Staff information

PNNL Publications

2024

• Zhou Y., P. Jiang, P. Chen, E. Jia, C.S. Welch, Q. Zhao, and J.A. Dhas, et al. 2024. "Novel Principal Component Analysis Tool based on Python for Analysis of Complex Spectra of Time-of-Flight Secondary Ion Mass Spectrometry." Journal of Vacuum Science & Technology A: International Journal Devoted to Vacuum, Surfaces, and Films A42, no. 2:Art. No. 023204. PNNL-SA-189615. doi:10.1116/6.0003355

2023

• Bowman M.M., A.E. Heath, T. Varga, A. Battu, R.K. Chu, J.G. Toyoda, and T. Cheeke, et al. 2023. "One thousand soils for molecular understanding of belowground carbon cycling." Frontiers in Soil Science 3. PNNL-SA-183617. doi:10.3389/fsoil.2023.1120425
• Graham E.B., H. Song, S.R. Grieger, V.A. Garayburu-Caruso, J.C. Stegen, K. Bladon, and A.N. Myers-Pigg. 2023. "Potential bioavailability of representative pyrogenic organic matter compounds in comparison to natural dissolved organic matter pools." Biogeosciences 20, no. 16:3449-3457. PNNL-SA-189608. doi:10.5194/bg-20-3449-2023
• Hudiburg T., J. Mathias, K. Bartowitz, D. Berardi, K. Bryant, E.B. Graham, and C. Kolden, et al. 2023. "Terrestrial carbon dynamics in an era of increasing wildfire." Nature Climate Change 13, no. 12:1306 - 1316. PNNL-SA-192593. doi:10.1038/s41558-023-01881-4
• McDowell N.G., K.J. Anderson-Teixeira, J.A. Biederman, D.D. Breshears, Y. Fang, L. Fernandez De Una, and E.B. Graham, et al. 2023. "Ecohydrological Decoupling under Changing Disturbances and Climate." One Earth 6, no. 3:251-266. PNNL-SA-189590. doi:10.1016/j.oneear.2023.02.007
• Naasko K.I., D.T. Naylor, E.B. Graham, S.P. Couvillion, R.E. Danczak, N. Tolic, and C.D. Nicora, et al. 2023. "Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry." mBio 14, no. 5:Art. No. e01758-23. PNNL-SA-187582. doi:10.1128/mbio.01758-23
• Turetcaia A., V.A. Garayburu-Caruso, M.H. Kaufman, R.E. Danczak, J.C. Stegen, R.K. Chu, and J.G. Toyoda, et al. 2023. "Rethinking Aerobic Respiration in the Hyporheic Zone Under Variation in Carbon and Nitrogen Stoichiometry." Environmental Science & Technology 57, no. 41:15499-15510. PNNL-SA-190231. doi:10.1021/acs.est.3c04765

2022

• Borton M.A., S. Collins, E.B. Graham, V.A. Garayburu-Caruso, A.E. Goldman, M. De Melo, and L. Renteria, et al. 2022. "It takes a village: using a crowdsourced approach to investigate organic matter composition in global rivers through the lens of ecological theory." Frontiers in Water 4. PNNL-SA-169359. doi:10.3389/frwa.2022.870453
• Dwivedi D., A. Santos, M. Barnard, T. Crimmins, A. Malhotra, K.A. Rod, and K. Aho, et al. 2022. "Biogeosciences Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science." Earth and Space Science 9, no. 3:Art. No. e2021EA002119. PNNL-SA-172157. doi:10.1029/2021EA002119
• Hu J., Q. Chen, S. Zhong, Y. Liu, Q. Gao, E.B. Graham, and H. Chen, et al. 2022. "Insight into Co-Hosts of Nitrate Reduction Genes and Antibiotic Resistance Genes in an Urban River of the Qinghai-Tibet Plateau." Water Research 225. PNNL-SA-172262. doi:10.1016/j.watres.2022.119189
• Isabwe A., J.R. Yang, Y. Wang, D.M. Wilkinson, E.B. Graham, H. Chen, and J. Yang. 2022. "Riverine bacterioplankton and phytoplankton assembly along an environmental gradient induced by urbanization." Limnology and Oceanography 67, no. 9:1943-1958. PNNL-SA-139753. doi:10.1002/lno.12179
• Roebuck, Jr. J.A., K. Bladon, D. Donahue, E.B. Graham, S.R. Grieger, K. Morgenstern, and M. Norwood, et al. 2022. "Spatiotemporal controls on the delivery of dissolved organic matter to streams following a wildfire." Geophysical Research Letters 49, no. 16:e2022GL099535. PNNL-SA-173675. doi:10.1029/2022GL099535
• Ward A.S., A.I. Packman, S. Bernal Berenguer, N. Brekenfeld, J. Drummond, E.B. Graham, and D. Hannah, et al. 2022. "Advancing river corridor science beyond disciplinary boundaries with an inductive approach to catalyse hypothesis generation." Hydrological Processes 36, no. 4:Art. No. e14540. PNNL-SA-162331. doi:10.1002/hyp.14540

