Staff information

Jim Fredrickson

Biological Sciences Division
Laboratory Fellow
Pacific Northwest National Laboratory
PO Box 999
MSIN: P7-54
Richland, WA 99352
E-mail:

Biography

Dr. Fredrickson specializes in Microbial Ecology and Environmental Microbiology. Since joining Pacific Northwest National Laboratory in 1985, he has focused his research efforts in subsurface microbiology and biogeochemistry. He has been responsible for laboratory and field research programs investigating the microbial ecology and biogeochemistry of geologically diverse subsurface environments and is recognized nationally and internationally for these efforts. He is currently a Laboratory Fellow in the Biological Sciences Division at PNNL.

Dr. Fredrickson has also served as Subprogram Coordinator for the U.S. Department of Energy’s Subsurface Science Program from 1991 to the present. In this role, he coordinated the technical aspects of DOE’s Deep Subsurface Microbiology Subprogram at the national level and assists DOE’s Program Manager in setting programmatic research directions. In 2005 Dr. Fredrickson was appointed Chief Scientist for the Genomics: GTL program. In this capacity, Dr. Fredrickson serves as a spokesperson for the GTL program to the science community.

Research Interests

Microbial ecology
Environmental microbiology
Subsurface microbiology and biogeochemistry

Education and Credentials

B.S. Soil Sciences, University of Wisconsin-Stevens Point, 1978
M.S. Soil Sciences, Washington State University, 1982
Ph.D. Soil Microbiology,Washington State University, 1984

Affiliations and Professional Service

Editor-in-Chief of Microbial Ecology (1995-2005)
Editorial Board Member Environmental Microbiology
Past Editorial Board Member of Applied and Environmental Microbiology
Served as Chairman of Division N (Microbial Ecology), American Society for Microbiology (1995-1997)
Divisional Group III Representative for the American Society for Microbiology (1998-2000)
Ad hoc reviewer for Science, Geochimica et Cosmochimica Acta, Geomicrobiology Journal, Journal of Bacteriology, Soil Biology and Biochemistry, Environmental Science and Technology, Canadian Journal of Microbiology, Chemical Geology and Molecular Ecology;
1998 ASM Foundation Lecturer
Member of the American Society for Microbiology
Member of the Organizing Committee for the 1993 International Conference on Subsurface Microbiology, Bath, England and the 1996 International Symposium on Subsurface Microbiology, Davos, Switzerland
1996 DOE-Environmental Management Science Program, Bioremediation Section Peer-review panel

Awards and Recognitions

1985 Emil Truog Award, Outstanding Ph.D. Thesis in the Field of Soil Science; Soil Science Society of America
1985 Washington State University Outstanding Thesis Award
Adjunct Graduate Faculty Appointment, Washington State University - served on five graduate committees to date
1991 U.S. DOE Certificate of Appreciation for "Outstanding Research in Microbiology and for Program Planning that Contributed to the Development of a Fundamental Research Program in Biodegradation and Microbial Physiology"
Adjunct Faculty Appointment, University of Idaho
American Society for Microbiology Foundation Lecturer, 1998-2000
Member, American Academy of Microbiology, 1999
Advisory Committee Member, UCLA-DOE Institute for Genomics and Proteomics
Co-chaired a colloquium sponsored by the American Academy of Microbiology, 2004. Systems Microbiology: Beyond Microbial Genomics (report published by the American Academy of Microbiology)
Member of the Committee on the Astrobiology Strategy for the Exploration of Mars (2006-2007)
Selection Committee 2006 Ernest Orlando Lawrence Award in Environmental Science & Technology
Fellow, American Association for the Advancement of Science

