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Fundamental and Computational Sciences Directorate

Staff information

James Stegen

Ecosystem Science
Earth Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352

PNNL Publications


  • Damerow J., C. Varadharajan, K.E. Boye, E.L. Brodie, M. Burrus, D. Chadwick, and R. Crystal-Ornelas, et al. 2021. "Sample identifiers and metadata to support data management and reuse in multidisciplinary ecosystem sciences." Data Science Journal 20, no. 1:Article No. 11. PNNL-SA-158301. doi:10.5334/dsj-2021-011
  • Danczak R.E., A.E. Goldman, R.K. Chu, J.G. Toyoda, V.A. Garayburu-Caruso, N. Tolic, and E.B. Graham, et al. 2021. "Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties." Science of the Total Environment 788. PNNL-SA-156110. doi:10.1016/j.scitotenv.2021.147409
  • Dove N.C., A.M. Veach, W. Muchero, T. Wahl, J.C. Stegen, C.W. Schadt, and M. Cregger. 2021. "Assembly of the Populus microbiome is temporally dynamic and determined by selective and stochastic factors." mSphere 6, no. 3:e01316-20. PNNL-SA-158824. doi:10.1128/mSphere.01316-20
  • Fudyma J.D., R.K. Chu, N. Grachet, J.C. Stegen, and M.M. Tfaily. 2021. "Coupled biotic-abiotic processes control biogeochemical cycling of dissolved organic matter in the Columbia River hyporheic zone." Frontiers in Water 2. PNNL-SA-158822. doi:10.3389/frwa.2020.574692
  • Kaufman M.H., J. Warden, M.B. Cardenas, J.C. Stegen, E.B. Graham, and J.M. Brown. 2021. "Evaluating the laboratory flume microbiome as a window into natural riverbed biogeochemistry." Frontiers in Water 3. PNNL-SA-147077. doi:10.3389/frwa.2021.596260
  • Sengupta A., J.C. Stegen, B. Bond-Lamberty, A. Rivas-Ubach, J. Zheng, P. Handakumbura, and C.G. Norris, et al. 2021. "Antecedent conditions determine the biogeochemical response of coastal soils to seawater exposure." Soil Biology and Biochemistry 153. PNNL-SA-154783. doi:10.1016/j.soilbio.2020.108104
  • Sengupta A., S.J. Fansler, R.K. Chu, R.E. Danczak, V.A. Garayburu-Caruso, L. Renteria, and H. Song, et al. 2021. "Disturbance triggers non-linear microbe-environment feedbacks." Biogeosciences 18, no. 16:4773-4789. PNNL-SA-157144. doi:10.5194/bg-18-4773-2021
  • Song H., J.C. Stegen, E.B. Graham, and T.D. Scheibe. 2021. "Historical Contingency in Microbial Resilience to Hydrologic Perturbations." Frontiers in Water 3. PNNL-SA-156061. doi:10.3389/frwa.2021.590378
  • Tagestad J.D., N.D. Ward, D. Butman, and J.C. Stegen. 2021. "Small Streams Dominate US Tidal Reaches and Will be Disproportionately Impacted by Sea-level Rise." Science of the Total Environment 753. PNNL-SA-145873. doi:10.1016/j.scitotenv.2020.141944


