Highlights & Publications

Highlights

APRIL 30, 2024
Research Highlight

Unraveling Microbial Redox Dynamics

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Green leaf on brown soil
FEBRUARY 22, 2024
Research Highlight

An R Package for NMR Data Processing

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The logo of the nmrrr package for R with some sample output showing processed NMR spectra.
MARCH 5, 2024
Feature

How Does a River Breathe?

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A view of the Columbia River from Hanford’s 300 Area
OCTOBER 16, 2023
Research Highlight

Ecosystem Metabolism in the Columbia River Contrasts with Small Rivers

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The Columbia River under a blue, cloudless sky, seen from a rocky riverbank.
SEPTEMBER 12, 2023
Research Highlight

Increasing Catchment Size Enhances the Variety of Functions Provided by Organic Matter in Rivers

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columbia river
JULY 6, 2023
Research Highlight

Riverbed Sediment Activity Is Influenced by Organic Carbon Concentration and Organic Matter Diversity

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A view of the East River
APRIL 10, 2023
Research Highlight

Wildfire Burn Severity Drives Short-Term Impacts on Water Chemistry

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confluence of the McKenzie River and Bear Creek

Data Packages 

Find RC-SFA data packages at https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA 

Publications

2024

  • Barnes, M. E., Johnson, D. W., Hart, S. C. 2024. The Median Isn't the Message: soil nutrient hot spots have a disproportionate influence on biogeochemical structure across years, seasons, and depths. Biogeochemistry, 167, (1), 75-95; doi: 10.1007/s10533-023-01107-x
  • Myers-Pigg, A. N., Grieger, S., Roebuck, J. A., Jr., Barnes, M. E., Bladon, K. D., Bailey, J. D., Barton, R., Chu, R. K., Graham, E. B., Homolka, K. K., Kew, W., Lipton, A. S., Scheibe, T., Toyoda, J. G., Wagner, S. 2024. Experimental open air burning of vegetation enhances organic matter chemical heterogeneity compared to laboratory burns. Environmental Science & Technology, 58, (22), 9679-9688; doi: 10.1021/acs.est.3c10826Barnes, M. E., Johnson, D. W., Hart, S. C. 2024. The Median Isn't the Message: soil nutrient hot spots have a disproportionate influence on biogeochemical structure across years, seasons, and depths. Biogeochemistry, 167, (1), 75-95; doi: 10.1007/s10533-023-01107-x.
  • Gonzalez-Duque, D., Gomez-Velez, J. D., Zarnetske, J. P., Chen, X. Y., Scheibe, T. D. 2024. Sinuosity-Driven Hyporheic Exchange: Hydrodynamics and Biogeochemical Potentials. Water Resources Research, 60, (4), e2023WR036023; doi: 10.1029/2023WR036023.
  • Hou, Z. J., Ward, N. D., Myers-Pigg, A. N., Lin, X., Waichler, S. R., Wiese Moore, C., Norwood, M. J., Regier, P., Yabusaki, S. B. 2024. Quantifying drivers of methane hydrobiogeochemistry in a tidal river floodplain system. Water, 16, (1),  doi: 10.3390/w16010171.
  • Roebuck, J. A., Rod, K. A., Garayburu‐Caruso, V. A., Chu, R. K., Goldman, A. E., Renteria, L., Taylor, M., Stegen, J. C. 2024. Linkages between mineral element composition of soils and sediments with hyporheic zone dissolved organic matter chemistry across the contiguous United States. Geophysical Research Letters, 51, (6),  doi: 10.1029/2023gl106220.
  • Roebuck Jr, J. A., Myers‐Pigg, A. N., Garayburu‐Caruso, V., Stegen, J. 2024. Investigating the impacts of solid phase extraction on dissolved organic matter optical signatures and the pairing with high‐resolution mass spectrometry data across a freshwater stream network. Limnology and Oceanography: Methods,  doi: 10.1002/lom3.10603.
  • Zheng, J., Scheibe, T. D., Boye, K., Song, H.-S. 2024. Thermodynamic control on the decomposition of organic matter across different electron acceptors. Soil Biology and Biochemistry, 109364; doi: 10.1016/j.soilbio.2024.109364.

