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Environmental Significace of the Groundwater-Surface Water Interaction Zone


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Dai H., Chen X., Ye M., Song X., Hammond G., Hu B. X. and Zachara J. (2019) Using Bayesian networks for sensitivity analysis of complex biogeochemical models. Water Resources Research, 55; doi: 10.1029/2018WR023589.

Gao Z., Liu H., Missik J., Yao J., Huang M., Chen X., Arntzen E. and Mcfarland D. (2019) Mechanistic links between underestimated CO2 fluxes and non-closure of the surface energy balance in a semi-arid sagebrush ecosystem. Environmental Research Letters, 14, 044016; doi: 10.1088/1748-9326/ab082d.

Graham E. B., Stegen J. C., Huang M., Chen X. and Scheibe T. D. (2019) Subsurface biogeochemistry is a missing link between ecology and hydrology in dam-impacted river corridors. Science of The Total Environment, 657, 435-445; doi: 10.1016/j.scitotenv.2018.11.414.

Hou Z., Scheibe T. D., Murray C. J., Perkins W. A., Arntzen E. V., Ren H., Mackley R. D. and Richmond M. C. (2019) Identification and mapping of riverbed sediment facies in the Columbia River through integration of field observations and numerical simulations. Hydrological Processes, 33, 1245-1259; doi: 10.1002/hyp.13396.

Meile C. and Scheibe T. D. (2019) Reactive transport modeling of microbial dynamics. Elements, 15, 111-116; doi: 10.2138/gselements.15.2.111.

Missik J. E. C., Liu H. P., Gao Z. M., Huang M. Y., Chen X. Y., Arntzen E., Mcfarland D. P., Ren H. Y., Titzler P. S., Thomle J. N. and Goldman A. (2019) Groundwater-river water exchange enhances growing season evapotranspiration and carbon uptake in a semiarid riparian ecosystem. Journal of Geophysical Research-Biogeosciences, 124, 99-114; doi: 10.1029/2018jg004666.

Sengupta A., Stegen J., Neto A., Wang Y., Neilson J., Chorover J., Troch P. A. and Maier R. M. (2019) Assessing microbial community patterns during incipient soil formation from basalt. Journal of Geophysical Research: Biogeosciences, 124; doi: 10.1029/2017JG004315.

Shuai P., Chen X., Song X., Hammond G. E., Zachara J., Royer P., Ren H., Perkins W. A., Richmond M. C. and Huang M. (2019) Dam operations and subsurface hydrogeology control dynamics of hydrologic exchange flows in a regulated river reach. Water Resources Research, 55; doi: 10.1029/2018wr024193.

Singh T., Wu L., Gomez-Velez J. D., Lewandowski J., Hannah D. M. and Krause S. (2019) Dynamic hyporheic zones: exploring the role of peak flow events on bedform-induced hyporheic exchange. Water Resources Research, 55, 218-235; doi: 10.1029/2018wr022993.

Song X., Chen X., Ye M., Dai Z., Hammond G. and Zachara J. M. (2019) Delineating facies spatial distribution by integrating ensemble data assimilation and indicator geostatistics with level-set transformation. Water Resources Research, 55; doi: 10.1029/2018wr023262.


Bao J., Zhou T., Huang M. Y., Hou Z. S., Perkins W., Harding S., Titzler S., Hammond G., Ren H. Y., Thorne P., Suffield S., Murray C. and Zachara J. (2018) Modulating factors of hydrologic exchanges in a large-scale river reach: Insights from three-dimensional computational fluid dynamics simulations. Hydrological Processes, 32, 3446-3463; doi: 10.1002/hyp.13266.

Feng Y., Chen R., Stegen J. C., Guo Z., Zhang J., Li Z. and Lin X. (2018) Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions. Molecular Ecology, 27, 5238-5251; doi: 10.1111/mec.14914.

Gao M., Li H.-Y., Liu D., Tang J., Chen X., Chen X., Blöschl G. and Ruby Leung L. (2018) Identifying the dominant controls on macropore flow velocity in soils: A meta-analysis. Journal of Hydrology, 567, 590-604; doi: 10.1016/j.jhydrol.2018.10.044

Graham E., Crump A., Kennedy D., Arntzen E., Fansler S., Purvine S. O., Nicora C., Nelson W., Tfaily M. and Stegen J. (2018) Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone. Science of the Total Environment, 642, 742-753; doi: 10.1016/j.scitotenv.2018.05.256.

Graham E. B., Gabor R. S., Schooler S., McKnight D. M., Nemergut D. R. and Knelman J. E. (2018) Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition. PeerJ, 6, e4575; doi: 10.7717/peerj.4575.

Grant S. B., Gomez-Velez J. D. and Ghisalberti M. (2018) Modeling the effects of turbulence on hyporheic exchange and local-to-global nutrient processing in streams. Water Resources Research, 54; doi: 10.1029/2018WR023078.

Hall E. K., Bernhard E. S., Bier R. L., Bradford M. A., Boot C. M., Cotner J. B., del Giorgio P. A., Evans S. E., Graham E. B., Jones S. E., Lennon J. T., Locey K. J., Nemergut D., Osborne B. B., Rocca J. D., Schimel J. S., Waldrop M. P. and Wallenstein M. W. (2018) Understanding how microbiomes influence the systems they inhabit. Nature Microbiology, 3, 977-982; doi: 10.1038/s41564-018-0201-z.

