Skip to Main Content U.S. Department of Energy
Environmental Significace of the Groundwater-Surface Water Interaction Zone

Highlights

2018

For the Hyporheic Zone, a Novel Thermodynamic Mechanism
For the Hyporheic Zone, a Novel Thermodynamic Mechanism
J.C. Stegen, et al., "Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology." Nature Communications 585 (2018). DOI: 10.1038/s41467-018-02922-9

2017

New Insights Into How Shoreline Vegetation Protects Soil-Bound Carbon
New Insights Into How Shoreline Vegetation Protects Soil-Bound Carbon
E. Graham, et al. 2017. Carbon inputs from riparian vegetation limit oxidation of physically-bound organic carbon via biochemical and thermodynamic processes. JGR Biogeosciences. DOI:10.1101/105486.

Researchers Fill Scientific Gaps of Understanding Regarding Temperate Reservoir Emissions
Researchers Fill Scientific Gaps of Understanding Regarding Temperate Reservoir Emissions
Benjamin L. Miller, et al. Methane Ebullition in Temperate Hydropower Reservoirs and Implications for US Policy on Greenhouse Gas Emissions. Environmental Management. 2017 DOI 10.1007/s00267-017-0909-1.

Improving Accuracy of Subsurface Flow and Transport Models
Improving Accuracy of Subsurface Flow and Transport Models
Tartakovsky, A. M., Panzeri, M., Tartakovsky, G. D., & Guadagnini, A. 2017. Uncertainty quantification in scale-dependent models of flow in porous media. Water Resources Research, 53, 9392-9401. DOI: 10.1002/2017WR020905

3-D View and Fine Resolution: Keys to Coupled Land Model System
3-D View and Fine Resolution: Keys to Coupled Land Model System
Bisht, G., Huang, M., Zhou, T., Chen, X., Dai, H., Hammond, G. E., Riley, W. J., Downs, J. L., Liu, Y., and Zachara, J. M.: Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulate stream-aquifer-land interactions (CP v1.0), Geosci. Model Dev., 10, 4539-4562, DOI: 10.5194/gmd-10-4539-2017, 2017.

Making Sense of Chromium Migration and Immobilization in the Hyporheic Zone
Making Sense of Chromium Migration and Immobilization in the Hyporheic Zone
Yuanyuan Liu, et al. "Coupled Hydro-Biogeochemical Processes Controlling Cr Reductive Immobilization in Columbia River Hyporheic Zone." Environ. Sci. Technol., 2017, 51 (3), pp 1508-1517. DOI: 10.1021/acs.est.6b05099

The Impossible Task of Replicating Numerical Models in Multiphase Flow Experiments
The Impossible Task of Replicating Numerical Models in Multiphase Flow Experiments
B Ling, et al., "Modeling variability in porescale multiphase flow experiments." Advances in Water Resources. 105, (2017), DOI: 10.1016/j.advwatres.2017.04.005
In-Soil Imaging of a Live Plant

In-Soil Imaging of a Live Plant
X Yang et al., "What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root soil system." Rhizosphere Vol. 3 Part 2, June 2017, 259-262. DOI: 10.1016/j.rhizosph.2017.04.017

QWhere Riverbed and Groundwater Mix

Dynamic Water Conditions Greatly Impact Nitrogen in Hyporheic Zones
Yuanyuan Liu, et al. "Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation Activity and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns." Environ. Sci. Technol., 2017, 51 (9), pp 4877-4886 DOI: 10.1021/acs.est.6b05018

QWhere Riverbed and Groundwater Mix

Where Riverbed and Groundwater Mix, a Cocktail for Ecological Changes
Robert E. Danczak, et al. "Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments." Journal of Geophysical Research 35, 221 (2016). doi: 10.1002/2016JG003527

Quantifying Shallow Water Hydrologic Exchanges
Quantifying Shallow Water Hydrologic Exchanges
T Zhou, et al., "A New Approach to Quantify Shallow Water Hydrologic Exchanges in a Large Regulated River Reach." Water 2017, 9(9), 703; doi:10.3390/w9090703

Microbial Acceleration of Aerobic Pyrite Oxidation

Microbial Acceleration of Aerobic Pyrite Oxidation by a Chemolithoautotrophic Bacteria from Hanford 300 Area Sediments
Percak-Dennett, E. M., S. He, B. J. Converse, H. Konishi, H. Xu, C. S. Chan et al. 2017. Microbial acceleration of aerobic microbial pyrite oxidation at circumneutral pH. Geobiology 15:690-703.

Microbial Fe(III)-oxide Reduction
Microbial Fe(III)-oxide Reduction Dominates over Fe(III)-phyllosilicate Reduction in Sediments
Wu, T., A. M. Griffin, C. A. Gorski, E. S. Shelobolina, H. Xu, R. K. Kukkadapu, and E. E. Roden. 2017. Interactions between Fe(III)-oxides and Fe(III)-phyllosilicates during microbial reduction 2: Natural subsurface sediments. Geomicrobiol. J. 34:231-241.
Structure and function of attached microbial communities
Structure and function of attached microbial communities in the Columbia River hyporheic corridor
Stern, N., M. Ginder-Vogel, J. C. Stegen, E. Arntzen, D. W. Kennedy, B. R. Larget, and E. E. Roden. 2017. Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Appl. Environ. Microbiol. 83:e00260-00217.
Modeling Microbial Ecology in the Hyporheic Zone
Modeling Microbial Ecology in the Hyporheic Zone
E.B. Graham, A.R. Crump, C.T. Resch, S. Fansler, E. Arntzen, D.W. Kennedy, J.K. Fredrickson, J.C. Stegen, "Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes." Environ Microbiol. 2017 Apr;19(4):1552-1567. doi: 10.1111/1462-2920.13720.