  • Anderson C.G., B. Bond-Lamberty, and J.C. Stegen. 2020. "Active layer depth and soil properties impact specific leaf area variation and ecosystem productivity in a boreal forest." PLOS ONE 15, no. 12:Article No.e0232506. PNNL-SA-120124. doi:10.1371/journal.pone.0232506
  • Danczak R.E., R. Daly, M. Borton, J.C. Stegen, S. Roux, K.C. Wrighton, and M. Wilkins. 2020. "Ecological assembly processes are coordinated between bacterial and viral communities in fractured shale ecosystems." mSystems 5, no. 2:Article No. e00098-20. PNNL-SA-147222. doi:10.1128/mSystems.00098-20
  • Danczak R.E., R.K. Chu, S.J. Fansler, A.E. Goldman, E.B. Graham, M.M. Tfaily, and J.G. Toyoda, et al. 2020. "Using metacommunity ecology to understand environmental metabolomes." Nature Communications 11, no. 1:Article No. 6369. PNNL-SA-152827. doi:10.1038/s41467-020-19989-y
  • Garayburu-Caruso V.A., J.C. Stegen, H. Song, L. Renteria, J.R. Wells, W.L. Garcia, and C.T. Resch, et al. 2020. "Carbon limitation leads to thermodynamic regulation of aerobic metabolism." Environmental Science & Technology Letters 7, no. 7:517-524. PNNL-SA-150146. doi:10.1021/acs.estlett.0c00258
  • Garayburu-Caruso V.A., R.E. Danczak, J.C. Stegen, L. Renteria, M.L. McCall, A.E. Goldman, and R.K. Chu, et al. 2020. "Using Community Science to Reveal the Global Chemogeography of River Metabolomes." Metabolites 10, no. 12:518. PNNL-SA-157277. doi:10.3390/metabo10120518
  • Ji M., W. Kong, J.C. Stegen, L. Yue, F. Wang, X. Dong, and D.A. Cowan, et al. 2020. "Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils." Environmental Microbiology 22, no. 6:2261-2272. PNNL-SA-140351. doi:10.1111/1462-2920.14993
  • Nelson W.C., E.B. Graham, A.R. Crump, S.J. Fansler, E.V. Arntzen, D.W. Kennedy, and J.C. Stegen. 2020. "Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome." PLoS One 15, no. 1:Article No. e0228165. PNNL-SA-125632. doi:10.1371/journal.pone.0228165
  • Pennington S.C., N.G. McDowell, P. Megonigal, J.C. Stegen, and B. Bond-Lamberty. 2020. "Localized basal area affects soil respiration temperature sensitivity in a coastal deciduous forest." Biogeosciences 17, no. 3:771-780. PNNL-SA-143158. doi:10.5194/bg-17-771-2020
  • Song H., J.C. Stegen, E.B. Graham, J. Lee, V.A. Garayburu-Caruso, W.C. Nelson, and X. Chen, et al. 2020. "Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling." Frontiers in Microbiology 11. PNNL-SA-151734. doi:10.3389/fmicb.2020.531756
  • Villa J.A., G. Smith, Y. Ju, L. Renteria, J.C. Angle, E.V. Arntzen, and S.F. Harding, et al. 2020. "Methane and nitrous oxide porewater concentrations and surface fluxes of a regulated river." Science of the Total Environment 715. PNNL-SA-149661. doi:10.1016/j.scitotenv.2020.136920
  • Wang J., P. Legendre, J. Soininen, C. Yeh, E.B. Graham, J.C. Stegen, and E. Casamayor, et al. 2020. "Temperature drives local contributions to beta diversity in mountain streams: stochastic and deterministic processes." Global Ecology and Biogeography 29, no. 3:420-432. PNNL-SA-132470. doi:10.1111/geb.13035
  • Wang W., N.G. McDowell, S.C. Pennington, C. Grossiord, R.T. Leff, A. Sengupta, and N.D. Ward, et al. 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. PNNL-SA-153708. doi:10.1016/j.agrformet.2020.108163


  • Graham E.B., J.C. Stegen, M. Huang, X. Chen, and T.D. Scheibe. 2019. "Subsurface biogeochemistry is a missing link between ecology and hydrology in dam-impacted river corridors." Science of the Total Environment 657. PNNL-SA-132468. doi:10.1016/j.scitotenv.2018.11.414
  • Sengupta A., J.C. Stegen, A. Neto, Y. Wang, J.W. Neilson, T. Tatarin, and E.A. Hunt, et al. 2019. "Assessing microbial community patterns under incipient soil formation from basalt." Journal of Geophysical Research. Biogeosciences 124, no. 4:941-958. PNNL-SA-127573. doi:10.1029/2017JG004315
  • Ward A.S., S.M. Wondzell, N.M. Schmadel, S. Herzog, J.P. Zarnetske, V. Baranov, and P. Blaen, et al. 2019. "Spatial and temporal variation in river corridor exchange across a 5th order mountain stream network." Hydrology and Earth System Sciences 23, no. 12:5199-5225. PNNL-SA-140824. doi:10.5194/hess-23-5199-2019


