PNNL

James Stegen is an internationally-recognized expert in ecological theory, the interface between microbial ecology and hydro-biogeochemistry, and distributed open watershed science. He is the lead investigator for research linking microbial communities to subsurface biogeochemistry and multi-scale linkages among soil microbiomes, carbon-cycling, and permafrost. Stegen also has demonstrated leadership in building multidisciplinary research teams that integrate computational simulation, experimentation, and observation.

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

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

• 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-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.

• DOE Early Career Research Program Award (2019)
• Linus Pauling Distinguished Postdoctoral Award (2011)

• National Science Foundation Postdoctoral Fellow (2009)

• 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.

Google Scholar

2021 

• 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., 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.