LAB PUBLICATIONS

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For a collection of non-peer reviewed articles (blog posts, essays, popular press articles) click here

Zee Book!
Schlesinger, W.H. and E.S. Bernhardt. 2020. Biogeochemistry: an analysis of global change, 4th edition. Elsevier. 672pp.

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Journal Articles
If you do not have personal or institutional access please request a reprint from emily.bernhardt "at" duke.edu
Authors who are or were members of the Bernhardt lab when work reported was conducted are indicated by underline

2021

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Ury et al. 2021 Ecological Applications

Carter et al. 2021 Limnology and Oceanography

White et al. 2021 Ecosystems

Simonin et al. 2021. Ecological Applications

• Delesantro, J.M., J.M. Duncan, D. Riveros-Iregui, J.R. Blaszczak, E.S. Bernhardt, D.L. Urban, L.E. Band. 2021. Characterizing and Classifying Urban Watersheds with Compositional and Structural Attributes. Hydrological Processes. e14339 doi: 10.1002/hyp.14339
• White, E.E., E.A. Ury, E.S. Bernhardt, X. Yang. 2021. Climate change driving widespread loss of forested wetlands throughout the North American Coastal Plain. Ecosystems. doi: 10.1007/s10021-021-00686-w
• Ross, M.R.V., F. Nippgen, B.L. McGlynn, C. Thomas, A. Brooks, R. Shriver, E. Moore, E.S Bernhardt. 2021.  Mountaintop mining legacies constrain ecological, hydrological and biogeochemical recovery trajectories.  Environmental Research Letters 16: 075004. doi: 10.1088/1748-9326/ac09ac
• Simonin, M., J.D. Rocca, J.R. Gerson, E. Moore, J. Craine, N. Fierer, M. Ross, A. Brooks, and E.S. Bernhardt. 2021. Consistent declines in aquatic biodiversity across diverse domains of life in rivers impacted by surface coal mining. Ecological Applications doi: 10.1002/eap.2389
• Likens, G.E., D. Buso, E.S. Bernhardt and E. Rosi. 2021. A century of change: reconstructing the biogeochemical history of Hubbard Brook. Hydrological Processes 35: e14256. doi: 10.1002/hyp.14256
• Gerson, J.R., D.M. Walters, C.A. Eagles-Smith, and E.S. Bernhardt.  Lethal impacts of selenium counterbalance the potential reduction in mercury bioaccumulation for freshwater organisms. Environmental Pollution 287: 117293. doi: 10.1016​/j.envpol.2021.117293
• Carter A.M., J.R. Blaszczak, J.B. Heffernan JB, E.S. Bernhardt. 2021. Hypoxia dynamics and spatial distribution in a low gradient river. Limnology and Oceanography. 66: 2251-2265. dio: 10.1002/lno11751
• Ury, E., X. Yang, J.P. Wright and E.S. Bernhardt. 2021. Rapid deforestation of a coastal landscape driven by sea level rise and extreme events. Ecological Applications doi: 10.1002/eap.2339
• ​Savoy, P., E.S. Bernhardt, L. Kirk, M. Cohen and J.B. Heffernan. 2021. A seasonally dynamic model of light at the stream surface. Freshwater Science. doi/10.1086/714270
• Rüegg, Janine, Caitlin C. Conn, Elizabeth P. Anderson, Tom J. Battin, Emily S. Bernhardt, Marta Boix Canadell, Sophia M. Bonjour, Jacob D. Hosen, Nicholas S. Marzolf, and Charles B. Yackulic. Thinking like a consumer: Linking aquatic basal metabolism and consumer dynamics. Limnology and Oceanography Letters 6, no. 1 (February 2021): 1–17. https://doi.org/10.1002/lol2.10172.

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• Campbell, J. L., L. E. Rustad, S. W. Bailey, E. S. Bernhardt, C. T. Driscoll, M. B. Green, P. M. Groffman, et al. “Watershed studies at the Hubbard Brook Experimental Forest: Building on a long legacy of research with new approaches and sources of data.” Hydrological Processes 35, no. 1 (January 1, 2021). https://doi.org/10.1002/hyp.14016.
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• Green, M. B., L. H. Pardo, S. W. Bailey, J. L. Campbell, W. H. McDowell, E. S. Bernhardt, and E. J. Rosi. “Predicting high-frequency variation in stream solute concentrations with water quality sensors and machine learning.” Hydrological Processes 35, no. 1 (January 1, 2021). https://doi.org/10.1002/hyp.14000.
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2020

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Rocca et al. 2020

Gerson, Topp et al. 2020

Naslund et al. 2020

• Gerson, Jacqueline R., David M. Walters, Collin A. Eagles-Smith, Emily S. Bernhardt, and Jessica E. Brandt. “Do Two Wrongs Make a Right? Persistent Uncertainties Regarding Environmental Selenium-Mercury Interactions.” Environmental Science & Technology 54, no. 15 (August 2020): 9228–34. https://doi.org/10.1021/acs.est.0c01894.
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• Perrotta, Brittany G., Marie Simonin, Jeffrey A. Back, Steven M. Anderson, Astrid Avellan, Christina M. Bergemann, Benjamin T. Castellon, et al. “Copper and Gold Nanoparticles Increase Nutrient Excretion Rates of Primary Consumers.” Environmental Science & Technology 54, no. 16 (August 2020): 10170–80. https://doi.org/10.1021/acs.est.0c02197.
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• Naslund, Laura C., Jacqueline R. Gerson, Alexander C. Brooks, David M. Walters, and Emily S. Bernhardt. “Contaminant Subsidies to Riparian Food Webs in Appalachian Streams Impacted by Mountaintop Removal Coal Mining.” Environmental Science & Technology 54, no. 7 (April 2020): 3951–59. https://doi.org/10.1021/acs.est.9b05907.
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• Rocca, Jennifer D., Marie Simonin, Emily S. Bernhardt, Alex D. Washburne, and Justin P. Wright. “Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing.” Ecology 101, no. 3 (March 2020): e02956. https://doi.org/10.1002/ecy.2956.
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• Avellan, Astrid, Marie Simonin, Steven M. Anderson, Nicholas K. Geitner, Nathan Bossa, Eleanor Spielman-Sun, Emily S. Bernhardt, et al. “Differential Reactivity of Copper- and Gold-Based Nanomaterials Controls Their Seasonal Biogeochemical Cycling and Fate in a Freshwater Wetland Mesocosm.” Environmental Science & Technology 54, no. 3 (February 2020): 1533–44. https://doi.org/10.1021/acs.est.9b05097.
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• Ury, Emily A., Steven M. Anderson, Robert K. Peet, Emily S. Bernhardt, and Justin P. Wright. “Succession, regression and loss: does evidence of saltwater exposure explain recent changes in the tree communities of North Carolina's Coastal Plain?” Annals of Botany 125, no. 2 (February 2020): 255–64. https://doi.org/10.1093/aob/mcz039.
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• Bier, R. L., J. J. Wernegreen, R. J. Vilgalys, J. C. Ellis, and E. S. Bernhardt. “Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage.” Limnology and Oceanography 65, no. S1 (January 1, 2020): S277–92. https://doi.org/10.1002/lno.11301.
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• Geitner, N. K., C. Ogilvie Hendren, G. Cornelis, R. Kaegi, J. R. Lead, G. V. Lowry, I. Lynch, et al. “Harmonizing across environmental nanomaterial testing media for increased comparability of nanomaterial datasets.” Environmental Science: Nano 7, no. 1 (January 1, 2020): 13–36. https://doi.org/10.1039/c9en00448c.
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• Gerson, Jacqueline R., Simon N. Topp, Claudia M. Vega, John R. Gardner, Xiao Yang, Luis E. Fernandez, Emily S. Bernhardt, and Tamlin M. Pavelsky. “Artificial lake expansion amplifies mercury pollution from gold mining.” Science Advances 6, no. 48 (November 27, 2020). https://doi.org/10.1126/sciadv.abd4953.
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• Gerson, J. R., L. C. Naslund, Y. T. Liu, H. Hsu-Kim, C. T. Driscoll, M. R. V. Ross, M. N. Waters, and E. S. Bernhardt. “Mercury and selenium loading in mountaintop mining impacted alkaline streams and riparian food webs.” Biogeochemistry 150, no. 1 (August 1, 2020): 109–22. https://doi.org/10.1007/s10533-020-00690-7.
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2019