  • Bottos E.M., D.W. Kennedy, E.B. Romero, S.J. Fansler, J.M. Brown, L.M. Bramer, and R.K. Chu, et al. 2018. "Dispersal Limitation and Thermodynamic Constraints Govern Spatial Structure of Permafrost Microbial Communities." FEMS Microbiology Ecology 94, no. 8:fiy110. PNNL-SA-130968. doi:10.1093/femsec/fiy110
  • Feng Y., R. Chen, J.C. Stegen, Z. Guo, J. Zhang, Z. Li, and X. Lin. 2018. "Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions." Molecular Ecology 27, no. 24:5238-5251. PNNL-SA-129546. doi:10.1111/mec.14914
  • Graham E.B., A.R. Crump, D.W. Kennedy, E.V. Arntzen, S.J. Fansler, S.O. Purvine, and C.D. Nicora, et al. 2018. "Multi ‘omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone." Science of the Total Environment 642. PNNL-SA-133671. doi:10.1016/j.scitotenv.2018.05.256
  • Song X., X. Chen, J.C. Stegen, G. Hammond, H. Song, H. Dai, and E.B. Graham, et al. 2018. "Drought Conditions Maximize the Impact of High-Frequency Flow Variations on Thermal Regimes and Biogeochemical Function in the Hyporheic Zone." Water Resources Research 54, no. 10:7361-7382. PNNL-SA-123922. doi:10.1029/2018WR022586
  • Stegen J.C. 2018. "At the nexus of history, ecology, and hydrobiogeochemistry: Improved predictions across scales through integration." mSystems 3, no. 2:Article No. e00167-17. PNNL-SA-130397. doi:10.1128/mSystems.00167-17
  • Stegen J.C., and A.E. Goldman. 2018. "WHONDRS: A community resource for studying dynamic river corridors." mSystems 3, no. 5:Article Number e00151-18. PNNL-SA-136150. doi:10.1128/mSystems.00151-18
  • Stegen J.C., E.M. Bottos, and J.K. Jansson. 2018. "A Unified Conceptual Framework for Prediction and Control of Microbiomes." Current Opinion in Microbiology 44. PNNL-SA-133248. doi:10.1016/j.mib.2018.06.002
  • Zhou T., J. Bao, M. Huang, Z. Hou, E.V. Arntzen, X. Song, and S.F. Harding, et al. 2018. "Riverbed Hydrologic Exchange Dynamics in a Large Regulated River Reach." Water Resources Research 54, no. 4:2715-2730. PNNL-SA-123666. doi:10.1002/2017WR020508


  • Graham E.B., J.C. Stegen, A.R. Crump, C.T. Resch, S.J. Fansler, E.V. Arntzen, and D.W. Kennedy, et al. 2017. "Organic carbon thermodynamics elucidate spatiotemporal mechanisms governing hyporheic zone biogeochemical cycling." In Proceedings of the Subsurface Biogeochemical Research and Terrestrial Ecosystem Science Joint Meeting April 25-26, 2017, Potomac, Maryland. Washington, District Of Columbia:US Department of Energy, Office of Biological and Environmental Research. PNNL-SA-125130.
  • Graham E.B., M.M. Tfaily, A.R. Crump, A.E. Goldman, L.M. Bramer, E.V. Arntzen, and E.B. Romero, et al. 2017. "Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes." Journal of Geophysical Research. Biogeosciences 122, no. 12:3188-3205. PNNL-SA-125144. doi:10.1002/2017JG003967
  • Hou Z., W.C. Nelson, J.C. Stegen, C.J. Murray, E.V. Arntzen, A.R. Crump, and D.W. Kennedy, et al. 2017. "Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies." Scientific Reports 7. PNNL-SA-121286. doi:10.1038/s41598-017-12275-w
  • Jurburg S.D., I. Nunes, J.C. Stegen, X. Le Roux, A. Prieme, S.J. Sorensen, and J. Falcao Salles. 2017. "Autogenic Succession and Deterministic Recovery Following Disturbance in Soil Bacterial Communities." Scientific Reports 7. PNNL-SA-120407. doi:10.1038/srep45691
  • Liu C., M. Yao, J.C. Stegen, J. Rui, J. Li, and X. Li. 2017. "Long-term Nitrogen Addition affects the Phylogenetic Turnover of Soil Microbial Community Responding to Moisture Pulse." Scientific Reports 7. PNNL-SA-127737. doi:10.1038/s41598-017-17736-w
  • Song H., D.G. Thomas, J.C. Stegen, M. Li, C. Liu, X. Song, and X. Chen, et al. 2017. "Regulation-structured dynamic metabolic model provides a potential mechanism for delayed enzyme response in denitrification process." Frontiers in Microbiology 8. PNNL-SA-129317. doi:10.3389/fmicb.2017.01866
  • Stegen J.C., C.G. Anderson, B. Bond-Lamberty, A.R. Crump, X. Chen, and N.J. Hess. 2017. "Soil respiration across a permafrost transition zone: spatial structure and environmental correlates." Biogeosciences 14, no. 18:4341-4354. PNNL-SA-122396. doi:10.5194/bg-14-4341-2017
  • Stern N., M.A. Ginder-Vogel, J.C. Stegen, E.V. Arntzen, D.W. Kennedy, B.R. Larget, and E.E. 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, no. 16:Article No. e00260-17. PNNL-SA-129379. doi:10.1128/AEM.00260-17
  • Yan Q., J.C. Stegen, Y. Yu, Y. Deng, X. Li, S. Wu, and L. Dai, et al. 2017. "Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China)." Molecular Ecology 26, no. 14:3839-3850. PNNL-SA-120283. doi:10.1111/mec.14151