2023

  • Ahamed, F., You, Y., Burgin, A., Stegen, J. C., Scheibe, T. D., Song, H.-S. 2023. Exploring the determinants of organic matter bioavailability through substrate-explicit thermodynamic modeling. Frontiers in Water, 5, 1169701; doi: 10.3389/frwa.2023.1169701.
  • Butler, Z., Good, S., Haagsma, M., Segura, C., Hu, H. 2023. Relationship between isotope ratios in precipitation and stream water across watersheds of the National Ecological Observation Network. Hydrological Processes, 37, (11),  doi: 10.1002/hyp.15018.
  • Chen, K., Chen, X., Stegen, J. C., Villa, J. A., Bohrer, G., Song, X., Chang, K. Y., Kaufman, M., Liang, X., Guo, Z., Roden, E. E., Zheng, C. 2023. Vertical hydrologic exchange flows control methane emissions from riverbed sediments. Environmental Science & Technology, 57, (9), 4014-4026; doi: 10.1021/acs.est.2c07676.
  • Chen, K., Yang, S., Roden, E. E., Chen, X., Chang, K. Y., Guo, Z., Liang, X., Ma, E., Fan, L., Zheng, C. 2023. Influence of vertical hydrologic exchange flow, channel flow, and biogeochemical kinetics on CH4 emissions from rivers. Water Resources Research, 59, (12),  doi: 10.1029/2023wr035341.
  • Chen, X. Y., Dwivedi, D., Michael, H. A. 2023. Editorial: Hydrology, ecology, and nutrient biogeochemistry at the terrestrial-aquatic interface. Frontiers in Environmental Science, 11,  doi: 10.3389/fenvs.2023.1322708.
  • Cui, Y., Wen, S., Stegen, J. C., Hu, A., Wang, J. 2023. Chemodiversity of riverine dissolved organic matter: Effects of local environments and watershed characteristics. Water Research, 121054; doi: 10.1016/j.watres.2023.121054.
  • Danczak, R. E., Garayburu-Caruso, V. A., Renteria, L., McKever, S. A., Otenburg, O. C., Grieger, S. R., Son, K., Kaufman, M. H., Fulton, S. G., Roebuck, J. A., Myers-Pigg, A. N., Stegen, J. C. 2023. Riverine organic matter functional diversity increases with catchment size. Frontiers in Water, 5, 1087108; doi: 10.3389/frwa.2023.1087108.
  • Fulton, S. G., Stegen, J. C., Kaufman, M. H., Dowd, J., Thompson, A. 2023. Laboratory evaluation of open source and commercial electrical conductivity sensor precision and accuracy: How do they compare? PLoS One, 18, (5), e0285092; doi: 10.1371/journal.pone.0285092.
  • Graham, E. B., Song, H.-S., Grieger, S., Garayburu-Caruso, V. A., Stegen, J. C., Bladon, K. D., Myers-Pigg, A. N. 2023. Potential bioavailability of representative pyrogenic organic matter compounds in comparison to natural dissolved organic matter pools. Biogeosciences, 20, (16), 3449-3457; doi: 10.5194/bg-20-3449-2023.
  • Karra, S. K., Apte, S. V., He, X., Scheibe, T. D. 2023. Pore-resolved investigation of turbulent open channel flow over a randomly packed permeable sediment bed. Journal of Fluid Mechanics, 971,  doi: 10.1017/jfm.2023.636.
  • Kaufman, M. H., Torgeson, J., Stegen, J. C. 2023. Metabolic multireactor: Practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments. PLoS One, 18, (7), e0284256; doi: 10.1371/journal.pone.0284256.
  • McDowell, N. G., Anderson-Teixeira, K., Biederman, J. A., Breshears, D. D., Fang, Y., Fernández-de-Uña, L., Graham, E. B., Mackay, D. S., McDonnell, J. J., Moore, G. W., Nehemy, M. F., Stevens Rumann, C. S., Stegen, J., Tague, N., Turner, M. G., Chen, X. 2023. Ecohydrological decoupling under changing disturbances and climate. One Earth, 6, (3), 251-266; doi: 10.1016/j.oneear.2023.02.007.
  • Moreland, K. C., Barnes, M. E., O'Geen, A., Dove, N., Hart, S. C., Berhe, A. A. 2023. Climatic controls on soil and saprock nitrogen distribution and persistence in the Sierra Nevada. Journal of Plant Nutrition and Soil Science, 186, (1), 116-129; doi: 10.1002/jpln.202200218.
  • Patel, K. F., Myers‐Pigg, A. N., Bond‐Lamberty, B., Barnes, M. E. 2023. nmrrr: A reproducible workflow for binning and visualizing NMR spectra from environmental samples. Journal of Geophysical Research: Biogeosciences, 128, (12),  doi: 10.1029/2023jg007768.
  • Pavlopoulos, G. A., Baltoumas, F. A., Liu, S., Selvitopi, O., Camargo, A. P., Nayfach, S., Azad, A., Roux, S., Call, L., Ivanova, N. N., Chen, I. M., Paez-Espino, D., Karatzas, E., Novel Metagenome Protein Families, C., Iliopoulos, I., Konstantinidis, K., Tiedje, J. M., Pett-Ridge, J., Baker, D., Visel, A., Ouzounis, C. A., Ovchinnikov, S., Buluc, A., Kyrpides, N. C. 2023. Unraveling the functional dark matter through global metagenomics. Nature, 622, (7983), 594-602; doi: 10.1038/s41586-023-06583-7.
  • Perez, G., Gomez-Velez, J. D., Chen, X., Scheibe, T. 2023. The directional unit hydrograph model: Connecting streamflow response to storm dynamics. Journal of Hydrology, 627, (Part A), 130422; doi: 10.1016/j.jhydrol.2023.130422.
  • Rodríguez-Ramos, J., Oliverio, A., Borton, M. A., Danczak, R., Mueller, B. M., Schulz, H., Ellenbogen, J., Flynn, R. M., Daly, R. A., Schopflin, L., Shaffer, M., Goldman, A., Lewandowski, J., Stegen, J. C., Wrighton, K. C. 2023. Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream. Frontiers in Microbiomes, 2,  doi: 10.3389/frmbi.2023.1199766.
  • Roley, S., Hall, B., Perkins, W., Garayburu-Caruso, V., Stegen, J. C. 2023. Coupled primary production and respiration in a large river contrasts with smaller rivers and streams. Limnology and Oceanography, 9999, 1-15; doi: 10.1002/lno.12435.
  • Shuai, P., Jiang, P., Coon, E. T., Chen, X. 2023. The importance of explicitly representing the streambed in watershed models. Hydrological Processes, 37, (12),  doi: 10.1002/hyp.15043.
  • Stadler, M., Barnard, M. A., Bice, K., de Melo, M. L., Dwivedi, D., Freeman, E. C., Garayburu-Caruso, V. A., Linkhorst, A., Mateus-Barros, E., Shi, C., Tanentzap, A. J., Meile, C. 2023. Applying the core-satellite species concept: Characteristics of rare and common riverine dissolved organic matter. Frontiers in Water, 5, 1156042; doi: 10.3389/frwa.2023.1156042.
  • Stegen, J. C., Garayburu-Caruso, V. A., Danczak, R. E., Goldman, A. E., Renteria, L., Torgeson, J. M., Hager, J. 2023. Maximum respiration rates in hyporheic zone sediments are primarily constrained by organic carbon concentration and secondarily by organic matter chemistry. Biogeosciences, 20, (14), 2857-2867; doi: 10.5194/bg-20-2857-2023.
  • Turetcaia, A. B., Garayburu-Caruso, V. A., Kaufman, M. H., Danczak, R. E., Stegen, J. C., Chu, R. K., Toyoda, J. G., Cardenas, M. B., Graham, E. B. 2023. Rethinking aerobic respiration in the hyporheic zone under variation in carbon and nitrogen stoichiometry. Environmental Science & Technology, 57, (41), 15499-15510; doi: 10.1021/acs.est.3c04765.
  • Xiao, Y., Sloan, J., Hepworth, C., Fradera-Soler, M., Mathers, A., Thorley, R., Baillie, A., Jones, H., Chang, T., Chen, X., Yaapar, N., Osborne, C. P., Sturrock, C., Mooney, S. J., Fleming, A. J., Zhu, X. G. 2023. Defining the scope for altering rice leaf anatomy to improve photosynthesis: a modelling approach. New Phytologist, 237, (2), 441-453; doi: 10.1111/nph.18564.