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• Brooks, A., M. R. V. Ross, F. Nippgen, B. McGlynn, and E. Bernhardt. “Excess Nitrate Export in Mountaintop Removal Coal Mining Watersheds.” Journal of Geophysical Research: Biogeosciences 124, no. 12 (December 1, 2019): 3867–80. https://doi.org/10.1029/2019JG005174.
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• Chamberlin, Catherine A., Emily S. Bernhardt, Emma J. Rosi, and James B. Heffernan. “Stoichiometry and daily rhythms: experimental evidence shows nutrient limitation decouples N uptake from photosynthesis.” Ecology 100, no. 10 (October 2019): e02822. https://doi.org/10.1002/ecy.2822.
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• Koenig, Lauren E., Ashley M. Helton, Philip Savoy, Enrico Bertuzzo, James B. Heffernan, Robert O. Hall, and Emily S. Bernhardt. “Emergent productivity regimes of river networks.” Limnology and Oceanography Letters 4, no. 5 (October 2019): 173–81. https://doi.org/10.1002/lol2.10115.
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• Simonin, Marie, Kristofor A. Voss, Brooke A. Hassett, Jennifer D. Rocca, Si-Yi Wang, Raven L. Bier, Christy R. Violin, Justin P. Wright, and Emily S. Bernhardt. “In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient.” Environmental Microbiology 21, no. 10 (October 2019): 3653–68. https://doi.org/10.1111/1462-2920.14694.
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• Savoy, P., A. P. Appling, J. B. Heffernan, E. G. Stets, J. S. Read, J. W. Harvey, and E. S. Bernhardt. “Metabolic rhythms in flowing waters: An approach for classifying river productivity regimes.” Limnology and Oceanography 64, no. 5 (September 1, 2019): 1835–51. https://doi.org/10.1002/lno.11154.
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• Helton, A. M., M. Ardón, and E. S. Bernhardt. “Hydrologic Context Alters Greenhouse Gas Feedbacks of Coastal Wetland Salinization.” Ecosystems 22, no. 5 (August 15, 2019): 1108–25. https://doi.org/10.1007/s10021-018-0325-2.                                                             Full Text
• Blaszczak, J. R., J. M. Delesantro, Y. Zhong, D. L. Urban, and E. S. Bernhardt. “Watershed urban development controls on urban streamwater chemistry variability.” Biogeochemistry 144, no. 1 (June 15, 2019): 61–84. https://doi.org/10.1007/s10533-019-00572-7.
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• Blaszczak, J. R., J. M. Delesantro, D. L. Urban, M. W. Doyle, and E. S. Bernhardt. “Scoured or suffocated: Urban stream ecosystems oscillate between hydrologic and dissolved oxygen extremes.” Limnology and Oceanography 64, no. 3 (May 1, 2019): 877–94. https://doi.org/10.1002/lno.11081.
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• Tully, K., K. Gedan, R. Epanchin-Niell, A. Strong, E. S. Bernhardt, T. Bendor, M. Mitchell, et al. “The invisible flood: The chemistry, ecology, and social implications of coastal saltwater intrusion.” Bioscience 69, no. 5 (May 1, 2019): 368–78. https://doi.org/10.1093/biosci/biz027.
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• Brandt, Jessica E., Marie Simonin, Richard T. Di Giulio, and Emily S. Bernhardt. “Beyond Selenium: Coal Combustion Residuals Lead to Multielement Enrichment in Receiving Lake Food Webs.” Environmental Science & Technology 53, no. 8 (April 2019): 4119–27. https://doi.org/10.1021/acs.est.9b00324.
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• Wen, Y., E. S. Bernhardt, W. Deng, W. Liu, J. Yan, E. M. Baruch, and C. M. Bergemann. “Salt effects on carbon mineralization in southeastern coastal wetland soils of the United States.” Geoderma 339 (April 1, 2019): 31–39. https://doi.org/10.1016/j.geoderma.2018.12.035.
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• Reinhold, A. M., G. C. Poole, C. Izurieta, A. M. Helton, and E. S. Bernhardt. “Constraint-based simulation of multiple interactive elemental cycles in biogeochemical systems.” Ecological Informatics 50 (March 1, 2019): 102–21. https://doi.org/10.1016/j.ecoinf.2018.12.008.
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• Rocca, J.D., M. Simonin, J.R. Blaszczak, J.G. Ernakovich, S.M. Gibbons, F.S. Midani, and A.D. Washburne. 2019. The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities. Frontiers in Microbiology. Online first.