PNNL Publications

2008

Marshall MJ, AE Plymale, DW Kennedy, L Shi, Z Wang, SB Reed, A Dohnalkova, CJ Simonson, C Liu, D Saffarini, MF Romine, JM Zachara, AS Beliaev, and JK Fredrickson. 2008. "Hydrogenase- and Outer Membrane c-Type Cytochrome-Facilitated Reduction of Technetium(VII) by Shewanella oneidensis MR-1." Environmental Microbiology 10(1):125-136. doi:10.1111/j.1462-2920.2007.01438.x
Pinchuk GE, CG Ammons, DE Culley, SM Li, JS McLean, MF Romine, KH Nealson, JK Fredrickson, and AS Beliaev. 2008. "Utilization of DNA as a Sole Source of Phosphorus, Carbon, and Energy by Shewanella spp.: Ecological and Physiological Implications for Dissimilatory Metal Reduction." Applied and Environmental Microbiology 74(4):1198-1208. doi:10.1128/AEM.02026-07
Elias DA, SL Tollaksen, DW Kennedy, HM Mottaz, CS Giometti, JS Mclean, EA Hill, GE Pinchuk, MS Lipton, JK Fredrickson, and YA Gorby. 2008. "The Influence of Cultivation Methods on Shewanella oneidensis Physiology and Proteome Expression ." Archives of Microbiology 189(4):313-324. doi:10.1007/s00203-007-0321-y
Fredrickson JK, and JM Zachara. 2008. "Electron Transfer at the Microbe-Mineral Interface: A Grand Challenge in Biogeochemistry." Geobiology 6(3):245-253.
Fredrickson JK, MF Romine, AS Beliaev, JM Auchutung, ME Driscoll, TS Gardner, KH Nealson, AL Osterman, GE Pinchuk, JL Reed, D Rodionov, JLM Rodrigues, D Saffarini, MH Serres, AM Spormann, IB Zhulin, and JM Tiedje. 2008. "Towards Environmental Systems Biology of Shewanella." Nature Reviews. Microbiology 6(8):592-603. doi:10.1038/nrmicro1947
Fredrickson JK, SMW Li, E Gaidamakova, V Matrosova, M Zhai, HM Sulloway, JC Scholten, MG Brown,, DL Balkwill, and MJ Daly. 2008. "Protein Oxidation: Key to Bacterial Desiccation Resistance?" The ISME Journal 2(4):393-403. doi:10.1038/ismej.2007.116
Mclean JS, GE Pinchuk, OV Geydebrekht, CL Bilskis, BA Zakrajsek, EA Hill, D Saffarini, MF Romine, YA Gorby, JK Fredrickson, and AS Beliaev. 2008. "Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1." Environmental Microbiology 10(7):1861-1876. doi:10.1111/j.1462-2920.2008.01608.x
Mclean JS, PD Majors, CL Reardon, CL Bilskis, SB Reed, MF Romine, and JK Fredrickson. 2008. "Investigations of Structure and Metabolism within Shewanella oneidensis MR-1 Biofilms ." Journal of Microbiological Methods 74(1):47-56.
Shi L, S Deng, MJ Marshall, Z Wang, DW Kennedy, A Dohnalkova, HM Mottaz, EA Hill, YA Gorby, AS Beliaev, DJ Richardson, JM Zachara, and JK Fredrickson. 2008. " Direct Involvement of Type II Secretion System in Extracellular Translocation of Shewanella oneidensis Outer Membrane Cytochromes MtrC and OmcA." Journal of Bacteriology 190(15):5512-5516. doi:10.1128/JB.00514-08
Zhang H, X Tang, GR Munske, NL Zakharova, L Yang, C Zheng, MA Wolff, N Tolic, GA Anderson, L Shi, MJ Marshall, JK Fredrickson, and JE Bruce. 2008. "In Vivo Identification of the Outer Membrane Protein OmcA-MtrC Interaction Network in Shewanella oneidensis MR-1 Cells Using Novel Hydrophobic Chemical Cross-Linkers." Journal of Proteome Research 7(4):1712-1720. doi:10.1021/pr7007658

