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Biological Sciences Staff information

David Kennedy

Microbiology
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352
509/371-6680

PNNL Publications

2013

  • 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

2012

  • Lee JH, JK Fredrickson, RK Kukkadapu, MI Boyanov, KM Kemner, X Lin, DW Kennedy, BN Bjornstad, A Konopka, DA Moore, CT Resch, and JL Phillips. 2012. "Microbial Reductive Transformation of Phyllosilicate Fe(III) and U(VI) in Fluvial Subsurface Sediments." Environmental Science & Technology 46(7):3721-3730.  doi:10.1021/es204528m
  • Lin X, DW Kennedy, AD Peacock, JP McKinley, CT Resch, JK Fredrickson, and A Konopka. 2012. "Distribution of microbial biomass and the potential for anaerobic respiration in Hanford Site 300 Area subsurface sediment." Applied and Environmental Microbiology 78(3):759-767. 
  • Lin X, DW Kennedy, JK Fredrickson, BN Bjornstad, and A Konopka. 2012. "Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site." Environmental Microbiology 14(2):414-425.  doi:10.1111/j.1462-2920.2011.02659.x
  • Liu J, Z Wang, SM Belchik, M Edwards, C Liu, DW Kennedy, ED Merkley, MS Lipton, JN Butt, D Richardson, JM Zachara, JK Fredrickson, KM Rosso, and L Shi. 2012. "Identification and Characterization of MtoA: a Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-oxidizing Bacterium Sideroxydans lithotrophicus ES-1." Frontiers in Microbiological Chemistry 3:Article No. 37.  doi:10.3389/fmicb.2012.00037
  • Shi Z, JM Zachara, L Shi, Z Wang, DA Moore, DW Kennedy, and JK Fredrickson. 2012. "Redox reactions of reduced flavin mononucleotide (FMN), riboflavin (RBF), and anthraquinone-2,6-disulfonate (AQDS) with ferrihydrite and lepidocrocite." Environmental Science & Technology 46(21):11644-11652.  doi:10.1021/es301544b

2011

  • Lee JH, DW Kennedy, A Dohnalkova, DA Moore, P Nachimuthu, SB Reed, and JK Fredrickson. 2011. "Manganese sulfide formation via concomitant microbial manganese oxide and thiosulfate reduction." Environmental Microbiology 13(12):3275-3288.  doi:10.1111/j.1462-2920.2011.02587.x
  • Lee JH, DW Kennedy, A Dohnalkova, DA Moore, P Nachimuthu, SB Reed, and JK Fredrickson. 2011. "Manganese sulfide formation via concomitant microbial manganese oxide and thiosulfate reduction." Environmental Microbiology 13(12):3275-3288.  doi:10.1111/j.1462-2920.2011.02587.x
  • Lin X, DW Kennedy, JK Fredrickson, BN Bjornstad, and A Konopka. 2011. "Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site." Environmental Microbiology 14(2):414-425.  doi:10.1111/j.1462-2920.2011.02659.x
  • Belchik SM, DW Kennedy, A Dohnalkova, Y Wang, PC Sevinc, HJ Wu, Y Lin, HP Lu, JK Fredrickson, and L Shi. 2011. "Extracellular Reduction of Hexavalent Chromium by Cytochromes MtrC and OmcA of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 77(12):4035-4041.  doi:10.1128/AEM.02463-10
  • Cao B, B Ahmed, DW Kennedy, Z Wang, L Shi, MJ Marshall, JK Fredrickson, NG Isern, PD Majors, and H Beyenal. 2011. "Contribution of Extracellular Polymeric Substances from Shewanella sp. HRCR-1 Biofilms to U(VI) Immobilization." Environmental Science & Technology 45(13):5483-5490.  doi:10.1021/es200095j
  • Plymale AE, JK Fredrickson, JM Zachara, A Dohnalkova, SM Heald, DA Moore, DW Kennedy, MJ Marshall, CM Wang, CT Resch, and P Nachimuthu. 2011. "Competitive Reduction of Pertechnetate (99TcO4-) by Dissimilatory Metal Reducing Bacteria and Biogenic Fe(II) ." Environmental Science & Technology 45(3):951-957. 
  • Shi L, SM Belchik, Z Wang, DW Kennedy, A Dohnalkova, MJ Marshall, JM Zachara, and JK Fredrickson. 2011. "Identification and Characterization of UndA-HRCR-6, an Outer Membrane Endecaheme c-Type Cytochrome of Shewanella sp. Strain HRCR-6 ." Applied and Environmental Microbiology 77(15):5521-5523.  doi:10.1128/AEM.00614-11
  • Zachara JM, RK Kukkadapu, T Peretyazhko, ME Bowden, CM Wang, DW Kennedy, DA Moore, and BW Arey. 2011. "The Mineralogic Transformation of Ferrihydrite Induced by Heterogeneous Reaction with Bioreduced Anthraquinone Disulfonate (AQDS) and the Role of Phosphate." Geochimica et Cosmochimica Acta 75(21):6330-6349.  doi:10.1016/j.gca.2011.06.030