2018

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• Appling, Alison P., Jordan S. Read, Luke A. Winslow, Maite Arroita, Emily S. Bernhardt, Natalie A. Griffiths, Robert O. Hall, et al. “The metabolic regimes of 356 rivers in the United States.” Scientific Data 5 (December 11, 2018): 180292. https://doi.org/10.1038/sdata.2018.292.
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• Brandt, J. E., N. E. Lauer, A. Vengosh, E. S. Bernhardt, and R. T. Di Giulio. “Strontium Isotope Ratios in Fish Otoliths as Biogenic Tracers of Coal Combustion Residual Inputs to Freshwater Ecosystems.” Environmental Science and Technology Letters 5, no. 12 (December 11, 2018): 718–23. https://doi.org/10.1021/acs.estlett.8b00477.
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• Marinos, Richard E., John L. Campbell, Charles T. Driscoll, Gene E. Likens, William H. McDowell, Emma J. Rosi, Lindsey E. Rustad, and Emily S. Bernhardt. “Give and Take: A Watershed Acid Rain Mitigation Experiment Increases Baseflow Nitrogen Retention but Increases Stormflow Nitrogen Export.” Environmental Science & Technology 52, no. 22 (November 8, 2018): 13155–65. https://doi.org/10.1021/acs.est.8b03553.
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• Avellan, Astrid, Marie Simonin, Eric McGivney, Nathan Bossa, Eleanor Spielman-Sun, Jennifer D. Rocca, Emily S. Bernhardt, et al. “Gold nanoparticle biodissolution by a freshwater macrophyte and its associated microbiome.” Nature Nanotechnology 13, no. 11 (November 2018): 1072–77. https://doi.org/10.1038/s41565-018-0231-y.
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• Marinos, Richard E., and Emily S. Bernhardt. “Soil carbon losses due to higher pH offset vegetation gains due to calcium enrichment in an acid mitigation experiment.” Ecology 99, no. 10 (October 2018): 2363–73. https://doi.org/10.1002/ecy.2478.
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• *Baruch, E. M., K. A. Voss, J. R. Blaszczak, J. Delesantro, D. L. Urban, and E. S. Bernhardt. “Not all pavements lead to streams: Variation in impervious surface connectivity affects urban stream ecosystems.” Freshwater Science 37, no. 3 (September 1, 2018): 673–84. https://doi.org/10.1086/699014.
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• Colman, Benjamin P., Leanne F. Baker, Ryan S. King, Cole W. Matson, Jason M. Unrine, Stella M. Marinakos, Danielle E. Gorka, and Emily S. Bernhardt. “Dosing, Not the Dose: Comparing Chronic and Pulsed Silver Nanoparticle Exposures.” Environmental Science & Technology 52, no. 17 (September 2018): 10048–56. https://doi.org/10.1021/acs.est.8b01700.
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• Covino, T. P., E. S. Bernhardt, and J. B. Heffernan. “Measuring and interpreting relationships between nutrient supply, demand, and limitation.” Freshwater Science 37, no. 3 (September 1, 2018): 448–55. https://doi.org/10.1086/699202.
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• Geitner, Nicholas K., Jane L. Cooper, Astrid Avellan, Benjamin T. Castellon, Brittany G. Perrotta, Nathan Bossa, Marie Simonin, et al. “Size-Based Differential Transport, Uptake, and Mass Distribution of Ceria (CeO2) Nanoparticles in Wetland Mesocosms.” Environmental Science & Technology 52, no. 17 (September 2018): 9768–76. https://doi.org/10.1021/acs.est.8b02040.
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• Hall, Ed K., Emily S. Bernhardt, Raven L. Bier, Mark A. Bradford, Claudia M. Boot, James B. Cotner, Paul A. Del Giorgio, et al. “Understanding how microbiomes influence the systems they inhabit.” Nature Microbiology 3, no. 9 (September 2018): 977–82. https://doi.org/10.1038/s41564-018-0201-z.
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• Hassett, B. A., E. B. Sudduth, K. A. Somers, D. L. Urban, C. R. Violin, S. Y. Wang, J. P. Wright, R. M. Cory, and E. S. Bernhardt. “Pulling apart the urbanization axis: patterns of physiochemical degradation and biological response across stream ecosystems.” Freshwater Science 37, no. 3 (September 1, 2018): 653–72. https://doi.org/10.1086/699387.
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• Simonin, Marie, Benjamin P. Colman, Steven M. Anderson, Ryan S. King, Matthew T. Ruis, Astrid Avellan, Christina M. Bergemann, et al. “Engineered nanoparticles interact with nutrients to intensify eutrophication in a wetland ecosystem experiment.” Ecological Applications : A Publication of the Ecological Society of America 28, no. 6 (September 2018): 1435–49. https://doi.org/10.1002/eap.1742.
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• Ross, M. R. V., F. Nippgen, B. A. Hassett, B. L. McGlynn, and E. S. Bernhardt. “Pyrite Oxidation Drives Exceptionally High Weathering Rates and Geologic CO2 Release in Mountaintop-Mined Landscapes.” Global Biogeochemical Cycles 32, no. 8 (August 1, 2018): 1182–94. https://doi.org/10.1029/2017GB005798.
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• Blaszczak, J. R., M. K. Steele, B. D. Badgley, J. B. Heffernan, S. E. Hobbie, J. L. Morse, E. N. Rivers, et al. “Sediment chemistry of urban stormwater ponds and controls on denitrification.” Ecosphere 9, no. 6 (June 1, 2018). https://doi.org/10.1002/ecs2.2318.
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• Rohr, J. R., E. S. Bernhardt, M. W. Cadotte, and W. H. Clements. “The ecology and economics of restoration: When, what, where, and how to restore ecosystems.” Ecology and Society 23, no. 2 (June 1, 2018). https://doi.org/10.5751/ES-09876-230215.
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• Bernhardt, E. S., J. B. Heffernan, N. B. Grimm, E. H. Stanley, J. W. Harvey, M. Arroita, A. P. Appling, et al. “The metabolic regimes of flowing waters.” Limnology and Oceanography 63 (March 1, 2018): S99–118. https://doi.org/10.1002/lno.10726.
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• Ardón, M., A. M. Helton, and E. S. Bernhardt. “Salinity effects on greenhouse gas emissions from wetland soils are contingent upon hydrologic setting: a microcosm experiment.” Biogeochemistry, January 1, 2018. https://doi.org/10.1007/s10533-018-0486-2.
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• Bhattachan, A., R. E. Emanuel, M. Ardón, E. S. Bernhardt, S. M. Anderson, M. G. Stillwagon, E. A. Ury, T. K. BenDor, and J. P. Wright. “Evaluating the effects of land-use change and future climate change on vulnerability of coastal landscapes to saltwater intrusion.” Elementa 6 (January 1, 2018). https://doi.org/10.1525/elementa.316.
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• Gerson, J. R., C. T. Driscoll, H. Hsu-Kim, and E. S. Bernhardt. “Senegalese artisanal gold mining leads to elevated total mercury and methylmercury concentrations in soils, sediments, and rivers.” Elementa 6 (January 1, 2018). https://doi.org/10.1525/elementa.274.
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• Pericak, Andrew A., Christian J. Thomas, David A. Kroodsma, Matthew F. Wasson, Matthew R. V. Ross, Nicholas E. Clinton, David J. Campagna, Yolandita Franklin, Emily S. Bernhardt, and John F. Amos. “Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine.” Plos One 13, no. 7 (January 2018): e0197758. https://doi.org/10.1371/journal.pone.0197758.
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• Simonin, Marie, Benjamin P. Colman, Weiyi Tang, Jonathan D. Judy, Steven M. Anderson, Christina M. Bergemann, Jennifer D. Rocca, Jason M. Unrine, Nicolas Cassar, and Emily S. Bernhardt. “Plant and Microbial Responses to Repeated Cu(OH)2 Nanopesticide Exposures Under Different Fertilization Levels in an Agro-Ecosystem.” Frontiers in Microbiology 9 (January 2018): 1769. https://doi.org/10.3389/fmicb.2018.01769.
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2017

