Emily S. Bernhardt | Scholars@Duke

Emily S. Bernhardt
James B. Duke Distinguished Professor

Emily Bernhardt is an ecosystem ecologist and biogeochemist whose research is principally concerned with tracking the movement of elements through ecological systems. Dr. Bernhardt's research aims to document the extent to which the structure and function of aquatic ecosystems is being altered by land use change (urbanization, agriculture, mining) global change (rising CO₂ , rising sea levels) and chemical pollution. Ultimately this information is necessary to determine whether and how ecosystem change can be mitigated or prevented through active ecosystem management.

Current Appointments & Affiliations

James B. Duke Distinguished Professor, Biology, Trinity College of Arts & Sciences 2019
Professor of Biology, Biology, Trinity College of Arts & Sciences 2016
Professor, Environmental Sciences and Policy, Nicholas School of the Environment 2016
Professor, Marine Science and Conservation, Nicholas School of the Environment 2021
Faculty Network Member of The Energy Initiative, Nicholas Institute-Energy Initiative, Initiatives 2015
Associate of the Duke Initiative for Science & Society, Duke Science & Society, Initiatives 2017

Contact Information

Box 90338, Durham, NC 27708-0000
Ffsc 3313, Durham, NC 27708
emily.bernhardt@duke.edu (919) 660-7318
Bernhardt lab

Background
Education, Training, & Certifications
- Ph.D., Cornell University 2001
- B.S., University of North Carolina - Chapel Hill 1996
Previous Appointments & Affiliations
- Jerry G. and Patricia Crawford Hubbard Professor, Biology, Trinity College of Arts & Sciences 2017 - 2019
- Associate Professor in the Department of Biology, Biology, Trinity College of Arts & Sciences 2010 - 2016
- Associate Professor, Environmental Sciences and Policy, Nicholas School of the Environment 2012 - 2016
- Assistant Professor of Biology, Biology, Trinity College of Arts & Sciences 2004 - 2010
- Assistant Professor of Earth and Ocean Sciences, Earth and Climate Sciences, Nicholas School of the Environment 2005 - 2008
- Assistant Research Professor, Biology, Trinity College of Arts & Sciences 2003 - 2004
Leadership & Clinical Positions at Duke
- Chair, Department of Biology, July 1, 2020 - June 30, 2023
Recognition
In the News
- MAY 2, 2023 Duke Today
  
  Three Faculty Elected to National Academy of Sciences
- FEB 23, 2023 Duke Today
  
  Faculty Exchange Ideas on Duke’s Climate Commitment in Academic Council
- MAR 25, 2022
  
  Let's Talk About Climate Change: Conversations to Build Climate Literacy Among Students
- MAR 10, 2022
  
  Intellectual Breakthroughs
- FEB 18, 2022
  
  Tracking the Pulse of Our Nation’s Rivers, Like a Fitbit for Streams
- JAN 28, 2022
  
  Modern Day Gold Rush Turns Pristine Rainforests into Heavily Polluted Mercury Sinks
- JAN 27, 2022 Duke Research Blog
  
  As Oceans Rise, Finding the Tipping Point for Coastal Wetlands
- SEP 1, 2021
  
  Mountaintop Mining Causes 40 Percent Loss of Aquatic Biodiversity
- APR 5, 2021
  
  Mapping North Carolina’s Ghost Forests From 430 Miles Up
- APR 6, 2020
  
  Stream Pollution From Mountaintop Mining Doesn’t Stay Put in the Water
- MAY 15, 2019 Interdisciplinary Studies
  
  Emily Bernhardt on Hunting Down Mercury Pollution
- MAY 7, 2019
  
  Duke Adds 21 Faculty to Distinguished Faculty Rank
- JUL 25, 2018
  
  Mapping Mountaintop Coal Mining’s Yearly Spread in Appalachia
- JUN 25, 2018
  
  Nanomaterials Could Mean More Algae Outbreaks for Wetlands, Waterways
- OCT 10, 2017 Duke Research Blog
  
  Students Bring Sixty Years of Data to Life on the Web
- AUG 17, 2017 Duke Health News
  
  Lab Tests Show Molecule Appears to Spur Cell Death in Tumors, Inflammation
- JUL 14, 2017 Nicholas School of the Environment
  
  Mountaintop Coal Mining Causes Appalachian Rivers to Run 'Consistently Saltier'
- APR 18, 2017
  
  Five Faculty Named Bass Fellows for Excellence in Teaching and Research
- JAN 24, 2017 Nicholas School of the Environment
  