2016

Modeling Microbial Ecology in the Hyporheic Zone
Modeling Microbial Ecology in the Hyporheic Zone
E.B. Graham, A.R. Crump, C.T. Resch, S. Fansler, E. Arntzen, D.W. Kennedy, J.K. Fredrickson, J.C. Stegen, "Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes." Environ Microbiol. 2017 Apr;19(4):1552-1567. doi: 10.1111/1462-2920.13720.
Better Models of Subsurface Microbial Communities
A new model for microbial communities in the hyporheic zone
Emily B. Graham, Alex R. Crump, Charles T. Resch, Sarah Fansler, Evan Arntzen, David W. Kennedy, Jim K. Fredrickson and James C. Stegen
Better Models of Subsurface Microbial Communities
Towards Better Models of Subsurface Microbial Communities
Stegen, J.C., Konopka, A., McKinley, J.P., Murray, C., Lin, X., Miller, M.D., Kennedy, D.W., Miller, E.A., Resch, C.T., and Fredrickson, J.K.
Columbia River Hyporheic Zone Tackles Contaminants, Greenhouse Gases
Environmental Monitor, article by Lori Balster, April 19, 2016.
Tracking Complex Transport
Tracking Complex Transport and Reaction Processes in the Groundwater-Surface Water Interaction Zone
Zachara, J.M., Chen, X., Murray, C., and Hammond, G.E.
Small Internal Pores
Small Internal Pores in Soil and Geologic Materials Influence the Biogeochemical Behavior of Larger Environmental Systems
Zachara, J.M., Brantley, S., Chorover, J., Ewing, R.P., Kerisit S., Liu, C., Perfect, E., Rother, G., and Stack, A.G.

2015

Dynamic Metabolic Modeling of Denitrifying Bacterial Growth: The Cybernetic Approach
Song, HS, and Liu, C.
The Effect of Transport Heterogeneity on Redox Reaction Rates at the Pore and Continuum Scale
Liu, Y., Liu, C., Zhang, C., Yang, X, and Zachara, J,M.
Groundwater-Surface Water Mixing in the Hyporheic Zone Stimulates Organic Carbon Turnover
Stegen, J.C., Fredrickson, J., Wilkins, M.J., Konopka, A., Nelson, W.C., Arntzen, E., Chrisler, W.B., Chu, R.K., Danczak, R., Fansler, S., Kennedy, D., Resch, C.T., Tfaily, M.
Intercomparison of 3D Pore-Scale Modeling Methods
Yang, X., Y. Mehmani, W. A. Perkins, A. Pasquali, M. Schoenherr, K. Kim, M. Perego, M. L. Parks, N. Trask, M. T. Balhoff, M. C. Richmond, M. Geier, M. Krafczyk, L.-S. Luo, A. M. Tartakovsky, and T. D. Scheibe
The Reduced Genomes of Parcubacteria (OD1) Contain Signatures of a Symbiotic Lifestyle
Nelson, W.C. and Stegen, J.C.
Hybrid multiscale simulation of a mixing-controlled reaction
Scheibe T. D., Schuchardt K., Agarwal K., Chase J., Yang X., Palmer B. J., Tartakovsky A. M., Elsethagen T. and Redden G.
Four-dimensional electrical conductivity monitoring of stage-driven river water intrusion: accounting for water table effects using a transient mesh boundary and conditional inversion constraints
Johnson, T., R. Versteeg, J. Thomle, G. Hammond, X. Chen, and J. Zachara
Estimating and mapping ecological processes influencing microbial community assembly
Stegen, J., X. Lin, J. Fredrickson, and A. Konopka

2014

A trans-outer membrane porin-cytochrome protein complex for extracellular electron transfer by Geobacter sulfurreducens PCA
Liu Y., Z. Wang , J. Liu, C. Levar, M. J. Edwards, J. Babauta, D. Kennedy, Z. Shi, H. Beyenal, D. R. Bond, T. A. Clark, J. N. Butt, D. J. Richardson, K. M. Rosso, J. Zachara, J. Fredrickson and L. Shi.
Fe(II)- and sulfide-facilitated reduction of 99Tc(VII)O4- in microbially reduced hyporheic zone sediments
Lee, J., J. Zachara, J. Fredrickson, S. Heald, J. McKinley, A. Plymale, C. Resch, and D. Moore.
Pore-scale and multi-scale numerical simulation of flow and transport in a laboratory-scale column
Scheibe, T.D., W. Perkins., M. Richmond, M. M. McKinley, P. Romero-Gomez, M. Oostrom, T. Wietsma, J. Serkowski, and J. Zachara.
Evaluating the performance of parallel subsurface simulators: an illustrative example with PFLOTRAN
Hammond, G.E., P.C. Lichtner and R.T. Mills.
Effect of subgrid heterogeneity on scaling geochemical and biogeochemical reactions: A case of U(VI) desorption
Liu C, J Shang, H Shan and JM Zachara.
Single-cell genomics reveals metabolic strategies for microbial growth and survival in an oligotrophic aquifer
Wilkins, M. J., D. W. Kennedy, C. J. Castelle, E. K. Field, R. Stepanauskas, J. K.Fredrickson, and A. E. Konopka.

Navigation

Research Activities

Related Websites