• Eagle, A. J., L. P. Olander, K. L. Locklier, J. B. Heffernan, and E. S. Bernhardt. “Fertilizer management and environmental factors drive n2o and no3 losses in corn: A meta-analysis.” Soil Science Society of America Journal 81, no. 5 (September 1, 2017): 1191–1202. https://doi.org/10.2136/sssaj2016.09.0281.
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• Nippgen, Fabian, Matthew R. V. Ross, Emily S. Bernhardt, and Brian L. McGlynn. “Creating a More Perennial Problem? Mountaintop Removal Coal Mining Enhances and Sustains Saline Baseflows of Appalachian Watersheds.” Environmental Science & Technology 51, no. 15 (August 2017): 8324–34. https://doi.org/10.1021/acs.est.7b02288.
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• Arnold, M. C., R. L. Bier, T. T. Lindberg, E. S. Bernhardt, and R. T. Di Giulio. “Biofilm mediated uptake of selenium in streams with mountaintop coal mine drainage.” Limnologica 65 (July 1, 2017): 10–13. https://doi.org/10.1016/j.limno.2017.05.002.
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• Voss, K. A., and E. S. Bernhardt. “Effects of mountaintop removal coal mining on the diversity and secondary productivity of Appalachian rivers.” Limnology and Oceanography 62, no. 4 (July 1, 2017): 1754–70. https://doi.org/10.1002/lno.10531.
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• Bernhardt, Emily S., Joanna R. Blaszczak, Cari D. Ficken, Megan L. Fork, Kendra E. Kaiser, and Erin C. Seybold. “Control Points in Ecosystems: Moving Beyond the Hot Spot Hot Moment Concept.” Ecosystems. 20, no. 4 (June 2017): 665–82. https://doi.org/10.1007/s10021-016-0103-y.
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• Bernhardt, E. S., E. J. Rosi, and M. O. Gessner. “Synthetic chemicals as agents of global change.” Frontiers in Ecology and the Environment 15, no. 2 (March 1, 2017): 84–90. https://doi.org/10.1002/fee.1450.
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• Brandt, Jessica E., Emily S. Bernhardt, Gary S. Dwyer, and Richard T. Di Giulio. “Selenium Ecotoxicology in Freshwater Lakes Receiving Coal Combustion Residual Effluents: A North Carolina Example.” Environmental Science & Technology 51, no. 4 (February 6, 2017): 2418–26. https://doi.org/10.1021/acs.est.6b05353.
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• Ardón, M., A. M. Helton, M. D. Scheuerell, and E. S. Bernhardt. “Fertilizer legacies meet saltwater incursion: Challenges and constraints for coastal plain wetland restoration.” Elementa 5 (January 1, 2017). https://doi.org/10.1525/elementa.236.
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• Lee, Marissa R., Emily S. Bernhardt, Peter M. van Bodegom, J Hans C. Cornelissen, Jens Kattge, Daniel C. Laughlin, Ülo Niinemets, et al. “Invasive species' leaf traits and dissimilarity from natives shape their impact on nitrogen cycling: a meta-analysis.” The New Phytologist 213, no. 1 (January 2017): 128–39. https://doi.org/10.1111/nph.14115.
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2016

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• Hiers, J Kevin, Stephen T. Jackson, Richard J. Hobbs, Emily S. Bernhardt, and Leonie E. Valentine. “The Precision Problem in Conservation and Restoration.” Trends in Ecology & Evolution 31, no. 11 (November 2016): 820–30. https://doi.org/10.1016/j.tree.2016.08.001.
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• Weathers, K. C., P. M. Groffman, E. Van Dolah, E. Bernhardt, N. B. Grimm, K. McMahon, J. Schimel, et al. “Frontiers in Ecosystem Ecology from a Community Perspective: The Future is Boundless and Bright.” Ecosystems 19, no. 5 (August 1, 2016): 753–70. https://doi.org/10.1007/s10021-016-9967-0.
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• Baalousha, Mohammed, Yi Yang, Marina E. Vance, Benjamin P. Colman, Samantha McNeal, Jie Xu, Joanna Blaszczak, Meredith Steele, Emily Bernhardt, and Michael F. Hochella. “Outdoor urban nanomaterials: The emergence of a new, integrated, and critical field of study.” The Science of the Total Environment 557–558 (July 2016): 740–53. https://doi.org/10.1016/j.scitotenv.2016.03.132.
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• Rosi-Marshall, Emma J., Emily S. Bernhardt, Donald C. Buso, Charles T. Driscoll, and Gene E. Likens. “Acid rain mitigation experiment shifts a forested watershed from a net sink to a net source of nitrogen.” Proceedings of the National Academy of Sciences of the United States of America 113, no. 27 (July 2016): 7580–83. https://doi.org/10.1073/pnas.1607287113.
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• Singh, Nitin K., Wilmer M. Reyes, Emily S. Bernhardt, Ruchi Bhattacharya, Judy L. Meyer, Jennifer D. Knoepp, and Ryan E. Emanuel. “Hydro-Climatological Influences on Long-Term Dissolved Organic Carbon in a Mountain Stream of the Southeastern United States.” Journal of Environmental Quality 45, no. 4 (July 2016): 1286–95. https://doi.org/10.2134/jeq2015.10.0537.
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• Somers, K. A., E. S. Bernhardt, B. L. Mcglynn, and D. L. Urban. “Downstream Dissipation of Storm Flow Heat Pulses: A Case Study and its Landscape-Level Implications.” Journal of the American Water Resources Association 52, no. 2 (April 1, 2016): 281–97. https://doi.org/10.1111/1752-1688.12382.
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• Di Giulio, R. T., E. S. Bernhardt, A. Vengosh, H. Hsu-Kim, and J. E. Brandt. “Legacy impacts of coal combusion residues in freshwater ecosystems in North Carolina.” Water Resources Research Institute News of the University of North Carolina, no. 464 (March 1, 2016).
• Ross, Matthew R. V., Brian L. McGlynn, and Emily S. Bernhardt. “Deep Impact: Effects of Mountaintop Mining on Surface Topography, Bedrock Structure, and Downstream Waters.” Environmental Science & Technology 50, no. 4 (February 4, 2016): 2064–74. https://doi.org/10.1021/acs.est.5b04532.
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• Ardón, Marcelo, Ashley M. Helton, and Emily S. Bernhardt. “Drought and saltwater incursion synergistically reduce dissolved organic carbon export from coastal freshwater wetlands.” Biogeochemistry. 127, no. 2–3 (February 2016): 411–26. https://doi.org/10.1007/s10533-016-0189-5.
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2015