 

2022

  • Acharya, B. S., Ahmmed, B., Chen, Y., Davison, J. H., Haygood, L., Hensley, R. T., Kumar, R., Lerback, J., Liu, H., Mehan, S., Mehana, M., Patil, S. D., Persaud, B. D., Sullivan, P. L., URycki, D. 2022. Hydrological Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science. Earth and Space Science, 9, (4), e2022EA002320; doi: 10.1029/2022EA002320.
  • Apte, S. V., Oujia, T., Matsuda, K., Kadoch, B., He, X., Schneider, K. 2022. Clustering of inertial particles in turbulent flow through a porous unit cell. Journal of Fluid Mechanics, 937, A9; doi: 10.1017/jfm.2022.100.
  • Arora, B., Briggs, M., Zarnetske, J., Stegen, J. C., Gomez-Velez, J., Dwivedi, D., Steefel, C. 2022. Hot Spots and Hot Moments in the Critical Zone: Identification of and Incorporation into Reactive Transport Models. In Biogeochemistry of the Critical Zone. Advances in Critical Zone Science, Wymore, A. S., Yang, W. H., Silver, W. L., McDowell, W. H., Chorover, J., Eds. Springer-Nature: 2022.
  • Bao, J., Chen, Y., Fang, Y., Song, X., Perkins, W., Duan, Z., Shuai, P., Ren, H., Hou, Z., Richmond, M., He, X., Scheibe, T. 2022. Modeling framework for evaluating the impacts of hydrodynamic pressure on hydrologic exchange fluxes and residence time for a large-scale river section over a long-term period. Environmental Modelling & Software, 148, 105277; doi: 10.1016/j.envsoft.2021.105277.
  • Borton, M. A., Collins, S. M., Graham, E. B., Garayburu-Caruso, V. A., Goldman, A. E., de Melo, M., Renteria, L., Stegen, J. C., , W. C. C. 2022. It takes a village: Using a crowdsourced approach to investigate organic matter composition in global rivers through the lens of ecological theory. Frontiers in Water, 4, 870453; doi: 10.3389/frwa.2022.870453.
  • Chen, K. W., Chen, X. Y., Song, X. H., Briggs, M. A., Jiang, P. S., Shuai, P., Hammond, G., Zhan, H. B., Zachara, J. M. 2022. Using ensemble data assimilation to estimate transient hydrologic exchange flow under highly dynamic flow conditions. Water Resources Research, 58, (5),  doi: 10.1029/2021WR030735.
  • Chen, Y., Bao, J., Fang, Y., Perkins, W. A., Ren, H., Song, X., Duan, Z., Hou, Z., He, X., Scheibe, T. D. 2022. Modeling of streamflow in a 30km long reach spanning 5 years using OpenFOAM 5.x. Geoscientific Model Development, 15, (7), 2917-2947; doi: 10.5194/gmd-15-2917-2022.
  • Dwivedi, D., Steefel, C. I., Arora, B., Banfield, J., Bargar, J., Boyanov, M. I., Brooks, S. C., Chen, X., Hubbard, S. S., Kaplan, D., Kemner, K. M., Nico, P. S., O’Loughlin, E. J., Pierce, E. M., Painter, S. L., Scheibe, T. D., Wainwright, H. M., Williams, K. H., Zavarin, M. 2022. From legacy contamination to watershed systems science: A review of scientific insights and technologies developed through DOE-supported research in water and energy security. Environmental Research Letters, 17, (4), 043004; doi: 10.1088/1748-9326/ac59a9.
  • Fremin, B. J., Bhatt, A. S., Kyrpides, N. C., Sengupta, A., Sczyrba, A., Maria da Silva, A., Buchan, A., Gaudin, A., Brune, A., Hirsch, A. M., Neumann, A., Shade, A., Visel, A., Campbell, B., Baker, B., Hedlund, B. P., Crump, B. C., Currie, C., Kelly, C., Craft, C., Hazard, C., Francis, C., Schadt, C. W., Averill, C., Mobilian, C., Buckley, D., Hunt, D., Noguera, D., Beck, D., Valentine, D. L., Walsh, D., Sumner, D., Lymperopoulou, D., Bhaya, D., Bryant, D. A., Morrison, E., Brodie, E., Young, E., Lilleskov, E., Högfors-Rönnholm, E., Chen, F., Stewart, F., Nicol, G. W., Teeling, H., Beller, H. R., Dionisi, H., Liao, H.-L., Beman, J. M., Stegen, J., Tiedje, J., Jansson, J., VanderGheynst, J., Norton, J., Dangl, J., Blanchard, J., Bowen, J., Macalady, J., Pett-Ridge, J., Rich, J., Payet, J. P., Gladden, J. D., Raff, J. D., Klassen, J. L., Tarn, J., Neufeld, J., Gravuer, K., Hofmockel, K., Chen, K.-H., Konstantinidis, K., DeAngelis, K. M., Partida-Martinez, L. P., Meredith, L., Chistoserdova, L., Moran, M. A., Scarborough, M., Schrenk, M., Sullivan, M., David, M., O'Malley, M. A., Medina, M., Habteselassie, M., Ward, N. D., Pietrasiak, N., Mason, O. U., Sorensen, P. O., Estrada de los Santos, P., Baldrian, P., McKay, R. M., Simister, R., Stepanauskas, R., Neumann, R., Malmstrom, R., Cavicchioli, R., Kelly, R., Hatzenpichler, R., Stocker, R., Cattolico, R. A., Ziels, R., Vilgalys, R., Blumer-Schuette, S., Crowe, S., Roux, S., Hallam, S., Lindow, S., Brawley, S. H., Tringe, S., Woyke, T., Whitman, T., Bianchi, T., Mock, T., Donohue, T., James, T. Y., Kalluri, U. C., Karaoz, U., Denef, V., Liu, W.-T., Whitman, W., Ouyang, Y. 2022. Thousands of small, novel genes predicted in global phage genomes. Cell Reports, 39, (12), 110984; doi: 10.1016/j.celrep.2022.110984.
