James C. Stegen

Earth Scientist

Biography

James C. Stegen is an internationally recognized scientist who works to rapidly translate scientific discovery into actionable knowledge through large-scale, open, and distributed science research. His research integrates ecological theory, microbial ecology, and hydrobiogeochemistry to advance understanding of Earth system processes.

Stegen’s research generates broadly applicable insights into how events—such as wildfires, droughts, and floods—cascade through river networks and shape key ecosystem functions like water flow and material transformations in streambed sediments. By connecting these dynamics to underlying microbial and biogeochemical processes, his work has impact from molecular to global scales. Stegen’s leadership at the Pacific Northwest National Laboratory (PNNL) has catalyzed several transformative research directions, including:

Redefining approaches to environmental system science by pioneering large-scale, distributed science efforts that generate transferable insights through coordinated, multi-site investigations;
Bridging disciplines to open new fields of study, such as integrating ecological theory with organic chemistry to understand energy flow in environmental systems; and
Developing multiscale analysis methods that connect molecular mechanisms to ecosystem functions to address complex environmental challenges.

He serves as principal investigator of PNNL’s River Corridor Scientific Focus Area, where Stegen has played a pivotal role in integrating field observations, laboratory experimentation, and predictive modeling. He also co-founded both the Integrated Coordinated Open Networked (ICON) Science Cooperative and the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS)—initiatives aimed at fostering geographically distributed, open-access science.

Stegen is the author of more than 150 peer-reviewed publications, including in Nature, Science, Nature Communications, and Nature Microbiology, with over 20,000 citations. He’s also been on Clarivate’s most Highly Cited Researchers list each year from 2020–2024. In addition to publishing dozens of publicly accessible datasets, he is regularly invited to present his research at scientific conferences, Department of Energy Office of Science meetings, and institutional seminars.

Stegen is a recipient of the prestigious 2025 Presidential Early Career Award for Scientists and Engineers (PECASE)—one of only six other PNNL researchers to receive this honor in nearly three decades. In 2019, he was also an awardee of the Department of Energy’s Early Career Research program, which afforded him transformative support to expand his research portfolio at the Laboratory.

He earned his BS and MS in biology from Central Washington University and Eastern Washington University, respectively, and received his PhD in ecology and evolution from the University of Arizona. Following a National Science Foundation postdoctoral fellowship at the University of North Carolina at Chapel Hill, Stegen joined PNNL in 2011 as a Linus Pauling Distinguished Fellow. Since 2013, he has served as a staff scientist in PNNL’s Earth and Biological Sciences Directorate and, since 2020, as joint faculty at Washington State University's School of the Environment, where he actively mentors the next generation of scientists.

Stegen’s interdisciplinary approach—anchored in multidimensional science and AI-driven methodologies—yields transferrable insights that connect diverse environmental processes to the nation’s most complex challenges.

Press Releases Related to Research

Understanding Large River Corridors: Multidisciplinary Instrumentation and Modeling

Mighty Microbes Where Rivers Run

Columbia River Hyporheic Zone Tackles Contaminants, Greenhouse Gases

Education

PhD in Ecology & Evolution, University of Arizona, 2009
MS in Biology, Eastern Washington University, 2004
BA in Biology, Central Washington University, 2000

Affiliations and Professional Service

2015-Present, Member of the American Geophysical Union (AGU)
2019-Present, Member of the Society for Freshwater Science (SFS)
2005-2018, Member of the Ecological Society of America (ESA)
Co-founder and co-director of the Integrated, Coordinated, Open, and Network (ICON) Science Cooperative (2021-present)
Co-leading an international effort towards integration across critical zone observatories/science (2019-2020)
Lead of the DOE Workshop “Leveraging Distributed Research Networks to Understand Watershed Systems” (January 2019). Organized and lead webinars around the workshop topics (2018–2019)
Advisory board member for DOE’s ESS-DIVE data archive (2018–present)
Participant in DOE’s Cyberinfrastructure working group (2019-2020)
Co-organizer of the SBR town hall and associated breakout sessions at DOE’s Environmental System Sciences Principal Investigator (ESS-PI) meeting (2019)
Invited speaker at International Symposium on Aquatic Microbial Ecology (2020), American Society for Microbiology Annual Meeting (2020), Applied and Environmental Microbiology Gordon Research Conference (2019), American Chemical Society Annual Conference (2019), DOE’s ESS-PI meeting (2019), DOE’s Biological and Environmental Research Advisory Committee meeting (2019), DOE-BER (2018), United States Geologic Survey headquarters (2018), Colorado State University (2018), Central Washington University (2018), Ecological Society of America Annual Meeting (2017), University of British Columbia (2016), Ecological Society of America Annual Meeting (2016), University of Arizona (2015), University of Groningen (2014), University of North Carolina (2011), Metabolic Basis of Ecology Gordon Research Conference (2010)
(Co-)Convener of AGU Fall meeting sessions, town halls, workshops: (Co-)Convener of AGU Fall meeting sessions, town halls, workshops: Oral Session: Biogeochemical and Hydrological Functioning Across Scales in River Corridors I, Town Hall: New and Expanding Community-Driven Research Programs to Understand Watershed and Coastal Processes (2020), Town Hall: Open Innovation in the Geosciences for Mutual Benefit and Accelerated Discovery (2020), Workshop: Toward an International Critical Zone Network-of-Networks for the Next Generation Through Shared Science, Tools, Data and Philosophy (2020), Biogeochemical and hydrological functioning across scales in river corridors (2019), Open Science Successes and Challenges: Learning from Biogeoscience Use-Cases (2019), Towards Predictive Understanding of the Frequency and Outcomes of Compounding Disturbances across Terrestrial and Aquatic Ecosystems (2019), Town Hall: Coordinated Open Science by Design to Transform the Geosciences (2019), Workshop: International Critical Zone Network-of-Networks (2019), River Corridor Biogeochemical and Hydrologic Dynamics Across Scales (2018), Town Hall for WHONDRS (2018), Characterizing Spatial and Temporal Variability of Hydrological and Biogeochemical Processes Across Scales (2017), Understanding and Predicting Hydrobiogeochemical Responses of Terrestrial-Aquatic Ecosystems to Perturbation (2016)
Lead principal investigator for WHONDRS: Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems (2017–Present)
2016 - Invited participant and writing team for DOE’s Terrestrial Aquatic Interfaces
Co-chair of 2012 Gordon Research Seminar on Metabolic Ecology
2009-2011 Invited participant in National Center for Ecological Analysis and Synthesis working group on Beta-Diversity.

Awards and Recognitions

Presidential Early Career Award for Scientists and Engineers (PECASE; 2025)
Clarivate’s Most Highly Cited Researchers List (2020, 2021, 2022, 2023, & 2024)
DOE Early Career Research Program Award (2019)
Linus Pauling Distinguished Postdoctoral Award (2011)
National Science Foundation Postdoctoral Fellow (2009)

Patents

Systems and Methods for Determining Ground Water-Surface Water Interactions. Status: Filed, Pending. IPID: 31300-E. Patent Master ID: 9708.
Automated Open Channel Field Oxygen Consumption Chamber. Status: IP, Evolving. IPID: 31633-E.

Publications

Google Scholar

2025

Regier, P., Son, K., Chen, X., Fang, Y., Jiang, P., Taylor, M., Wollheim, W.M. and Stegen, J., 2025. Allometric scaling of hyporheic respiration across basins in the Pacific Northwest United States. Journal of Geophysical Research: Biogeosciences, 130(3), p.e2024JG008344.
Stegen, J., Burgin, A. J., Busch, M. H., Fisher, J. B., Ladau, J., Abrahamson, J., Kinsman-Costello, L., Li, L., Chen, X., Datry, T., McDowell, N., Tatariw, C., Braswell, A., Deines, J. M., Guimond, J. A., Regier, P., Rod, K., Bam, E. K. P., Fluet-Chouinard, E., Forbrich, I., Jaeger, K. L., O'Meara, T., Scheibe, T., Seybold, E., Sweetman, J. N., Zheng, J., Allen, D. C., Herndon, E., Middleton, B. A., Painter, S., Roche, K., Scamardo, J., Vander Vorste, R., Boye, K., Wohl, E., Zimmer, M., Hondula, K., Laan, M., Marshall, A., Patel, K. F. 2025. Reviews and syntheses: Variable inundation across Earth's terrestrial ecosystems. Biogeosciences, 22, (4), 995-1034; doi: 10.5194/bg-22-995-2025.
Stegen, J. C., Garayburu-Caruso, V. A., Danczak, R. E., Chu, R. K., Goldman, A. E., McKever, S., Renteria, L., Toyoda, J. 2025. Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear. Scientific Reports, 15, (1), doi: 10.1038/s41598-024-76675-5.
Borton, M. A., McGivern, B. B., Willi, K. R., Woodcroft, B. J., Mosier, A. C., Singleton, D. M., Bambakidis, T., Pelly, A., Daly, R. A., Liu, F., Freiburger, A., Edirisinghe, J. N., Faria, J. P., Danczak, R., Leleiwi, I., Goldman, A. E., Wilkins, M. J., Hall, E. K., Pennacchio, C., Roux, S., Eloe-Fadrosh, E. A., Good, S. P., Sullivan, M. B., Wood-Charlson, E. M., Miller, C. S., Ross, M. R. V., Henry, C. S., Crump, B. C., Stegen, J. C., Wrighton, K. C. 2025. A functional microbiome catalogue crowdsourced from North American rivers. Nature, 637, (8044), 103-112; doi: 10.1038/s41586-024-08240-z.