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• Bier, Raven L., Emily S. Bernhardt, Claudia M. Boot, Emily B. Graham, Edward K. Hall, Jay T. Lennon, Diana R. Nemergut, et al. “Linking microbial community structure and microbial processes: an empirical and conceptual overview.” Fems Microbiology Ecology 91, no. 10 (October 2015). https://doi.org/10.1093/femsec/fiv113.
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• Helton, Ashley M., Marcelo Ardón, and Emily S. Bernhardt. “Thermodynamic constraints on the utility of ecological stoichiometry for explaining global biogeochemical patterns.” Ecology Letters 18, no. 10 (October 2015): 1049–56. https://doi.org/10.1111/ele.12487.
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• Gorka, Danielle E., Joshua S. Osterberg, Carley A. Gwin, Benjamin P. Colman, Joel N. Meyer, Emily S. Bernhardt, Claudia K. Gunsch, Richard T. DiGulio, and Jie Liu. “Reducing Environmental Toxicity of Silver Nanoparticles through Shape Control.” Environmental Science & Technology 49, no. 16 (August 2015): 10093–98. https://doi.org/10.1021/acs.est.5b01711.
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• Bier, Raven L., Kristofor A. Voss, and Emily S. Bernhardt. “Bacterial community responses to a gradient of alkaline mountaintop mine drainage in Central Appalachian streams.” The Isme Journal 9, no. 6 (June 2015): 1378–90. https://doi.org/10.1038/ismej.2014.222.
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• Duncan, J. M., L. E. Band, P. M. Groffman, and E. S. Bernhardt. “Mechanisms driving the seasonality of catchment scale nitrate export: Evidence for riparian ecohydrologic controls.” Water Resources Research 51, no. 6 (June 1, 2015): 3982–97. https://doi.org/10.1002/2015WR016937.
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• Arnold, Mariah C., Lisa A. Friedrich, T Ty Lindberg, Matthew Ross, Norman M. Halden, Emily Bernhardt, Vince P. Palace, and Richard T. Di Giulio. “Microchemical analysis of selenium in otoliths of two West Virginia fishes captured near mountaintop removal coal mining operations.” Environmental Toxicology and Chemistry 34, no. 5 (May 2015): 1039–44. https://doi.org/10.1002/etc.2885.
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• Helton, A. M., M. S. Wright, E. S. Bernhardt, G. C. Poole, R. M. Cory, and J. A. Stanford. “Dissolved organic carbon lability increases with water residence time in the alluvial aquifer of a river floodplain ecosystem.” Journal of Geophysical Research G: Biogeosciences 120, no. 4 (April 1, 2015): 693–706. https://doi.org/10.1002/2014JG002832.
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• Yang, Yi, Benjamin P. Colman, Emily S. Bernhardt, and Michael F. Hochella. “Importance of a nanoscience approach in the understanding of major aqueous contamination scenarios: case study from a recent coal ash spill.” Environmental Science & Technology 49, no. 6 (March 2015): 3375–82. https://doi.org/10.1021/es505662q.
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• Voss, K. A., R. S. King, and E. S. Bernhardt. “From a line in the sand to a landscape of decisions: A hierarchical diversity decision framework for estimating and communicating biodiversity loss along anthropogenic gradients.” Methods in Ecology and Evolution 6, no. 7 (January 1, 2015): 795–805. https://doi.org/10.1111/2041-210X.12379.
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2014

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• Payn, R. A., A. M. Helton, G. C. Poole, C. Izurieta, A. J. Burgin, and E. S. Bernhardt. “A generalized optimization model of microbially driven aquatic biogeochemistry based on thermodynamic, kinetic, and stoichiometric ecological theory.” Ecological Modelling 294 (December 4, 2014): 1–18. https://doi.org/10.1016/j.ecolmodel.2014.09.003.
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• Schoepfer, V. A., E. S. Bernhardt, and A. J. Burgin. “Iron clad wetlands: Soil iron-sulfur buffering determines coastal wetland response to salt water incursion.” Journal of Geophysical Research: Biogeosciences 119, no. 12 (December 1, 2014): 2209–19. https://doi.org/10.1002/2014JG002739.
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• Appling, A. P., E. S. Bernhardt, and J. A. Stanford. “Floodplain biogeochemical mosaics: A multidimensional view of alluvial soils.” Journal of Geophysical Research G: Biogeosciences 119, no. 8 (August 1, 2014): 1538–53. https://doi.org/10.1002/2013JG002543.
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• Helton, Ashley M., Emily S. Bernhardt, and Anna Fedders. “Biogeochemical regime shifts in coastal landscapes: the contrasting effects of saltwater incursion and agricultural pollution on greenhouse gas emissions from a freshwater wetland.” Biogeochemistry. 120, no. 1–3 (August 2014): 133–47. https://doi.org/10.1007/s10533-014-9986-x.
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• Carmichael, M. J., E. S. Bernhardt, S. L. Bräuer, and W. K. Smith. “The role of vegetation in methane flux to the atmosphere: should vegetation be included as a distinct category in the global methane budget?” Biogeochemistry. 119, no. 1–3 (June 2014): 1–24. https://doi.org/10.1007/s10533-014-9974-1.
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• Colman, Benjamin P., Benjamin Espinasse, Curtis J. Richardson, Cole W. Matson, Gregory V. Lowry, Dana E. Hunt, Mark R. Wiesner, and Emily S. Bernhardt. “Emerging contaminant or an old toxin in disguise? Silver nanoparticle impacts on ecosystems.” Environmental Science & Technology 48, no. 9 (May 2014): 5229–36. https://doi.org/10.1021/es405454v.
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2013

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• Ardón, Marcelo, Jennifer L. Morse, Benjamin P. Colman, and Emily S. Bernhardt. “Drought-induced saltwater incursion leads to increased wetland nitrogen export.” Global Change Biology 19, no. 10 (October 2013): 2976–85. https://doi.org/10.1111/gcb.12287.
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• Bernhardt, Emily S. “Ecology. Cleaner lakes are dirtier lakes.” Science (New York, N.Y.) 342, no. 6155 (October 2013): 205–6. https://doi.org/10.1126/science.1245279.
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• Baron, J. S., E. K. Hall, B. T. Nolan, J. C. Finlay, E. S. Bernhardt, J. A. Harrison, F. Chan, and E. W. Boyer. “The interactive effects of excess reactive nitrogen and climate change on aquatic ecosystems and water resources of the United States.” Biogeochemistry. 114, no. 1–3 (July 2013): 71–92. https://doi.org/10.1007/s10533-012-9788-y.
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• Sudduth, E. B., S. S. Perakis, and E. S. Bernhardt. “Nitrate in watersheds: Straight from soils to streams?” Journal of Geophysical Research: Biogeosciences 118, no. 1 (March 1, 2013): 291–302. https://doi.org/10.1002/jgrg.20030.
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• Morse, Jennifer L., and Emily S. Bernhardt. “Using 15N tracers to estimate N2O and N2 emissions from nitrification and denitrification in coastal plain wetlands under contrasting land-uses.” Soil Biology & Biochemistry 57 (February 2013): 635–43. https://doi.org/10.1016/j.soilbio.2012.07.025.
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• Cha, Y., C. A. Stow, and E. S. Bernhardt. “Impacts of dreissenid mussel invasions on chlorophyll and total phosphorus in 25 lakes in the USA.” Freshwater Biology 58, no. 1 (January 1, 2013): 192–206. https://doi.org/10.1111/fwb.12050.
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• Colman, Benjamin P., Christina L. Arnaout, Sarah Anciaux, Claudia K. Gunsch, Michael F. Hochella, Bojeong Kim, Gregory V. Lowry, et al. “Low concentrations of silver nanoparticles in biosolids cause adverse ecosystem responses under realistic field scenario.” Plos One 8, no. 2 (January 2013): e57189. https://doi.org/10.1371/journal.pone.0057189.
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• Levard, Clement, Ernest M. Hotze, Benjamin P. Colman, Amy L. Dale, Lisa Truong, X. Y. Yang, Audrey J. Bone, et al. “Sulfidation of silver nanoparticles: natural antidote to their toxicity.” Environmental Science & Technology 47, no. 23 (January 2013): 13440–48. https://doi.org/10.1021/es403527n.
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• Lutz, Brian D., Emily S. Bernhardt, and William H. Schlesinger. “The environmental price tag on a ton of mountaintop removal coal.” Plos One 8, no. 9 (January 2013): e73203. https://doi.org/10.1371/journal.pone.0073203.
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• Riegel, Joseph B., Emily Bernhardt, and Jennifer Swenson. “Estimating above-ground carbon biomass in a newly restored coastal plain wetland using remote sensing.” Plos One 8, no. 6 (January 2013): e68251. https://doi.org/10.1371/journal.pone.0068251.
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• Somers, K. A., E. S. Bernhardt, J. B. Grace, B. A. Hassett, E. B. Sudduth, S. Wang, and D. L. Urban. “Streams in the urban heat island: Spatial and temporal variability in temperature.” Freshwater Science 32, no. 1 (January 1, 2013): 309–26. https://doi.org/10.1899/12-046.1.
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• Wang, S. -. Y., E. S. Bernhardt, and J. P. Wright. “Urban stream denitrifier communities are linked to lower functional resistance to multiple stressors associated with urbanization.” Hydrobiologia, 2013, 1–11. https://doi.org/10.1007/s10750-013-1747-7.
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2012