Harvey J., Gomez-Velez J., Schmadel N., Scott D., Boyer E., Alexander R., Eng K., Golden H., Kettner A., Konrad C., Moore R., Pizzuto J., Schwarz G., Soulsby C. and Choi J. (2018) How hydrologic connectivity regulates water quality in river corridors. JAWRA Journal of the American Water Resources Association, 1-13; doi: 10.1111/1752-1688.12691.

Korneev S. V., Yang X., Zachara J. M., Scheibe T. D. and Battiato I. (2018) Downscaling-based segmentation for unresolved images of highly heterogeneous granular porous samples. Water Resources Research, 54, 2871-2890; doi: 10.1002/2018wr022886.

Mays D. C. and Scheibe T. D. (2018) Groundwater contamination, subsurface processes, and remediation methods: Overview of the special issue of water on groundwater contamination and remediation. Water, 10, 1708; doi: 10.3390/w10121708.

Meile C. and Scheibe T. D. (2018) Reactive transport modeling and biogeochemical cycling. In Reactive Transport Modeling: Applications in Subsurface Energy and Environmental Problems, Y. Xiao, F. Whitaker, T. Xu, and C. Steefel (Eds.), Chapter 10, Wiley Press, 485-510.

Song X., Chen X., Stegen J., Hammond G., Song H., Dai H., Graham E. B. and Zachara J. (2018) Drought conditions maximize the impact of high-frequency flow variations on thermal regimes and biogeochemical function in the hyporheic zone. Water Resources Research, 54; doi: 10.1029/2018WR022586.

Stegen J. (2018) At the nexus of history, ecology, and hydrobiogeochemistry: Improved predictions across scales through integration. mSystems, 3, e00167-00117; doi: 10.1128/mSystems.00167-17.

Stegen J., Bottos E. and Jansson J. (2018) A unified conceptual framework for prediction and control of microbiomes. Current Opinion in Microbiology, 44, 20-27; doi: 10.1016/j.mib.2018.06.002.

Stegen J. and Goldman A. (2018) WHONDRS: A community resource for studying dynamic river corridors. mSystems, 3, e00151-00118; doi: 10.1128/mSystems.00151-18.

Stegen J., Johnson T., Fredrickson J., Wilkins M. J., Konopka A., Nelson W. C., Arntzen E., Chrisler W. B., Chu R. K., Fansler S., Graham, E., Kennedy D., Resch C. T., Tfaily M. and Zachara, J. M. (2018) Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology. Nature Communications, 9(1) doi: 10.1038/s41467-018-02922-9.

Stern N., Mejia J., He S. M., Yang Y., Ginder-Vogel M. and Roden E. E. (2018) Dual role of humic substances as electron donor and shuttle for dissimilatory iron reduction. Environmental Science & Technology, 52, 5691-5699; doi: 10.1021/acs.est.7b06574.

Wang C., Gomez-Velez J. D. and Wilson J. L. (2018) The importance of capturing topographic features for modeling groundwater flow and transport in mountainous watersheds. Water Resources Research, 54, 10,313-310,338; doi: 10.1029/2018WR023863.

Wu L., Singh T., Gomez-Velez J., Nützmann G., Wörman A., Krause S. and Lewandowski J. (2018) Impact of dynamically changing discharge on hyporheic exchange processes under gaining and losing groundwater conditions. Water Resources Research, 54, 10,076-010,093; doi: 10.1029/2018wr023185.

Xu F., Liu Y. and Liu C. (2018) A generalized-rate model for describing and scaling redox kinetics in sediments containing variable redox-reactive materials. Environmental Science & Technology, 52, 5268-5276; doi: 10.1021/acs.est.7b06354.

Yan A., Liu C., Liu Y. and Xu F. (2018) Effect of ion exchange on the rate of aerobic microbial oxidation of ammonium in hyporheic zone sediments. Environmental Science and Pollution Research, 25, 8880-8887; doi: 10.1007/s11356-018-1217-x.

Yang C., Zhang Y. K., Liu Y. Y., Yang X. F. and Liu C. X. (2018) Model-based analysis of the effects of dam-induced river water and groundwater interactions on hydro-biogeochemical transformation of redox sensitive contaminants in a hyporheic zone. Water Resources Research, 54, 5973-5985; doi: 10.1029/2018wr023286.

Yang Q. C., Almendinger J. E., Zhang X. S., Huang M. Y., Chen X. Y., Leng G. Y., Zhou Y. Y., Zhao K. G., Asrar G. R., Srinivasan R. and Li X. (2018) Enhancing SWAT simulation of forest ecosystems for water resource assessment: A case study in the St. Croix River basin. Ecological Engineering, 120, 422-431; doi: 10.1016/j.ecoleng.2018.06.020.

Zhou T., Bao J., Huang M., Hou Z., Arntzen E., Song X., Harding S., Titzler S., Murray C., Perkins W., Chen X., Stegen J., Hammond G., Thorne J. and Zachara J. (2018) Riverbed hydrologic exchange dynamics in a large regulated river reach. Water Resources Research, 54; doi: 10.1002/2017WR020508.


Bisht G., Huang M., Zhou T., Chen X., Dai H., Hammond G., Riley W., Downs J., Liu Y. and Zachara J. (2017) Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulate stream-aquifer-land interactions (CP v1.0). Geoscientific Model Development, 10, 4539-4562, doi: 10.5194/gmd-10-4539-2017.