2024

Cui Y, W. S., Stegen J, Hu A, Wang J. 2024. Chemodiversity of riverine dissolved organic matter: Effects of local environments and watershed characteristics. . 2024 February; 250:121054-. doi: 10.1016/j.watres.2023.121054. Water Research, doi:
Freire-Zapata, V., Holland-Moritz, H., Cronin, D. R., Aroney, S., Smith, D. A., Wilson, R. M., Ernakovich, J. G., Woodcroft, B. J., Bagby, S. C., Team, E. F., Coordinators, E. B. I., Rich, V. I., Sullivan, M. B., Stegen, J. C., Tfaily, M. M. 2024. Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient. Nature Microbiology, doi: 10.1038/s41564-024-01800-z.
Gary, S. F., Scheibe, T. D., Rexer, E., Torreira, A. V., Garayburu‐Caruso, V. A., Goldman, A., Stegen, J. C. 2024. Prediction of distributed river sediment respiration rates using community‐generated data and machine learning. Journal of Geophysical Research: Machine Learning and Computation, 1, (3), e2024JH000199; doi: 10.1029/2024jh000199.
Hu, A., Jang, K. S., Tanentzap, A. J., Zhao, W., Lennon, J. T., Liu, J., Li, M., Stegen, J., Choi, M., Lu, Y., Feng, X., Wang, J. 2024. Thermal responses of dissolved organic matter under global change. Nature Communications, 15, (1), 576; doi: 10.1038/s41467-024-44813-2.
Kew, W., Myers-Pigg, A., Chang, C. H., Colby, S. M., Eder, J., Tfaily, M. M., Hawkes, J., Chu, R. K., Stegen, J. C. 2024. Reviews and syntheses: Opportunities for robust use of peak intensities from high-resolution mass spectrometry in organic matter studies. Biogeosciences, 21, (20), 4665-4679; doi: 10.5194/bg-21-4665-2024.
Larsen, S., Coleine, C., Albanese, D., Stegen, J. C., Selbmann, L., Donati, C. 2024. Geology and elevation shape bacterial assembly in Antarctic endolithic communities. Science of the Total Environment, 907, doi: 10.1016/j.scitotenv.2023.168050.
Price, A. N., Zimmer, M. A., Bergstrom, A., Burgin, A. J., Seybold, E. C., Krabbenhoft, C. A., Zipper, S., Busch, M. H., Dodds, W. K., Walters, A., Rogosch, J. S., Stubbington, R., Walker, R. H., Stegen, J. C., Datry, T., Messager, M., Olden, J., Godsey, S. E., Shanafield, M., Lytle, D., Burrows, R., Kaiser, K. E., Allen, G. H., Mims, M. C., Tonkin, J. D., Bogan, M., Hammond, J. C., Boersma, K., Myers-Pigg, A. N., DelVecchia, A., Allen, D., Yu, S., Ward, A. 2024. Biogeochemical and community ecology responses to the wetting of non-perennial streams. Nature Water, 2, (9), 815-826; doi: 10.1038/s44221-024-00298-3.
Quiroga, M. V., Stegen, J. C., Mataloni, G., Cowan, D., Lebre, P. H., Valverde, A. 2024. Microdiverse bacterial clades prevail across Antarctic wetlands. Molecular Ecology, 33, (1), e17189; doi: 10.1111/mec.17189.
Roebuck, J. A., Rod, K. A., Garayburu‐Caruso, V. A., Chu, R. K., Goldman, A. E., Renteria, L., Taylor, M., Stegen, J. C. 2024. Linkages between mineral element composition of soils and sediments with hyporheic zone dissolved organic matter chemistry across the contiguous United States. Geophysical Research Letters, 51, (6), doi: 10.1029/2023gl106220.
Roebuck Jr, J. A., Myers‐Pigg, A. N., Garayburu‐Caruso, V., Stegen, J. 2024. Investigating the impacts of solid phase extraction on dissolved organic matter optical signatures and the pairing with high‐resolution mass spectrometry data across a freshwater stream network. Limnology and Oceanography: Methods, 22, (4), 241-253; doi: 10.1002/lom3.10603.
Ryan, K. A., Garayburu-Caruso, V. A., Crump, B. C., Bambakidis, T., Raymond, P. A., Liu, S. D., Stegen, J. C. 2024. Riverine dissolved organic matter transformations increase with watershed area, water residence time, and Damkohler numbers in nested watersheds. Biogeochemistry, 167, (10), 1203-1224; doi: 10.1007/s10533-024-01169-5.

2023

Adebayo, M. B., Bailey, V. L., Chen, X. Y., Hopple, A. M., Jiang, P. S., Li, B., Li, Z., Martin-Hayden, J. M., Megonigal, J. P., Regier, P. J., Rich, R., Stegen, J. C., Smith, R. W., Ward, N. D., Woodard, S. C., Doro, K. O. 2023. A hydrogeophysical framework to assess infiltration during a simulated ecosystem-scale flooding experiment. Journal of Hydrology, 626, doi: 10.1016/j.jhydrol.2023.130243.
Ahamed, F., You, Y., Burgin, A., Stegen, J. C., Scheibe, T. D., Song, H.-S. 2023. Exploring the determinants of organic matter bioavailability through substrate-explicit thermodynamic modeling. Frontiers in Water, 5, 1169701; doi: 10.3389/frwa.2023.1169701.
Arora, B., Kuppel, S., Wellen, C., Oswald, C., Groh, J., Payandi-Rolland, D., Stegen, J., Coffinet, S. 2023. Building cross-site and cross-network collaborations in critical zone science. Journal of Hydrology, 618, doi: 10.1016/j.jhydrol.2023.129248.
Chen, K., Chen, X., Stegen, J. C., Villa, J. A., Bohrer, G., Song, X., Chang, K. Y., Kaufman, M., Liang, X., Guo, Z., Roden, E. E., Zheng, C. 2023. Vertical hydrologic exchange flows control methane emissions from riverbed sediments. Environmental Science & Technology, 57, (9), 4014-4026; doi: 10.1021/acs.est.2c07676.
Cui, Y., Wen, S., Stegen, J. C., Hu, A., Wang, J. 2023. Chemodiversity of riverine dissolved organic matter: Effects of local environments and watershed characteristics. Water Research, 121054; doi: 10.1016/j.watres.2023.121054.
Danczak, R. E., Garayburu-Caruso, V. A., Renteria, L., McKever, S. A., Otenburg, O. C., Grieger, S. R., Son, K., Kaufman, M. H., Fulton, S. G., Roebuck, J. A., Myers-Pigg, A. N., Stegen, J. C. 2023. Riverine organic matter functional diversity increases with catchment size. Frontiers in Water, 5, 1087108; doi: 10.3389/frwa.2023.1087108.
Fulton, S. G., Stegen, J. C., Kaufman, M. H., Dowd, J., Thompson, A. 2023. Laboratory evaluation of open source and commercial electrical conductivity sensor precision and accuracy: How do they compare? PLoS One, 18, (5), e0285092; doi: 10.1371/journal.pone.0285092.
Graham, E. B., Song, H.-S., Grieger, S., Garayburu-Caruso, V. A., Stegen, J. C., Bladon, K. D., Myers-Pigg, A. N. 2023. Potential bioavailability of representative pyrogenic organic matter compounds in comparison to natural dissolved organic matter pools. Biogeosciences, 20, (16), 3449-3457; doi: 10.5194/bg-20-3449-2023.
Hopple, A. M., Doro, K. O., Bailey, V. L., Bond-Lamberty, B., McDowell, N., Morris, K. A., Myers-Pigg, A., Pennington, S. C., Regier, P., Rich, R., Sengupta, A., Smith, R., Stegen, J., Ward, N. D., Woodard, S. C., Megonigal, J. P. 2023. Attaining freshwater and estuarine-water soil saturation in an ecosystem-scale coastal flooding experiment. Environmental Monitoring and Assessment, 195, (3), 425; doi: 10.1007/s10661-022-10807-0.
Kaufman, M. H., Torgeson, J., Stegen, J. C. 2023. Metabolic multireactor: Practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments. PLoS One, 18, (7), e0284256; doi: 10.1371/journal.pone.0284256.
Li, X., Stegen, J. C., Yu, Y., Huang, J. 2023. Coordination and divergence in community assembly processes across co-occurring microbial groups separated by cell size. Front Microbiol, 14, 1166322; doi: 10.3389/fmicb.2023.1166322.
McDowell, N. G., Anderson-Teixeira, K., Biederman, J. A., Breshears, D. D., Fang, Y., Fernández-de-Uña, L., Graham, E. B., Mackay, D. S., McDonnell, J. J., Moore, G. W., Nehemy, M. F., Stevens Rumann, C. S., Stegen, J., Tague, N., Turner, M. G., Chen, X. 2023. Ecohydrological decoupling under changing disturbances and climate. One Earth, 6, (3), 251-266; doi: 10.1016/j.oneear.2023.02.007.
Pavlopoulos, G. A., Baltoumas, F. A., Liu, S., Selvitopi, O., Camargo, A. P., Nayfach, S., Azad, A., Roux, S., Call, L., Ivanova, N. N., Chen, I. M., Paez-Espino, D., Karatzas, E., Novel Metagenome Protein Families, C., Iliopoulos, I., Konstantinidis, K., Tiedje, J. M., Pett-Ridge, J., Baker, D., Visel, A., Ouzounis, C. A., Ovchinnikov, S., Buluc, A., Kyrpides, N. C. 2023. Unraveling the functional dark matter through global metagenomics. Nature, 622, (7983), 594-602; doi: 10.1038/s41586-023-06583-7.
Rodríguez-Ramos, J., Oliverio, A., Borton, M. A., Danczak, R., Mueller, B. M., Schulz, H., Ellenbogen, J., Flynn, R. M., Daly, R. A., Schopflin, L., Shaffer, M., Goldman, A., Lewandowski, J., Stegen, J. C., Wrighton, K. C. 2023. Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream. Frontiers in Microbiomes, 2, doi: 10.3389/frmbi.2023.1199766.
Roley, S., Hall, B., Perkins, W., Garayburu-Caruso, V., Stegen, J. C. 2023. Coupled primary production and respiration in a large river contrasts with smaller rivers and streams. Limnology and Oceanography, 9999, 1-15; doi: 10.1002/lno.12435.
Stegen, J. C., Garayburu-Caruso, V. A., Danczak, R. E., Goldman, A. E., Renteria, L., Torgeson, J. M., Hager, J. 2023. Maximum respiration rates in hyporheic zone sediments are primarily constrained by organic carbon concentration and secondarily by organic matter chemistry. Biogeosciences, 20, (14), 2857-2867; doi: 10.5194/bg-20-2857-2023.
Turetcaia, A. B., Garayburu-Caruso, V. A., Kaufman, M. H., Danczak, R. E., Stegen, J. C., Chu, R. K., Toyoda, J. G., Cardenas, M. B., Graham, E. B. 2023. Rethinking aerobic respiration in the hyporheic zone under variation in carbon and nitrogen stoichiometry. Environmental Science & Technology, 57, (41), 15499-15510; doi: 10.1021/acs.est.3c04765.