2021

• Chen X., R.M. Lee, D. Dwivedi, K. Son, Y. Fang, X. Zhang, and E.B. Graham, et al. "Integrating Field Observations and Reactive Transport Modeling to Predict Watershed Water Quality under Environmental Perturbations."
• Chen X., R.M. Lee, D. Dwivedi, K. Son, Y. Fang, X. Zhang, and E.B. Graham, et al. 2021. "Integrating Field Observations and Process-based Modeling to Predict Watershed Water Quality under Environmental Perturbations." Journal of Hydrology 602. PNNL-SA-148272. doi:10.1016/j.jhydrol.2020.125762
• Danczak R.E., A.E. Goldman, R.K. Chu, J.G. Toyoda, V.A. Garayburu-Caruso, N. Tolic, and E.B. Graham, et al. 2021. "Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties." Science of the Total Environment 788. PNNL-SA-156110. doi:10.1016/j.scitotenv.2021.147409
• Graham E.B., and P. Smith. 2021. "Crowdsourcing global perspectives in ecology using social media." Frontiers in Ecology and Evolution 9. PNNL-SA-153135. doi:10.3389/fevo.2021.588894
• Graham E.B., C. Averill, B. Bond-Lamberty, J.E. Knelman, S. Krause, A.L. Peralta, and A. Shade, et al. 2021. "Toward a generalizable framework of disturbance ecology through crowdsourced science." Frontiers in Ecology and Evolution 9. PNNL-SA-151971. doi:10.3389/fevo.2021.588940
• Kaufman M.H., J. Warden, M.B. Cardenas, J.C. Stegen, E.B. Graham, and J.M. Brown. 2021. "Evaluating a laboratory flume microbiome as a window into natural riverbed biogeochemistry." Frontiers in Water 3. PNNL-SA-147077. doi:10.3389/frwa.2021.596260
• Knelman J.E., S.K. Schmidt, and E.B. Graham. 2021. "Cyanobacteria in early soil development of deglaciated forefields: Dominance of non-heterocytous filamentous cyanobacteria and phosphorus limitation of N-fixing Nostocales." Soil Biology and Biochemistry 154. PNNL-SA-159501. doi:10.1016/j.soilbio.2020.108127
• Liu W., E.B. Graham, Y. Dong, L. Zhong, J. Zhang, C. Qiu, and R. Chen, et al. 2021. "Balanced stochastic versus deterministic assembly processes benefit diverse yet uneven ecosystem functions in representative agroecosystems." Environmental Microbiology 23, no. 1:391-404. PNNL-SA-157815. doi:10.1111/1462-2920.15326
• Plymale A.E., J.R. Wells, C.I. Pearce, C.J. Brislawn, E.B. Graham, T. Cheeke, and J.L. Allen, et al. 2021. "Niche partitioning of microbial communities at an ancient vitrified hillfort: implications for vitrified radioactive waste disposal." Geomicrobiology Journal 38, no. 1:36-56. PNNL-SA-150253. doi:10.1080/01490451.2020.1807658
• Song H., J.C. Stegen, E.B. Graham, and T.D. Scheibe. 2021. "Historical Contingency in Microbial Resilience to Hydrologic Perturbations." Frontiers in Water 3. PNNL-SA-156061. doi:10.3389/frwa.2021.590378
• Wu R., M.R. Davison, W.C. Nelson, E.B. Graham, S.J. Fansler, Y. Farris, and S.L. Bell, et al. 2021. "DNA viral diversity, abundance and functional potential vary across grassland soils with a range of historical moisture regimes." mBio 12, no. 6:e02595-21. PNNL-SA-166275. doi:10.1128/mBio.02595-21