Dai H., M. Ye, A. P. Walker and X. Chen (2017) A new process sensitivity index to identify important system processes under process model and parametric uncertainty. Water Resources Research, 53(4): 3476-3490, doi: 10.1002/2016WR019715.

Dai H., Chen X., Ye M., Song X. and Zachara J. (2017) A geostatistics informed hierarchical sensitivity analysis method for complex groundwater flow and transport modeling. Water Resources Research, 53(5): 4327-4343, doi: 10.1002/2016WR019756.

Gao Z., Russell E. S., Missik J. E. C., Huang M., Chen X., Strickland C. E., Clayton R., Arntzen E., Ma Y., and Liu H.* (2017) A novel approach to evaluate soil heat flux calculation: An analytical review of nine methods, Journal of Geophysical Research - Atmospheres, 122, doi: 10.1002/2017JD027160.

Goldman, A. E., Graham, E. B., Crump, A. R., Kennedy, D. W., Romero, E. B., Anderson, C. G., Dana, K. L., Resch, C. T., Fredrickson, J. K., and Stegen, J. C. (2017), Biogeochemical cycling at the aquatic-terrestrial interface is linked to parafluvial hyporheic zone inundation history. Biogeosciences, 14, 4229-4241, doi: 10.5194/bg-14-4229-2017.

Graham, E. B., Crump, A. R., Resch, C. T., Fansler, S., Arntzen, E., Kennedy, D. W., Fredrickson, J. K. and Stegen, J. C. (2017), Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes. Environ Microbiol, 19: 1552-1567. doi: 10.1111/1462-2920.13720. download data

Graham E. and Stegen J. (2017) Dispersal-based microbial community assembly decreases biogeochemical function. Processes, 5, 65, doi: 10.3390/pr5040065.

Graham E. B., Tfaily M., Crump A. R., Goldman A., Bramer L., Arntzen E., Romero E., Resch C. T., Kennedy D. and Stegen J. (2017) Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes. JGR Biogeosciences, 122, 3188-3205; doi: 10.1101/105486.

Hou Z., Nelson W. C., Stegen J., Arntzen E., Murray C., Crump A. R., Scheibe T. D., Fredrickson J. and Zachara J. (2017) Geochemical and microbial community attributes in relation to hyporheic zone geological facies. Scientific Reports, 7, 12006, doi:10.1038/s41598-017-12275-w.

Jiao Y., Lei H., Yang D., Huang M., Liu D. and Yuan X. (2017) Impact of vegetation dynamics on hydrological processes in a semi-arid basin using a land surface-hydrology coupled model. Journal of Hydrology, 551:116-131, doi:10.1029/2006WR005588.

Johnson T., Hammond G. E. and Chen X. (2017) PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data. Computers and Geosciences, 99, 72-80; doi:10.1016/j.cageo.2016.09.006.

Johnson T. and Thomle J. (2017) 3-D decoupled inversion of complex conductivity data in the real number domain. Geophysical Journal International, 212, 284-296, doi: 10.1093/gji/ggx416.

Li L., Maher K., Navarre-Sitchler A., Druhan J., Meile C., Lawrence C., Moore J., Perdrial J., Sullivan P., Thompson A., Jin L., Bolton E. W., Brantley S. L., Dietrich W. E., Mayer K. U., Steefel C. I., Valocchi A., Zachara J., Kocar B., McIntosh J., Tutolo B. M., Kumar M., Sonnenthal E., Bao C. and Beisman J. (2017) Expanding the role of reactive transport models in critical zone processes. "Earth-Science Reviews," 165, 280-301; doi: 10.1016/j.earscirev.2016.09.001.

Li M., Gao Y., Qian W. J., Shi L., Liu Y., Nelson W. C., Nicora C. D., Resch C. T., Thompson C., Yan S., Fredrickson J. K., Zachara J. M. and Liu C. (2017) Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes. Environmental Microbiology Reports, 9, 512-521; doi: 10.1111/1758-2229.12558.

Li M., Qian W. J., Gao Y., Shi L. and Liu C. (2017) Functional enzyme-based approach for linking microbial community functions with biogeochemical process kinetics. Environmental Science & Technology," 51, 11848-11857; doi: 10.1021/acs.est.7b03158.

Ling B., Bao J., Oostrom M., Battiato I. and Tartakovsky A. M. (2017) Modeling variability in porescale multiphase flow experiments. Advances in Water Resources, 105: 29-38, doi: 10.1016/j.advwatres.2017.04.005.

Liu C., Yao M., Stegen J., Rui J., Li J. and Li X. (2017) Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse. Scientific Reports, 7, 17492; doi: 10.1038/s41598-017-17736-w 1.

Liu, Y, F. Xu and C. Liu (2017), Coupled hydro-biogeochemical processes controlling Cr reductive immobilization in Columbia River hyporheic zone, Environmental Science & Technology, 51(3), 1508-1517, doi: 10.1021/acs.est.6b05099.

Liu Y., Liu C., Nelson W. C., Shi L., Xu F., Liu Y. D., Yan A., Zhong L. R., Thompson C., Fredrickson J. and Zachara J. (2017) Effect of water chemistry and hydrodynamics on nitrogen transformation and microbial community functional potential in hyporheic zone sediment columns. Environmental Science & Technology, 51(9): 4877-4886, doi: 10.1021/acs.est.6b05018

Miller B. L., Arntzen E. V., Goldman A. and Richmond M. C. (2017) Methane ebullition in temperate hydropower reservoirs and implications for U.S. policy on greenhouse gas emissions. Environmental Management, 56, 1-15; doi: 10.1007/s00267-017-0909-1.