2022

Arora B., Briggs M., Zarnetske J., Stegen J. C., Gomez-Velez J., Dwivedi D. and Steefel C. (2022). Hot Spots and Hot Moments in the Critical Zone: Identification of and Incorporation into Reactive Transport Models. Biogeochemistry of the Critical Zone. Advances in Critical Zone Science. A. S. Wymore, W. H. Yang, W. L. Silver, W. H. McDowell and J. Chorover, Springer-Nature. doi: 10.1007/978-3-030-95921-0_2.
Borton M. A., Collins S. M., Graham E. B., Garayburu-Caruso V. A., Goldman A. E., de Melo M., Renteria L., Stegen J. C. and W. C. C. (2022) It takes a village: Using a crowdsourced approach to investigate organic matter composition in global rivers through the lens of ecological theory. Frontiers in Water, 4, 870453; doi: 10.3389/frwa.2022.870453.
Danczak R. E., Sengupta A., Fansler S. J., Chu R. K., Garayburu-Caruso V. A., Renteria L., Toyoda J., Wells J. and Stegen J. C. (2022) Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly. Frontiers in Microbiology, 13, 803420; doi: 10.3389/fmicb.2022.803420.
Fremin B. J.Bhatt A. S.Kyrpides N. C.Sengupta A.Sczyrba A.Maria da Silva A.Buchan A. Gaudin A. Brune A. Hirsch A. M. Neumann A. Shade A. Visel A. Campbell B. Baker B. Hedlund B. P. Crump B. C.Currie C. Kelly C. Craft C. Hazard C. Francis C. Schadt C. W. Averill C. Mobilian C. Buckley D. Hunt D. Noguera D. Beck D. Valentine D. L. Walsh D. Sumner D Lymperopoulou D. Bhaya D. Bryant D. A. Morrison E. Brodie E. Young E. Lilleskov E. Högfors-Rönnholm E. Chen F. Stewart F. Nicol G. W. Teeling H. Beller H. R. Dionisi H. Liao H.-L. Beman J. M. Stegen J. Tiedje J. Jansson J. VanderGheynst J. Norton J. Dangl J. Blanchard J. Bowen J. Macalady J. Pett-Ridge J. Rich J. Payet J. P. Gladden J. D. Raff J. D. Klassen J. L. Tarn J. Neufeld J. Gravuer K. Hofmockel K. Chen K.-H. Konstantinidis K. DeAngelis K. M. Partida-Martinez L. P. Meredith L. Chistoserdova L. Moran M. A. Scarborough M. Schrenk M. Sullivan M. David M. O'Malley M. A. Medina M. Habteselassie M. Ward N. D. Pietrasiak N. Mason O. U. Sorensen P. O. Estrada de los Santos P. Baldrian P. McKay R. M. Simister R. Stepanauskas R. Neumann R. Malmstrom R. Cavicchioli R. Kelly R. Hatzenpichler R. Stocker R. Cattolico R. A. Ziels R. Vilgalys R. Blumer-Schuette S., et al. (2022) Thousands of small, novel genes predicted in global phage genomes. Cell Reports, 39, 110984; doi: https://doi.org/10.1016/j.celrep.2022.110984.
Goldman A. E., Emani S. R., Perez-Angel L. C., Rodriguez-Ramos J. A. and Stegen J. C. (2022) Integrated, Coordinated, Open, and Networked (ICON) Science to Advance the Geosciences: Introduction and Synthesis of a Special Collection of Commentary Articles. Earth and Space Science, 9, e2021EA002099; doi: 10.1029/2021EA002099.
Hu A., Jang K. S., Meng F., Stegen J., Tanentzap A. J., Choi M., Lennon J. T., Soininen J. and Wang J. (2022) Microbial and environmental processes shape the link between organic matter functional traits and composition. Environmental Science & Technology, 56, 10504-10516; doi: 10.1021/acs.est.2c01432.
Hu W., Hou Q., Delgado-Baquerizo M., Stegen J. C., Du Q., Dong L., Ji M., Sun Y., Yao S., Gong H., Xiong J., Xia R., Liu J., Aqeel M., Akram M. A., Ran J. and Deng J. (2022) Continental-scale niche differentiation of dominant topsoil archaea in drylands. Environ Microbiol, Submitted; ISMEJ-21-00550A; doi: 10.1111/1462-2920.16099.
Johnson T., Thomle J., Stickland C., Goldman A. and Stegen J. (2022) Riverbed temperature and 4D ERT monitoring reveals heterogenous horizontal and vertical groundwater-surface water exchange flows under dynamic stage conditions. Frontiers in Earth Science, 10; doi: 10.3389/feart.2022.910058.
Kaufman M. H., Ghosh R. N., Grate J., Shooltz D. D., Freeman M. J., Ball T. M., Loloee R., McIntire C. W., Wells J., Strickland C., Vermeul V., Rod K. A., Mackley R., Lin X., Ren H., Goldman A. and Stegen J. (2022) Dissolved oxygen sensor in an automated hyporheic sampling system reveals biogeochemical dynamics. PLOS Water, 1, e0000014; doi: 10.1371/journal.pwat.0000014.
Larsen S., Albanese D., Stegen J., Franceschi P., Coller E., Zanzotti R., Ioriatti C., Stefani E., Pindo M., Cestaro A. and Donati C. (2022) Distinct and temporally stable assembly mechanisms shape bacterial and fungal communities in vineyard soils. Microbial Ecology; doi: 10.1007/s00248-022-02065-x.
Leonard L. T., Vanzin G. F., Garayburu-Caruso V. A., Lau S. S., Beutler C. A., Newman A. W., Mitch W. A., Stegen J. C., Williams K. H. and Sharp J. O. (2022) Disinfection byproducts formed during drinking water treatment reveal an export control point for dissolved organic matter in a subalpine headwater stream. Water Research X, 15, 100144; doi: 10.1016/j.wroa.2022.100144.
Little C. J., Rizzuto M., Luhring T. M., Monk J. D., Nowicki R. J., Paseka R. E., Stegen J. C., Symons C. C., Taub F. B. and Yen J. (2022) Movement with meaning: integrating information into meta-ecology. Oikos, 2022, e08892; doi: 10.1111/oik.08892.
Nelson A. R., Toyoda J., Chu R. K., Tolić N., Garayburu-Caruso V. A., Saup C. M., Renteria L., Wells J. R., Stegen J. C., Wilkins M. J. and Danczak R. E. (2022) Implications of sample treatment on characterization of riverine dissolved organic matter. Environmental Science: Processes & Impacts, 24, 773-782; doi: 10.1039/D2EM00044J.
Quiroga M. V., Valverde A., Mataloni G., Casa V., Stegen J. C. and Cowan D. (2022) The ecological assembly of bacterial communities in Antarctic wetlands varies across levels of phylogenetic resolution. Environmental Microbiology, 24, 3486-3499; doi: 10.1111/1462-2920.15912.
Rodriguez-Ramos, J. A., et al. (2022). Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments. Msystems: e0051622.doi: 10.1128/msystems.00516-22.
Rubinstein R. L., Borton M. A., Zhou H., Shaffer M., Hoyt D. W., Stegen J., Henry C. S., Wrighton K. C. and Versteeg R. (2022) ORT: A workflow linking genome-scale metabolic models with reactive transport codes. Bioinformatics, 38, 778-784; doi: 10.1093/bioinformatics/btab753.
Shaffer J. P., Nothias L. F., Thompson L. R., Sanders J. G., Salido R. A., Couvillion S. P., Brejnrod A. D., Lejzerowicz F., Haiminen N., Huang S., Lutz H. L., Zhu Q., Martino C., Morton J. T., Karthikeyan S., Nothias-Esposito M., Duhrkop K., Bocker S., Kim H. W., Aksenov A. A., Bittremieux W., Minich J. J., Marotz C., Bryant M. M., Sanders K., Schwartz T., Humphrey G., Vasquez-Baeza Y., Tripathi A., Parida L., Carrieri A. P., Beck K. L., Das P., Gonzalez A., McDonald D., Ladau J., Karst S. M., Albertsen M., Ackermann G., DeReus J., Thomas T., Petras D., Shade A., Stegen J., Song S. J., Metz T. O., Swafford A. D., Dorrestein P. C., Jansson J. K., Gilbert J. A., Knight R. and Earth Microbiome Project C. (2022). Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nature Microbiology 7,(12), 2128-2150; doi: 10.1038/s41564-022-01266-x.
Stegen J. C., Fansler S. J., Tfaily M. M., Garayburu-Caruso V. A., Goldman A. E., Danczak R. E., Chu R. K., Renteria L., Tagestad J. and Toyoda J. (2022) Organic matter transformations are disconnected between surface water and the hyporheic zone. Biogeosciences, 19, 3099-3110; doi: 10.5194/bg-19-3099-2022.
Ward A. S., Packman A., Bernal S., Brekenfeld N., Drummond J., Graham E., Hannah D. M., Klaar M., Krause S., Kurz M., Li A. G., Lupon A., Mao F., Roca M. E. M., Ouellet V., Royer T. V., Stegen J. C. and Zarnetske J. P. (2022) Advancing river corridor science beyond disciplinary boundaries with an inductive approach to catalyse hypothesis generation. Hydrological Processes, 36, e14540; doi: 10.1002/hyp.14540.
Wu, R., Bottos, E. M., Danna, V. G., Stegen, J. C., Jansson, J. K., Davison, M. R. 2022. RNA Viruses Linked to Eukaryotic Hosts in Thawed Permafrost. mSystems, 7, (6), e0058222; doi: 10.1128/msystems.00582-22.