  • Hammond, G. E. 2022. The PFLOTRAN reaction sandbox. Geoscientific Model Development Discussion, 2022, 1-26; doi: 10.5194/gmd-2021-284.
  • Hills, D. J., Damerow, J. E., Ahmmed, B., Catolico, N., Chakraborty, S., Coward, C. M., Crystal‐Ornelas, R., Duncan, W. D., Goparaju, L. N., Lin, C., Liu, Z., Mudunuru, M. K., Rao, Y., Rovetto, R. J., Sun, Z., Whitehead, B. P., Wyborn, L., Yao, T. 2022. Earth and Space Science Informatics Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science. Earth and Space Science, 9, (4), e2021EA002108; doi: 10.1029/2021ea002108.
  • Isabwe, A., Yang, J. R., Wang, Y., Wilkinson, D. M., Graham, E. B., Chen, H., Yang, J. 2022. Riverine bacterioplankton and phytoplankton assembly along an environmental gradient induced by urbanization. Limnology and Oceanography, 67, (9), 1943-1958; doi: 10.1002/lno.12179.
  • Jiang, P. S., Chen, X. Y., Missik, J. E. C., Gao, Z. M., Liu, H. P., Verbeke, B. A. 2022. Encoding diel hysteresis and the Birch effect in dryland soil respiration models through knowledge-guided deep learning. Frontiers in Environmental Science, 10,  doi: 10.3389/fenvs.2022.1035540.
  • Jiang, P. S., Son, K., Mudunuru, M. K., Chen, X. Y. 2022. Using Mutual Information for Global Sensitivity Analysis on Watershed Modeling. Water Resources Research, 58, (10), 2022WR032932; doi: 10.1029/2022WR032932.
  • Johnson, T., Thomle, J., Stickland, C., Goldman, A., Stegen, J. 2022. Riverbed temperature and 4D ERT monitoring reveals heterogenous horizontal and vertical groundwater-surface water exchange flows under dynamic stage conditions. Frontiers in Earth Science, 10,  doi: 10.3389/feart.2022.910058.
  • Kaufman, M. H., Ghosh, R. N., Grate, J., Shooltz, D. D., Freeman, M. J., Ball, T. M., Loloee, R., McIntire, C. W., Wells, J., Strickland, C., Vermeul, V., Rod, K. A., Mackley, R., Lin, X., Ren, H., Goldman, A., Stegen, J. 2022. Dissolved oxygen sensor in an automated hyporheic sampling system reveals biogeochemical dynamics. PLOS Water, 1, (4), e0000014; doi: 10.1371/journal.pwat.0000014.
  • Leonard, L. T., Vanzin, G. F., Garayburu-Caruso, V. A., Lau, S. S., Beutler, C. A., Newman, A. W., Mitch, W. A., Stegen, J. C., Williams, K. H., Sharp, J. O. 2022. Disinfection byproducts formed during drinking water treatment reveal an export control point for dissolved organic matter in a subalpine headwater stream. Water Research X, 15, 100144; doi: 10.1016/j.wroa.2022.100144.
  • Little, C. J., Rizzuto, M., Luhring, T. M., Monk, J. D., Nowicki, R. J., Paseka, R. E., Stegen, J. C., Symons, C. C., Taub, F. B., Yen, J. 2022. Movement with meaning: integrating information into meta-ecology. Oikos, 2022, (8), e08892; doi: 10.1111/oik.08892.
  • Maltz, M. R., Carey, C. J., Freund, H. L., Botthoff, J. K., Hart, S. C., Stajich, J. E., Aarons, S. M., Aciego, S. M., Blakowski, M., Dove, N. C., Barnes, M. E., Pombubpa, N., Aronson, E. L. 2022. Landscape topography and regional drought alters dust microbiomes in the Sierra Nevada of California. Frontiers in Microbiology, 13, 856454; doi: 10.3389/fmicb.2022.856454.
  • Mudunuru, M. K., Son, K., Jiang, P., Hammond, G., Chen, X. 2022. Scalable deep learning for watershed model calibration. Frontiers in Earth Science, 10,  doi: 10.3389/feart.2022.1026479.
  • Nelson, A. R., Toyoda, J., Chu, R. K., Tolić, N., Garayburu-Caruso, V. A., Saup, C. M., Renteria, L., Wells, J. R., Stegen, J. C., Wilkins, M. J., Danczak, R. E. 2022. Implications of sample treatment on characterization of riverine dissolved organic matter. Environmental Science: Processes & Impacts, 24, (5), 773-782; doi: 10.1039/D2EM00044J.
  • Ren, H. Y., Cromwell, E., Kravitz, B., Chen, X. Y. 2022. Technical note: Using long short-term memory models to fill data gaps in hydrological monitoring networks. Hydrology and Earth System Sciences, 26, (7), 1727-1743; doi: 10.5194/hess-26-1727-2022.