  Synthetic Chemicals Understudied Drivers of Environmental Change
- JUN 24, 2016
  
  Neutralizing Acidic Forest Soils Boosts Tree Growth but Causes Spike in Nitrogen Export
- MAR 22, 2016 The Atlantic
  
  Jedediah Purdy: The violent remaking of Appalachia
- FEB 9, 2016 Charleston Gazette-Mail
  
  Almost level: Study details how mining flattens W.Va.
- FEB 5, 2016
  
  Central Appalachia Flatter Due to Mountaintop Mining
- OCT 6, 2015
  
  Nicholas Faculty Launch Five-Year Project to Research Stream Biomes
- SEP 13, 2013 International Business Times
  
  Area as big as Washington D.C. needs to be mined every 81 days to meet U.S. coal demand
- SEP 12, 2013
  
  Calculating the True Cost of a Ton of Mountaintop Removal Coal
Awards & Honors
Expertise
Subject Headings
Global Scholarship
- Research
  - United States of America (Country)
Research
Selected Grants
- LTER: Long Term Ecological Research at the Hubbard Brook Experimental Forest. awarded by Cary Institute of Ecosystem Studies 2023 - 2029
- MRA: Continental-scale controls on instream and catchment contributions to greenhouse gas fluxes from rivers awarded by National Science Foundation 2021 - 2026
- THELORACS: Tree Health Evaluated using LiDAR, Optical, and Radar Applications across Coastal Systems awarded by University of Virginia - Charlottesville 2022 - 2025
- Collaborative Research: MRA: MACRO-Sheds: Comparative Ecosystem Biogeochemistry at Continental Scales awarded by National Science Foundation 2019 - 2024
- DISES RCN: SWISLR - Saltwater Intrusion and Sea Level Rise in rural landscapes: Assessing Risk and Identifying Mitigation and Adaptation Options for Rural Coastal Plain Communities. awarded by National Science Foundation 2021 - 2024
- LTREB: Streams to Screens: Bringing the Hubbard Brook Watershed Ecosystem Record (HB-WatER) into the 21st Century awarded by Cary Institute of Ecosystem Studies 2019 - 2024
- Ecosystem Function Model Analysis on the Roanoke River awarded by Army Corps of Engineers 2021 - 2023
- River Ecosystem Phenology in an Increasingly Ice-free World awarded by National Aeronautics and Space Administration 2020 - 2023
- Macrosystems, Collaborative Research: Defining Stream Biomes Beyond the Steady State awarded by National Science Foundation 2015 - 2023
- Center for Environmental Implications of Nanotechnology awarded by National Science Foundation 2008 - 2021
- Community Coalescence: Disentangling Assembly Processes using Aquatic Microbial Communities awarded by National Science Foundation 2018 - 2021
- Collaborative Research: Salinization of the inland coastal plain through saltwater intrusion: landscapes in transition along the leading edge of climate change awarded by National Science Foundation 2015 - 2020
- Mountain top mining effects on watershed hydrology and biogeochemistry awarded by National Science Foundation 2014 - 2019
- DISSERTATION RESEARCH: Will Ecosystem Recovery From Acid Precipitation Jeopardize Soil Carbon Storage? awarded by National Science Foundation 2017 - 2019
- RCN: Smart Civic Engagement in Rapidly Urbanizing Regions awarded by North Carolina State University 2018
- REU Site: Research Experiences for Undergraduates in Environmental Implications of Nanotechnology awarded by National Science Foundation 2014 - 2018
- Streams in urbanizing landscapes: from syndrome diagnosis to watershed prescription awarded by National Science Foundation 2013 - 2018
- DISSERTATION RESEARCH: Pulsed and Pressed: the Interactive Effects of Disturbance Intensity and Complex Chemical Exposure on the Productivity of Urban Stream Ecosystems awarded by National Science Foundation 2016 - 2018
- Legacy impacts of coal combustion residues on freshwater ecosystems in North Carolina awarded by Water Resources Research Institute 2015 - 2016
- Duke Forest FACE Experiment: Forest-Atmosphere Carbon Transfer and Storage awarded by Department of Energy 2001 - 2015
- Bernhardt Sabbatical Research Agreement awarded by Forschungsverbund Berlin e.V. 2014 - 2015
- Nitrogen Losses: A Meta-analysis of 4R Nutrient Management in U.S. Corn-Based Systems awarded by Foundation for Agronomic Research 2014 - 2015
- REU: Research Experience for Undergraudates on Environmental Implications of Nanotechnology awarded by National Science Foundation 2010 - 2014
- Collaborative Research: Coupled Element Cycles of C, N and S in Southeastern Coastal Plain and Wetland Ecosystems awarded by National Science Foundation 2010 - 2013
- COLLABORATIVE RESEARCH: Reconciling human and natural systems for the equitable provision of ecosystem services in the Triangle of North Carolina awarded by National Science Foundation 2009 - 2013
- DISSERTATION RESEARCH:Impact of watershed urbanization and climate change on stream denitrifier community structure and function awarded by National Science Foundation 2010 - 2012