2007

Zachara JM, JK Fredrickson, RK Kukkadapu, and YA Gorby. 2007. "Anaerobic Microbial-Mineral Processes with Fe(III) Oxides: Experimental Considerations and Approaches." Chapter 4 in Methods for Investigating Microbial-Mineral Interactions: CMS Workshop Lectures, vol. 14, ed. Patricia A. Maurice and Leslie A. Warren, pp. 117-165. The Clay Minerals Society, West Lafayette, IN.
Biju VP, D Pan, YA Gorby, JK Fredrickson, JS Mclean, D Saffarini, and HP Lu. 2007. "Combined Spectroscopic and Topographic Characterization of Nanoscale Domains and Their Distributions of a Redox Protein on Bacterial Cell Surfaces ." Langmuir 23(3):1333-1338. doi:10.1021/la061343z
Bretschger O, A Obraztsova, CA Sturm, IS Chang, YA Gorby, SB Reed, DE Culley, CL Reardon, S Barua, MF Romine, J Zhou, AS Beliaev, R Bouhenni, D Saffarini, F Mansfeld, BH Kim, JK Fredrickson, and KH Nealson. 2007. "Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants." Applied and Environmental Microbiology 73(21):7003-7012. doi:10.1128/AEM.01087-07
Daly MJ, E Gaidamakova, V Matrosova, A Vasilenko, M Zhai, RD leapman, B Lai, B Ravel, SMW Li, KM Kemner, and JK Fredrickson. 2007. "Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance." PLoS Biology 5(4):e92. doi:10.1371/journal.pbio.0050092
Deflaun MF, JK Fredrickson, H Dong, SM Pfiffner, TC Onstott, DL Balkwill, SH Streger, E Stackebrandt, S Knoessen, and E van Heerden. 2007. "Isolation and Characterization of a Geobacillus thermoleovorans Strain from an Ultra-Deep South African Gold Mine." Systematic and Applied Microbiology 30(2):152-164.
Hartshorne RS, BN Jepson, TA Clarke, SJ Field, JK Fredrickson, JM Zachara, L Shi, JN Butt, and D Richardson. 2007. "Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors." Journal of Biological Inorganic Chemistry 12(7):1083-1094. doi:10.1007/s00775-007-0278-y
Lee JH, MG Kim, B Yoo, NV Myung, J Maeng, T Lee, A Dohnalkova, JK Fredrickson, MJ Sadowsky, and HG Hur. 2007. "Biogenic formation of photoactive arsenic-sulfide nanotubes by Shewanella sp. strain HN-41 ." Proceedings of the National Academy of Sciences of the United States of America 104(51):20410-20415. doi:10.1073/pnas.0707595104
Shi L, TC Squier, JM Zachara, and JK Fredrickson. 2007. "Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes." Molecular Microbiology 65(1):12-20. doi:10.1111/j.1365-2958.2007.05783.x