  • Danczak R.E., A.H. Sawyer, K.H. Williams, J.C. Stegen, C. Hobson, and M.J. Wilkins. 2016. "Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments." Journal of Geophysical Research. Biogeosciences 121, no. 12:2976-2987. PNNL-SA-123167. doi:10.1002/2016JG003527
  • Stegen J.C., A. Konopka, J. McKinely, C.J. Murray, X. Lin, M.D. Miller, and D.W. Kennedy, et al. 2016. "Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies." Scientific Reports. PNNL-SA-117630. doi:10.1038/srep30553
  • Stegen J.C., A.H. Hurlbert, B. Bond-Lamberty, X. Chen, C.G. Anderson, R.K. Chu, and F. Dini-Andreote, et al. 2016. "Aligning the Measurement of Microbial Diversity with Macroecological Theory." Frontiers in Microbiology 7. PNNL-SA-122085. doi:10.3389/fmicb.2016.01487
  • Stegen J.C., J.K. Fredrickson, M.J. Wilkins, A. Konopka, W.C. Nelson, E.V. Arntzen, and W.B. Chrisler, et al. 2016. "Groundwater-Surface Water Mixing Shifts Ecological Assembly Processes and Stimulates Organic Carbon Turnover." Nature Communications 7. PNNL-SA-111962. doi:10.1038/ncomms11237


  • Dini-Andreote F., J.C. Stegen, J.D. van Elsas, and J. Falcao 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, no. 11:E1326-E1332. PNNL-SA-105908. doi:10.1073/pnas.1414261112
  • Martinez I., J.C. Stegen, M.X. Maldonado-Gómez, A. Eren, P.M. Siba, A.R. Greenhill, and J. Walter. 2015. "The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes." Cell Reports 11, no. 4:527-538. PNNL-SA-107911. doi:10.1016/j.celrep.2015.03.049
  • Nelson W.C., and J.C. Stegen. 2015. "The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle." Frontiers in Microbiology 6. PNNL-SA-112374. doi:10.3389/fmicb.2015.00713
  • Stegen J.C., X. Lin, J.K. Fredrickson, and A. Konopka. 2015. "Estimating and mapping ecological processes influencing microbial community assembly." Frontiers in Microbiology 6. PNNL-SA-96713. doi:10.3389/fmicb.2015.00370


  • Hurlbert A.H., and J.C. Stegen. 2014. "On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions." Frontiers in Genetics 5. PNNL-SA-104983. doi:10.3389/fgene.2014.00420
  • Hurlbert A.H., and J.C. Stegen. 2014. "When should species richness be energy-limited, and how would we know?." Ecology Letters 17, no. 4:401-413. PNNL-SA-97830. doi:10.1111/ele.12240


  • Bailey V.L., S.J. Fansler, J.C. Stegen, and L.A. McCue. 2013. "Linking Microbial Community Structure to ß-Glucosidic Function in Soil Aggregates." The ISME Journal 7, no. 10:2044-2053. PNNL-SA-90744. doi:10.1038/ismej.2013.87
  • Lindemann S.R., J.J. Moran, J.C. Stegen, R.S. Renslow, J.R. Hutchison, J.K. Cole, and A. Dohnalkova, et al. 2013. "The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington: Community Structural Responses to Seasonal Cycling." Frontiers in Microbiology 4. PNNL-SA-96936. doi:10.3389/fmicb.2013.00323
  • Stegen J.C., X. Lin, J.K. Fredrickson, X. Chen, D.W. Kennedy, C.J. Murray, and M.L. Rockhold, et al. 2013. "Quantifying Community Assembly Processes and Identifying Features that Impose Them." The ISME Journal 7. PNNL-SA-86535. doi:10.1038/ismej.2013.93
  • Wang J., J. Shen, Y. Wu, C. Tu, J. Soininen, J.C. Stegen, and J. He, et al. 2013. "Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes." The ISME Journal 7, no. 7:1310-1321. PNNL-SA-90907. doi:10.1038/ismej.2013.30


  • Stegen J.C., X. Lin, A. Konopka, and J.K. Fredrickson. 2012. "Stochastic and Deterministic Assembly Processes in Subsurface Microbial Communities." The ISME Journal 6, no. 9:1653-1664. PNNL-SA-84131. doi:10.1038/ismej.2012.22

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