- Quantifying the Impact of Floodplain Trees on River-Borne Nitrogen Removal awarded by Environmental Protection Agency 2008 - 2011
- Career: Potential for the recovery of biogeochemical function in degraded stream ecosystems awarded by National Science Foundation 2006 - 2011
- The National River Restoration Science Synthesis Project awarded by Environmental Protection Agency 2005
External Relationships
- Banco Bilbao Vizcaya Argentaria (BBVA) Foundation
- Cary Institute of Ecosystem Studies
- Elsevier
- National Ecological Observatory Network (NEON), Battelle Corporation
- US Department of Justice
- University of Virginia Environmental Resilience Institute
Publications & Artistic Works
Selected Publications
- Books
  - Schlesinger, W. H., and E. S. Bernhardt. Biogeochemistry: An Analysis of Global Change, Third Edition, 2013. https://doi.org/10.1016/C2010-0-66291-2.
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  - Schlesinger, W. H., and E. S. Bernhardt. Biogeochemistry: an Analysis of Global Change. Academic Press, 2013.
- Academic Articles
  - Rumschlag, Samantha L., Michael B. Mahon, Devin K. Jones, William Battaglin, Jonny Behrens, Emily S. Bernhardt, Paul Bradley, et al. “Density declines, richness increases, and composition shifts in stream macroinvertebrates.” Science Advances 9, no. 18 (May 2023): eadf4896. https://doi.org/10.1126/sciadv.adf4896.
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  - DelVecchia, A. G., S. Rhea, K. S. Aho, E. H. Stanley, E. R. Hotchkiss, A. Carter, and E. S. Bernhardt. “Variability and drivers of CO2, CH4, and N2O concentrations in streams across the United States.” Limnology and Oceanography 68, no. 2 (February 1, 2023): 394–408. https://doi.org/10.1002/lno.12281.
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  - Rhea, Spencer, Nicholas Gubbins, Amanda G. DelVecchia, Matthew R. V. Ross, and Emily S. Bernhardt. “User-focused evaluation of National Ecological Observatory Network streamflow estimates.” Scientific Data 10, no. 1 (February 2023): 89. https://doi.org/10.1038/s41597-023-01983-w.
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  - Rhea, Spencer, Nicholas Gubbins, Amanda G. DelVecchia, Matthew R. V. Ross, and Emily S. Bernhardt. “Author Correction: User-focused evaluation of National Ecological Observatory Network streamflow estimates.” Scientific Data 10, no. 1 (February 2023): 109. https://doi.org/10.1038/s41597-023-02026-0.
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  - Battin, Tom J., Ronny Lauerwald, Emily S. Bernhardt, Enrico Bertuzzo, Lluís Gómez Gener, Robert O. Hall, Erin R. Hotchkiss, et al. “River ecosystem metabolism and carbon biogeochemistry in a changing world.” Nature 613, no. 7944 (January 2023): 449–59. https://doi.org/10.1038/s41586-022-05500-8.
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  - Vlah, M. J., S. Rhea, E. S. Bernhardt, W. Slaughter, N. Gubbins, A. G. DelVecchia, A. Thellman, and M. R. V. Ross. “MacroSheds: A synthesis of long-term biogeochemical, hydroclimatic, and geospatial data from small watershed ecosystem studies.” Limnology and Oceanography Letters, January 1, 2023. https://doi.org/10.1002/lol2.10325.
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  - Rosi, Emma J., Emily S. Bernhardt, Christopher T. Solomon, Gene E. Likens, William H. McDowell, and Irena F. Creed. “Give long-term datasets World Heritage status.” Science (New York, N.Y.) 378, no. 6625 (December 2022): 1180–81. https://doi.org/10.1126/science.adg0508.
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  - Carter, A. M., A. G. DelVecchia, and E. S. Bernhardt. “Patterns and Drivers of Dissolved Gas Concentrations and Fluxes Along a Low Gradient Stream.” Journal of Geophysical Research: Biogeosciences 127, no. 11 (November 1, 2022). https://doi.org/10.1029/2022JG007048.
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  - Bernhardt, Emily. “Coastal freshwater wetlands squeezed between migrating salt marshes and working lands.” Science Advances 8, no. 26 (July 2022): eadd1628. https://doi.org/10.1126/sciadv.add1628.
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  - Delesantro, J. M., J. M. Duncan, D. Riveros-Iregui, J. R. Blaszczak, E. S. Bernhardt, D. L. Urban, and L. E. Band. “The Nonpoint Sources and Transport of Baseflow Nitrogen Loading Across a Developed Rural-Urban Gradient.” Water Resources Research 58, no. 7 (July 1, 2022). https://doi.org/10.1029/2021WR031533.
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  - White, E. E., E. A. Ury, E. S. Bernhardt, and X. Yang. “Climate Change Driving Widespread Loss of Coastal Forested Wetlands Throughout the North American Coastal Plain.” Ecosystems 25, no. 4 (June 1, 2022): 812–27. https://doi.org/10.1007/s10021-021-00686-w.