Percak-Dennett E., He S., Converse B., Konishi H., Xu H., Corcoran A., Noguera D., Chan C., Bhattacharyya A., Borch T., Boyd E. and Roden E. E. (2017) Microbial acceleration of aerobic pyrite oxidation at circumneutral pH. Geobiology, 15, 690-703; DOI: 10.1111/gbi.12241.

Qafoku O., Pearce C. I., Neumann A., Kovarik L., Zhu M., Ilton E. S., Bowden M. E., Resch C. T., Arey B. W., Arenholz E., Felmy A. R. and Rosso K. M. (2017) Tc(VII) and Cr(VI) interaction with naturally reduced ferruginous smectite from a redox transition zone. Environmental Science & Technology, 51, 9042-9052; doi: 10.1021/acs.est.7b02191.

Renslow R., Ahmed B., Nunez J. R., Cao, B., Majors, P. D., Fredrickson J. K. and Beyenal H. (2017) Modeling substrate utilization, metabolite production, and uranium immobilization in Shewanella oneidensis biofilms. Frontiers in Environmental Science, 50: 30, doi: 10.3389/fenvs.2017.00030.

Song H.-S., Goldberg N., Mahajan A. and Ramkrishna D. (2017) Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming. Bioinformatics, 33, 2345-2353; DOI: 10.1093/bioinformatics/btx171.

Song H.-S., Thomas D., Stegen J., Li M., Liu C., Song X., Chen X., Fredrickson J., Zachara J. and Scheibe T. D. (2017) Regulation-structured dynamic metabolic model provides a potential mechanism for delayed enzyme response in denitrification process. Frontiers in Microbiology, 8, 1866; DOI: 10.3389/fmicb.2017.01866.

Stern N., Ginder-Vogel M. A., Stegen J. C., Arntzen E., Kennedy D., Larget B. R. and Roden E. (2017) Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology, 83, e00260-00217; DOI: 10.1128/AEM.00260-17.

Tartakovsky A. M., Panzeri M., Tartakovsky G. D. and Guadagnini A. (2017) Uncertainty quantification in scale-dependent models of flow in porous media. Water Resources Research, 53: 9392-9401, doi: 10.1002/2017WR020905.

Wu T., Griffin A. M., Gorski C. A., Shelobolina E. S., Xu H., Kukkadapu R. K. and Roden E. E. (2017) Interactions between Fe(III)-oxides and Fe(III)-phyllosilicates during microbial reduction 2: Natural subsurface sediments. Geomicrobiology Journal; DOI: 10.1080/01490451.2016.1174758.

Xia Y., Mocko D., Huang M., Rodell M., Mitchell K. E., Cai X. and Ek M. B. (2017) Comparison and assessment of three advanced land surface models in simulating terrestrial water storage components over the United States. Journal of Hydrometeorology; DOI: 10.1175/JHM-D-16-0112.1.

Xu F., Liu Y., Zachara J., Bowden M., Kennedy D., Plymale A. E. and Liu C. (2017) Redox transformation and reductive immobilization of Cr(VI) in Columbia River hyporheic zone sediments. Journal of Hydrology, 555, 278-287; doi: 10.1016/j.jhydrol.2017.10.016.

Xu Z. and Tartakovsky A. M. (2017) Method of model reduction and multifidelity models for solute transport in random layered porous media. Physical Review E, 96, 033314; doi: 10.1103/PhysRevE.96.033314.

Yan Q., Stegen J., Yu Y., Deng Y., Li X. B., Wu S., Dai L., Zhang X., Li J., Wang C., Ni J., Li X. B., Hu H., Feng W., Ning D., He Z., Von Nostrand J. D., Wu L. and Zhou J. (2017) Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China). Molecular Ecology, 26(14): 3839-3850, doi: 10.1111/mec.14151.

Yan Z., Liu C., Liu Y. and Bailey V. L. (2017) Multiscale investigation on biofilm distribution and its impact on macroscopic biogeochemical reaction rates. Water Resources Research, 53(11): 8698-8714, doi: 10.1002/2017WR020570.

Yang, X., T. Varga, C. Liu, and T. D. Scheibe (2017) 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, 3(2): 259-262, doi: 10.1016/j.rhisph.2017.04.017.

Zhou T., Huang M., Bao J., Hou Z., Arntzen E., Mackley R. D., Crump A., Goldman A., Song X., Xu Y. and Zachara J. (2017) A new approach to quantify shallow water hydrologic exchanges in a large regulated river reach. Water 9, 703; DOI: 10.3390/w9090703.


Barajas-Solano D. A. and Tartakovsky A. M. (2016) Hybrid multiscale finite volume method for advection-diffusion-reaction equations. Multiscale Modeling and Simulation, 14, 1341-1376; DOI: 10.1137/15M1022537.

Battiato I. (2016) Multiscale models of flow and transport. In Handbook of Groundwater Engineering, J. H. Cushman and D. M. Tartakovsky (Eds.). CRC Press, ISBN-10: 1498703046.

Bowen L., Tartakovsky A. M. and Battiato I. (2016) Dispersion controlled by permeable surfaces: surface properties and scaling. Journal of Fluid Mechanics, 801, 13-42; DOI: 10.1017/jfm.2016.431.

