlying observations from the field.

Funding Information

This material by ENIGMA, a Science Focus Area at Lawrence Berkeley National Laboratory, is based upon work supported by the U.S. DOE, Office of Science, BER program under contract number DE-AC02-05CH11231.