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  - Gerson, Jacqueline R., Natalie Szponar, Arianna Agostini, Rand Alotaibi, Bridget Bergquist, Arabella Chen, Luis E. Fernandez, et al. “Chemistry of surface water, precipitation, throughfall, leaves, sediment, soil, and air near a gold mining region in Peru.” Ecology 103, no. 5 (May 2022): e3666. https://doi.org/10.1002/ecy.3666.
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  - Anderson, Steven M., Emily A. Ury, Paul J. Taillie, Eric A. Ungberg, Christopher E. Moorman, Benjamin Poulter, Marcelo Ardón, Emily S. Bernhardt, and Justin P. Wright. “Salinity thresholds for understory plants in coastal wetlands.” Plant Ecology. 223, no. 3 (March 2022): 323–37. https://doi.org/10.1007/s11258-021-01209-2.
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  - Bernhardt, Emily S., Phil Savoy, Michael J. Vlah, Alison P. Appling, Lauren E. Koenig, Robert O. Hall, Maite Arroita, et al. “Light and flow regimes regulate the metabolism of rivers.” Proceedings of the National Academy of Sciences of the United States of America 119, no. 8 (February 2022): e2121976119. https://doi.org/10.1073/pnas.2121976119.
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  - Gerson, Jacqueline R., Natalie Szponar, Angelica Almeyda Zambrano, Bridget Bergquist, Eben Broadbent, Charles T. Driscoll, Gideon Erkenswick, et al. “Amazon forests capture high levels of atmospheric mercury pollution from artisanal gold mining.” Nature Communications 13, no. 1 (January 2022): 559. https://doi.org/10.1038/s41467-022-27997-3.
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  - Gray, Austin D., and Emily Bernhardt. “Are nitrogen and carbon cycle processes impacted by common stream antibiotics? A comparative assessment of single vs. mixture exposures.” Plos One 17, no. 1 (January 2022): e0261714. https://doi.org/10.1371/journal.pone.0261714.
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  - Jin, Lingrong, Jacqueline R. Gerson, Jennifer D. Rocca, Emily S. Bernhardt, and Marie Simonin. “Alkaline mine drainage drives stream sediment microbial community structure and function.” The Science of the Total Environment 805 (January 2022): 150189. https://doi.org/10.1016/j.scitotenv.2021.150189.
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  - Ury, E. A., J. P. Wright, M. Ardón, and E. S. Bernhardt. “Saltwater intrusion in context: soil factors regulate impacts of salinity on soil carbon cycling.” Biogeochemistry 157, no. 2 (January 1, 2022): 215–26. https://doi.org/10.1007/s10533-021-00869-6.
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  - Usseglio-Viretta, F. L. E., P. Patel, E. Bernhardt, A. Mistry, P. P. Mukherjee, J. Allen, S. J. Cooper, J. Laurencin, and K. Smith. “MATBOX: An Open-source Microstructure Analysis Toolbox for microstructure generation, segmentation, characterization, visualization, correlation, and meshing.” Softwarex 17 (January 2022): 100915–100915. https://doi.org/10.1016/j.softx.2021.100915.
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  - Naslund, Laura C., Jacqueline R. Gerson, Alexander C. Brooks, Amy D. Rosemond, David M. Walters, and Emily S. Bernhardt. “Ecosystem modification and network position impact insect-mediated contaminant fluxes from a mountaintop mining-impacted river network.” Environmental Pollution (Barking, Essex : 1987) 291 (December 2021): 118257. https://doi.org/10.1016/j.envpol.2021.118257.
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  - Gerson, Jacqueline R., Rebecca Dorman, Collin Eagles-Smith, Emily S. Bernhardt, and David Walters. “Lethal impacts of selenium counterbalance the potential reduction in mercury bioaccumulation for freshwater organisms.” Environmental Pollution (Barking, Essex : 1987) 287 (October 2021): 117293. https://doi.org/10.1016/j.envpol.2021.117293.
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  - Delesantro, J. M., J. M. Duncan, D. Riveros-Iregui, J. R. Blaszczak, E. S. Bernhardt, D. L. Urban, and L. E. Band. “Characterizing and classifying urban watersheds with compositional and structural attributes.” Hydrological Processes 35, no. 9 (September 1, 2021). https://doi.org/10.1002/hyp.14339.
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  - Simonin, Marie, Jennifer D. Rocca, Jacqueline R. Gerson, Eric Moore, Alexander C. Brooks, Lauren Czaplicki, Matthew R. V. Ross, Noah Fierer, Joseph M. Craine, and Emily S. Bernhardt. “Consistent declines in aquatic biodiversity across diverse domains of life in rivers impacted by surface coal mining.” Ecological Applications : A Publication of the Ecological Society of America 31, no. 6 (September 2021): e02389. https://doi.org/10.1002/eap.2389.
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  - Ross, M. R. V., F. Nippgen, B. L. McGlynn, C. J. Thomas, A. C. Brooks, R. K. Shriver, E. M. Moore, and E. S. Bernhardt. “Mountaintop mining legacies constrain ecological, hydrological and biogeochemical recovery trajectories.” Environmental Research Letters 16, no. 7 (July 1, 2021). https://doi.org/10.1088/1748-9326/ac09ac.