  • Rodriguez-Ramos, J. A., Borton, M. A., McGivern, B. B., Smith, G. J., Solden, L. M., Shaffer, M., Daly, R. A., Purvine, S. O., Nicora, C. D., Eder, E. K., Lipton, M., Hoyt, D. W., Stegen, J. C., Wrighton, K. C. 2022. Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments. mSystems, e0051622; doi: 10.1128/msystems.00516-22.
  • Roebuck, J. A., Bladon, K. D., Donahue, D., Graham, E. B., Grieger, S., Morgenstern, K., Norwood, M. J., Wampler, K. A., Erkert, L., Renteria, L., Danczak, R., Fricke, S., Myers‐Pigg, A. N. 2022. Spatiotemporal controls on the delivery of dissolved organic matter to streams following a wildfire. Geophysical Research Letters, 49, (16),  doi: 10.1029/2022gl099535.
  • Rubinstein, R. L., Borton, M. A., Zhou, H., Shaffer, M., Hoyt, D. W., Stegen, J., Henry, C. S., Wrighton, K. C., Versteeg, R. 2022. ORT: A workflow linking genome-scale metabolic models with reactive transport codes. Bioinformatics, 38, (3), 778-784; doi: 10.1093/bioinformatics/btab753.
  • Shaffer, J. P., Nothias, L. F., Thompson, L. R., Sanders, J. G., Salido, R. A., Couvillion, S. P., Brejnrod, A. D., Lejzerowicz, F., Haiminen, N., Huang, S., Lutz, H. L., Zhu, Q., Martino, C., Morton, J. T., Karthikeyan, S., Nothias-Esposito, M., Duhrkop, K., Bocker, S., Kim, H. W., Aksenov, A. A., Bittremieux, W., Minich, J. J., Marotz, C., Bryant, M. M., Sanders, K., Schwartz, T., Humphrey, G., Vasquez-Baeza, Y., Tripathi, A., Parida, L., Carrieri, A. P., Beck, K. L., Das, P., Gonzalez, A., McDonald, D., Ladau, J., Karst, S. M., Albertsen, M., Ackermann, G., DeReus, J., Thomas, T., Petras, D., Shade, A., Stegen, J., Song, S. J., Metz, T. O., Swafford, A. D., Dorrestein, P. C., Jansson, J. K., Gilbert, J. A., Knight, R., Earth Microbiome Project, C. 2022. Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nature Microbiology, 7, (12), 2128-2150; doi: 10.1038/s41564-022-01266-x.
  • Simmonds, M. B., Riley, W. J., Agarwal, D. A., Chen, X., Cholia, S., Crystal-Ornelas, R., Coon, E. T., Dwivedi, D., Hendrix, V. C., Huang, M., Jan, A., Kakalia, Z., Kumar, J., Koven, C. D., Li, L., Melara, M., Ramakrishnan, L., Ricciuto, D. M., Walker, A. P., Zhi, W., Zhu, Q., Varadharajan, C. 2022. Guidelines for publicly archiving terrestrial model data to enhance usability, intercomparison, and synthesis. Data Science Journal, 21, (1),  doi: 10.5334/dsj-2022-003.
  • Son, K., Fang, Y., Gomez-Velez, J. D., Chen, X. 2022. Spatial microbial respiration variations in the hyporheic zones within the Columbia River Basin. Journal of Geophysical Research: Biogeosciences, 127, (11), e2021JG006654; doi: 10.1029/2021JG006654.
  • Son, K., Fang, Y., Gomez‐Velez, J. D., Byun, K., Chen, X. 2022. Combined effects of stream hydrology and land use on basin‐scale hyporheic zone denitrification in the Columbia River Basin. Water Resources Research, 58, (12),  doi: 10.1029/2021wr031131.
  • Ward, A. S., Packman, A., Bernal, S., Brekenfeld, N., Drummond, J., Graham, E., Hannah, D. M., Klaar, M., Krause, S., Kurz, M., Li, A. G., Lupon, A., Mao, F., Roca, M. E. M., Ouellet, V., Royer, T. V., Stegen, J. C., Zarnetske, J. P. 2022. Advancing river corridor science beyond disciplinary boundaries with an inductive approach to catalyse hypothesis generation. Hydrological Processes, 36, (4), e14540; doi: 10.1002/hyp.14540.
  • Yang, J., Ye, M., Chen, X., Dai, H., Walker, A. P. 2022. Process interactions can change process ranking in a coupled complex system under process model and parametric uncertainty. Water Resources Research, 58, (3),  doi: 10.1029/2021wr029812.
  • Yang, Y., Berhe, A. A., Barnes, M. E., Moreland, K. C., Tian, Z., Kelly, A. E., Bales, R. C., O'Geen, A. T., Goulden, M. L., Hartsough, P., Hart, S. C. 2022. Climate warming alters nutrient storage in seasonally dry forests: insights from a 2,300 m elevation gradient. Global Biogeochemical Cycles, 36, (11),  doi: 10.1029/2022gb007429.
  • Yang, Y., Berhe, A. A., Hunsaker, C. T., Johnson, D. W., Safeeq, M., Barnes, M. E., McCorkle, E. P., Stacy, E. M., Bales, R. C., Bart, R. R., Goulden, M. L., Hart, S. C. 2022. Impacts of climate and disturbance on nutrient fluxes and stoichiometry in mixed-conifer forests. Biogeochemistry, 158, (1), 1-20; doi: 10.1007/s10533-021-00882-9.
  • Yao J., Yuan, W., Gao, H., Liu, H., Chen, X., Ma, Y., Arntzen, E., McFarland, D. P. 2022. Impact of shifts in vegetation phenology on the carbon balance of a semiarid sagebrush ecosystem. Remote Sensing, 14, (23), 5924; doi: 10.3390/rs14235924 