Danczak R., Sawyer A. H., Williams K., Stegen J., Hobson C. and Wilkins M. J. (2016) Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments. Journal of Geophysical Research: Biogeosciences, 121, 2976-2987; DOI: 10.1002/2016JG003527.

Graham E. B., Crump A. R., Resch C. T., Fansler S., Arntzen E., Kennedy D., Fredrickson J. and Stegen J. (2016) Coupling spatiotemporal community assembly processes to changes in microbial metabolism. Frontiers in Microbiology, 7, 1949; DOI: 10.3389/fmicb.2016.01949, download data.

Ito A., Inatomi M., Huntzinger D. N., Schwalm C., Michalak A. M., Cook R., King A. W., Mao J. F., Wei Y. X., Mac Post W., Wang W. L., Arain M. A., Huang S., Hayes D. J., Ricciuto D. M., Shi X. Y., Huang M. Y., Lei H. M., Tian H. Q., Lu C. Q., Yang J., Tao B., Jain A., Poulter B., Peng S. S., Ciais P., Fisher J. B., Parazoo N., Schaefer K., Peng C. H., Zeng N. and Zhao F. (2016) Decadal trends in the seasonal-cycle amplitude of terrestrial CO2 exchange resulting from the ensemble of terrestrial biosphere models. Tellus Series B-Chemical and Physical Meteorology, 68, 28968; DOI: 10.3402/Tellusb.V68.28968.

Korneev S. and Battiato I. (2016) Sequential homogenization of reactive transport in polydispers porous media. SIAM Multiscale Modeling and Simulation, 14, 1301-1318; DOI: 10.1137/16M1074278.

Leng G., Huang M., Voisin N., Zhang X., Asrar G. R. and Leung L. R. (2016) Emergence of new hydrologic regimes of surface water resources in the Conterminous United States under future warming. Environmental Research Letters, 11, 114003; DOI: 10.1088/1748-9326/11/11/114003.

Renslow R., Lindemann S. and Song H. (2016) A generalized spatial measure for resilience of microbial systems. Frontiers in Microbiology, 7, 443; doi: 10.3389/fmicb.2016.00443.

Shi L., Dong H., Reguera G., Beyenal H., Lu A., Liu J., Yu H. and Fredrickson J. (2016) Extracellular electron transfer mechanisms between microorganisms and minerals. Nature Reviews Microbiology, 14, 651-662; DOI: 10.1038/nrmicro.2016.93.

Stegen JC, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Danczak RE, Fansler SJ, Kennedy DW, Resch CT, Tfaily MM. (2016) Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover. Nature Communications 7, 11237; doi:10.1038/ncomms11237.

Stegen J. C., Konopka A., McKinley J., Murray C., Lin X., Miller M. D., Kennedy D., Miller E. A., Resch C. T. and Fredrickson J. (2016) Coupling among microbial communities, biogeochemistry, and mineralogy across biogeochemical facies. Scientific Reports, 6, 30553; DOI: 10.1038/srep30553.

Veach A. M., Stegen J. C., Brown S. P., Dodds W. K. and Jumpponen A. (2016) Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem. Molecular Ecology, 25, 4674-4688; DOI: 10.1111/mec.13784.

Wu T., Kukkadapu R., Griffin A. M., Gorski C. A., Konishi C. A., Xu H. and Roden E. (2016) Interactions between Fe(III)-oxides and Fe(III)-phyllosilicates during microbial reduction 1: Synthetic sediments Geomicrobiology Journal, 33, 793-806; DOI: 10.1080/0149045.1.2015.1117546.

Xie X., Liu Y., Pi K., Liu C., Li J., Duan M. and Wang Y. (2016) In situ Fe-sulfide for arsenic removal under reducing conditions. Journal of Hydrology, 534, 42-49; DOI: 10.1016/j.jhydrol.2015.12.057.

Xie X., Pi K., Liu Y., Liu C., Li J., Zhang L., Zhu Y., Su C., Ma T. and Wang Y. (2016) In situ arsenic remediation by aquifer iron coating: Field trial in the Datong basin, China. Journal of Hazardous Materials, 302, 19-26; doi: 10.1016/j.jhazmat.2015.09.055.

Yan S., Liu Y. Y., Liu C. X., Shi L., Shang J. Y., Shan H. M., Zachara J., Fredrickson J., Kennedy D., Resch C. T., Thompson C. and Fansler S. (2016) Nitrate bioreduction in redox-variable low permeability sediments. Science of the Total Environment, 539, 185-195; doi: 10.1016/j.scitotenv.2015.08.122.

Yang X. F., Mehmani Y., Perkins W. A., Pasquali A., Schonherr M., Kim K., Perego M., Parks M. L., Trask N., Balhoff M. T., Richmond M. C., Geier M., Krafczyk M., Luo L. S., Tartakovsky A. M. and Scheibe T. D. (2016) Intercomparison of 3D pore-scale flow and solute transport simulation methods. Advances in Water Resources, 95, 176-189; DOI: 10.1016/j.advwatres.2015.09.015.

Zachara JM, Brantley SL, Chorover JD, Ewing RP, Kerisit SN, Liu C, Perfect E, Rother G and Stack AG. (2016) Internal domains of natural porous media revealed: Critical locations for transport, storage, and chemical reaction. Environmental Science & Technology, 50, 2811-2829; doi: 10.1021/acs.est.5b05015.