2021

Chen X., Lee R. M., Dwivedi D., Son K., Fang Y., Zhang X., Graham E., Stegen J., Fisher J. B., Moulton D. and Scheibe T. D. (2021) Integrating field observations and process-based modeling to predict watershed water quality under environmental perturbations. Journal of Hydrology, 602, 125762; doi: 10.1016/j.jhydrol.2020.125762.
Damerow J., Varadharajan C., Boye K., Brodie E. L., Burrus M., Chadwick D., Crystal-Ornelas R., Elbashandy H., Eloy Alves R., Ely K., Goldman A., Haberman T., Hendrix V., Kakalia Z., Kemner K. M., Kersting A., Merino N., O'Brien F., Perzan Z., Robles E., Sorensen P., Stegen J. C., Walls R., Weisenhorn P., Zavarin M. and Agarwal D. (2021) Sample identifiers and metadata to support data management and reuse in multidisciplinary ecosystem sciences. Data Science Journal, 20, 1-19; doi: 10.5334/dsj-2021-011.
Danczak R. E., Goldman A. E., Chu R. K., Toyoda J. G., Garayburu-Caruso V. A., Tolic N., Graham E. B., Morad J. W., Renteria L., Wells J. R., Herzog S. P., Ward A. S. and Stegen J. C. (2021) Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties. Science of the Total Environment, 788, 147409; doi: 10.1016/j.scitotenv.2021.147409.
Dove N. C., Veach A. M., Muchero W., Wahl T., Stegen J. C., Schadt C. W. and Cregger M. A. (2021) Assembly of the populus microbiome is temporally dynamic and determined by selective and stochastic factors. Msphere, 6, e01316-01320; doi: 10.1128/mSphere.01316-20.
Fegel T. S., Boot C. M., Covino T. P., Elder K., Hall E. K., Starr B., Stegen J. C. and Rhoades C. C. (2021) Amount and reactivity of dissolved organic matter export are affected by land cover change from old‐growth to second‐growth forests in headwater ecosystems. Hydrological Processes, 35, e14343; doi: 10.1002/hyp.14343.
Fudyma J. D., Chu R., Grachet N. G., Stegen J. C. and Tfaily M. (2021) Coupled biotic-abiotic processes control biogeochemical cycling of dissolved organic matter in the Columbia River hyporheic zone. Frontiers in Water, 2, 574692; doi: 10.3389/frwa.2020.574692.
Goldman A., Emani S., Perez-Angel L. C., Rodriguez-Ramos J., Stegen J. C. and Fox P. (2021) Special collection on open collaboration across geosciences. Eos, 102; doi: 10.1029/2021EO153180.
Hou Z., Ren H., Murray C. J., Song X., Fang Y., Arntzen E. V., Chen X., Stegen J. C., Huang M., Gomez-Velez J. D., Duan Z., Perkins W. A., Richmond M. C. and Scheibe T. D. (2021) A novel construct for scaling groundwater–river interactions based on machine-guided hydromorphic classification. Environmental Research Letters, 16, 104016; doi: 10.1088/1748-9326/ac24ce.
Kaufman M. H., Warden J. G., Cardenas M. B., Stegen J. C., Graham E. B. and Brown J. (2021) Evaluating a laboratory flume microbiome as a window into natural riverbed biogeochemistry. Frontiers in Water, 3, 596260; doi: 10.3389/frwa.2021.596260.
Nayfach S., Roux S., Seshadri R., Udwary D., Varghese N., Schulz F., Wu D. Y., Paez-Espino D., Chen I. M., Huntemann M., Palaniappan K., Ladau J., Mukherjee S., Reddy T. B. K., Nielsen T., Kirton E., Faria J. P., Edirisinghe J. N., Henry C. S., Jungbluth S. P., Chivian D., Dehal P., Wood-Charlson E. M., Arkin A. P., Tringe S. G., Visel A., Woyke T., Mouncey N. J., Ivanova N. N., Kyrpides N. C., Eloe-Fadrosh E. A. and Consortium I. M. D. (2021) A genomic catalog of Earth's microbiomes (Nov, 10.1038/s41587-020-0718-6, 2020). Nature Biotechnology, 39, 521-521; doi: 10.1038/s41587-021-00898-4.
Sengupta A., Volkmann T. H. M., Danczak R. E., Stegen J. C., Dontsova K., Abramson N., Bugaj A. S., Volk M. J., Matos K. A., Meira-Neto A. A., Barberán A., Neilson J. W., Maier R. M., Chorover J., Troch P. A. and Meredith L. K. (2021) Contrasting community assembly forces drive microbial structural and potential functional responses to precipitation in an incipient soil system. Frontiers in Microbiology, 12; doi: 10.3389/fmicb.2021.754698.
Sengupta A., Fansler S. J., Chu R. K., Danczak R. E., Garayburu-Caruso V. A., Renteria L., Song H.-S., Toyoda J., Wells J. and Stegen J. C. (2021) Disturbance triggers non-linear microbe–environment feedbacks. Biogeosciences Discussion, 18, 4773-4789; doi: 10.5194/bg-18-4773-2021.
Sengupta A., Stegen J. C., Bond-Lamberty B., Rivas-Ubach A., Zheng J., Handakumbura P. P., Norris C., Peterson M. J., Yabusaki S. B., Bailey V. L. and Ward N. D. (2021) Antecedent conditions determine the biogeochemical response of coastal soils to seawater exposure. Soil Biology and Biochemistry, 153, 108104; doi: https://doi.org/10.1016/j.soilbio.2020.108104.
Song H.-S., Stegen J. C., Graham E. B. and Scheibe T. D. (2021) Historical contingency in microbial resilience to hydrologic perturbations. Frontiers in Water, 3; doi: 10.3389/frwa.2021.590378.
Tagestad J., Ward N. D., Butman D. and Stegen J. C. (2021) Small streams dominate US tidal reaches and will be disproportionately impacted by sea-level rise. Science Total Environment, 753, 141944; doi: 10.1016/j.scitotenv.2020.141944.