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• Colman, Benjamin P., Si-Yi Wang, Melanie Auffan, Mark R. Wiesner, and Emily S. Bernhardt. “Antimicrobial effects of commercial silver nanoparticles are attenuated in natural streamwater and sediment.” Ecotoxicology (London, England) 21, no. 7 (October 2012): 1867–77. https://doi.org/10.1007/s10646-012-0920-5.
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• Phillips, Richard P., Ina C. Meier, Emily S. Bernhardt, A Stuart Grandy, Kyle Wickings, and Adrien C. Finzi. “Roots and fungi accelerate carbon and nitrogen cycling in forests exposed to elevated CO2.” Ecology Letters 15, no. 9 (September 2012): 1042–49. https://doi.org/10.1111/j.1461-0248.2012.01827.x.
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• Bernhardt, Emily S., Brian D. Lutz, Ryan S. King, John P. Fay, Catherine E. Carter, Ashley M. Helton, David Campagna, and John Amos. “How many mountains can we mine? Assessing the regional degradation of Central Appalachian rivers by surface coal mining.” Environmental Science & Technology 46, no. 15 (August 2012): 8115–22. https://doi.org/10.1021/es301144q.
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• Lutz, B. D., P. J. Mulholland, and E. S. Bernhardt. “Long-term data reveal patterns and controls on stream water chemistry in a forested stream: Walker branch, Tennessee.” Ecological Monographs 82, no. 3 (August 1, 2012): 367–87. https://doi.org/10.1890/11-1129.1.
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• Izurieta, C., G. Poole, R. A. Payn, I. Griffith, R. Nix, A. Helton, E. Bernhardt, and A. J. Burgin. “Development and application of a simulation environment (NEO) for integrating empirical and computational investigations of system-level complexity.” 2012 International Conference on Information Science and Applications, Icisa 2012, July 30, 2012. https://doi.org/10.1109/ICISA.2012.6220928.
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• Lowry, Gregory V., Benjamin P. Espinasse, Appala Raju Badireddy, Curtis J. Richardson, Brian C. Reinsch, Lee D. Bryant, Audrey J. Bone, et al. “Long-term transformation and fate of manufactured ag nanoparticles in a simulated large scale freshwater emergent wetland.” Environmental Science & Technology 46, no. 13 (July 2012): 7027–36. https://doi.org/10.1021/es204608d.
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• Morse, J. L., M. Ardón, and E. S. Bernhardt. “Using environmental variables and soil processes to forecast denitrification potential and nitrous oxide fluxes in coastal plain wetlands across different land uses.” Journal of Geophysical Research: Biogeosciences 117, no. 2 (June 1, 2012). https://doi.org/10.1029/2011JG001923.
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• Lutz, B. D., E. S. Bernhardt, B. J. Roberts, R. M. Cory, and P. J. Mulholland. “Distinguishing dynamics of dissolved organic matter components in a forested stream using kinetic enrichments.” Limnology and Oceanography 57, no. 1 (January 1, 2012): 76–89. https://doi.org/10.4319/lo.2012.57.1.0076.
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• Yin, Liyan, Benjamin P. Colman, Bonnie M. McGill, Justin P. Wright, and Emily S. Bernhardt. “Effects of silver nanoparticle exposure on germination and early growth of eleven wetland plants.” Plos One 7, no. 10 (January 2012): e47674. https://doi.org/10.1371/journal.pone.0047674.​                                                                                                                                                                              Full Text

2011

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• Lindberg, T Ty, Emily S. Bernhardt, Raven Bier, A. M. Helton, R Brittany Merola, Avner Vengosh, and Richard T. Di Giulio. “Cumulative impacts of mountaintop mining on an Appalachian watershed.” Proceedings of the National Academy of Sciences of the United States of America 108, no. 52 (December 12, 2011): 20929–34. https://doi.org/10.1073/pnas.1112381108.
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• Baulch, Helen M., Emily H. Stanley, and Emily S. Bernhardt. “Can algal uptake stop NO3(-) pollution?” Nature 477, no. 7366 (September 28, 2011): E3. https://doi.org/10.1038/nature10418.
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• Bernhardt, E. S., and M. A. Palmer. “Evaluating river restoration.” Ecological Applications 21, no. 6 (September 1, 2011): 1925. https://doi.org/10.1890/11-0644.1.
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• Bernhardt, Emily S., and Margaret A. Palmer. “River restoration: the fuzzy logic of repairing reaches to reverse catchment scale degradation.” Ecological Applications : A Publication of the Ecological Society of America 21, no. 6 (September 2011): 1926–31. https://doi.org/10.1890/10-1574.1.
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• Sudduth, Elizabeth B., Brooke A. Hassett, Peter Cada, and Emily S. Bernhardt. “Testing the field of dreams hypothesis: functional responses to urbanization and restoration in stream ecosystems.” Ecological Applications : A Publication of the Ecological Society of America 21, no. 6 (September 2011): 1972–88. https://doi.org/10.1890/10-0653.1.
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• Violin, Christy R., Peter Cada, Elizabeth B. Sudduth, Brooke A. Hassett, David L. Penrose, and Emily S. Bernhardt. “Effects of urbanization and urban stream restoration on the physical and biological structure of stream ecosystems.” Ecological Applications : A Publication of the Ecological Society of America 21, no. 6 (September 2011): 1932–49. https://doi.org/10.1890/10-1551.1.
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• Muehlbauer, J. D., M. W. Doyle, and E. S. Bernhardt. “Macroinvertebrate community responses to a dewatering disturbance gradient in a restored stream.” Hydrology and Earth System Sciences 15, no. 6 (June 20, 2011): 1771–83. https://doi.org/10.5194/hess-15-1771-2011.
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• Helton, A. M., G. C. Poole, J. L. Meyer, W. M. Wollheim, B. J. Peterson, P. J. Mulholland, E. S. Bernhardt, et al. “Thinking outside the channel: Modeling nitrogen cycling in networked river ecosystems.” Frontiers in Ecology and the Environment 9, no. 4 (May 1, 2011): 229–38. https://doi.org/10.1890/080211.
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• Drake, John E., Anne Gallet-Budynek, Kirsten S. Hofmockel, Emily S. Bernhardt, Sharon A. Billings, Robert B. Jackson, Kurt S. Johnsen, et al. “Increases in the flux of carbon belowground stimulate nitrogen uptake and sustain the long-term enhancement of forest productivity under elevated CO₂.” Ecology Letters 14, no. 4 (April 2011): 349–57. https://doi.org/10.1111/j.1461-0248.2011.01593.x.
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• Cheng, Y., L. Yin, S. Lin, M. Wiesner, E. Bernhardt, and J. Liu. “Toxicity reduction of polymer-stabilized silver nanoparticles by sunlight.” Journal of Physical Chemistry C 115, no. 11 (March 24, 2011): 4425–32. https://doi.org/10.1021/jp109789j.
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• Bernhardt, Emily S., and Margaret A. Palmer. “The environmental costs of mountaintop mining valley fill operations for aquatic ecosystems of the Central Appalachians.” Annals of the New York Academy of Sciences 1223 (March 2011): 39–57. https://doi.org/10.1111/j.1749-6632.2011.05986.x.
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• Lutz, Brian D., Emily S. Bernhardt, Brian J. Roberts, and Patrick J. Mulholland. “Examining the coupling of carbon and nitrogen cycles in Appalachian streams: the role of dissolved organic nitrogen.” Ecology 92, no. 3 (March 2011): 720–32. https://doi.org/10.1890/10-0899.1.
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• Yin, Liyan, Yingwen Cheng, Benjamin Espinasse, Benjamin P. Colman, Melanie Auffan, Mark Wiesner, Jerome Rose, Jie Liu, and Emily S. Bernhardt. “More than the ions: the effects of silver nanoparticles on Lolium multiflorum.” Environmental Science & Technology 45, no. 6 (March 2011): 2360–67. https://doi.org/10.1021/es103995x.
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• Phillips, Richard P., Adrien C. Finzi, and Emily S. Bernhardt. “Enhanced root exudation induces microbial feedbacks to N cycling in a pine forest under long-term CO2 fumigation.” Ecology Letters 14, no. 2 (February 2011): 187–94. https://doi.org/10.1111/j.1461-0248.2010.01570.x.
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• Doyle, Martin W., and Emily S. Bernhardt. “What is a stream?” Environmental Science & Technology 45, no. 2 (January 2011): 354–59. https://doi.org/10.1021/es101273f.
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• Wang, Si-Yi, Elizabeth B. Sudduth, Matthew D. Wallenstein, Justin P. Wright, and Emily S. Bernhardt. “Watershed urbanization alters the composition and function of stream bacterial communities.” Plos One 6, no. 8 (January 2011): e22972. https://doi.org/10.1371/journal.pone.0022972.
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2010