Zachara JM, Chen X, Murray CJ and Hammond G. (2016) River stage influences on uranium transport in a hydrologically dynamic groundwater-surface water transition zone. Water Resources Research, 52 (published online March 4); doi: 10.1002/2015WR018009. download data

Zhang X., Liu C., Hu B. X. and Hu Q. (2016) Grain-size based additivity models for scaling multi-rate surface complexation in subsurface sediments. Mathematical Geosciences, 48, 511-535; DOI: 10.1007/s11004-015-9620-z.

Zhu W. H., Shi M. R., Yu D., Liu C. X., Huang T. L. and Wu F. C. (2016) Characteristics and Kinetic Analysis of AQS Transformation and Microbial Goethite Reduction: Insight into "Redox mediator-Microbe-Iron oxide" Interaction Process. Scientific Reports, 6, doi: 10.1038/Srep23718.


Batuk O. N., Conradson S. D., Aleksandrova O. N., Boukhalfa H., Burakov B. E., Clark D. L., Czerwinski K. R., Felmy A. R., Lezama-Pacheco J. S., Kalmykov S. N., Moore D. A., Myasoedov B. F., Reed D., Reilly D. D., Roback R. C., Vlasova I. E., Webb S. M. and Wilkerson M. P. (2015) Multiscale speciation of U and Pu at Chernobyl, Hanford, Los Alamos, McGuire AFB, Mayak, and Rocky Flats. Environmental Science & Technology, 49, 6474-6484; doi: 10.1021/es506145b.

Beckwith C. R., Edwards M. J., Lawes M., Shi L., Butt J. N., Richardson D. J. and Clarke T. A. (2015) Characterization of MtoD from Sideroxydans lithotrophicus: a cytochrome c electron shuttle used in lithoautotrophic growth. Frontiers in Microbiology, 6, 332; doi: 10.3389/Fmicb.2015.00332.

Breuer M., Rosso K. M. and Blumberger J. (2015) Flavin binding to the deca-heme cytochrome MtrC: Insights from computational molecular simulation. Biophysical Journal, 109, 2614-2624; doi: 10.1016/j.bpj.2015.10.038.

Breuer M., Rosso K. M., Blumberger J. and Butt J. N. (2015) Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities. Journal of the Royal Society Interface, 12, 20141117, doi: 10.1098/Rsif.2014.1117.

Byrne J. M., Klueglein N., Pearce C., Rosso K. M., Appel E. and Kappler A. (2015) Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria. Science, 347, 1473-1476; doi: 10.1126/science.aaa4834.

Converse B., McKinley J., Resch C. T. and Roden E. (2015) Microbial mineral colonization across a subsurface redox transition zone. Frontiers in Microbiology, 6, 858; doi: 10.3389/fmicb.2015.00858.

Edwards M., White G., Norman M., Tome-Fernandez A., Ainsworth E., Shi L., Fredrickson J., Zachara J., Butt J., Richardson D. and Clarke T. A. (2015) Redox linked flavin sites in extracellular decaheme proteins involved in microbe-mineral electron transfer. Science Reports, 5, 11677; doi: 10.1038/srep11677.

Johnson, T., R. Versteeg, J. Thomle, G. Hammond, X. Chen, and J. Zachara (2015). 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, Water Resources Research., 51, doi:10.1002/2014WR016129.

Lee J., Fredrickson J., Plymale A. E., Dohnalkova A., Resch C. T., McKinley J. and Shi L. (2015) An autotrophic H2-oxidizing, nitrate-respiring, Tc(VII)-reducing Acidovorax sp. isolated from a subsurface oxic-anoxic transition zone. Environmental Microbiology Reports, 7, 395-403; doi: 10.1111/1758-2229.12263.

Liu C., Liu Y., Kerisit S. and Zachara J. M. (2015) Pore-scale process coupling and effective surface reaction rates in heterogeneous materials. In Reviews in Mineralogy & Geochemistry: Pore-Scale Geochemical Processes (eds. C. Steefel, S. Emmanuel, and L. M. Anovitz), The Mineralogical Society of America, Chantilly, VA, 191-216.

Liu, Y., Fredrickson, J., Zachara, J., Shi, L. (2015). Direct involvement of ombB, omaB, and omcB genes in extracellular reduction of Fe(III) by Geobacter sulfurreducens PCA. Frontiers in Microbiology 6. doi: 10.3389/fmicb.2015.01075

Liu Y., Liu C., Kukkadapu R., McKinley J., Zachara J., Plymale A. E., Miller M. D., Varga T. and Resch C. T. (2015) 99Tc(VII) retardation, reduction, and redox rate scaling in naturally reduced sediments. Environmental Science & Technology, 49, 13403-13412; doi: 10.1021/acs.est.5b03273.

Liu Y., Liu C., Zhang C., Yang X. and Zachara J. (2015) Pore and continuum scale study of the effect of subgrid transport heterogeneity on redox reaction rates. Geochimica et Cosmochimica Acta, 163, 140-155; doi: 10.1016/j.gca.2015.04.039.