2020

Anderson C. G., Bond-Lamberty B. and Stegen J. C. (2020) Active layer depth and soil properties impact specific leaf area variation and ecosystem productivity in a boreal forest. PLoS One, 15, e0232506; doi: 10.1371/journal.pone.0232506.
Bao Y., Feng Y., Stegen J. C., Wu M., Chen R., Liu W., Zhang J., Li Z. and Lin X. (2020) Straw chemistry links the assembly of bacterial communities to decomposition in paddy soils. Soil Biology and Biochemistry, 148, 107866; doi: https://doi.org/10.1016/j.soilbio.2020.107866.
Danczak R. E., Chu R. K., Fansler S. J., Goldman A. E., Graham E. B., Tfaily M. M., Toyoda J. and Stegen J. C. C. (2020) Using metacommunity ecology to understand environmental metabolomes. Nature Communications, 11, 6369; doi: 10.1038/s41467-020-19989-y.
Danczak R. E., Daly R. A., Borton M. A., Stegen J. C. C., Roux S., Wrighton K. C. and Wilkins M. J. (2020) Ecological assembly processes are coordinated between bacterial and viral communities in fractured shale ecosystems. Msystems, 5, e00098-00020; doi: 10.1128/mSystems.00098-20.
Garayburu-Caruso V. A., Danczak R. E., Stegen J. C., Renteria L., Mccall M., Goldman A. E., Chu R. K., Toyoda J., Resch C. T., Torgeson J. M., Wells J., Fansler S., Kumar S. and Graham E. B. (2020) Using community science to reveal the global chemogeography of river metabolomes. Metabolites, 10, 518; doi: 10.3390/metabo10120518.
Garayburu-Caruso V. A., Stegen J. C., Song H.-S., Renteria L., Wells J., Garcia W., Resch C. T., Goldman A. E., Chu R. K., Toyoda J. and Graham E. B. (2020) Carbon limitation leads to thermodynamic regulation of aerobic metabolism. Environmental Science & Technology Letters, 7, 517-524; doi: 10.1021/acs.estlett.0c00258.
Goldman A., Emani S., Perez-Angel L. C., Rodriguez-Ramos J., Stegen J. C. and Fox P. (2020) Special collection on open collaboration across geosciences. Eos.
Ji M., Kong W., Stegen J., Yue L., Wang F., Dong X., Cowan D. A. and Ferrari B. C. (2020) Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils. Environmental Microbiology, 22, 2261-2272; doi: 10.1111/1462-2920.14993.
Kattge J.Bonisch G.Diaz S.Lavorel S.Prentice I. C.Leadley P.Tautenhahn S.Werner G. D. A.Aakala T.Abedi M.Acosta A. T. R.Adamidis G. C.Adamson K.Aiba M.Albert C. H.Alcantara J. M.Alcazar C. C.Aleixo I.Ali H.Amiaud B.Ammer C.Amoroso M. M.Anand M.Anderson C.Anten N.Antos J.Apgaua D. M. G.Ashman T. L.Asmara D. H.Asner G. P.Aspinwall M.Atkin O.Aubin I.Baastrup-Spohr L.Bahalkeh K.Bahn M.Baker T.Baker W. J.Bakker J. P.Baldocchi D.Baltzer J.Banerjee A.Baranger A.Barlow J.Barneche D. R.Baruch Z.Bastianelli D.Battles J.Bauerle W.Bauters M.Bazzato E.Beckmann M.Beeckman H.Beierkuhnlein C.Bekker R.Belfry G.Belluau M.Beloiu M.Benavides R.Benomar L.Berdugo-Lattke M. L.Berenguer E.Bergamin R.Bergmann J.Bergmann Carlucci M.Berner L.Bernhardt-Romermann M.Bigler C.Bjorkman A. D.Blackman C.Blanco C.Blonder B.Blumenthal D.Bocanegra-Gonzalez K. T.Boeckx P.Bohlman S.Bohning-Gaese K.Boisvert-Marsh L.Bond W.Bond-Lamberty B.Boom A.Boonman C. C. F.Bordin K.Boughton E. H.Boukili V.Bowman D.Bravo S.Brendel M. R.Broadley M. R.Brown K. A.Bruelheide H.Brumnich F.Bruun H. H.Bruy D.Buchanan S. W.Bucher S. F.Buchmann N.Buitenwerf R.Bunker D. E.Burger J., et al. (2020) TRY plant trait database - enhanced coverage and open access. Global Change Biology, 26, 119-188; doi: 10.1111/gcb.14904.
Lin X., Ren H., Goldman A., Stegen J. C. and Scheibe T. D. (2020) WHONDRS-GUI: A web application for global survey of surface water metabolites. PeerJ, 8, e9277; doi: 10.7717/peerj.9277.
Nelson W. C., Graham E. B., Crump A. R., Fansler S. J., Arntzen E. V., Kennedy D. W. and Stegen J. C. (2020) Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome. PLOS ONE, 15, e0228165; doi: 10.1371/journal.pone.0228165.
Song H.-S., Stegen J. C., Graham E. B., Lee J.-Y., Garayburu-Caruso V. A., Nelson W. C., Chen X., Moulton J. D. and Scheibe T. D. (2020) Representing organic matter thermodynamics in biogeochemical reactions via substrate-explicit modeling. Frontiers in Microbiology, 11; doi: 10.3389/fmicb.2020.531756.
Thomle J., Strickland C., Johnson T. C., Zhu Y. and Stegen J. (2020) A flux detection probe to quantify dynamic groundwater-surface water exchange in the hyporheic zone. Ground Water, 58, 892-900; doi: 10.1111/gwat.13001.
Villa J. A., Smith G. J., Ju Y., Renteria L., Angle J. C., Arntzen E., Harding S. F., Ren H., Chen X., Sawyer A. H., Graham E. B., Stegen J. C., Wrighton K. C. and Bohrer G. (2020) Methane and nitrous oxide porewater concentrations and surface fluxes of a regulated river. Science of the Total Environment, 715, 136920; doi: 10.1016/j.scitotenv.2020.136920.
Wang J. J., Legendre P., Soininen J., Yeh C. F., Graham E., Stegen J. C., Casamayor E. O., Zhou J. Z., Shen J. and Pan F. Y. (2020) Temperature drives local contributions to beta diversity in mountain streams: Stochastic and deterministic processes. Global Ecology and Biogeography, 29, 420-432; doi: 10.1111/geb.13035.
Wang W., McDowell N. G., Pennington S., Grossiord C., Leff R. T., Sengupta A., Ward N. D., Sezen U. U., Rich R., Megonigal J. P., Stegen J. C., Bond-Lamberty B. and Bailey V. (2020) Tree growth, transpiration, and water-use efficiency between shoreline and upland red maple (Acer rubrum) trees in a coastal forest. Agricultural and Forest Meteorology, 295, 108163; doi: https://doi.org/10.1016/j.agrformet.2020.108163.