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  - Ury, Emily A., Xi Yang, Justin P. Wright, and Emily S. Bernhardt. “Rapid deforestation of a coastal landscape driven by sea-level rise and extreme events.” Ecological Applications : A Publication of the Ecological Society of America 31, no. 5 (July 2021): e02339. https://doi.org/10.1002/eap.2339.
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  - Carter, A. M., J. R. Blaszczak, J. B. Heffernan, and E. S. Bernhardt. “Hypoxia dynamics and spatial distribution in a low gradient river.” Limnology and Oceanography 66, no. 6 (June 1, 2021): 2251–65. https://doi.org/10.1002/lno.11751.
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  - Likens, G. E., D. C. Buso, E. S. Bernhardt, and E. Rosi. “A century of change: Reconstructing the biogeochemical history of Hubbard Brook.” Hydrological Processes 35, no. 6 (June 1, 2021). https://doi.org/10.1002/hyp.14256.
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  - Savoy, P., E. Bernhardt, L. Kirk, M. J. Cohen, and J. B. Heffernan. “A seasonally dynamic model of light at the stream surface.” Freshwater Science 40, no. 2 (June 1, 2021): 286–301. https://doi.org/10.1086/714270.
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  - Rüegg, J., C. C. Conn, E. P. Anderson, T. J. Battin, E. S. Bernhardt, M. Boix Canadell, S. M. Bonjour, J. D. Hosen, N. S. Marzolf, and C. B. Yackulic. “Thinking like a consumer: Linking aquatic basal metabolism and consumer dynamics.” Limnology and Oceanography Letters 6, no. 1 (February 1, 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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  - 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 2020): eabd4953. https://doi.org/10.1126/sciadv.abd4953.
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  - 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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  - Gerson, Jacqueline R., Laura C. Naslund, Yu-Ting Liu, Heileen Hsu-Kim, Charles T. Driscoll, Matthew R. V. Ross, Matthew N. Waters, and Emily S. Bernhardt. “Mercury and selenium loading in mountaintop mining impacted alkaline streams and riparian food webs.” Biogeochemistry. 150, no. 1 (August 2020): 109–22. https://doi.org/10.1007/s10533-020-00690-7.
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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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  - 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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  - 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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  - 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, L. E., A. M. Helton, P. Savoy, E. Bertuzzo, J. B. Heffernan, R. O. Hall, and E. S. Bernhardt. “Emergent productivity regimes of river networks.” Limnology and Oceanography Letters 4, no. 5 (October 1, 2019): 173–81. https://doi.org/10.1002/lol2.10115.
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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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  - Tully, K., K. Gedan, R. Epanchin-Niell, A. Strong, E. S. Bernhardt, T. Bendor, M. Mitchell, et al. “Corrigendum: The invisible flood: The chemistry, ecology, and social implications of coastal saltwater intrusion (BioScience (2019) 69,5 (368–378) DOI: 10.1093/biosci/biz027).” Bioscience 69, no. 9 (September 1, 2019). https://doi.org/10.1093/biosci/biz083.
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  - Helton, Ashley M., Marcelo Ardón, and Emily S. Bernhardt. “Hydrologic Context Alters Greenhouse Gas Feedbacks of Coastal Wetland Salinization.” Ecosystems. 22, no. 5 (August 2019): 1108–25. https://doi.org/10.1007/s10021-018-0325-2.
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  - Blaszczak, Joanna R., Joseph M. Delesantro, Ying Zhong, Dean L. Urban, and Emily S. Bernhardt. “Watershed urban development controls on urban streamwater chemistry variability.” Biogeochemistry. 144, no. 1 (June 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, Jennifer, Marie Simonin, Justin Wright, Alex Washburne, and Emily Bernhardt. “Rare Microbial Taxa Emerge When Communities Collide: Freshwater and Marine Microbiome Responses to Experimental Seawater Intrusion,” 2019. https://doi.org/10.1101/550756.
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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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  - 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 2018): 180292. https://doi.org/10.1038/sdata.2018.292.