Mao J., Fu W., Shi X., Ricciuto D. M., Fisher J. B., Dickinson R. E., Wei Y., Shem W., Piao S., Wang K., Schwalm C. R., Tian H., Mu M., Arain A., Ciais P., Cook R., Dai Y., Hayes D., Hoffman F. M., Huang M., Huang S., Huntzinger D. N., Ito A., Jain A., King A. W., Lei H., Lu C., Michalak A. M., Parazoo N., Peng C., Peng S., Poulter B., Schaefer K., Jafarov E., Thornton P. E., Wang W., Zeng N., Zeng Z., Zhao F., Zhu Q. and Zhu Z. (2015) Disentangling climatic and anthropogenic controls on global terrestrial evapotranspiration trends. Environmental Research Letters, 10, 094008; DOI: 10.1088/1748-9326/10/9/094008.

Nelson W. C. and Stegen J. C. (2015) The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. Frontiers in Microbiology, 6, 713; doi: 10.3389/fmicb.2015.00713.

Scheibe T. D., Perkins W. A., Richmond M. C., McKinley M. I., Romero-Gomez P. D. J., Oostrom M., Wietsma T. W., Serkowski J. A. and Zachara J. M. (2015) Pore-scale and multiscale numerical simulation of flow and transport in a laboratory-scale column. Water Resources Research, 51, 1023-1035; doi: 10.1002/2014wr015959.

Scheibe T. D., Schuchardt K., Agarwal K., Chase J., Yang X., Palmer B. J., Tartakovsky A. M., Elsethagen T. and Redden G. (2015) Hybrid multiscale simulation of a mixing-controlled reaction. Advances in Water Resources, 83, 228-239; doi:10.1016/j.advwatres.2015.06.006.

Scheibe T. D., Yang X., Chen X. and Hammond G. E. (2015) A hybrid multiscale framework for subsurface flow and transport simulations. Procedia Computer Science, 51, 1098-1107; doi: 10.1016/j.procs.2015.05.276, 2015.

Song H. and Liu C. (2015) Dynamic metabolic modeling of denitrifying bacterial growth: The cybernetic approach. Industrial & Engineering Chemistry Research, 54, 10221-10227; doi: 10.1021/acs.iecr.5b01615.

Song H., Renslow R., Fredrickson J. and Lindemann S. (2015) Integrating ecological and engineering concepts of resilience in microbial communities. Frontiers in Microbiology 6, 1298; doi: 10.3389/fmicb.2015.01298.

Stegen J. C., Lin X., Fredrickson J. K. and Konopka A. E. (2015) Estimating and mapping ecological processes influencing microbial community assembly. Frontiers in Microbiology, 6, 370; doi: 10.3389/fmicb.2015.00370.

Tian H., Lu C., Yang J., Banger K., Huntzinger D. N., Schwalm C. R., Michalak A. M., Cook R. B., Ciais P., Hayes D. J., Huang M., Ito A., Jain A. K., Lei H., Mao J., Pan S., Post W. M., Peng S., Poulter B., Ren W., Ricciuto D. M., Schaefer K., Shi X., Tao B., Wang W., Wei Y., Yang Q., Zhang B. and Zeng N. (2015) Global patterns of soil carbon stocks and fluxes as simulated by multiple terrestrial biosphere models: sources and magnitude of uncertainty. Global Biogeochemical Cycles, 29, 775-792; doi: 10.1002/2014GB005021.

Wang Z. M., Shi Z., Shi L., White G. F., Richardson D. J., Clarke T. A., Fredrickson J. K. and Zachara J. M. (2015) Effects of soluble flavin on heterogeneous electron transfer between surface-exposed bacterial cytochromes and iron oxides. Geochimica Et Cosmochimica Acta, 163, 299-310; doi: 10.1016/j.gca.2015.03.039.

Wilkins M. J. and Fredrickson J. (2015) Chapter 5: The Terrestrial Subsurface Ecosystem. In Ehrlich's Geomicrobiology, Sixth Edition (eds. CRC Press, Taylor & Francis Group, 69-95.

Xie, X., Wang, Y., Fu, P., Liu, C., Li, J., Liu, Y., Wang, Z., Duan, M., Mapoma, H. (2015). In situ treatment of arsenic contaminated groundwater by aquifer iron coating: Experimental study. Science of the Total Environment 527, 38-46. doi: 10.1016/j.scitotenv.2015.05.002

Yan, S., Liu, Y., Liu, C., Shi, L., Shang, J., Shan, H., Zachara, J., Fredrickson, J., Kennedy, D., Resch, C.T., Thompson, C., Fansler, S. (2015). Nitrate bioreduction in redox-variable low permeability sediments. Science of the Total Environment 539, 185-195. doi: 10.1016/j.scitotenv.2015.08.122


Breuer M., Rosso K. M. and Blumberger J. (2014) Electron flow in multi-heme bacterial cytochromes is a balancing act between heme electronic interaction and redox potentials. Proceedings of the National Academy of Sciences, 111, 611-616; doi: 10.1073/pnas.1316156111.

Buck E. C., Moore D. A., Czerwinski K. R., Conradson S. D., Batuk O. N. and Felmy A. R. (2014) Nature of nano-sized plutonium particles in soils at the Hanford site. Radiochimica Acta, 102, 1059-1068; doi: 10.1515/ract-2013-2103.

Edwards M. J., Baiden N. A., Johs A., Tomanicek S. J., Liang L. Y., Shi L., Fredrickson J. K., Zachara J. M., Gates A. J., Butt J. N., Richardson D. J. and Clarke T. A. (2014) The X-ray crystal structure of Shewanella oneidensis OmcA reveals new insight at the microbe-mineral interface. FEBS Letters, 588, 1886-1890; doi: 10.1016/j.febslet.2014.04.013.

