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Physical Sciences Division
Research Highlights

March 2012

Digging Deeper in the Dirt

Targeted metagenomic analyses reveal underground microbes that may influence and alter contaminant fate and transport at Hanford Site

Results: Inherited from a legacy of nuclear production, the Hanford Site is very dynamic belowground where contaminants, such as uranium and nitrate, may react with microorganisms in ways that affect their movement through the subsurface. In a recent study of subsurface sediments at this southeastern Washington State site, scientists at Pacific Northwest National Laboratory characterized the vertical distribution of microbes over multiple geologic formations.

They found these organisms can influence groundwater geochemistry as a consequence of biogeochemical activities, such as the reduction of sulfate, iron, and nitrate. Based on their findings, the scientists identified transition zones in the sediment layers, including an active zone where they believe cycling between oxidized and reduced forms of chemicals is occurring.


Relative abundances of phylogenetic and functional microbial groups, normalized to total Bacteria and Archaea 16S rRNA gene copy numbers. Upper and lower dotted lines represent the Hanford-Ringold contact and Ringold oxic-anoxic interface, respectively (from Lin et al., 2012, Applied and Environmental Microbiology 78(3):759-767).

Why It Matters: These analyses will improve understanding of the site's subsurface microbial ecology and help clarify how microbial communities affect fate and transport of contaminants in the sediments and groundwater as well as the cycling of other naturally occurring elements.

Dr. Allan Konopka, PNNL Laboratory Fellow and head of the microbiology group at PNNL, explained: "To predict the extent to which the indigenous microbial community can affect the fate and transport of contaminants through groundwater, it's essential to determine how the distribution of specific microbes and geochemical conditions interact to create ‘hot spots' of microbial activity."

In the past, the impact of microorganisms that transform contaminants in the subsurface was given relatively little consideration in environmental management of the Department of Energy's Hanford Site. Hence, little research exists on the site's underground microorganisms.

But during the last decade, scientists have realized the importance of microbial biogeochemical reactions on contaminants. These reactions can modify contaminant solubility, result in the precipitation or dissolution of mineral phases, and transform other elements in ways that can impact groundwater quality. This study not only fulfills a need to elucidate Hanford's subsurface microbial ecology, but it may support future efforts for understanding how microorganisms may impact subsurface contaminant plumes at Hanford as they migrate towards the Columbia River.

Methods: The scientists recovered subsurface sediments from a 52-m-deep borehole cored in the Hanford Site's 300. They performed microbial analyses on 17 sediment samples across multiple geologic formations: the oxygen-containing, or oxic, coarse-grained Hanford formation; the oxic, fine-grained upper Ringold formation; and the reduced Ringold formation.

The researchers extracted DNA from the cores and used quantitative polymerase chain reaction (qPCR) to amplify fragments of genes that were diagnostic for particular biogeochemical processes, such as denitrification and sulfate reduction. They then were able to analyze the sequence of these amplified fragments and determine which specific microbes were most abundant in mediating these processes in the subsurface.

Their research showed that the most elevated biomass levels occur in the Hanford formation, while strata below 17.4 m (such as the Ringold formation) had significantly less biomass. Further, they were able to relate the heterogeneity in sediment properties that occurs vertically, such as contact between the Hanford and Ringold formations, as well as the boundary between oxidized and reduced Ringold sediments, to differences in the functional properties of the microbial community. 

Analysis of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold contact and the Ringold oxic-anoxic interface. Analyses showed that the region just below the contact between the Hanford and Ringold formations is likely a zone of active biogeochemical redox cycling.

What's Next? Future work will determine the rates at which these bacteria drive biogeochemical reactions in the Hanford Site subsurface. In particular, it will be important to determine what compounds serve as natural energy sources for the native microbial populations that catalyze the biotransformation of natural compounds and environmental contaminants. 

Acknowledgments: This research was supported by DOE's Office of Biological and Environmental Research as part of the Subsurface Biogeochemistry Research Program's Scientific Focus Area and Integrated Field-Scale Research Challenge at PNNL.

The research team includes former PNNL staff member Xueju Lin; Allan Konopka, David Kennedy, James McKinley, Tom Resch, and James Fredrickson, all PNNL; and Aaron Peacock, Haley & Aldrich, Inc.

Reference:  Lin X, D Kennedy, A Peacock, J McKinley, CT Resch, J Fredrickson, and A Konopka. 2012. "Distribution of Microbial Biomass and Potential for Anaerobic Respiration in Hanford Site 300 Area Subsurface Sediment." Applied and Environmental Microbiology 78(3):759-767. DOI:10.1128/AEM.07404-11.


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