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Linking Microbial Communities to Subsurface Geochemistry and Hydrology at the Field-Scale

EMSL Project ID


Background and Key Challenges:
A major challenge in subsurface science is understanding how microbial communities, geochemistry, and hydrology interactively govern the fate and transport of contaminants. Key insights required to meet this challenge have been achieved primarily through a bottom-up research paradigm that focuses on processes and phenomena at small spatial scales. Recent years have seen an increased appreciation of the subsurface as a complex system characterized by emergent properties difficult to predict from small-scale phenomena alone. This is particularly relevant for subsurface systems contaminated at the ‘field-scale’ (~one to many km2). Effective, field-scale remediation requires the existing bottom-up paradigm be complemented with a top-down, field-scale approach. To implement a top-down research program relevant to the fate and transport of subsurface contaminants one must simultaneously characterize multiple microbiological, geochemical and hydrological properties at the spatial scale of contamination. EMSL is unique in providing the capabilities necessary to realize such an approach.

The Hanford 300 Area contains a uranium-contaminated unconfined aquifer that regularly interacts (hydrologically) with the Columbia River. Recent studies suggest that subsurface microbial communities in this system are strongly influenced by river-water intrusion, sediment composition and redox state. Currently unknown is how and the degree to which these factors influence the composition, function and metabolic activity of microbial communities across the spatial scale of contamination (~1km2). We aim to fill these knowledge gaps. Our first year of work will focus on river-water intrusion, and test three hypotheses (see ‘Project Description’) which propose mechanisms through which river-water intrusion influences microbial and geochemical components of the Hanford 300 Area subsurface. In the second and third years, we will combine field and laboratory experiments to test hypotheses aimed at understanding how river-water intrusion, sediment composition and redox state jointly influence microbial-geochemical feedbacks.

We will leverage multiple EMSL capabilities to analyze field/experimental samples and to conduct manipulative lab experiments. In the first year we will study the influence of river intrusion using field samples taken before, during, and after river elevation rise, from existing wells and river locations. Year two will couple additional field sampling across the subsurface redox transition zone with field experiments that manipulate sediment composition. Year three will focus on laboratory experiments aimed at more mechanistic understanding. Samples will be analyzed using EMSL’s (i) mass-spectrometry capabilities to characterize proteomes of microbial communities; (ii) SOLiD sequencing capabilities to characterize taxonomic composition of microbial communities; (iii) flow cytometer to estimate community-level metabolic activity; and (iv) carbon analyzer to quantify dissolved organic carbon. The resulting data will be used in a comparative statistical framework to test hypotheses. EMSL’s flow-cell capabilities will be used to conduct laboratory experiments that manipulate river intrusion, organic carbon supply, sediment composition, and redox state.

Expected Results:
In the first year we expect to find (i) the influence of river-water intrusion to be mediated by direct inputs of river-associated microbes and organic carbon; (ii) that increasing levels of river-water intrusion cause microbial community composition and function to become more stochastic through space and time; and (iii) that inputs of river-derived organic carbon will boost microbial community metabolic activity. We further expect to identify microbial taxa and functional proteins that are consistently related to river-water intrusion and organic carbon concentration.

Project Details

Project type
Large-Scale EMSL Research
Start Date
End Date


Principal Investigator

James Stegen
Pacific Northwest National Laboratory


Mary Lipton
Environmental Molecular Sciences Laboratory

Team Members

David Kennedy
Pacific Northwest National Laboratory

Allan Konopka
Pacific Northwest National Laboratory

James Fredrickson
Pacific Northwest National Laboratory

Related Publications

Stegen JC, TC Johnson, JK Fredrickson, MJ Wilkins, AE Konopka, WC Nelson, EV Arntzen, WB Chrisler, RK Chu, SJ Fansler, EB Graham, DW Kennedy, CT Resch, MM Tfaily, and JM Zachara. 2018. "Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology." Nature Communications 9:Article No. 585. doi:10.1038/s41467-018-02922-9