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Fundamental and Computational Sciences Directorate

Staff information

James Stegen

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

PNNL Publications


  • Zhou T, J Bao, M Huang, Z Hou, EV Arntzen, X Song, SF Harding, PS Titzler, H Ren, CJ Murray, WA Perkins, X Chen, JC Stegen, G Hammond, PD Thorne, and JM Zachara. 2018. "Riverbed Hydrologic Exchange Dynamics in a Large Regulated River Reach." Water Resources Research 54(4):2715-2730.  doi:10.1002/2017WR020508
  • Stegen JC, TC Johnson, JK Fredrickson, MJ Wilkins, AE Konopka, WC Nelson, EV Arntzen, WB Chrisler, RK Chu, SJ Fansler, EB Graham, DW Kennedy, CT Resch, MM Tfaily, and JM Zachara. 2018. "Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology." Nature Communications 9:Article No. 585.  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." The ISME Journal 12(4):1072-1083.  doi:10.1038/s41396-018-0082-4


  • Graham EB, and JC Stegen. 2017. "Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function." Processes 5(4):Article No. 65.  doi:10.3390/pr5040065
  • Graham EB, AR Crump, CT Resch, SJ Fansler, EV 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, MM Tfaily, AR Crump, AE Goldman, LM Bramer, EV Arntzen, EB 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(12):3,188-3,205.  doi:10.1002/2017JG003967
  • Graham EB, MM Tfaily, AR Crump, AE Goldman, LM Bramer, EV Arntzen, EB 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(12):3188-3205.  doi:10.1002/2017JG003967
  • 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(18):4229-4241.  doi:10.5194/bg-14-4229-2017
  • Hou Z, WC Nelson, JC Stegen, CJ Murray, EV 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:Article No. 12006.  doi:10.1038/s41598-017-12275-w
  • Jurburg SD, I Nunes, JC Stegen, X Le Roux, A Prieme, SJ Sorensen, and J Falcao Salles. 2017. "Autogenic Succession and Deterministic Recovery Following Disturbance in Soil Bacterial Communities." Scientific Reports 7:Article No. 45691.  doi:10.1038/srep45691
  • Liu C, M Yao, JC 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:Article No. 17492.  doi:10.1038/s41598-017-17736-w
  • Song HS, DG Thomas, JC Stegen, M Li, C Liu, X Song, X 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 8:1866.  doi:10.3389/fmicb.2017.01866
  • Stegen JC, CG Anderson, B Bond-Lamberty, AR Crump, X Chen, and NJ Hess. 2017. "Soil respiration across a permafrost transition zone: spatial structure and environmental correlates." Biogeosciences 14(18):4341-4354.  doi:10.5194/bg-14-4341-2017
  • Stern N, MA Ginder-Vogel, JC Stegen, EV 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(16):Article No. e00260-17.  doi:10.1128/AEM.00260-17
  • Yan Q, JC Stegen, Y Yu, Y Deng, X Li, S Wu, L Dai, X Zhang, J Li, C Wang, J Ni, X Li, H Hu, F Xiao, W Feng, D Ning, Z He, JD Van Nostrand, L Wu, and J Zhou. 2017. "Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China)." Molecular Ecology 26(14):3839-3850.  doi:10.1111/mec.14151


  • Graham EB, AR Crump, CT Resch, SJ Fansler, EV Arntzen, DW Kennedy, JK Fredrickson, and JC Stegen. 2016. "Coupling spatiotemporal community assembly processes to ecosystem function." Frontiers in Microbiology 7:Article No. 1949.  doi:10.3389/fmicb.2016.01949
  • 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(12):2976-2987.  doi:10.1002/2016JG003527
  • Stegen JC, A Konopka, J McKinely, CJ Murray, X 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):30553.  doi:10.1038/srep30553
  • Stegen JC, AH Hurlbert, B Bond-Lamberty, X Chen, CG Anderson, RK Chu, F Dini-Andreote, SJ Fansler, NJ Hess, and MM Tfaily. 2016. "Aligning the Measurement of Microbial Diversity with Macroecological Theory." Frontiers in Microbiology 7:Article No. 1487.  doi:10.3389/fmicb.2016.01487
  • Stegen JC, JK Fredrickson, MJ Wilkins, A Konopka, WC Nelson, EV Arntzen, WB Chrisler, RK Chu, RE Danczak, SJ Fansler, DW Kennedy, CT Resch, and MM Tfaily. 2016. "Groundwater-Surface Water Mixing Shifts Ecological Assembly Processes and Stimulates Organic Carbon Turnover." Nature Communications 7:11237.  doi:10.1038/ncomms11237


  • Dini-Andreote F, JC Stegen, JD 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(11):E1326-E1332.  doi:10.1073/pnas.1414261112
  • Martinez I, JC Stegen, MX Maldonado-Gómez, 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(4):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:Article No. 713.  doi:10.3389/fmicb.2015.00713
  • Stegen JC, X Lin, JK Fredrickson, and A Konopka. 2015. "Estimating and mapping ecological processes influencing microbial community assembly." Frontiers in Microbiology 6:Article No. 370.  doi:10.3389/fmicb.2015.00370


  • Hurlbert AH, and JC Stegen. 2014. "On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions." Frontiers in Genetics 5:Article No. 420.  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(4):401-413.  doi:10.1111/ele.12240


  • Bailey VL, SJ Fansler, JC Stegen, and LA McCue. 2013. "Linking Microbial Community Structure to ß-Glucosidic Function in Soil Aggregates." The ISME Journal 7(10):2044-2053.  doi:10.1038/ismej.2013.87
  • Lindemann SR, JJ Moran, JC Stegen, RS Renslow, JR Hutchison, JK Cole, A Dohnalkova, J Tremblay, K Singh, S Malfatti, F Chen, S 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 4:323.  doi:10.3389/fmicb.2013.00323
  • Stegen JC, X Lin, JK Fredrickson, X Chen, DW Kennedy, CJ Murray, ML Rockhold, and A Konopka. 2013. "Quantifying Community Assembly Processes and Identifying Features that Impose Them." The ISME Journal 7:2069-2079.  doi:10.1038/ismej.2013.93
  • Wang J, J Shen, Y Wu, C Tu, J Soininen , JC Stegen, J He, X Liu, L Zhang, and E Zhang. 2013. "Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes." The ISME Journal 7(7):1310-1321.  doi:10.1038/ismej.2013.30


  • Stegen JC, X Lin, A Konopka, and JK Fredrickson. 2012. "Stochastic and Deterministic Assembly Processes in Subsurface Microbial Communities." The ISME Journal 6(9):1653-1664.  doi:10.1038/ismej.2012.22

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