2019

Brislawn CJ, EB Graham, K Dana P Ihardt, SJ Fansler, WB Chrisler, JB Cliff, JC Stegen, JJ Moran, and HC Bernstein. 2019. “Forfeiting the priority effect: turnover defines biofilm community succession.” ISME Journal, 13, 1865-1877; doi: 10.1038/s41396-019-0396-x.
Graham EB, JC Stegen, MY Huang, XY Chen, TD and Scheibe. 2019. “Subsurface biogeochemistry is a missing link between ecology and hydrology in dam-impacted river corridors.” Science of the Total Environment, 657, 435-445; doi: 10.1016/j.scitotenv.2018.11.414.
Pennington SC, NG McDowell, JP Megonigal, JC Stegen, and B Bond-Lamberty. 2019. “Tree proximity affects soil respiration dynamics in a coastal temperate deciduous forest.” Biogeosciences Discuss., 2019, 1-27; doi: 10.5194/bg-2019-218.
Scott DT, JD Gomez-Velez, CN Jones, and JW Harvey. 2019. “Floodplain inundation spectrum across the United States.” Nature Communications, 10, 5194; doi: 10.1038/s41467-019-13184-4.
Sengupta A, JC Stegen, AAM Neto, YD Wang, JW Neilsont, J Chorover, PA Troch, and RM Maier. 2019. “Assessing microbial community patterns during incipient soil formation from basalt.” Journal of Geophysical Research-Biogeosciences, 124, 941-958; doi: 10.1029/2017jg004315.
Sengupta A, J Indivero, C Gunn, MM Tfaily, RK Chu, J Toyoda, VL Bailey, ND Ward, and JC Stegen. 2019. “Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities.” Biogeosciences, 16, 3911-3928; doi: 10.5194/bg-16-3911-2019.
Wang JJ, P Legendre, J Soininen, CF Yeh, E Graham, J Stegen, EO Casamayor, JZ Zhou, J Shen, and FY Pan. 2019. “Temperature drives local contributions to beta diversity in mountain streams: Stochastic and deterministic processes.” Global Ecology and Biogeography; doi: 10.1111/geb.13035.
Ward AS, SM Wondzell, NM Schmadel, S Herzog, JP Zarnetske, V Baranov, PJ Blaen, N Brekenfeld, R Chu, R Derelle, J Drummond, JH Fleckenstein, V Garayburu-Caruso, E Graham, D Hannah, CJ Harman, J Hixson, JLA Knapp, S Krause, MJ Kurz, J Lewandowski, AG Li, E Marti, M Miller, AM Milner, K Neil, L Orsini, AI Packman, S Plont, L Renteria, K Roche, T Royer, C Segura, J Stegen, J Toyoda, J Wells, and NI Wisnoski. 2019. “Spatial and temporal variation in river corridor exchange across a 5th-order mountain stream network.” Hydrology and Earth System Sciences, 23, 5199-5225; doi: 10.5194/hess-23-5199-2019.
Ward AS, JP Zarnetske, V Baranov, PJ Blaen, N Brekenfeld, R Chu, R Derelle, J Drummond, JH Fleckenstein, V Garayburu-Caruso, E Graham, D Hannah, CJ Harman, S Herzog, J Hixson, JLA Knapp, S Krause. MJ, Kurz, J Lewandowski, A Li, E Martí, M Miller, AM Milner, K Neil, L Orsini, AI Packman, S Plont, L Renteria, K Roche, T Royer, NM Schmadel, C Segura, J Stegen, J Toyoda, J Wells, NI Wisnoski, and SM Wondzell. 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, 1567-1581; doi: 10.5194/essd-11-1567-2019.
Chu R, A Goldman, SC Brooks, R Danczak, V Garayburu-Caruso, E Graham, M Jones, X Lin, JW Morad, H Ren, L Renteria, C Resch, M Tfaily, M Tolic, J Toyoda, J Wells, and J Stegen. 2019. “WHONDRS 48 Hour Diel Cycling Study at the East Fork Poplar Creek in Tennessee, USA.” ESS-DIVE Dataset, Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS); Pacific Northwest National Laboratory, Richland, WA; doi: 10.15485/1577278.
Danczak R, A Goldman, R Chu, V Garayburu-Caruso, E Graham, X He, X Lin, C Meile, JW Morad, H Ren, L Renteria, C Resch, J Rooze, J Schalles, M Tfaily, J Thomle, H Tolic, J Toyoda, J Wells, and J Stegen. 2019. “WHONDRS 48 Hour Diel Cycling Study at the Altamaha River in Georgia, USA. ESS-DIVE Dataset.” Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS); Pacific Northwest National Laboratory, Richland, WA; doi: 10.15485/1577263.
Garayburu-Caruso V, A Goldman, R Chu, RE Danczak, E Graham, X Lin, JW Morad, H Ren, L Renteria, C Resch, M Tfaily, H Tolic, J Toyoda, J Wells, and J Stegen. 2019. “WHONDRS 48 Hour Diel Cycling Study at the Columbia River in Washington, USA.” ESS-DIVE Dataset, Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS); Pacific Northwest National Laboratory, Richland, WA; doi: 10.15485/1577265.
Goldman A, S Arnon, E Bar-Zeev, R Chu, R Danczak, V Garayburu-Caruso, E Graham, X Lin, JW Morad, H Ren, L Renteria, C Resch, M Tfaily, H Tolic, J Toyoda, J Wells, and J Stegen. 2019. “WHONDRS 48 Hour Diel Cycling Study at the Jordan River, Israel.” ESS-DIVE Dataset, Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS); Pacific Northwest National Laboratory, Richland, WA; doi: 10.15485/1577266.
Renteria L, A Goldman, R Chu, R Danczak, V Garayburu-Caruso, E Graham, X Lin, JW Morad, H Ren, C Resch, M Tfaily, H Tolic, J Toyoda, J Wells, K Znotinas, and J Stegen. 2019. “WHONDRS 48 Hour Diel Cycling Study at the Nisqually River, Washington, USA.” ESS-DIVE Dataset, Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS); Pacific Northwest National Laboratory, Richland, WA; doi: 10.15485/1576995.
Stegen J., Goldman A., Blackburn S. E., Chu R., Danczak R., Garayburu-Caruso V., Graham E., Grieshauber C., Lin X., Morad J. W., Ren H., Renteria L., Resch C., Tfaily M., Tolic N., Toyoda J. G., Wells J. R. and Znotinas K. (2019) WHONDRS Surface Water Sampling for Metabolite Biogeography. ESS-DIVE Dataset, Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS); Pacific Northwest National Laboratory, Richland, WA; doi: 10.15485/1484811.
Stegen J, A Goldman, R Chu, R Danczak, V Garayburu-Caruso, E Graham, X Lin, JW Morad, H Ren, L Renteria, C Resch, M Tfaily, N Tolic, JG Toyoda, and JR Wells. 2019. “WHONDRS 48 Hour Diel Cycling Study at HJ Andrews Experimental Forest Watershed 1 (WS1).” ESS-DIVE Dataset, Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS); Pacific Northwest National Laboratory, Richland, WA; doi: 10.15485/1509695.
Wells J, A Goldman, R Chu, R Danczak, V Garayburu-Caruso, E Graham, J Lewandowski, X Lin, K Meinikmann, JW Morad, B Muller B, H Ren, L Renteria, C Resch, H Schulz, M Tfaily, H Tolic H, J Toyoda, and J Stegen. 2019 “WHONDRS 48 Hour Diel Cycling Study at the Erpe River, Germany.” ESS-DIVE Dataset, Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS); Pacific Northwest National Laboratory, Richland, WA; doi: 10.15485/1577260.

2018

Bottos EM, DW Kennedy, EB Romero, SJ Fansler, JM Brown, LM Bramer, RK Chu, MM Tfaily, JK Jansson, and JC Stegen. 2018. “Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities.” FEMS Microbiology Ecology, 94; doi: 10.1093/femsec/fiy110.
Feng YZ, RR Chen, JC Stegen, ZY Guo, JW Zhang, ZP Li, and XG Lin. 2018. “Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions.” Molecular Ecology, 27, 5238-5251; doi: 10.1111/mec.14914.
Graham EB, AR Crump, DW Kennedy, E Arntzen, S Fansler, SO Purvine, CD Nicora, W Nelson, MM Tfaily, and JC Stegen. 2018. “Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone.” Science of the Total Environment, 642, 742-753; doi: 10.1016/j.scitotenv.2018.05.256.
Song X, X Chen, J Stegen, G Hammond, H Song, H Dai, EB Graham, and J Zachara. 2018. “Drought conditions maximize the impact of high-frequency flow variations on thermal regimes and biogeochemical function in the hyporheic zone.” Water Resources Research, 54; doi: 10.1029/2018WR022586.
Stegen JC. 2018. “At the nexus of history, ecology, and hydrobiogeochemistry: improved predictions across scales through integration.” Msystems, 3; doi: 10.1128/mSystems.00167-17.
Stegen JC, EM Bottos, and JK Jansson. 2018. “A unified conceptual framework for prediction and control of microbiomes.” Current Opinion in Microbiology, 44, 20-27; doi: 10.1016/j.mib.2018.06.002.
Stegen JC and AE Goldman. 2018. “WHONDRS: A community resource for studying dynamic river corridors.” Msystems, 3; doi: 10.1128/mSystems.00151-18.
Stegen JC, T Johnson, JK Fredrickson, MJ Wilkins, AE Konopka, WC Nelson, EV Arntzen, WB Chrisler, RK Chu, SJ Fansler, EB Graham, DW Kennedy, CT Resch, M Tfaily, and J Zachara. 2018. “Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.” Nature Communications, 9; doi: 10.1038/s41467-018-02922-9.
Tripathi BM, JC Stegen, M Kim, K Dong, JM Adams, and YK Lee. 2018. “Soil pH mediates the balance between stochastic and deterministic assembly of bacteria.” ISME Journal, 12, 1072-1083; doi: 10.1038/s41396-018-0082-4.
Zhou T, J Bao, MY Huang, ZS Hou, E Arntzen, XH Song, SF Harding, PS Titzler, HY Ren, CJ Murray, WA Perkins, XY Chen, JC Stegen, GE Hammond, PD Thorne, and JM Zachara. 2018. “Riverbed hydrologic exchange dynamics in a large regulated river reach.” Water Resources Research, 54, 2715-2730; doi: 10.1002/2017wr020508.