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• Ardón, M., S. Montanari, J. L. Morse, M. W. Doyle, and E. S. Bernhardt. “Phosphorus export from a restored wetland ecosystem in response to natural and experimental hydrologic fluctuations.” Journal of Geophysical Research: Biogeosciences 115, no. 4 (December 1, 2010). https://doi.org/10.1029/2009JG001169.
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• Ardón, Marcelo, Jennifer L. Morse, Martin W. Doyle, and Emily S. Bernhardt. “The Water Quality Consequences of Restoring Wetland Hydrology to a Large Agricultural Watershed in the Southeastern Coastal Plain.” Ecosystems. 13, no. 7 (November 2010): 1060–78. https://doi.org/10.1007/s10021-010-9374-x.
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• Bernhardt, Emily S., Benjamin P. Colman, Michael F. Hochella, Bradley J. Cardinale, Roger M. Nisbet, Curtis J. Richardson, and Liyan Yin. “An ecological perspective on nanomaterial impacts in the environment.” Journal of Environmental Quality 39, no. 6 (November 2010): 1954–65. https://doi.org/10.2134/jeq2009.0479.
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• Lowry, Gregory V., Ernest M. Hotze, Emily S. Bernhardt, Dionysios D. Dionysiou, Joel A. Pedersen, Mark R. Wiesner, and Baoshan Xing. “Environmental occurrences, behavior, fate, and ecological effects of nanomaterials: an introduction to the special series.” Journal of Environmental Quality 39, no. 6 (November 2010): 1867–74. https://doi.org/10.2134/jeq2010.0297.
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• Palmer, M. A., E. S. Bernhardt, W. H. Schlesinger, K. N. Eshleman, E. Foufoula Georgiou, M. S. Hendryx, A. D. Lemly, et al. “Environmental and Human Health Consequences of Mountaintop Removal Mining.” Science 327 (January 2010): 148–49.
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• Palmer, M. A., H. L. Menninger, and E. Bernhardt. “River restoration, habitat heterogeneity and biodiversity: A failure of theory or practice?” Freshwater Biology 55: 205–22. https://doi.org/10.1111/j.1365-2427.2009.02372.x.
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2009

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• Phillips, Richard P., Emily S. Bernhardt, and William H. Schlesinger. “Elevated CO2 increases root exudation from loblolly pine (Pinus taeda) seedlings as an N-mediated response.” Tree Physiology 29, no. 12 (December 2009): 1513–23. https://doi.org/10.1093/treephys/tpp083.
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• Wenger, S. J., A. H. Roy, C. R. Jackson, E. S. Bernhardt, T. L. Carter, S. Filoso, C. A. Gibson, et al. “Twenty-six key research questions in urban stream ecology: An assessment of the state of the science.” Journal of the North American Benthological Society 28, no. 4 (December 1, 2009): 1080–98. https://doi.org/10.1899/08-186.1.
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• Wiesner, Mark R., Gregory V. Lowry, Kimberly L. Jones, Michael F. Hochella, Richard T. Di Giulio, Elizabeth Casman, and Emily S. Bernhardt. “Decreasing uncertainties in assessing environmental exposure, risk, and ecological implications of nanomaterials.” Environmental Science & Technology 43, no. 17 (September 2009): 6458–62. https://doi.org/10.1021/es803621k.
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• Wright, J., A. Symstad, J. M. Bullock, K. Engelhardt, L. Jackson, and E. Bernhardt. “Restoring biodiversity and ecosystem function: Will an integrated approach improve results?,” July 30, 2009. https://doi.org/10.1093/acprof:oso/9780199547951.003.0012.
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• Colman, Benjamin P., Melanie Auffan, Curtis J. Richardson, Emily S. Bernhardt, and Mark Wiesner. “Impacts of nanosilver on microbial activity in wetlands and streams.” Geochimica Et Cosmochimica Acta 73, no. 13 (June 1, 2009): A238–A238.
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2008

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• Craig, L. S., M. A. Palmer, D. C. Richardson, S. Filoso, E. S. Bernhardt, B. P. Bledsoe, M. W. Doyle, et al. “Stream restoration strategies for reducing river nitrogen loads.” Frontiers in Ecology and the Environment 6, no. 10 (December 1, 2008): 529–38. https://doi.org/10.1890/070080.
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• Phillips, R. P., Y. Erlitz, R. Bier, and E. S. Bernhardt. “New approach for capturing soluble root exudates in forest soils.” Functional Ecology 22, no. 6 (December 1, 2008): 990–99. https://doi.org/10.1111/j.1365-2435.2008.01495.x.
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• Bernhardt, E. S., and W. H. McDowell. “Twenty years apart: Comparisons of DOM uptake during leaf leachate releases to Hubbard Brook valley streams in 1979 versus 2000.” Journal of Geophysical Research: Biogeosciences 113, no. 3 (September 28, 2008). https://doi.org/10.1029/2007JG000618.
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• Poole, G. C., S. J. O’Daniel, K. L. Jones, W. W. Woessner, E. S. Bernhardt, A. M. Helton, J. A. Stanford, B. R. Boer, and T. J. Beechie. “Hydrologic spiralling: The role of multiple interactive flow paths in stream ecosystems.” River Research and Applications 24, no. 7 (September 1, 2008): 1018–31. https://doi.org/10.1002/rra.1099.
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• Bernhardt, Emily S., Lawrence E. Band, Christopher J. Walsh, and Philip E. Berke. “Understanding, managing, and minimizing urban impacts on surface water nitrogen loading.” Annals of the New York Academy of Sciences 1134 (January 2008): 61–96. https://doi.org/10.1196/annals.1439.014.
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2007