Felmy A. R., Moore D. A., Buck E. C., Conradson S. D., Kukkadapu R., Sweet L., Abrecht D. and Ilton E. S. (2014) The solubility of 242PuO2 in the presence of aqueous Fe(II). The impact of precipitate preparation Radiochimica Acta, 102, 861-874; doi: 10.1515/ract-2013-2187.

Hammond G. E., Lichtner P. C. and Mills R. T. (2014) Evaluating the performance of parallel subsurface simulators: An illustrative example with PFLOTRAN. Water Resources Research, 50, 208-228; doi: 10.1002/2012WR013483.

Kerisit S. and Liu C. X. (2014) Molecular dynamics simulations of uranyl and uranyl carbonate adsorption at aluminosilicate surfaces. Environmental Science & Technology, 48, 3899-3907; doi: 10.1021/es405387c.

Lee J.-H., Zachara J. M., Fredrickson J. K., Heald S. M., McKinley J. P., Plymale A. E., Resch C. T. and Moore D. A. (2014) Fe(II)- and sulfide-facilitated reduction of 99Tc(VII)O4- in microbially reduced hyporheic zone sediments. Geochimica et Cosmochimica Acta, 136, 247-264; doi: 10.1016/j.gca.2013.08.017.

Lilova K. I., Pearce C. I., Rosso K. M. and Navrotsky A. (2014) Energetics of spinels in the Fe-Ti-O system at the nanoscale. Chemphyschem, 15, 3655-3662, doi: 10.1002/cphc.201402441.

Liu C. X., Shang J. Y., Shan H. M. and Zachara J. M. (2014) Effect of subgrid heterogeneity on scaling geochemical and biogeochemical reactions: A case of U(VI) desorption. Environmental Science & Technology, 48, 1745-1752; doi: 10.1021/es404224j.

Liu Y., Wang Z., Liu J., Levar C., Edwards M. J., Babauta J., Kennedy D., Shi Z., Beyenal H., Bond D. R., Clark T. A., Butt J. N., Richardson D. J., Rosso K. M., Zachara J., Fredrickson J. and Shi L. (2014) A trans-outer membrane porin-cytochrome protein complex for extracellular electron transfer by Geobacter sulfurreducens PCA. Environmental Microbiology Reports, 6, 776-785; doi: 10.1111/1758-2229.12204.

Ma R., Liu C. X., Greskowiak J., Prommer H., Zachara J. and Zheng C. M. (2014) Influence of calcite on uranium(VI) reactive transport in the groundwater-river mixing zone. Journal of Contaminant Hydrology, 156, 27-37; doi: 10.1016/j.jconhyd.2013.10.002.

Ma R., Zheng C., Liu C., Greskowiak J., Prommer H. and Zachara J. (2014) Assessment of controlling processes for field-scale uranium reactive transport under highly transient flow conditions. Water Resources Research, 50, 1006-1024; doi: 10.1002/2013WR013835.

Pearce C. I., Liu J., Baer D. R., Qafoku O., Heald S. M., Arenholz E., Grosz A. E., McKinley J. P., Resch C. T., Bowden M. E., Engelhard M. H. and Rosso K. M. (2014) Characterization of natural titanomagnetites (Fe3-xTixO4) for studying heterogeneous electron transfer to Tc(VII) in the Hanford subsurface. Geochimica et Cosmochimica Acta, 128, 114-127; doi: 10.1016/j.gca.2013.12.010.

Shang J. Y., Liu C., Wang Z. and Zachara J. M. (2014) Long-term kinetics of U(VI) desorption from sediments. Water Resources Research, 50, 855-870; doi: 10.1002/2013WR013949.

Shi L., Fredrickson J. K. and Zachara J. M. (2014) Genomic analyses of bacterial porin-cytochrome gene clusters. Frontiers in Microbiology, 5, 657. doi: 10.3389/fmicb.2014.00657

Singer D. M., Guo H. and Davis J. A. (2014) U(VI) and Sr(II) batch sorption and diffusion kinetics into mesoporous silica (MCM-41). Chemical Geology, 390, 152-163; doi: 10.1016/j.chemgeo.2014.10.027.

Smith D. M. A. and Rosso K. M. (2014) Possible dynamically gated conductance along heme wires in bacterial multiheme cytochromes. Journal of Physical Chemistry B, 118, 8505-8512; doi: 10.1021/jp502803y.

Wang Z. M., Zachara J. M., Shang J. Y., Jeon C., Liu J. and Liu C. X. (2014) Investigation of U(VI) adsorption in quartz-chlorite mineral mixtures. Environmental Science & Technology, 48, 7766-7773; doi: 10.1021/Es500537g.

Wilkins M. J., Kennedy D. W., Castelle C. S., Field E. K., Stepanauskas R., Fredrickson J. K. and Konopka A. (2014) Single-cell genomics reveal metabolic strategies for growth and survival in an oligotrophic aquifer. Microbiology, 160, 362-372; doi: 10.1099/mic.0.073965-0.

Zhang X., Liu C., Hu B. X. and Zhang G. (2014) Uncertainty analysis of multi-rate kinetics of uranium desorption from sediments. Journal of Contaminant Hydrology, 156, 1-15; doi: 10.1016/j.jconhyd.2013.10.001.


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