2010

  • Peretyazhko T, JM Zachara, DW Kennedy, JK Fredrickson, BW Arey, JP McKinley, CM Wang, A Dohnalkova, and Y Xia. 2010. "Ferrous Phosphate Surface Precipitates Resulting from the Reduction of Intragrain 6-line Ferrihydrite by Shewanella oneidensis MR-1 ." Geochimica et Cosmochimica Acta 74(13):3751-3767.  doi:10.1016/j.gca.2010.04.008
  • Peretyazhko T, JM Zachara, DW Kennedy, JK Fredrickson, BW Arey, JP McKinley, CM Wang, A Dohnalkova, and Y Xia. 2010. "Ferrous phosphate surface precipitates resulting from the reduction of intragrain 6-line ferrihydrite by Shewanella oneidensis MR-1." Geochimica et Cosmochimica Acta 74(13):3751-3767.  doi:10.1016/j.gca.2010.04.008
  • Gao H, S Barua, Y Liang, L Wu, Y Dong, SB Reed, J Chen, DE Culley, DW Kennedy, Y Yang, Z He, KH Nealson, JK Fredrickson, JM Tiedje, MF Romine, and J Zhou. 2010. "Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration." Microbial Biotechnology 3(4):455-466.  doi:10.1111/j.1751-7915.2010.00181.x
  • Reardon CL, A Dohnalkova, P Nachimuthu, DW Kennedy, D Saffarini, BW Arey, L Shi, Z Wang, DA Moore, JS Mclean, DM Moyles, MJ Marshall, JM Zachara, JK Fredrickson, and AS Beliaev. 2010. "Role of Outer-Membrane Cytochromes MtrC and OmcA in the Biomineralization of Ferrihydrite by Shewanella oneidensis MR-1." Geobiology 8(1):56-68.  doi:10.1111/j.1472-4669.2009.00226.x

2009

  • Marshall MJ, A Dohnalkova, DW Kennedy, AE Plymale, SH Thomas, FE Loffler, R Sanford, JM Zachara, JK Fredrickson, and AS Beliaev. 2009. "Electron donor-dependent radionuclide reduction and nanoparticle formation by Anaeromyxobacter dehalogenans strain 2CP-C." Environmental Microbiology 11(2):534-543. 
  • Bose S, MF Hochella, YA Gorby, DW Kennedy, DE Mccready, AS Madden, and BH Lower. 2009. "Bioreduction of hematite nanoparticles by the dissimilatory iron reducing bacterium Shewanella oneidensis MR-1." Geochimica et Cosmochimica Acta 73(4):962-976. 
  • Fredrickson JK, JM Zachara, AE Plymale, SM Heald, JP McKinley, DW Kennedy, C Liu, and P Nachimuthu. 2009. "Oxidative Dissolution Potential of Biogenic and Abiogenic TcO2 in Subsurface Sediments." Geochimica et Cosmochimica Acta 73(8):962-976.  doi:10.1016/j.gca.2009.01.027
  • Sharp J, EJ Schofield, H Veeramani, E Suvorova, DW Kennedy, MJ Marshall, A Mehta, JR Bargar, and R Bernier-Latmani. 2009. "Structural similarities between biogenic uraninites produced by phylogenetically and metabolically diverse bacteria." Environmental Science & Technology 43(21):8295-8301. 

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
  • 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
  • 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

2006

  • 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. 
  • Dohnalkova A, CL Bilskis, and DW Kennedy. 2006. " TEM Study of Manganese Biosorption by Cyanobacterium Synechocystis 6803 ." In Microscopy and Microanalysis 2006, Chicago, Illinois, USA, July 30 - August 3, 2005. Published in Microscopy and Microanalysis, vol. 12, no. Supplement S02, pp. 444-445.  Cambridge University Press, Cambridge, United Kingdom.  doi:10.1017/S1431927606064051
  • 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. 
  • 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
  • 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. 
  • 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

2005

  • Liu C, JM Zachara, L Zhong, RK Kukkadapu, JE Szecsody, and DW Kennedy. 2005. "Influence of Sediment Bioreduction and Reoxidation on Uranium Sorption." Environmental Science and Technology 39(11):4125-4133. 
  • Kelly SD, KM Kemner, SC Brooks, JK Fredrickson, SL Carroll, DW Kennedy, JM Zachara, AE Plymale, and S Fendorf. 2005. "Ca-UO2-CO3 Complexation - Implications for Bioremediation of U(VI)." Physica Scripta T115:915-917.  doi:10.1238/Physica.Topical.115a00915
  • 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. 
  • Zhong L, C Liu, JM Zachara, DW Kennedy, JE Szecsody, and BD Wood. 2005. "Oxidative Remobilization of Biogenic Uranium (IV) Precipitates: Effects of Iron (II) and pH." Journal of Environmental Quality 34(5):1763-1771. 

2004

  • 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. 

2003

  • 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 . 

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. 
  • 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. 

2000

  • Amonette JE, DJ Workman, DW Kennedy, JS Fruchter, and YA Gorby. 2000. "Dechlorination of Carbon Tetrachloride by Fe(II) Associated with Goethite." Environmental Science and Technology 34:4606-4613. 
  • 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. 

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. 

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