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• Bernhardt, E. S., E. B. Sudduth, M. A. Palmer, J. D. Allan, J. L. Meyer, G. Alexander, J. Follastad-Shah, et al. “Restoring rivers one reach at a time: Results from a survey of U.S. river restoration practitioners.” Restoration Ecology 15, no. 3 (September 1, 2007): 482–93. https://doi.org/10.1111/j.1526-100X.2007.00244.x.
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• Fierer, Noah, Jennifer L. Morse, Sean T. Berthrong, Emily S. Bernhardt, and Robert B. Jackson. “Environmental controls on the landscape-scale biogeography of stream bacterial communities.” Ecology 88, no. 9 (September 2007): 2162–73. https://doi.org/10.1890/06-1746.1.
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• Follstad Shah, J. J., C. N. Dahm, S. P. Gloss, and E. S. Bernhardt. “River and riparian restoration in the southwest: Results of the National River Restoration Science Synthesis project.” Restoration Ecology 15, no. 3 (September 1, 2007): 550–62. https://doi.org/10.1111/j.1526-100X.2007.00250.x.
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• Hassett, B. A., M. A. Palmer, and E. S. Bernhardt. “Evaluating stream restoration in the Chesapeake Bay watershed through practitioner interviews.” Restoration Ecology 15, no. 3 (September 1, 2007): 563–72. https://doi.org/10.1111/j.1526-100X.2007.00251.x.
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• Kondolf, G. M., S. Anderson, R. Lave, L. Pagano, A. Merenlender, and E. S. Bernhardt. “Two decades of river restoration in California: What can we learn?” Restoration Ecology 15, no. 3 (September 1, 2007): 516–23. https://doi.org/10.1111/j.1526-100X.2007.00247.x.
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• Palmer, M., J. D. Allan, J. Meyer, and E. S. Bernhardt. “River restoration in the twenty-first century: Data and experiential knowledge to inform future efforts.” Restoration Ecology 15, no. 3 (September 1, 2007): 472–81. https://doi.org/10.1111/j.1526-100X.2007.00243.x.
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• Sudduth, E. B., J. L. Meyer, and E. S. Bernhardt. “Stream restoration practices in the southeastern United States.” Restoration Ecology 15, no. 3 (September 1, 2007): 573–83. https://doi.org/10.1111/j.1526-100X.2007.00252.x.
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• Warren, D. R., E. S. Bernhardt, R. O. Hall, and G. E. Likens. “Forest age, wood and nutrient dynamics in headwater streams of the Hubbard Brook Experimental Forest, NH.” Earth Surface Processes and Landforms 32, no. 8 (July 1, 2007): 1154–63. https://doi.org/10.1002/esp.1548.
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• Bernhardt, E. S., and M. A. Palmer. “Restoring streams in an urbanizing world.” Freshwater Biology 52, no. 4 (April 1, 2007): 738–51. https://doi.org/10.1111/j.1365-2427.2006.01718.x.
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2006

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• Bernhardt, E.S, S. E. Bunn, D. D. Hart, B. Malmqvist, T. Muotka, R. J. Naiman, C. Pringle, M. Reuss, and B. Van Wilgen. “Perspective: The challenge of ecologically sustainable water management.” Water Policy 8, no. 5 (October 25, 2006): 475–79. https://doi.org/10.2166/wp.2006.057.
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• Jenkinson, R. G., K. A. Barnas, J. H. Braatne, E. S. Bernhardt, M. A. Palmer, J. D. Allan, G. Alexander, et al. “Stream restoration databases and case studies: A guide to information resources and their utility in advancing the science and practice of restoration.” Restoration Ecology 14, no. 2 (June 1, 2006): 177–86. https://doi.org/10.1111/j.1526-100X.2006.00119.x.
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• Palmer, M. A., and E. S. Bernhardt. “Hydroecology and river restoration: Ripe for research and synthesis.” Water Resources Research 42, no. 3 (March 1, 2006). https://doi.org/10.1029/2005WR004354.
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• Schlesinger, W. H., K. H. Reckhow, and E. S. Bernhardt. “Global change: The nitrogen cycle and rivers.” Water Resources Research 42, no. 3 (March 1, 2006). https://doi.org/10.1029/2005WR004300.
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• Bernhardt, E. S., J. J. Barber, J. S. Pippen, L. Taneva, J. A. Andrews, and W. H. Schlesinger. “Long-term Effects of Free Air CO2 Enrichment (FACE) on Soil Respiration.” Biogeochemistry. 77, no. 1 (January 2006): 91–116. https://doi.org/10.1007/s10533-005-1062-0.
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2005

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• Bernhardt, E. S., M. A. Palmer, J. D. Allan, G. Alexander, K. Barnas, S. Brooks, J. Carr, et al. “Ecology. Synthesizing U.S. river restoration efforts.” Science (New York, N.Y.) 308, no. 5722 (April 2005): 636–37. https://doi.org/10.1126/science.1109769.
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• Palmer, M. A., E. S. Bernhardt, J. D. Allan, P. S. Lake, G. Alexander, S. Brooks, J. Carr, S. Clayton, C. N. Dahm, and J. Follstad Shah. “Standards for ecologically successful river restoration.” Journal of Applied Ecology. 42, no. 2 (April 2005): 208–17. https://doi.org/10.1111/j.1365-2664.2005.01004.x.
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• Bernhardt, E. S., G. E. Likens, R. O. Hall, D. C. Buso, S. G. Fisher, T. M. Burton, J. L. Meyer, et al. “Can't see the forest for the stream? In-stream processing and terrestrial nitrogen exports.” Bioscience 55, no. 3 (January 1, 2005): 219–30. https://doi.org/10.1641/0006-3568(2005)055[0219:ACSTFF]2.0.CO;2.
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• Hassett, B., M. Palmer, E. Bernhardt, S. Smith, J. Carr, and D. Hart. “Restoring watersheds project by project: Trends in Chesapeake Bay tributary restoration.” Frontiers in Ecology and the Environment 3, no. 5 (January 1, 2005): 259–67. https://doi.org/10.1890/1540-9295(2005)003[0259:RWPBPT]2.0.CO;2.
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• Palmer, M.A., E.S. Bernhardt, E.A. Chornesky, S.L. Collins, A.P. Dobson, C.S. Duke, B.D. Gold, R. Jacobson, S. Kingsland, R. Kranz, M.J Mappin, M.L. Martinez, F. Micheli, J.L. Morse, M.L Pace, M. Pascual, S. Palumbi, O.J. Reichman, A.L. Simons, A. Townsend, and M.G. Turner.  2005.  Ecological Science and Sustainability for the 21st Century.  Frontiers in Ecology and the Environment. 3: 4-11

Papers published before Emily Bernhardt joined Duke's faculty are available on her curriculum vitae or Google Scholar page