2017

Goldman AE, EB Graham, AR Crump, DW Kennedy, EB Romero, CG Anderson, KL Dana, CT Resch, JK Fredrickson, and JC Stegen. 2017. “Biogeochemical cycling at the aquatic-terrestrial interface is linked to parafluvial hyporheic zone inundation history.” Biogeosciences, 14, 4229-4241; doi: 10.5194/bg-14-4229-2017.
Graham EB, AR Crump, CT Resch, S Fansler, E Arntzen, DW Kennedy, JK Fredrickson, and JC Stegen. 2017. “Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes.” Environmental Microbiology, 19, 1552-1567; doi: 10.1111/1462-2920.13720.
Graham EB, AE Goldman, AR Crump, AE Goldman, LM Bramer, E Arntzen, E Romero, CT Resch, DW Kennedy, and JC Stegen. 2017. “Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes.” Journal of Geophysical Research-Biogeosciences, 122, 3188-3205; doi: 10.1002/2017jg003967.
Graham EB and JC Stegen. 2017. “Dispersal-based microbial community assembly decreases biogeochemical function.” Processes, 5; doi: 10.3390/pr5040065.
Hou Z, WC Nelson, JC Stegen, CJ Murray, E Arntzen, AR Crump, DW Kennedy, MC Perkins, TD Scheibe, JK Fredrickson, and JM Zachara. 2017. “Geochemical and microbial community attributes in relation to hyporheic zone geological facies.” Scientific Reports, 7; doi: 10.1038/s41598-017-12275-w.
Jurburg SD, I Nunes, JC Stegen, X Le Roux, A Prieme, SJ Sorensen, and JF Salles. 2017. “Autogenic succession and deterministic recovery following disturbance in soil bacterial communities.” Scientific Reports, 7; doi: 10.1038/srep45691.
Liu C, MJ Yao, JC Stegen, JP Rui, JB Li, and XZ Li. 2017. “Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse.” Scientific Reports, 7; doi: 10.1038/s41598-017-17736-w.
Song HS, DG Thomas, JC Stegen, MJ Li, CX Liu, XH Song, XY Chen, JK Fredrickson, JM Zachara, and TD Scheibe. 2017. “Regulation-structured dynamic metabolic model provides a potential mechanism for delayed enzyme response in denitrification process.” Frontiers in Microbiology, 8; doi: 10.3389/fmicb.2017.01866.
Stegen JC, CG Anderson, B Bond-Lamberty, AR Crump, X Chen, and N Hess. 2017. “Soil respiration across a permafrost transition zone: spatial structure and environmental correlates.” Biogeosciences, 14, 4341-4354; doi: 10.5194/bg-14-4341-2017.
Stern N, M Ginder-Vogel, JC Stegen, E Arntzen, DW Kennedy, BR Larget, and EE Roden. 2017. “Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia river hyporheic corridor.” Applied and Environmental Microbiology, 83; doi: 10.1128/AEM.00260-17.
Yan QY, JC Stegen, YH Yu, Y Deng, XH Li, S Wu, LL Dai, X Zhang, JJ Li, C Wang, JJ Ni, XM Li, HJ Hu, FS Xiao, WS Feng, DL Ning, ZL He, JD Van Nostrand, LY Wu, and JZ Zhou. 2017. “Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China).” Molecular Ecology, 26, 3839-3850; doi: 10.1111/mec.14151.

2016

Danczak RE, AH Sawyer, KH Williams, JC Stegen, C Hobson, and MJ Wilkins. 2016. “Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments.” Journal of Geophysical Research-Biogeosciences, 121, 2976-2987; doi: 10.1002/2016jg003527.
Graham EB, AR Crump, CT Resch, S Fansler, E Arntzen, DW Kennedy, JK Fredrickson, and JC Stegen. 2016. “Coupling spatiotemporal community assembly processes to changes in microbial metabolism.” Frontiers in Microbiology, 7; doi: 10.3389/fmicb.2016.01949.
Stegen JC, JK Fredrickson, MJ Wilkins, AE Konopka, WC Nelson, EV Arntzen, WB Chrisler, RK Chu, RE Danczak, SJ Fansler, DW Kennedy, CT Resch, and M Tfaily. 2016. “Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.” Nature Communications, 7; doi: 10.1038/ncomms11237.
Stegen JC, AH Hurlbert, B Bond-Lamberty, XY Chen, CG Anderson, RK Chu, F Dini-Andreote, SJ Fansler S. J., Hess N. J. and Tfaily M. (2016) Aligning the measurement of microbial diversity with macroecological theory. Frontiers in Microbiology, 7; doi: 10.3389/fmicb.2016.01487.
Stegen JC, A Konopka, JP McKinley, C Murray, XJ Lin, MD Miller, DW Kennedy, EA Miller, CT Resch, and JK Fredrickson. 2016. “Coupling among microbial communities, biogeochemistry, and mineralogy across biogeochemical facies.” Scientific Reports, 6; doi: 10.1038/srep30553.
Veach AM, JC Stegen, SP Brown, WK Dodds, and A Jumpponen. 2016. “Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem.” Molecular Ecology, 25, 4674-4688; doi: 10.1111/mec.13784.

2015

Dini-Andreote F, JC Stegen, JD van Elsas, and JF Salles. 2015. “Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession.” Proceedings of the National Academy of Sciences of the United States of America, 112, E1326-E1332; doi: 10.1073/pnas.1414261112.
Hu WG, Q Zhang, T Tian, DY Li, G Cheng, J Mu, QB Wu, FJ Niu, JC Stegen, LZ An, and HY Feng. 2015. “Relative roles of deterministic and stochastic processes in driving the vertical distribution of bacterial communities in a permafrost core from the Qinghai-Tibet Plateau, China.” Plos One, 10; doi: 10.1371/journal.pone.0145747.
Martinez I, JC Stegen, MX Maldonado-Gomez, AM Eren, PM Siba, AR Greenhill, and J Walter. 2015. “The gut microbiota of rural papua new guineans: Composition, diversity patterns, and ecological processes.” Cell Reports, 11, 527-538; doi: 10.1016/j.celrep.2015.03.049.
Nelson WC and JC Stegen. 2015. “The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle.” Frontiers in Microbiology, 6; doi: 10.3389/fmicb.2015.00713.
Stegen JC, XJ Lin, JK Fredrickson, and AE Konopka. 2015. “Estimating and mapping ecological processes influencing microbial community assembly.” Frontiers in Microbiology, 6; doi: 10.3389/fmicb.2015.00370.

2014

Hurlbert AH and JC Stegen. 2014. “On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions.” Frontiers in Genetics, 5; doi: 10.3389/fgene.2014.00420.
Hurlbert AH and JC Stegen. 2014. “When should species richness be energy limited, and how would we know?” Ecology Letters, 17, 401-413; doi: 10.1111/ele.12240.

2013

Bailey VL, SJ Fansler, JC Stegen, and LA Mccue. 2013. “Linking microbial community structure to beta-glucosidic function in soil aggregates.” ISME Journal, 7, 2044-2053; doi: 10.1038/ismej.2013.87.
Bentley LP, JC Stegen, VM Savage, DD Smith, EI von Allmen, JS Sperry, PB Reich, and BJ Enquist. 2013. “An empirical assessment of tree branching networks and implications for plant allometric scaling models.” Ecology Letters, 16, 1069-1078; doi: 10.1111/ele.12127.
Lindemann SR, JJ Moran, JC Stegen, RS Renslow, JR Hutchison, JK Cole, AC Dohnalkova, J Tremblay, K Singh, SA Malfatti, F Chen SG Tringe, H Beyenal, and JK Fredrickson. 2013. “The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling.” Frontiers in Microbiology, 4; doi: 10.3389/fmicb.2013.00323.
Moles AT, B Peco, IR Wallis, WJ Foley, AGB Poore, EW Seabloom, PA Vesk, AJ Bisigato, L Cella-Pizarro, CJ Clark, PS Cohen, WK Cornwell, W Edwards, R Ejrnaes, T Gonzales-Ojeda, BJ Graae, G Hay, FC Lumbwe, B Magana-Rodriguez, BD Moore, PL Peri, JR Poulsen, JC Stegen, R Veldtman, H Zeipel, NR Andrew, SL Boulter, ET Borer, JHC Cornelissen, AG Farji-Brener, JL DeGabriel, E Jurado, LA Kyhn, B Low, CPH Mulder, K Reardon-Smith, J Rodriguez-Velazquez, A De Fortier, Z Zheng, PG Blendinger, BJ Enquist, JM Facelli, T Knight, JD Majer, M Martinez-Ramos, P McQuillan, and FKC Hui. 2013. “Correlations between physical and chemical defences in plants: tradeoffs, syndromes, or just many different ways to skin a herbivorous cat?” New Phytologist, 198, 252-263; doi: 10.1111/nph.12116.
Stegen JC, AL Freestone, TO Crist, MJ Anderson, JM Chase, LS Comita, HV Cornell, KF Davies, SP Harrison, AH Hurlbert, BD Inouye, NJB Kraft, JA Myers, NJ Sanders, NG Swenson, and M Vellend. 2013. “Stochastic and deterministic drivers of spatial and temporal turnover in breeding bird communities.” Global Ecology and Biogeography, 22, 202-212; doi: 10.1111/j.1466-8238.2012.00780.x.
Stegen JC, XJ Lin, JK Fredrickson, XY Chen, DW Kennedy, CJ Murray, ML Rockhold, and A Konopka. 2013. “Quantifying community assembly processes and identifying features that impose them.” ISME Journal, 7, 2069-2079; doi: 10.1038/ismej.2013.93.
Wang JJ, J Shen, YC Wu, C Tu, J Soininen, JC Stegen, JZ He, XQ Liu, L Zhang, and EL Zhang. 2013. “Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes.” ISME Journal, 7, 1310-1321; doi: 10.1038/ismej.2013.30.