2020

• Danczak R.E., R.K. Chu, S.J. Fansler, A.E. Goldman, E.B. Graham, M.M. Tfaily, and J.G. Toyoda, et al. 2020. "Using metacommunity ecology to understand environmental metabolomes." Nature Communications 11, no. 1:Article No. 6369. PNNL-SA-152827. doi:10.1038/s41467-020-19989-y
• Fang Y., X. Chen, J.D. Gomez Velez, X. Zhang, Z. Duan, G. Hammond, and A.E. Goldman, et al. 2020. "A multirate mass transfer model to represent the interaction of multicomponent biogeochemical processes between surface water and hyporheic zones (SWAT-MRMT-R 1.0)." Geoscientific Model Development 13, no. 8:3553-3569. PNNL-SA-148784. doi:10.5194/gmd-13-3553-2020
• Garayburu-Caruso V.A., J.C. Stegen, H. Song, L. Renteria, J.R. Wells, W.L. Garcia, and C.T. Resch, et al. 2020. "Carbon limitation leads to thermodynamic regulation of aerobic metabolism." Environmental Science & Technology Letters 7, no. 7:517-524. PNNL-SA-150146. doi:10.1021/acs.estlett.0c00258
• Garayburu-Caruso V.A., R.E. Danczak, J.C. Stegen, L. Renteria, M.L. McCall, A.E. Goldman, and R.K. Chu, et al. 2020. "Using Community Science to Reveal the Global Chemogeography of River Metabolomes." Metabolites 10, no. 12:518. PNNL-SA-157277. doi:10.3390/metabo10120518
• Liu W., E.B. Graham, L. Zhong, J. Zhang, S. Li, X. Lin, and Y. Feng. 2020. "Long-term Stochasticity Combines with Short-term Variability in Assembly Processes to Underlie Rice Paddy Sustainability." Frontiers in Microbiology 11. PNNL-SA-140335. doi:10.3389/fmicb.2020.00873
• Liu W., E.B. Graham, L. Zhong, J. Zhang, W. Li, Z. Li, and X. Lin, et al. 2020. "Dynamic microbial assembly processes correspond to soil fertility in sustainable paddy agroecosystems." Functional Ecology 34, no. 6:1244-1256. PNNL-SA-151048. doi:10.1111/1365-2435.13550
• Naylor D.T., N.C. Sadler, A. Bhattacharjee, E.B. Graham, C.R. Anderton, R.S. McClure, and M.S. Lipton, et al. 2020. "Soil Microbiomes under Climate Change and Implications for Carbon Cycling." Annual Review of Environment and Resources 45. PNNL-SA-150059. doi:10.1146/annurev-environ-012320-082720
• Nelson W.C., E.B. Graham, A.R. Crump, S.J. Fansler, E.V. Arntzen, D.W. Kennedy, and J.C. Stegen. 2020. "Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome." PLoS One 15, no. 1:Article No. e0228165. PNNL-SA-125632. doi:10.1371/journal.pone.0228165
• Rue G., J. Darling, E.B. Graham, M.M. Tfaily, and D.M. Mcknight. 2020. "Dynamic changes in dissolved organic matter composition in a Mountain Lake under ice cover and relationships to changes in nutrient cycling and phytoplankton community composition." Aquatic Sciences 82, no. 1:Article No. 15. PNNL-SA-142564. doi:10.1007/s00027-019-0687-3
• Song H., J.C. Stegen, E.B. Graham, J. Lee, V.A. Garayburu-Caruso, W.C. Nelson, and X. Chen, et al. 2020. "Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling." Frontiers in Microbiology 11. PNNL-SA-151734. doi:10.3389/fmicb.2020.531756
• Villa J.A., G. Smith, Y. Ju, L. Renteria, J.C. Angle, E.V. Arntzen, and S.F. Harding, et al. 2020. "Methane and nitrous oxide porewater concentrations and surface fluxes of a regulated river." Science of the Total Environment 715. PNNL-SA-149661. doi:10.1016/j.scitotenv.2020.136920
• Wang J., P. Legendre, J. Soininen, C. Yeh, E.B. Graham, J.C. Stegen, and E. Casamayor, et al. 2020. "Temperature drives local contributions to beta diversity in mountain streams: stochastic and deterministic processes." Global Ecology and Biogeography 29, no. 3:420-432. PNNL-SA-132470. doi:10.1111/geb.13035
• Ward N.D., P. Megonigal, B. Bond-Lamberty, V.L. Bailey, D. Butman, E. Canuel, and H.L. Diefenderfer, et al. 2020. "Representing the Function and Sensitivity of Coastal Interfaces in Earth System Models." Nature Communications 11. PNNL-SA-147328. doi:10.1038/s41467-020-16236-2