2006

Liu C, BH Jeon, JM Zachara, Z Wang, A Dohnalkova, and JK Fredrickson. 2006. "Kinetics of Microbial Reduction of Solid Phase U(VI)." Environmental Science and Technology 40(20):6290-6296.
Marshall MJ, AS Beliaev, A Dohnalkova, DW Kennedy, L Shi, Z Wang, MI Boyanov, B Lai, KM Kemner, JS Mclean, SB Reed, DE Culley, VL Bailey, CJ Simonson, D Saffarini, MF Romine, JM Zachara, and JK Fredrickson. 2006. "c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis ." PloS Biology 4(8):1324-1333.
Brim H, JP Osborne, HM Kostandarithis, JK Fredrickson, LP Wackett, and MJ Daly. 2006. "Deinococcus radiodurans Engineered for Complete Toluene Degradation Facilitates Cr(VI) Reduction." Microbiology 152(8):2469-2477.
Elias DA, ME Monroe, RD Smith, JK Fredrickson, and MS Lipton. 2006. "Confirmation of the Expression of a Large Set of Conserved Hypothetical Proteins in Shewanella oneidensis MR-1." Journal of Microbiological Methods 66(2):223-233.
Fang R, DA Elias, ME Monroe, Y Shen, M McIntosh, P Wang, CD Goddard, SJ Callister, RJ Moore, YA Gorby, JN Adkins, JK Fredrickson, MS Lipton, and RD Smith. 2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5(4):714-725. doi:10.1074/mcp.M500301-MCP200
Gao H, A Obraztova, N Stewart, R Popa, JK Fredrickson, JM Tiedje, K Nealson, and J Zhou. 2006. "Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean ." International Journal of Systematic and Evolutionary Microbiology 56(8):1911-1916.
Gorby YA, S Yanina, JS Mclean, KM Rosso, DM Moyles, A Dohnalkova, TJ Beveridge, IS Chang, BH Kim, KS Kim, DE Culley, SB Reed, MF Romine, D Saffarini, EA Hill, L Shi, DA Elias, DW Kennedy, GE Pinchuk, K Watanabe, S Ishii, B Logan, KH Nealson, and JK Fredrickson. 2006. "Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms ." Proceedings of the National Academy of Sciences of the United States of America 103(30):11358-11363.
Harvey SD, GM Mong, RM Ozanich, JS Mclean, SM Goodwin, NB Valentine, and JK Fredrickson. 2006. "Preparation and evaluation of spore-specific affinity- augmented bio-imprinted beads." Analytical and Bioanalytical Chemistry 386(2):211-219. doi:10.1007/s00216-006-0622-z
Kovacik WP, Jr, K Takai, MR Mormile, JP McKinley, FJ Brockman, JK Fredrickson, and WE Holben. 2006. "Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S°-reducing bacteria in a sulfate-rich environment." Environmental Microbiology 8(1):141-155. doi:10.1111/j.1462-2920.2005.00876.x
Kukkadapu RK, JM Zachara, JK Fredrickson, JP McKinley, DW Kennedy, SC Smith, and H Dong. 2006. "Reductive Biotransformation of Fe in Shale-Limestone Saprolite Containing Fe(III) Oxides and Fe(II)/Fe(III) Phyllosilicates." Geochimica et Cosmochimica Acta 70(14):3662-3676. doi:10.1016/j.gca.2006.05.004
Lipton MS, MF Romine, ME Monroe, DA Elias, L Pasa-Tolic, GA Anderson, DJ Anderson, JK Fredrickson, KK Hixson, CD Masselon, HM Mottaz, N Tolic, and RD Smith. 2006. "AMT Tag Approach to Proteomic Characterization of Deinococcus Radiodurans and Shewanella Oneidensis ." In Microbial Proteomics, Methods of Biochemical Analysis, vol. 49, ed. I. Humphery-Smith and M. Hecker, pp. 113-134. John Wiley & Sons, Inc., Hoboken, NJ.
Roh Y, H Gao, H Vali, DW Kennedy, Z Yang, W Gao, A Dohnalkova, RD Stapleton, JW Moon, TJ Phelps, JK Fredrickson, and J Zhou. 2006. "Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium, Shewanella sp. Strain PV-4." Applied and Environmental Microbiology 72(5):3236-3244. doi:10.1128/AEM.72.5.3236-3244.2006
Shi L, B Chen, Z Wang, DA Elias, MU Mayer, YA Gorby, S Ni, BH Lower, DW Kennedy, DS Wunschel, HM Mottaz, MJ Marshall, EA Hill, AS Beliaev, JM Zachara, JK Fredrickson, and TC Squier. 2006. "Isolation of a High-Affinity Functional Protein Complex between OmcA and MtrC: Two Outer Membrane Decaheme c-type Cytochromes of Shewanella oneidensis MR-1 ." Journal of Bacteriology 188(13):4705-4714. doi:10.1128/JB.01966-05
Xiong Y, L Shi, B Chen, MU Mayer, BH Lower, londer, S Bose, MF Hochella, JM Zachara, JK Fredrickson, and TC Squier. 2006. "High-Affinity Binding and Direct Electron Transfer to Solid Metals by the Shewanella oneidensis MR-1 Outer Membrane c-type Cytochrome OmcA." Journal of the American Chemical Society 128(43):13978-13979. doi:10.1021/ja063526d