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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., 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 2018): 13155–65. https://doi.org/10.1021/acs.est.8b03553.
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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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  - Ardón, Marcelo, Ashley M. Helton, and Emily S. Bernhardt. “Salinity effects on greenhouse gas emissions from wetland soils are contingent upon hydrologic setting: a microcosm experiment.” Biogeochemistry. 140, no. 2 (September 2018): 217–32. https://doi.org/10.1007/s10533-018-0486-2.
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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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  - 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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  - 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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  - 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 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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  - 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).
  - 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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  - 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 2016): 2064–74. https://doi.org/10.1021/acs.est.5b04532.
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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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  - 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): fiv113. https://doi.org/10.1093/femsec/fiv113.
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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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  - 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 (July 1, 2015): 795–805. https://doi.org/10.1111/2041-210X.12379.
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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: 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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  - 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: 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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  - 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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  - Morse, Jennifer L., and Jennifer L. 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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  - 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 (Accepted).” Hydrobiologia, 2013, 1–11. https://doi.org/10.1007/s10750-013-1747-7.
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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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  - 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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  - Lowry, G. V., B. P. Espinasse, A. R. Badireddy, C. J. Richardson, B. C. Reinsch, L. D. Bryant, A. J. Bone, et al. “Long-Term Transformation and Fate of Manufactured Ag Nanoparticles in a Simulated Large Scale Freshwater Emergent Wetland.” Environmental Science & Technology, April 2012. https://doi.org/10.1021/es204608d.
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  - Appling, A. P., E. S. Bernhardt, J. Kimball, and J. A. Stanford. “Patterns and mechanisms of nitrogen accumulation during floodplain succession (Submitted).” Ecology, 2012.
  - Cha, Y., C. Stow, and E. S. Bernhardt. “Dreissenid invasion impacts on chlorophyll and total phosphorus in 25 US lake ecosystems.” Freshwater Biology, 2012.
  - Lutz, B. D., E. S. Bernhardt, B. J. Roberts, R. M. Cory, and P. J. Mulhollande. “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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  - Morse, J. L., and E. S. Bernhardt. “Using 15N dual tracers to estimate the relative contribution of nitrification and denitrification to N2O and N2 emissions in coastal plain wetlands under contrasting land uses and soil moisture conditions.” Soil Biology and Biochemistry, 2012.
  - Morse, Jennifer L., Marcelo Ardón, and Emily S. Bernhardt. “Greenhouse gas fluxes in southeastern U.S. coastal plain wetlands under contrasting land uses.” Ecological Applications : A Publication of the Ecological Society of America 22, no. 1 (January 2012): 264–80. https://doi.org/10.1890/11-0527.1.
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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 stream temperatures (Accepted).” Freshwater Science, 2012.
  - Sudduth, E. B., S. S. Perakis, and E. S. Bernhardt. “Nitrate in watersheds: straight from soils to streams? (Accepted)” Jgr Biogeosciences, 2012.