2019

• Brislawn C.J., E.B. Graham, K.L. Dana, P.D. Ilhardt, S.J. Fansler, W.B. Chrisler, and J.B. Cliff, et al. 2019. "Forfeiting the priority effect: turnover defines biofilm community succession." The ISME Journal 13, no. 7:1865-1877. PNNL-SA-133067. doi:10.1038/s41396-019-0396-x
• Graham E.B., F. Yang, S.L. Bell, and K.S. Hofmockel. 2019. "High Genetic Potential for Proteolytic Decomposition in Northern Peatland Ecosystems." Applied Environmental Microbiology 85, no. 10:Article No. e02851-18. PNNL-SA-136389. doi:10.1128/AEM.02851-18
• Graham E.B., J.C. Stegen, M. Huang, X. Chen, and T.D. Scheibe. 2019. "Subsurface biogeochemistry is a missing link between ecology and hydrology in dam-impacted river corridors." Science of the Total Environment 657. PNNL-SA-132468. doi:10.1016/j.scitotenv.2018.11.414
• Knelman J.E., S.K. Schmidt, V.A. Garayburu-Caruso, S. Kumar, and E.B. Graham. 2019. "Multiple, compounding disturbances in a forest ecosystem: Fire increases susceptibility of Soil Edaphic Properties, Bacterial Community Structure, and Function to Change with Extreme Precipitation Event." Soil Systems 3, no. 2:40. PNNL-SA-144296. doi:10.3390/soilsystems3020040
• Ward A.S., J.P. Zarnetske, V. Baranov, P. Blaen, N. Brekenfeld, R.K. Chu, and R. Derelle, et al. 2019. "Co-located contemporaneous mapping of morphological, hydrological, chemical, and biological conditions in a 5th order mountain stream network, Oregon, USA." Earth System Science Data 11, no. 4:1567-1581. PNNL-SA-140490. doi:10.5194/essd-11-1567-2019
• Ward A.S., S.M. Wondzell, N.M. Schmadel, S. Herzog, J.P. Zarnetske, V. Baranov, and P. Blaen, et al. 2019. "Spatial and temporal variation in river corridor exchange across a 5th order mountain stream network." Hydrology and Earth System Sciences 23, no. 12:5199-5225. PNNL-SA-140824. doi:10.5194/hess-23-5199-2019
• Zegeye E. 2019. "Selection, Succession, and Stabilization of Soil Microbial Consortia." mSystems 4, no. 4:Article Number e00055-19. PNNL-SA-146173. doi:10.1128/mSystems.00055-19
• Zegeye E., C.J. Brislawn, Y. Farris, S.J. Fansler, K.S. Hofmockel, J.K. Jansson, and A.T. Wright, et al. 2019. "Selection, succession and stabilization of soil microbial consortia." mSystems 4, no. 4:e00055-19. PNNL-SA-138630. doi:10.1128/mSystems.00055-19
• Zegeye E., C.J. Brislawn, Y. Farris, S.J. Fansler, K.S. Hofmockel, J.K. Jansson, and A.T. Wright, et al. 2019. "Selection, Succession, and Stabilization of Soil Microbial Consortia." mSystems 4, no. 4:Article Number e00055-19. PNNL-SA-146173. doi:10.1128/mSystems.00055-19