2005

Beliaev AS, DM Klingeman, J Klappenbach, L Wu, MF Romine, JM Tiedje, KH Nealson, JK Fredrickson, and J Zhou. 2005. "Global Transcriptome Analysis of Shewanella oneidensis MR-1 Exposed to Different Terminal Electron Acceptors." Journal of Bacteriology 187(20):7138-7145. doi:10.1128/JB.187.20.7138-7145.2005
Fredrickson JK, and DL Balkwill. 2005. "Geomicrobial Processes and Biodiversity in the Deep Terrestrial Subsurface." Geomicrobiology Journal 23(6):345 - 356 . doi:10.1080/01490450600875571
Fredrickson JK. 2005. "Between a Rock and a Hard Place: Geomicrobial Electron Transfer." Environmental Microbiology 7:475-476.
Majors PD, JS Mclean, JK Fredrickson, and RA Wind. 2005. "NMR methods for in-situ biofilm metabolism studies: spatial and temporal resolved measurements." Water Science and Technology 52(7):7-12.
Dichristina TJ, JK Fredrickson, and JM Zachara. 2005. "Enzymology of Electron Transport: Energy Generation with Geochemical Consequences." Chapter 3 in Molecular Geomicrobiology, Reviews in Mineralogy & Geochemistry, vol. 59, ed. J.F. Banfield, J. Cervini-Silva and K.H. Nealson, pp. 27-52. Mineralogical Society of America, Chantilly, VA.
Elias DA, ME Monroe, MJ Marshall, MF Romine, AS Beliaev, JK Fredrickson, GA Anderson, RD Smith, and MS Lipton. 2005. "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics based proteomics." Proteomics 5(12):3120-3130. doi:10.1002/pmic.200401140
Fredrickson JK, and MF Romine. 2005. "Genome-Assisted Analysis of Dissimilatory Metal-Reducing Bacteria." Current Opinion in Biotechnology 16(3):269-274.
Ghosal D, MV Omelchenko, E Gaidamakova, V Matrosova, A Vasilenko, A Venkateswaran, M Zhai, HM Kostandarithes, H Brim, KS Makarova, LP Wackett, JK Fredrickson, and MJ Daly. 2005. "How radiation kills cells: Survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress." FEMS Microbiology Reviews 29(2):361-375.
Kolker E, AF Picone, MY Galperin, MF Romine, R Higdon, KS Makarova, N Kolker, GA Anderson, X Qiu, KJ Auberry, G Babnigg, AS Beliaev, P Edlefsen, DA Elias, YA Gorby, T Holzman, J Klappenbach, K Konstantinidis, ML Land, MS Lipton, LA McCue, ME Monroe, L Pasa-Tolic, GE Pinchuk, SO Purvine, M Serres, S Tsapin, BA Zakrajsek, W Zhu, J Zhou, F Larimer, C Lawrence, M Riley, FR Collart, JR Yates, III, RD Smith, CS Giometti, K Nealson, JK Fredrickson, and JM Tiedje. 2005. "Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved functional annotations." Proceedings of the National Academy of Sciences of the United States of America 102(6):2099-2104.
Kukkadapu RK, JM Zachara, JK Fredrickson, DW Kennedy, A Dohnalkova, and DE McCready. 2005. "Ferrous Hydroxy Carbonate is a Stable Transformation Product of Biogenic Magnetite." American Mineralogist 90(2-3):510-515.
Majors PD, JS Mclean, GE Pinchuk, JK Fredrickson, YA Gorby, KR Minard, and RA Wind. 2005. "NMR methods for in-situ biofilm metabolism studies." Journal of Microbiological Methods 62(3):337-344.
Moser DP, TM Gihring, FJ Brockman, JK Fredrickson, DL Balkwill, ME Dollhopf, BS Lollar, L Pratt, E Boice, G Southam, G Wanger, B Baker, S Pfiffner, L Lin, and TC Onstott. 2005. " Desulfotomaculum spp.and Methanobacterium spp. Dominate a 4-5 km Deep Fault." Applied and Environmental Microbiology 71(12):8773-8783.

2004

Hu JZ, RA Wind, JS Mclean, YA Gorby, CT Resch, and JK Fredrickson. 2004. "High Resolution 1H NMR Spectroscopy of Metabolically Active Microorganisms Using Non-Destructive Magic Angle Spinning." Spectroscopy 19(12):98-103.
Rosso KM, DMAM Smith, Z Wang, CC Ainsworth, and JK Fredrickson. 2004. "Self-Exchange Electron Transfer Kinetics and Reduction Potentials for Anthraquinone Disulfonate." Journal of Physical Chemistry A 108(16):3292-3303.
Zachara JM, RK Kukkadapu, PL Gassman, A Dohnalkova, JK Fredrickson, and T Anderson. 2004. "Biogeochemical Transformation of Fe Minerals in a Petroleum-Contaminated Aquifer." Geochimica et Cosmochimica Acta 68(8):1791-1805.
Balkwill DL, TL Kieft, T Tsukuda, HM Kostandarithes, TC Onstott, S Macnaughton, J Bownas, and JK Fredrickson. 2004. "Identification of Iron-reducing Thermus strains as Thermus scotoductus." Extremophiles 8(1):37-44.
Daly MJ, E Gaidamakova, V Matrosova, A Vasilenko, M Zhai, A Venkateswaran, M Hess, MV Omelchenko, HM Kostandarithes, S Makarova, LP Wackett, JK Fredrickson, and D Ghosal. 2004. "Accumulation of Mn(II) in Deinococcus radiodurans Facilitates Gamma-Radiation Resistance." Science 306(5698):1025-1028.
Fredrickson JK, JM Zachara, DL Balkwill, DW Kennedy, SMW Li, HM Kostandarithes, MJ Daly, MF Romine, and FJ Brockman. 2004. "Geomicrobiology of High Level Nuclear Waste-Contaminated Vadose Sediments at the Hanford Site, Washington State." Applied and Environmental Microbiology 70(7):4230-4241.
Fredrickson JK, JM Zachara, DW Kennedy, RK Kukkadapu, JP McKinley, SM Heald, C Liu, and AE Plymale. 2004. "Reduction of TcO4- by sediment-associated biogenic Fe(II)." Geochimica et Cosmochimica Acta 68(15):3171-3187.
Kukkadapu RK, JM Zachara, JK Fredrickson, and DW Kennedy. 2004. "Biotransformation of Two-Line Silica-Ferrihydrite by a Dissimilatory Fe(III)-Reducing Bacterium: Formation of Carbonate Green Rust in the Presence of Phosphate." Geochimica et Cosmochimica Acta 68(13):2799-2814.
Lehman RM, SP O'Connell, A Banta, JK Fredrickson, AL Reysenbach, TL Kieft, and FS Colwell. 2004. "Microbiological Comparison of Core and Groundwater Samples Collected from a Fractured Basalt Aquifier with that of Dialysis Chamber Incubated in Situ." Geomicrobiology Journal 21(3):169-182.
Romine MF, DA Elias, ME Monroe, KJ Auberry, R Fang, JK Fredrickson, GA Anderson, RD Smith, and MS Lipton. 2004. "Validation of Shewanella oneidensis MR-1 Small Proteins by AMT Tag-based Proteome Analysis." OMICS. A Journal of Integrative Biology 8(3):239-254.