2021

  • Sengupta A., T. Volkmann, R.E. Danczak, J.C. Stegen, K. Dontsova, N. Abramson, and A. Bugaj, et al. 2021. "Contrasting community assembly forces drive microbial structural and functional responses to precipitation in an incipient soil system." Frontiers in Microbiology 12. PNNL-SA-166658. doi:10.3389/fmicb.2021.754698
  • He X., S.V. Apte, S. Karra, and O.N. Dogan. 2021. "A LES Study of Secondary Motion and Wall Shear Stresses in a Pipe Bend." Physics of Fluids 33, no. 11:Art. No. 115102. PNNL-SA-165081. doi:10.1063/5.0065338
  • Hou Z., H. Ren, C.J. Murray, X. Song, Y. Fang, E.V. Arntzen, and X. Chen, et al. 2021. "A Novel Construct for Scaling Groundwater-River Interactions Based on Machine-Guided Hydromorphic Classification." Environmental Research Letters 16, no. 10:104016. PNNL-SA-151112. doi:10.1088/1748-9326/ac24ce
  • Danczak R.E., A.E. Goldman, R.K. Chu, J.G. Toyoda, V.A. Garayburu-Caruso, N. Tolic, and E.B. Graham, et al. 2021. "Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties." Science of the Total Environment 788. PNNL-SA-156110. doi:10.1016/j.scitotenv.2021.147409
  • Song X., Y. Fang, J. Bao, H. Ren, Z. Duan, W.A. Perkins, and H. Zhou, et al. 2021. "Scale-dependent spatial variabilities of hydrological exchange flows and transit time in a large regulated river." Journal of Hydrology 598. PNNL-SA-152146. doi:10.1016/j.jhydrol.2021.126283
  • Dove N.C., A.M. Veach, W. Muchero, T. Wahl, J.C. Stegen, C.W. Schadt, and M. Cregger. 2021. "Assembly of the Populus microbiome is temporally dynamic and determined by selective and stochastic factors." mSphere 6, no. 3:e01316-20. PNNL-SA-158824. doi:10.1128/mSphere.01316-20
  • Chu H., X.R. Luo, Z. Ouyang, W.S. Chan, S. Dengel, S. Biraud, and M.S. Torn, et al. 2021. "Representativeness of Eddy-Covariance flux footprints for areas surrounding AmeriFlux sites." Agricultural and Forest Meteorology 301. PNNL-SA-157254. doi:10.1016/j.agrformet.2021.108350
  • Dwivedi D., S.E. Godsey, and T.D. Scheibe. 2021. "Editorial: Linking hydrological and biogeochemical processes in riparian corridors." Frontiers in Water 3. PNNL-SA-161453. doi:10.3389/frwa.2021.693763
  • Xiao Y., J.M. Sloan, C. Hepworth, C.P. Osborne, A.J. Flemming, X. Chen, and X. Zhu. 2021. "Estimating uncertainty: A Bayesian approach to modelling photosynthesis in C3 leaves." Plant, Cell & Environment 44, no. 5:1436-1450. PNNL-SA-161702. doi:10.1111/pce.13995
  • Missik J.E., H. Liu, Z. Gao, M. Huang, X. Chen, E.V. Arntzen, and D.P. McFarland, et al. 2021. "Groundwater regulates interannual variations in evapotranspiration in a riparian semiarid ecosystem." Journal of Geophysical Research: Atmospheres 126, no. 7:Article No. e2020JD033078. PNNL-SA-153611. doi:10.1029/2020jd033078
  • Ren H., X. Song, Y. Fang, Z. Hou, and T.D. Scheibe. 2021. "Machine Learning Analysis of Hydrologic Exchange Flows and Transit Time Distributions in a Large Regulated River." Frontiers in Artificial Intelligence 4. PNNL-SA-158855. doi:10.3389/frai.2021.648071
  • Conner A., M. Gooseff, X. Chen, E.V. Arntzen, and V.A. Garayburu-Caruso. 2021. "Groundwater Inflows to the Columbia River Along the Hanford Reach and Associated Nitrate Concentrations." Frontiers in Water 3. PNNL-SA-161403. doi:10.3389/frwa.2021.574684
  • Zhang Y., D. Zhou, W. Wei, J.M. Frame, H. Sun, A. Sun, and X. Chen. 2021. "Hierarchical Fractional Advection-Dispersion Equation (FADE) to Quantify Anomalous Transport in River Corridor over a Broad Spectrum of Scales: Theory and Applications." Mathematics 9, no. 7:790. PNNL-SA-160334. doi:10.3390/math9070790
  • Nayfach S., S. Roux, R. Seshadri, D. Udwary, N. Varghese, F. Schulz, and D. Wu, et al. 2021. "A genomic catalog of Earth‚Äôs microbiomes." Nature Biotechnology 39, no. 4:499‚Äì509. PNNL-SA-150672. doi:10.1038/s41587-020-0718-6
  • Damerow J., C. Varadharajan, K.E. Boye, E.L. Brodie, M. Burrus, D. Chadwick, and R. Crystal-Ornelas, et al. 2021. "Sample identifiers and metadata to support data management and reuse in  multidisciplinary ecosystem sciences." Data Science Journal 20, no. 1:Article No. 11. PNNL-SA-158301. doi:10.5334/dsj-2021-011
  • Graham E.B., C. Averill, B. Bond-Lamberty, J.E. Knelman, S. Krause, A.L. Peralta, and A. Shade, et al. 2021. "Toward a generalizable framework of disturbance ecology through crowdsourced science." Frontiers in Ecology and Evolution 9. PNNL-SA-151971. doi:10.3389/fevo.2021.588940
  • Wu R., X. Chen, G.E. Hammond, G. Bisht, X. Song, M. Huang, and G. Niu, et al. 2021. "Coupling Surface Flow with High-performance Subsurface Reactive Flow and Transport Code PFLOTRAN." Environmental Modelling & Software 137. PNNL-SA-156109. doi:10.1016/j.envsoft.2021.104959
  • Zhu B., M. Huang, Y. Cheng, X. Xie, Y. Liu, G. Bisht, and X. Chen. 2021. "Impact of vegetation physiology and phenology on watershed hydrology in a semiarid watershed in the Pacific Northwest in a changing climate." Water Resources Research 57, no. 3:e2020WR028394. PNNL-SA-154491. doi:10.1029/2020WR028394
  • Song H., J.C. Stegen, E.B. Graham, and T.D. Scheibe. 2021. "Historical Contingency in Microbial Resilience to Hydrologic Perturbations." Frontiers in Water 3. PNNL-SA-156061. doi:10.3389/frwa.2021.590378
  • Fudyma J.D., R.K. Chu, N. Grachet, J.C. Stegen, and M.M. Tfaily. 2021. "Coupled biotic-abiotic processes control biogeochemical cycling of dissolved organic matter in the Columbia River hyporheic zone." Frontiers in Water 2. PNNL-SA-158822. doi:10.3389/frwa.2020.574692
  • Liu W., E.B. Graham, Y. Dong, L. Zhong, J. Zhang, C. Qiu, and R. Chen, et al. 2021. "Balanced stochastic versus deterministic assembly processes benefit diverse yet uneven ecosystem functions in representative agroecosystems." Environmental Microbiology 23, no. 1:391-404. PNNL-SA-157815. doi:10.1111/1462-2920.15326

