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Bacteria to the Rescue

High-performance computing adds speed, clarity to uranium bioremediation research

 Site shot: Isosurfaces for aqueous U(VI) 40 days after initiating the 2008 field experiment at the Rifle Site. Enlarge Image.

Despite expectations for natural groundwater flow to clean up uranium-contaminated legacy waste sites, elevated uranium levels in groundwater plumes often persist. One remediation alternative for these sites involves stimulating indigenous bacteria to transform uranium to an immobile, solid-associated form. At the Integrated Field Research Challenge (IFRC) project in Rifle, Colorado, scientists are performing field biostimulation experiments to better understand the site-specific processes, properties, and conditions controlling uranium bioremediation. A key component of the research is development of a mathematical model based on the knowledge and understandings of the multidisciplinary Rifle IFRC science team. This model simulated a 2008 engineered bioremediation field experiment where pulsed acetate injection was used to stimulate metal-reducing bacteria to transform aqueous U(VI) into immobile U(IV). The simulations reproduced many important observations, including the timing and magnitude of iron, uranium, and sulfate reduction, as well as aqueous uranium concentration dynamics. To account for the high spatial and temporal resolution, large number of reactive species and minerals, and highly detailed uranium behavior at Rifle, researchers used the eSTOMP subsurface simulator on EMSL’s massively parallel supercomputer, Chinook, to model the 110-day in situ field experiment and 50 days of post-field behavior. Re-engineered to run on the most powerful computers, eSTOMP is the new “extreme-scale” version of PNNL’s Subsurface Transport Over Multiple Phases (STOMP) simulator. In this case, the principal eSTOMP modeling was completed in less than 12 hours versus 60 or more days (assuming available memory) running on a desktop system. 

Scientific impact: Scientists were able to incorporate more processes and process interactions of interest at higher levels of detail than earlier simulations of Rifle field studies. These included variably saturated flow and biogeochemical reactive transport through three-dimensional physically and chemically heterogeneous sediments, as well as new knowledge about the behavior and interaction of the stimulated microbial community with the subsurface geochemical environment. In addition to the metal-reducing bacteria that catalyze the formation of immobile U(IV), they demonstrated the importance of accounting for sulfate-reducing bacteria activity. A key finding is that uranium bioreduction is most effective when acetate concentrations are engineered to exceed the sulfate-reducing bacteria demand. The model also showed how uranium and acetate can be trapped in the unsaturated zone that results from the seasonal water table decline. Notably, the Rifle IFRC project has a variety of science—geology, geophysics, biogeochemistry, hydrology, microbiology, proteomics, etc.—behind it. Modeling can provide a framework for bridging and organizing those interactions, affording a true merger of scientific field research and technological simulation advancements. 

Societal impact: If engineered bioremediation is effective and viable for handling legacy uranium in aquifer systems, modeling via high-performance computers and comprehensively detailed simulation codes can offer better and more reliable site-specific assessments of risk and remediation performance. Moreover, modeling can be applied more efficiently to hypothesis testing, exploring alternatives, and uncertainty quantification, which may lead to better field experiments and solutions for improving contaminant reduction and removal from groundwater. 

Reference: Yabusaki SB, Y Fang, KH Williams, CJ Murray, AL Ward, RD Dayvault, SR Waichler, DR Newcomer, FA Spane, and PE Long. 2011. “Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment.” Journal of Contaminant Hydrology 126(3-4):271-290. DOI: 10.1016/j.jconhyd.2011.09.002. 

Acknowledgment: The work conducted at the Rifle IFRC site is supported by the Subsurface Biogeochemical Research Program in the Climate and Environmental Sciences Division of the Office of Biological and Environmental Research at the DOE’s Office of Science.

Released: December 06, 2011