2012

Hulshof CM, JC Stegen, NG Swenson, CAF Enquist, and BJ Enquist. 2012. “Interannual variability of growth and reproduction in Bursera simaruba: the role of allometry and resource variability.” Ecology, 93, 180-190; doi: 10.1890/11-0740.1.
Kraft NJB, NJ Sanders, JC Stegen, MJ Anderson, TO Crist, HV Cornell, M Vellend, JM Chase, LS Comita, KF Davies, AL Freestone, SP Harrison, BD Inouye, JA Myers, and NG Swenson. 2012. “Response to comments on "disentangling the drivers of beta diversity along latitudinal and elevational gradients." Science, 335; doi: 10.1126/science.1218697.
McClain CR, JC Stegen, and AH Hurlbert. 2012. “Dispersal, environmental niches and oceanic-scale turnover in deep-sea bivalves.” Proceedings of the Royal Society B-Biological Sciences, 279, 1993-2002; doi: 10.1098/rspb.2011.2166.
Price CA, JS Weitz, VM Savage, JC Stegen, A Clarke, DA Coomes, PS Dodds, RS Etienne, AJ Kerkhoff, K McCulloh, KJ Niklas, H Olff, and NG Swenson. 2012. “Testing the metabolic theory of ecology.” Ecology Letters, 15, 1465-1474; doi: 10.1111/j.1461-0248.2012.01860.x.
Stegen JC, BJ Enquist, and R Ferriere. 2012. “Eco-evolutionary community dynamics: Covariation between diversity and invasibility across temperature gradients.” American Naturalist, 180, E110-E126; doi: 10.1086/667577.
Stegen JC, R Ferriere, and BJ Enquist. 2012. “Evolving ecological networks and the emergence of biodiversity patterns across temperature gradients.” Proceedings of the Royal Society B-Biological Sciences, 279, 1051-1060; doi: 10.1098/rspb.2011.1733.
Stegen JC, XJ Lin, AE Konopka, and JK Fredrickson. 2012. “Stochastic and deterministic assembly processes in subsurface microbial communities.” ISME Journal, 6, 1653-1664; doi: 10.1038/ismej.2012.22.
Swenson NG, BJ Enquist, J Pither, AJ Kerkhoff, B Boyle, MD Weiser, JJ Elser, WF Fagan, J Forero-Montana, N Fyllas, NJB Kraft, JK Lake, AT Moles, S Patino, OL Phillips, CA Price, PB Reich, CA Quesada, JC Stegen, R Valencia, IJ Wright, SJ Wright, S Andelman, PM Jorgensen, TE Lacher, A Monteagudo, MP Nunez-Vargas, R Vasquez-Martinez, and KM Nolting. 2012. “The biogeography and filtering of woody plant functional diversity in North and South America.” Global Ecology and Biogeography, 21, 798-808; doi: 10.1111/j.1466-8238.2011.00727.x.
Swenson NG, JC Stegen, SJ Davies, DL Erickson, J Forero-Montana, AH Hurlbert, WJ Kress, J Thompson, M Uriarte, SJ Wright, and JK Zimmerman. 2012. “Temporal turnover in the composition of tropical tree communities: functional determinism and phylogenetic stochasticity.” Ecology, 93, 490-499; doi: 10.1890/11-1180.1.

2011

Anderson MJ, TO Crist, JM Chase, M Vellend, BD Inouye, AL Freestone, NJ Sanders, HV Cornell, LS Comita, KF Davies, SP Harrison, NJB Kraft, JC Stegen, and NG Swenson. 2011. “Navigating the multiple meanings of beta diversity: a roadmap for the practicing ecologist.” Ecology Letters, 14, 19-28; doi: 10.1111/j.1461-0248.2010.01552.x.
Kraft NJB, LS Comita, JM Chase, NJ Sanders, NG Swenson, TO Crist, JC Stegen, M Vellend, B Boyle, MJ Anderson, HV Cornell, KF Davies, AL Freestone, BD Inouye, SP Harrison, and JA Myers. 2011. “Disentangling the drivers of beta diversity along latitudinal and elevational gradients.” Science, 333, 1755-1758; doi: 10.1126/science.1208584.
Moles AT, IR Wallis, WJ Foley, DI Warton, JC Stegen, AJ Bisigato, L Cella-Pizarro, CJ Clark, PS Cohen, WK Cornwell, W Edwards, R Ejrnaes, T Gonzales-Ojeda, BJ Graae, G Hay, FC Lumbwe, B Magana-Rodriguez, BD Moore, PL Peri, JR Poulsen, R Veldtman, H von Zeipel, NR Andrew, SL Boulter, ET Borer, FF Campon, M Coll, AG Farji-Brener, J De Gabriel, E Jurado, LA Kyhn, B Low, CPH Mulder, K Reardon-Smith, J Rodriguez-Velazquez, EW Seabloom, PA Vesk, A van Cauter, MS Waldram, Z Zheng, PG Blendinger, BJ Enquist, JM Facelli, T Knight, JD Majer, M Martinez-Ramos, P McQuillan, and LD Prior. 2011. “Putting plant resistance traits on the map: a test of the idea that plants are better defended at lower latitudes.” New Phytologist, 191, 777-788; doi: 10.1111/j.1469-8137.2011.03732.x.
Stegen JC and AR Black. 2011. “Trophic ecology of an aquatic mite (Piona carnea) preying on Daphnia pulex: effects of predator density, nutrient supply and a second predator (Chaoborus americanus).” Hydrobiologia, 668, 171-182; doi: 10.1007/s10750-010-0454-x.
Stegen JC and AH Hurlbert. 2011. “Inferring ecological processes from taxonomic, phylogenetic and functional trait beta-diversity.” Plos One, 6; doi: 10.1371/journal.pone.0020906.
Stegen JC, NG Swenson, BJ Enquist, EP White, OL Phillips, PM Jorgensen, MD Weiser, AM Mendoza, and PN Vargas. 2011. “Variation in above-ground forest biomass across broad climatic gradients.” Global Ecology and Biogeography, 20, 744-754; doi: 10.1111/j.1466-8238.2010.00645.x.

2010

Doi H, M Cherif, T Iwabuchi, I Katano, JC Stegen, and M Striebel. 2010. “Integrating elements and energy through the metabolic dependencies of gross growth efficiency and the threshold elemental ratio.” Oikos, 119, 752-765; doi: 10.1111/j.1600-0706.2009.18540.x.
Stegen JC, BJ Enquist, and R Ferriere. 2010. “Advancing the metabolic theory of biodiversity (vol 12, pg 1001, 2009).” Ecology Letters, 13, 141-141.

2009

Stegen JC, BJ Enquist, and R Ferriere. 2009. “Advancing the metabolic theory of biodiversity.” Ecology Letters, 12, 1001-1015; doi: 10.1111/j.1461-0248.2009.01358.x.
Stegen JC and NG Swenson. 2009. “Functional trait assembly through ecological and evolutionary time.” Theoretical Ecology, 2, 239-250; doi: 10.1007/s12080-009-0047-3.
Stegen JC, NG Swenson, R Valencia, BJ Enquist, and J Thompson. 2009. “Above-ground forest biomass is not consistently related to wood density in tropical forests.” Global Ecology and Biogeography, 18, 617-625; doi: 10.1111/j.1466-8238.2009.00471.x.

2008

Stegen JC and EP White. 2008. “On the relationship between mass and diameter distributions in tree communities.” Ecology Letters, 11, 1287-1293; doi: 10.1111/j.1461-0248.2008.01242.x.

2004

Stegen JC, CM Gienger, and LX Sun. 2004. “The control of color change in the Pacific tree frog, Hyla regilla.” Canadian Journal of Zoology-Revue Canadienne De Zoologie, 82, 889-896; doi: 10.1139/Z04-068.