2003

Rosso KM, JM Zachara, JK Fredrickson, YA Gorby, and SC Smith. 2003. "Nonlocal Bacterial Electron Transfer to Hematite Surfaces." Geochimica et Cosmochimica Acta 67(5):1081-1087.
Baker BJ, DP Moser, BJ MacGregor, S Fishbain, M Wagner, NK Fry, B Jackson, N Speolstra, S Loos, K Takai, BS Lollar, JK Fredrickson, DL Balkwill, TC Onstott, CF Wimpee, and DA Stahl. 2003. "Related Assemblages of Sulphate-reducing Bacteria Associated with Ultradeep Gold Mines of South Africa and Deep Basalt Aquifers of Washington State." Environmental Microbiology 5(4):267-277.
Balkwill DL, JK Fredrickson, and MF Romine. 2003. "Sphingomonas and Related Genera." In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, 3rd ed. Release 3.14, ed. M. Dworkin. Springer-Verlag, New York, NY.
Brim H, A Venkateswaran, HM Kostandarithes, JK Fredrickson, and MJ Daly. 2003. "Engineering Deinococcus geothermailis for Bioremediation of High-Temperature Radioactive Waste Environments." Applied and Environmental Microbiology 69(8):4575-4582.
Brooks SC, JK Fredrickson, SL Carroll, DW Kennedy, JM Zachara, AE Plymale, SD Kelly, KM Kemner, and S Fendorf. 2003. "Inhibition of bacterial U(VI) reduction by calcium." Environmental Science and Technology 37(9):1850-1858.
Dong H, RK Kukkadapu, JK Fredrickson, JM Zachara, DW Kennedy, and HM Kostandarithes. 2003. "Microbial Reduction of Structural Fe(III) in Illite and Goethite." Environmental Science and Technology Vol. 37(7):1268-1276 .
Fredrickson JK, S Kota, RK Kukkadapu, C Liu, and JM Zachara. 2003. "Influence of Electron Donor/Acceptor Concentrations on Hydrous Ferric Oxide (HFO) Bioreduction." Biodegradation 14(2):91-103.
Kukkadapu RK, JM Zachara, JK Fredrickson, SC Smith, A Dohnalkova, and CK Russell. 2003. "Transformation of 2-line Ferrihydrite to 6-line Ferrihydrite under Oxic and Anoxic Conditions." American Mineralogist 88(11-12):1903-1914 pt. 2.
Mormile MR, MA Biesen, MC Gutierrez, A Ventosa, JB Pavlovich, TC Onstott, and JK Fredrickson. 2003. "Isolation of Halobacterium salinarum retrieved directly from halite brine inclusions." Environmental Microbiology 5(11):1094-1102.
Moser DP, JK Fredrickson, DR Geist, EV Arntzen, AD Peacock, SMW Li, CM Spadoni, and JP McKinley. 2003. "Biogeochemical Processes and Microbial Characteristics Across Groundwater - Surface Water Boundaries of the Hanford Reach of the Columbia River." Environmental Science and Technology 37(22):5127-5134.
Moser DP, TC Onstott, JK Fredrickson, FJ Brockman, DL Balkwill, GR Drake, S Pfiffner, DC White, K Takai, LM Pratt, J Fong, BS Lollar, G Slater, TJ Phelps, N Spoelstra, M Deflaun, G Southam, AT Welty, BJ Baker, and J Hoek. 2003. "Temporal Shifts in the Geochemistry and Microbial Community Structure of an Ultradeep Mine Borehole Following Isolation." Geomicrobiology Journal 20(6):517-548.
Onstott TC, DP Moser, S Pfiffner, JK Fredrickson, FJ Brockman, TJ Phelps, DC White, AD Peacock, DL Balkwill, R Hoover, L Krumholz, M Borscik, TL Kieft, and R Wilson. 2003. "Indigenous and Contaminant Microbes in Ultradeep Mines." Environmental Microbiology 5(11):1168-1191.
Takai K, MR Mormile, JP Mckinley, FJ Brockman, WE Holben, WP Kovacik, and JK Fredrickson. 2003. "Shifts in Archaeal Communities Associated with Lithological and Geochemical Variations in Subsurface Cretaceous Rock." Environmental Microbiology 5(4):309-320. doi:10.1046/j.1462-2920.2003.0421x