2018

• Graham E.B., A.R. Crump, D.W. Kennedy, E.V. Arntzen, S.J. Fansler, S.O. Purvine, and C.D. Nicora, et al. 2018. "Multi ‘omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone." Science of the Total Environment 642. PNNL-SA-133671. doi:10.1016/j.scitotenv.2018.05.256
• Graham E.B., R.S. Gabor, S. Schooler, D.M. Mcknight, D.R. Nemergut, and J. Knelman. 2018. "Oligotrophic Wetland Sediments Susceptible to Shifts in Microbiomes and Mercury Cycling with Dissolved Organic Matter Addition." PeerJ 6. PNNL-SA-120643. doi:10.7717/peerj.4575
• Hall E.K., E. Bernhardt, R. Bier, M. Bradford, C.M. Boot, J. Cotner, and P. del Giorgio, et al. 2018. "Understanding How Microbiomes Influence The Systems They Inhabit." Nature Microbiology 3, no. 9:977-982. PNNL-SA-136262. doi:10.1038/s41564-018-0201-z
• Knelman J.E., E.B. Graham, J. Prevey, M.S. Robeson, P. Kelly, E. Hood, and S.K. Schmidt. 2018. "Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession." Frontiers in Microbiology 9. PNNL-SA-129382. doi:10.3389/fmicb.2018.00128
• Plymale A.E., J.R. Wells, E.B. Graham, O. Qafoku, S.M. Brooks, and B.D. Lee. 2018. "Bacterial productivity in a ferrocyanide-contaminated aquifer at a nuclear waste site." Water 10, no. 8:Article No. 1072. PNNL-SA-135770. doi:10.3390/w10081072
• Song X., X. Chen, J.C. Stegen, G. Hammond, H. Song, H. Dai, and E.B. Graham, et al. 2018. "Drought Conditions Maximize the Impact of High-Frequency Flow Variations on Thermal Regimes and Biogeochemical Function in the Hyporheic Zone." Water Resources Research 54, no. 10:7361-7382. PNNL-SA-123922. doi:10.1029/2018WR022586

2017

• Goldman A.E., E.B. Graham, A.R. Crump, D.W. Kennedy, E.B. Romero, C.G. Anderson, and K.L. Dana, et al. 2017. "Biogeochemical cycling at the aquatic-terrestrial interface is linked to parafluvial hyporheic zone inundation history." Biogeosciences 14, no. 18:4229-4241. PNNL-SA-123674. doi:10.5194/bg-14-4229-2017
• Graham E.B., A.R. Crump, C.T. Resch, S.J. Fansler, E.V. Arntzen, D.W. Kennedy, and J.K. Fredrickson, et al. 2017. "Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes." Environmental Microbiology 19. PNNL-SA-122625. doi:10.1111/1462-2920.13720
• Graham E.B., and J.C. Stegen. 2017. "Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function." Processes 5, no. 4:Article No. 65. PNNL-SA-129385. doi:10.3390/pr5040065
• Graham E.B., J.C. Stegen, A.R. Crump, C.T. Resch, S.J. Fansler, E.V. Arntzen, and D.W. Kennedy, et al. 2017. "Organic carbon thermodynamics elucidate spatiotemporal mechanisms governing hyporheic zone biogeochemical cycling." In Proceedings of the Subsurface Biogeochemical Research and Terrestrial Ecosystem Science Joint Meeting April 25-26, 2017, Potomac, Maryland. Washington, District Of Columbia:US Department of Energy, Office of Biological and Environmental Research. PNNL-SA-125130.
• Graham E.B., M.M. Tfaily, A.R. Crump, A.E. Goldman, L.M. Bramer, E.V. Arntzen, and E.B. Romero, et al. 2017. "Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes." Journal of Geophysical Research: Biogeosciences 122, no. 12:3188-3205. PNNL-SA-125144. doi:10.1002/2017JG003967
• Knelman J., E.B. Graham, S. Ferrenberg, A. Lecoeuvre, A. Labrado, J. Darcy, and D.R. Nemergut, et al. 2017. "Rapid Shifts in Soil Nutrients and Decomposition Enzyme Activity in Early Succession Following Forest Fire." Forests 8, no. 9:347. PNNL-SA-120687. doi:10.3390/f8090347

2016

• Castle S.C., D.R. Nemergut, A. Grandy, J.W. Leff, E.B. Graham, E. Hood, and S.K. Schmidt, et al. 2016. "Biogeochemical drivers of microbial community convergence across actively retreating glaciers." Soil Biology and Biochemistry 101. PNNL-SA-120239. doi:10.1016/j.soilbio.2016.07.010
• Graham E.B., A.R. Crump, C.T. Resch, S.J. Fansler, E.V. Arntzen, D.W. Kennedy, and J.K. Fredrickson, et al. 2016. "Coupling spatiotemporal community assembly processes to ecosystem function." Frontiers in Microbiology 7. PNNL-SA-118464. doi:10.3389/fmicb.2016.01949