  - Yin, L., B. Colman, B. McGill, J. P. Wright, and E. S. Bernhardt. “Effects of Silver Nanoparticle Exposure on Germination and Early Growth of Eleven Wetland Plants.” Plos One 7 (2012): e47674.
  - 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 2011): 20929–34. https://doi.org/10.1073/pnas.1112381108.
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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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  - Baulch, Helen M., Emily H. Stanley, and Emily S. Bernhardt. “Can algal uptake stop NO3(-) pollution?” Nature 477, no. 7366 (September 2011): E3. https://doi.org/10.1038/nature10418.
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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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  - 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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  - 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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  - 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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  - 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, no. SUPPL. 1 (January 1, 2010): 205–22. https://doi.org/10.1111/j.1365-2427.2009.02372.x.
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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 E. 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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  - Ardón, Marcelo, and Emily S. Bernhardt. “Restoring Rivers and Streams,” March 15, 2009. https://doi.org/10.1002/9780470015902.a0020148.
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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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  - 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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  - 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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  - 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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  - 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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  - Fierer, N., J. L. Morse, S. Berthrong, E. S. Bernhardt, and R. B. Jackson. “The landscape-level biogeography of stream bacterial communities.” Ecology 88 (2007): 2162–73.
  - Kondolf, G. M., S. Anderson, R. Lave, L. Pagano, A. Merelender, and E. S. Bernhardt. “Two Decades of River Restoration in California: Trends in Implementation and Reporting.” Restoration Ecology 15 (2007): 516–23.
  - Palmer, M. A., J. D. Allan, J. L. Meyer, and E. S. Bernhardt. “River Restoration in the United States in the 21st Century.” Restoration Ecology 15 (2007): 472–81.
  - Sudduth, E. B., J. L. Meyer, and E. S. Bernhardt. “Stream restoration practices in the southeastern US.” Restoration Ecology 15 (2007): 573–83.
  - Bernhardt, E., 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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  - 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 (2005): 259–67.
  - Likens, G. E., D. C. Buso, B. K. Dresser, E. S. Bernhardt, R. O. Hall, K. H. Macneale, and S. W. Bailey. “Buffering an acidic stream in New Hampshire with a silicate mineral.” Restoration Ecology 12, no. 3 (September 1, 2004): 419–28. https://doi.org/10.1111/j.1061-2971.2004.00357.x.
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  - Palmer, Margaret, Emily Bernhardt, Elizabeth Chornesky, Scott Collins, Andrew Dobson, Clifford Duke, Barry Gold, et al. “Ecology. Ecology for a crowded planet.” Science (New York, N.Y.) 304, no. 5675 (May 2004): 1251–52. https://doi.org/10.1126/science.1095780.
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  - Bernhardt, E. S., G. E. Likens, D. C. Buso, and C. T. Driscoll. “Erratum: In-stream uptake dampens effects of major forest disturbance on watershed nitrogen export (Proceedings of the National Academy of Sciences of the United States of America (September 2, 2003) 100, 18 (10304-10308)).” Proceedings of the National Academy of Sciences of the United States of America 101, no. 16 (April 20, 2004): 6327. https://doi.org/10.1073/pnas.0401639101.
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  - Bernhardt, E. S., and G. E. Likens. “Controls on periphyton biomass in heterotrophic streams.” Freshwater Biology 49, no. 1 (January 1, 2004): 14–27. https://doi.org/10.1046/j.1365-2426.2003.01161.x.
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  - Palmer, M. A., D. D. Hart, J. D. Allan, and E. Bernhardt. “Bridging engineering, ecological, and geomorphic science to enhance riverine restoration: Local and national efforts.” Proceedings of the Symposium Protection and Restoration of Urban and Rural Streams, December 1, 2003, 29–37.