2020

  • Garayburu-Caruso V.A., R.E. Danczak, J.C. Stegen, L. Renteria, M.L. McCall, A.E. Goldman, and R.K. Chu, et al. 2020. "Using Community Science to Reveal the Global Chemogeography of River Metabolomes." Metabolites 10, no. 12:518. PNNL-SA-157277. doi:10.3390/metabo10120518
  • Danczak R.E., R.K. Chu, S.J. Fansler, A.E. Goldman, E.B. Graham, M.M. Tfaily, and J.G. Toyoda, et al. 2020. "Using metacommunity ecology to understand environmental metabolomes." Nature Communications 11, no. 1:Article No. 6369. PNNL-SA-152827. doi:10.1038/s41467-020-19989-y
  • Ahmmed B., M. Mudunuru, S. Karra, S.C. James, H. Viswanathan, and J. Dunbar. 2020. "PFLOTRAN-SIP: A PFLOTRAN Module for Simulating Spectral-induced Polarization of Electrical Impedance Data." Energies 13, no. 24:6552. PNNL-SA-157259. doi:10.3390/en13246552
  • Chen X., J.M. Zachara, V.R. Vermeul, G. Hammond, M.D. Freshley, and Y. Fang. 2020. "Understanding Contaminant Migration within a Dynamic River Corridor through Field Experiments and Reactive Transport Modeling." Frontiers in Water 2. PNNL-SA-151389. doi:10.3389/frwa.2020.533796
  • Ren H., Z. Hou, Z. Duan, X. Song, W.A. Perkins, M.C. Richmond, and E.V. Arntzen, et al. 2020. "Spatial Mapping of Riverbed Grain-size Distribution Using Machine Learning." Frontiers in Water 2. PNNL-SA-151819. doi:10.3389/frwa.2020.551627
  • Rizzo C., X. Song, F. De Barros, and X. Chen. 2020. "Temporal flow variations interact with spatial physical heterogeneity to impact solute transport in managed river corridors." Journal of Contaminant Hydrology 235. PNNL-SA-153233. doi:10.1016/j.jconhyd.2020.103713
  • Fang Y., X. Song, H. Ren, W.A. Perkins, P. Shuai, M.C. Richmond, and Z. Hou, et al. 2020. "High-performance simulation of dynamic hydrologic exchange and implications for surrogate flow and reactive transport modeling in a large river corridor." Frontiers in Water 2. PNNL-SA-153319. doi:10.3389/frwa.2020.564211
  • Song H., J.C. Stegen, E.B. Graham, J. Lee, V.A. Garayburu-Caruso, W.C. Nelson, and X. Chen, et al. 2020. "Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling." Frontiers in Microbiology 11. PNNL-SA-151734. doi:10.3389/fmicb.2020.531756
  • Danczak RE, RA Daly, MA Borton, JC Stegen, S Roux, KC Wrighton, and MJ Wilkins. (2020) “Ecological assembly processes are coordinated between bacterial and viral communities in fractured shale ecosystems.” Msystems, 5, e00098-00020; doi: 10.1128/mSystems.00098-20.
  • Ji M, W Kong, J Stegen, L Yue, F Wang, X Dong, DA Cowan, and BC Ferrari. (2020) “Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils.” Environmental Microbiology, 22, 2261-2272; doi: 10.1111/1462-2920.14993.
  • Liu W, EB Graham, L Zhong, J Zhang, S Li, X Lin, and Y Feng. (2020) “Long-term stochasticity combines with short-term variability in assembly processes to underlie rice paddy sustainability.” Frontiers in Microbiology, 11, 873; doi: 10.3389/fmicb.2020.00873.
  • Liu W, EB Graham, L Zhong, J Zhang, W Li, Z Li, X Lin, Y Feng, and J Wang. (2020) “Dynamic microbial assembly processes correspond to soil fertility in sustainable paddy agroecosystems.” Functional Ecology, 34, 1244-1256; doi: 10.1111/1365-2435.13550.
  • Graham EB and S Krause. (2020) “Social media sows consensus in disturbance ecology.” Nature, 577, 170; doi: 10.1038/d41586-020-00006-7 download data.
  • Kruegler J, J Gomez-Velez, LK Lautz, and TA Endreny. (2020) “Dynamic evapotranspiration alters hyporheic flow and residence times in the intrameander zone.” Water, 12, 424; doi: 10.3390/w12020424 download data.
  • Li B, X Liu, MH Kaufman, A Turetcaia, X Chen, and MB Cardenas. (2020) “Flexible and modular simultaneous modeling of flow and reactive transport in rivers and hyporheic zones.” Water Resources Research, 56; doi: 10.1029/2019wr026528download data.
  • Nelson WC, EB Graham, AR Crump, SJ Fansler, EV Arntzen, DW Kennedy, and JC Stegen. (2020) “Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome.” PLoS ONE, 15, e0228165; doi: 10.1371/journal.pone.0228165 download data.
  • Villa JA, GJ Smith, Y Ju, L Renteria, JC Angle, E Arntzen, SF Harding, H Ren, X Chen, AH Sawyer, EB Graham, JC Stegen, KC Wrighton, and G Bohrer. (2020) “Methane and nitrous oxide porewater concentrations and surface fluxes of a egulatedr river.” Science of The Total Environment, 715, 136920; doi: 10.1016/j.scitotenv.2020.136920. download data.
  • Wang JJ, P Legendre, J Soininen, CF Yeh, E Graham, JC Stegen, EO Casamayor, JZ Zhou, J Shen, and FY Pan. (2020) “Temperature drives local contributions to beta diversity in mountain streams: Stochastic and deterministic processes.” Global Ecology and Biogeography, 29, 420-432; doi: 10.1111/geb.13035 Front cover download data.
  • Wu L, JD Gomez-Velez, S Krause, T Singh, A Wörman, and J Lewandowski. (2020) “Impact of flow alteration and temperature variability on hyporheic exchange.” Water Resources Research, 56; doi: 10.1029/2019wr026225 download data.
  • Yao J, H Liu, J Huang, Z Gao, G Wang, D Li, H Yu, and X Chen. (2020) “Accelerated dryland expansion regulates future variability in dryland gross primary production.” Nature Communications, 11, 1665; doi: 10.1038/s41467-020-15515-2download data.
  • Zachara JM, X Chen, X Song, P Shuai, C Murray, and CT Resch. (2020) “Kilometer-scale hydrologic exchange flows in a gravel bed river corridor and their implications to solute migration.” Water Resources Research, 56, e2019WR02525; doi: 10.1029/2019wr025258 download data.
  • Garayburu-Caruso VA, et al., “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism.” Environmental Science & Technology Letters 7, 517-524 (2020). [DOI: 10.1021/acs.estlett.0c00258]