2002

Liu C, JM Zachara, JK Fredrickson, DW Kennedy, and A Dohnalkova. 2002. "Modeling the Inhibition of the Bacterial Reduction of U(VI) by beta-MnO2(S)(g)." Environmental Science and Technology 36(7):1452-1459.
Liu C, YA Gorby, JM Zachara, JK Fredrickson, and CF Brown. 2002. "Reduction Kinetics of Fe(III), Co(III), U(VI), Cr(VI), and Tc(VII) in Cultures of Dissimilatory Metal-reducing Bacteria." Biotechnology and Bioenegineering 80(6):637-649.
Zachara JM, RK Kukkadapu, JK Fredrickson, YA Gorby, and SC Smith. 2002. "Biomineralization of Poorly Crystalline Fe(III) Oxides by Dissimilatory Metal Reducing Bacteria (DMRB)." Geomicrobiology Journal 19:179-207.
Fredrickson JK, JM Zachara, DW Kennedy, C Liu, MC Duff, D Hunter, and A Dohnalkova. 2002. "Influence of Mn oxides on the reduction of U(VI) by the metal-reducing bacterium Shewanella putrefaciens." Geochimica et Cosmochimica Acta 66(18):3247-3262.
Lipton MS, L Pasa-Tolic, GA Anderson, DJ Anderson, DL Auberry, JR Battista, MJ Daly, JK Fredrickson, KK Hixson, HM Kostandarithes, CD Masselon, LM Markillie, RJ Moore, MF Romine, Y Shen, EF Strittmatter, N Tolic, HR Udseth, A Venkateswaran, KK Wong, R Zhao, and RD Smith. 2002. "Global Analysis of Deinococcus radiodurans Proteome by using Accruate Mass Tags." Proceedings of the National Academy of Sciences of the United States of America 99(17):11049-11054.
Rai D, YA Gorby, JK Fredrickson, DA Moore, and M Yui. 2002. "Reductive Dissolution of PuO2(am): The Effect of Fe(II) and Hydroquinone." Journal of Solution Chemistry 31(6):433-453.