  - Bernhardt, E. S., G. E. Likens, D. C. Buso, and C. T. Driscoll. “In-stream uptake dampens effects of major forest disturbance on watershed nitrogen export.” Proceedings of the National Academy of Sciences of the United States of America 100, no. 18 (September 2003): 10304–8. https://doi.org/10.1073/pnas.1233676100.
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  - Houlton, B. Z., C. T. Driscoll, T. J. Fahey, G. E. Likens, P. M. Groffman, E. S. Bernhardt, and D. C. Buso. “Nitrogen dynamics in ice storm-damaged forest ecosystems: Implications for nitrogen limitation theory.” Ecosystems 6, no. 5 (August 1, 2003): 431–43. https://doi.org/10.1007/s10021-002-0198-1.
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  - Bernhardt, E. S., R. O. Hall, and G. E. Likens. “Whole-system estimates of nitrification and nitrate uptake in streams of the Hubbard Brook Experimental Forest.” Ecosystems 5, no. 5 (August 1, 2002): 419–30. https://doi.org/10.1007/s10021-002-0179-4.
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  - Flecker, A. S., B. W. Taylor, E. S. Bernhardt, J. M. Hood, W. K. Cornwell, S. R. Cassatt, M. J. Vanni, and N. S. Altman. “Interactions between herbivorous fishes and limiting nutrients in a tropical stream ecosystem.” Ecology 83, no. 7 (July 1, 2002): 1831–44. https://doi.org/10.1890/0012-9658(2002)083[1831:IBHFAL]2.0.CO;2.
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  - Flecker, Alexander S., Brad W. Taylor, Emily S. Bernhardt, James M. Hood, William K. Cornwell, Shawn R. Cassatt, Michael J. Vanni, and Naomi S. Altman. “Interactions between Herbivorous Fishes and Limiting Nutrients in a Tropical Stream Ecosystem.” Ecology 83, no. 7 (July 2002): 1831–1831. https://doi.org/10.2307/3071768.
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  - Bernhardt, E. S., and G. E. Likens. “Dissolved organic carbon enrichment alters nitrogen dynamics in a forest stream.” Ecology 83, no. 6 (June 1, 2002): 1689–1700. https://doi.org/10.1890/0012-9658(2002)083[1689:DOCEAN]2.0.CO;2.
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  - Hall, R. J. O., E. S. Bernhardt, and G. E. Likens. “Relating nutrient uptake with transient storage in forested mountain streams.” Limnology and Oceanography 47, no. 1 (January 1, 2002): 255–65. https://doi.org/10.4319/lo.2002.47.1.0255.
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  - Bernhardt, E. S. “Lessons from kinetic releases of ammonium in streams of the Hubbard Brook Experimental Forest (HBEF).” Verhandlungen Internationale Vereingung Limnologie 28 (2002): 429–33.
  - Hall, R. O., K. H. Macneale, E. S. Bernhardt, M. Field, and G. E. Likens. “Biogeochemical responses of two forest streams to a 2-month calcium addition.” Freshwater Biology 46, no. 3 (April 7, 2001): 291–302. https://doi.org/10.1046/j.1365-2427.2001.00660.x.
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- Book Sections
  - Tockner, K., E. S. Bernhardt, A. Koska, and C. Zarfl. “A Global View on Future Major Water Engineering Projects.” In Water Resources Development and Management, 47–64, 2016. https://doi.org/10.1007/978-3-319-18971-0_4.
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  - Ross, M. R. V., E. S. Bernhardt, M. W. Doyle, and J. B. Heffernan. “Designer Ecosystems: Incorporating Design Approaches into Applied Ecology,” 40:419–43, 2015. https://doi.org/10.1146/annurev-environ-121012-100957.
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- Conference Papers
  - Gorka, Danielle E., Jonathan Litvak Jeger, Hongbo Zhang, Yanwen Ma, Benjamin P. Colman, Emily S. Bernhardt, and Jie Liu. “Phytotoxicity of soluble graphitic nanofibers to model plant species.” In Environmental Toxicology and Chemistry, 35:2941–47, 2016. https://doi.org/10.1002/etc.3478.
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  - Anciaux, Sarah K., Benjamin P. Colman, Emily S. Bernhardt, Justin Wright, and Bonny McGill. “Investigation of the bioaccumulation of silver nanoparticles.” In Abstracts of Papers of the American Chemical Society, Vol. 241. AMER CHEMICAL SOC, 2011.
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  - Phillips, Richard P., Adrien Finzi, and Emily Bernhardt. “Biogeochemical consequences of changes in root-derived carbon inputs to soil in a forest exposed to CO2 enrichment.” In Geochimica Et Cosmochimica Acta, 74:A815–A815. PERGAMON-ELSEVIER SCIENCE LTD, 2010.
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  - Aber, J. D., E. S. Bernhardt, F. A. Dijkstra, R. H. Gardner, K. H. Macneale, W. J. Parton, S. T. A. Pickett, D. L. Urban, and K. C. Weathers. “Standards of practice for review and publication of models: Summary of discussion.” In Models in Ecosystem Science, edited by C. D. Canham, J. J. Cole, and W. K. Lauenroth, 204–10. PRINCETON UNIV PRESS, 2003.
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