2019

2018

2017

  • Bisht G, M Huang, T Zhou, X Chen, H Dai, G Hammond, W Riley, J Downs, Y Liu, and J Zachara. (2017) “Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulatestream-aquifer-land interactions (CP v1.0).” Geoscientific Model Development, 10, 4539-4562, doi: 10.5194/gmd-10-4539-2017 download data.
  • Dai H, M Ye, AP 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: 10.1002/2016WR019715download data.
  • Dai H, X Chen, M Ye, X Song, and J Zachara. (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 download data.
  • Gao Z, ES Russell, JEC Missik, M Huang, X Chen, CE Strickland, R Clayton, E Arntzen, Y Ma, and H Liu.* (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 download data.
  • Goldman AE, EB Graham, AR Crump, DW Kennedy, EB Romero, CG Anderson, KL Dana, CT Resch, JK Fredrickson, and JC Stegen. (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 download data.
  • Graham, EB, AR Crump, CT Resch, S Fansler, E Arntzen, DW Kennedy, JK Fredrickson, and JC Stegen. (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 J Stegen. (2017) “Dispersal-based microbial community assembly decreases biogeochemical function.” Processes, 5, 65, doi: 10.3390/pr5040065 download data.
  • Graham EB, M Tfaily, AR Crump, A Goldman, L Bramer, E Arntzen, E Romero, CT Resch, D Kennedy, and J Stegen. (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 download data.
  • Hou Z, WC Nelson, J Stegen, E Arntzen, C Murray, AR Crump, TD Scheibe, J Fredrickson, and J Zachara. (2017) “Geochemical and microbial community attributes in relation to hyporheic zone geological facies.” Scientific Reports, 7, 12006, doi:10.1038/s41598-017-12275-w download data.
  • Jiao Y, H Lei, D Yang, M Huang, D Liu, and X Yuan. (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, GE Hammond, and X Chen. (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 download data.
  • Johnson T and J Thomle. (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 download data.
  • Li L, K Maher, A Navarre-Sitchler, J Druhan, C Meile, C Lawrence, J Moore, J Perdrial, P Sullivan, A Thompson, L Jin, EW Bolton, SL Brantley, WE Dietrich, KU Mayer, CI Steefel, A Valocchi, J Zachara. B, Kocar, J McIntosh, BM Tutolo, M Kumar, E Sonnenthal, C Bao, and J Beisman. (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 download data.
  • Li M, Y Gao, WJ Qian, L Shi, Y Liu, WC Nelson, CD Nicora, CT Resch, C Thompson, S Yan, JK Fredrickson, JM Zachara, and C Liu. (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 download data.
  • Li M, WJ Qian, Y Gao, L Shi, and C Liu. (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 download data.
  • Ling B, J Bao, M Oostrom, I Battiato, and AM Tartakovsky. (2017) “Modeling variability in porescale multiphase flow experiments.” Advances in Water Resources, 105: 29-38, doi: 10.1016/j.advwatres.2017.04.005 download data.
  • Liu C, M Yao, J Stegen, J Rui, J Li, and X Li. (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 1download data.
  • 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 download data.
  • Liu Y, C Liu, WC Nelson, L Shi. F, Xu, YD Liu, A Yan, LR Zhong, C Thompson, J Fredrickson, and J Zachara. (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.6b05018download data.
  • Miller BL, EV Arntzen, A Goldman, and MC Richmond. (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 download data.
  • Percak-Dennett E, S He, B Converse, H Konishi, H Xu, A Corcoran, D Noguera, C Chan, A Bhattacharyya, T Borch, E Boyd, and EE Roden. (2017) “Microbial acceleration of aerobic pyrite oxidation at circumneutral pH.” Geobiology, 15, 690-703; DOI: 10.1111/gbi.12241 download data.
  • Qafoku O, CI Pearce, A Neumann, L Kovarik, M Zhu, ES Ilton, ME Bowden, CT Resch, BW Arey, E Arenholz, AR Felmy, and KM Rosso. (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 download data.
  • Renslow R, B Ahmed, JR Nunez, B Cao, PD Majors, JK Fredrickson, and H Beyenal. (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 download data.
  • Song H-S, N Goldberg, A Mahajan, and D Ramkrishna. (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 download data.
  • Song H-S, D Thomas, J Stegen, M Li, C Liu, X Song, X Chen, J Fredrickson, J Zachara, and TD Scheibe. (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 download data.
  • Stern N, MA Ginder-Vogel, JC Stegen, E Arntzen, D Kennedy, BR Larget, and E Roden. (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 download data.
  • Tartakovsky AM, M Panzeri, GD Tartakovsky, and A Guadagnini. (2017) “Uncertainty quantification in scale-dependent models of flow in porous media.” Water Resources Research, 53: 9392-9401, doi: 10.1002/2017WR020905 download data.
  • Wu T, AM Griffin, CA Gorski, ES Shelobolina, H Xu, RK Kukkadapu, and EE Roden. (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 download data.
  • Xia Y, D Mocko, M Huang, M Rodell, KE Mitchell, X Cai, and MB Ek. (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 download data.
  • Xu F, Y Liu, J Zachara, M Bowden, D Kennedy, AE Plymale, and C Liu. (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 download data.
  • Xu Z and AM Tartakovsky. (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 download data.
  • Yan Q, J Stegen, Y Yu, Y Deng, XB Li, S Wu, L Dai, X Zhang, J Li, C Wang, J Ni, XB Li, H Hu, W Feng, D Ning, Z He, JD Von Nostrand, L Wu, and J Zhou. (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 download data.
  • Yan Z, C Liu, Y Liu, and VL Bailey. (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 download data.
  • Yang X, T Varga, C Liu, and TD 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.2017.04.017download data.
  • Zhou T, M Huang, J Bao, Z Hou, E Arntzen, RD Mackley, A Crump, A Goldman, X Song, Y Xu, and J Zachara. (2017) “A new approach to quantify shallow water hydrologic exchanges in a large regulated river reach.” Water 9, 703; DOI: 10.3390/w9090703 download data.

Related organizations

EMSL, the Environmental Molecular Sciences Laboratory

Research topics

Biology
Subsurface Science
Earth & Coastal Sciences
Microbiome Science