2001

Liu C, S Kota, JM Zachara, JK Fredrickson, and CK Brinkman. 2001. "Kinetic Analysis of the Bacterial Reduction of Goethite." Environmental Science and Technology 35:2482-2490.
Zachara JM, JK Fredrickson, SC Smith, and PL Gassman. 2001. "Solubilization of Fe(III) Oxide-Bound Trace Metals by a Dissimilatory Fe(III) Reducing Bacterium." Geochimica et Cosmochimica Acta 65(1):75-93.
Balkwill D, J Chen, M Deflaun, F Dobbs, H Dong, JK Fredrickson, M Fuller, M Green, T Ginn, T Griffin, W Holben, S Hubbard, W Johnson, PE Long, B Mailloux, E Majer, M Mcinerney, CJ Murray, T Onstott, T Phelps, TD Scheibe, D Swift, D White, and F Wobber. 2001. "Breakthroughs in field-scale bacterial transport." Eos 82(38):417, 423-425.
Fredrickson JK, JM Zachara, RK Kukkadapu, YA Gorby, SC Smith, and CF Brown. 2001. "Biotransformation of Ni-Substituted Hydrous Ferric Oxide by an Fe(III)-Reducing Bacterium." Environmental Science and Technology 35(4):703-712.
Kukkadapu RK, JM Zachara, SC Smith, JK Fredrickson, and C Liu. 2001. "Dissimilatory Bacterial Reduction of Al-Substituted Goethite in Subsurface Sediments." Geochimica et Cosmochimica Acta 65(17):2913-2924.
Shi T, JK Fredrickson, and DL Balkwill. 2001. "Biodegradation of polycyclic aromatic hydrocarbons by Sphingomonas strains isolated from the terrestrial subsurface." Journal of Industrial Microbiology and Biotechnology 26(5):283-289.
Takai K, DP Moser, M Deflaun, TC Onstott, and JK Fredrickson. 2001. "Archaeal Diversity in Waters from Deep South African Gold Mines." Applied and Environmental Microbiology 67(12):5750-5760.
Takai K, DP Moser, TC Onstott, N Spoelstra, SM Pfiffner, A Dohnalkova, and JK Fredrickson. 2001. "Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine." International Journal of Systematic and Evolutionary Microbiology 51(part 4):1245-1256.

2000

Wildung RE, YA Gorby, KM Krupka, NJ Hess, SMW Li, AE Plymale, JP McKinley, and JK Fredrickson. 2000. "Effect of Electron Donor and Solution Chemistry on the Products of Dissimilatory Reduction of Technetium by Shewanella putrefaciens." Applied and Environmental Microbiology 66(6):2451-2460.
Zachara JM, SC Smith, and JK Fredrickson. 2000. "The Effect of Biogenic Fe(II) on the Stability and Sorption of Co(II)EDTA2- to Goethite and a Subsurface Sediment." Geochimica et Cosmochimica Acta 64(8):1345-1362.
Brim HS, SC Mcfarlan, JK Fredrickson, KW Minton, M Zhai, LP Wackett, and M Daly. 2000. "Engineering deinococcus radiodurans for metal remediation in radioactive mixed waste environments." Nature Biotechnology 18:85-90.
Dong H, JK Fredrickson, DW Kennedy, JM Zachara, RK Kukkadapu, and TC Onstott. 2000. "Mineral Transformations Associated with the Microbial Reduction of Magnetite." Chemical Geology 169:299-318.
Fredrickson JK, JM Zachara, DW Kennedy, YA Gorby, SMW Li, and KM Krupka. 2000. "Reduction of U(VI) in Goethite (a-FeOOH) Suspensions by a Dissimilatory Metal-Reducing Bacterium." Geochimica et Cosmochimica Acta 64:3085-3098.
Fredrickson JK, HM Kostandarithes, SMW Li, AE Plymale, and MJ Daly. 2000. "Reduction of Fe(III) Cr(VI), and Te(VII) by Deinococcus Radiodurans R1." Applied and Environmental Microbiology 66(5):2006-2011.

1999

Romine MF, LC Stillwell, KK Wong, SJ Thurston, EC Sisk, CW Sensen, T Gaasterland, JK Fredrickson, and JD Saffer. 1999. "Complete sequence of a 184 kb catabolic plasmid from Sphingomonas aromaticivorans strain F199." Journal of Bacteriology 181(5):1585-1602.
Fredrickson JK, DL Balkwill, MF Romine, and T Shi. 1999. "Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp." Journal of Industrial Microbiology and Biotechnology 23(4-5):273-283.
Fredrickson JK, DL Balkwill, MF Romine, and T Shi. 1999. "Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp." Journal of Industrial Microbiology and Biotechnology 23:273-283.
Romine MF, JK Fredrickson, and SMW Li. 1999. "Induction of Aromatic Catabolic Activity in Sphingomonas Aromaticivorans Strain F199." Journal of Industrial Microbiology and Biotechnology 23:303-313.
Tobin KJ, TC Onstott, MF Deflaun, FS Colwell, and JK Fredrickson. 1999. "In situ imaging of microorganisms in geologic material." Journal of Microbiological Methods 37:201-213.

1998

Zachara JM, JK Fredrickson, SMW Li, DW Kennedy, SC Smith, and PL Gassman. 1998. "Bacterial Reduction of Crystalline Fe3+ Oxides in Single Phase Suspensions and Subsurface Materials." American Mineralogist 83(11-12):1426-1443.