Research Topics
| J K FredricksonSummaryAffiliation: Pacific Northwest National Laboratory Country: USA Publications
| Collaborators
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Detail Information
Publications
c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensisMatthew J Marshall
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
PLoS Biol 4:e268. 2006..In the environment, such association of UO(2) nanoparticles with biopolymers may exert a strong influence on subsequent behavior including susceptibility to oxidation by O(2) or transport in soils and sediments...- Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genusDmitry A Rodionov
Sanford Burnham Medical Research Institute, La Jolla, California, USA
BMC Genomics 12:S3. 2011..The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria... - Genomic encyclopedia of sugar utilization pathways in the Shewanella genusDmitry A Rodionov
Burnham Institute for Medical Research, La Jolla, California 92037, USA
BMC Genomics 11:494. 2010.... - Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington stateJames K Fredrickson
Pacific Northwest Laboratory, Richland, WA 99352, USA
Appl Environ Microbiol 70:4230-41. 2004.... 
Towards environmental systems biology of ShewanellaJames K Fredrickson
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Nat Rev Microbiol 6:592-603. 2008....- Electron transfer at the microbe-mineral interface: a grand challenge in biogeochemistryJ K Fredrickson
Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99352, USA
Geobiology 6:245-53. 2008..Collectively, the grand challenge will provide a detailed view of how organisms engage with mineral surfaces to exchange energy and electron density as required for life function... 
Genome-assisted analysis of dissimilatory metal-reducing bacteriaJames K Fredrickson
Pacific Northwest National Laboratory, PO Box 999, Richland, Washington 99352, USA
Curr Opin Biotechnol 16:269-74. 2005..It is anticipated that details of the mechanisms of metal ion respiration, and metabolism in general, will eventually be revealed by comprehensive, systems-level analyses enabled by functional genomics data...- Biotransformation of Ni-substituted hydrous ferric oxide by an Fe(III)-reducing bacteriumJ K Fredrickson
Pacific Northwest National Laboratory, P O Box 999, MSIN P7 50, Richland, Washington 99352, USA
Environ Sci Technol 35:703-12. 2001.... - Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1J K Fredrickson
Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Appl Environ Microbiol 66:2006-11. 2000.... - Influence of electron donor/acceptor concentrations on hydrous ferric oxide (HFO) bioreductionJames K Fredrickson
Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biodegradation 14:91-103. 2003..The respiration driven rate of Fe(II) formation from HFO is believed to be a primary factor governing the array of ferrous and ferric iron phases formed during reduction... - Effect of electron donor and solution chemistry on products of dissimilatory reduction of technetium by Shewanella putrefaciensR E Wildung
Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Appl Environ Microbiol 66:2451-60. 2000.... - Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mineK Takai
Pacific Northwest National Laboratory, Richland, WA 99352, USA
Int J Syst Evol Microbiol 51:1245-56. 2001..nov., sp. nov. is proposed (type strain SAGM1T = JCM 10712T = ATCC 700919T). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed... - Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptorsA S Beliaev
Biological Sciences Division, Pacific Northwest National Laboratory, P O Box 999, MS P7 50, Richland, Washington 99352, USA
J Bacteriol 187:7138-45. 2005..Moreover, the relative paucity and/or the constitutive nature of genes involved in electron transfer to metals is likely due to the low-specificity and the opportunistic nature of the metal-reducing electron transport pathways... - Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1J S McLean
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA99352, USA
Environ Microbiol 10:1861-76. 2008.... - Kinetic analysis of the bacterial reduction of goethiteC Liu
Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Environ Sci Technol 35:2482-90. 2001..Using independently estimated parameters, the developed model successfully described bacterial goethite reduction with variable FeOOH and lactate concentrations... - Electron donor-dependent radionuclide reduction and nanoparticle formation by Anaeromyxobacter dehalogenans strain 2CP-CMatthew J Marshall
Biological Sciences Division, Pacific Northwest National Laborotary, Richland, WA 99354, USA
Environ Microbiol 11:534-43. 2009..These findings expand our knowledge of the radionuclide reduction processes catalysed by Anaeromyxobacter spp. that may influence the fate and transport of radionuclide contaminants in the subsurface... - Environmental processes mediated by iron-reducing bacteriaJ K Fredrickson
Pacific Northwest National Laboratory, Washington 99352, USA
Curr Opin Biotechnol 7:287-94. 1996..In addition, the number of biotechnological applications of iron-reducing bacteria, including remediation of soils and sediments contaminated with metals, radionuclides and organics, is rapidly expanding... - Archaeal diversity in waters from deep South African gold minesK Takai
Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Appl Environ Microbiol 67:5750-60. 2001..Based on the phylogenetic analysis of archaeal strains and rDNA clones, including the newly discovered archaeal rDNA clones, the evolutionary relationship and the phylogenetic organization of the domain Archaea are reevaluated... - Role of outer-membrane cytochromes MtrC and OmcA in the biomineralization of ferrihydrite by Shewanella oneidensis MR-1C L Reardon
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
Geobiology 8:56-68. 2010..Collectively, these results highlight the importance of the outer-membrane cytochromes in the reductive transformation of FH and support a role for direct electron transfer from the OMCs at the cell surface to the mineral... - Hydrogenase- and outer membrane c-type cytochrome-facilitated reduction of technetium(VII) by Shewanella oneidensis MR-1Matthew J Marshall
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Environ Microbiol 10:125-36. 2008..c-Type cytochrome-catalysed Tc(VII) reduction could be a potentially important mechanism in environments where organic electron donor concentrations are sufficient to allow this reaction to dominate... - Kinetics of microbial reduction of Solid phase U(VI)Chongxuan Liu
Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Environ Sci Technol 40:6290-6. 2006..The results demonstrated that microbial reduction of solid-phase U(VI) is controlled by coupled biological, chemical, and physical processes... - Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromesLiang Shi
Pacific Northwest National Laboratory, Richland, Washington 99354, USA
Mol Microbiol 65:12-20. 2007..Thus, multihaem c-Cyts play critical roles in S. oneidensis MR-1- and G. sulfurreducens-mediated dissimilatory reduction of solid metal (hydr)oxides by facilitating ET across the bacterial cell envelope... - Protein oxidation: key to bacterial desiccation resistance?James K Fredrickson
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
ISME J 2:393-403. 2008..We present the case that survival of bacteria that inhabit dry-climate soils are highly dependent on mechanisms, which limit protein oxidation during dehydration... - Direct involvement of type II secretion system in extracellular translocation of Shewanella oneidensis outer membrane cytochromes MtrC and OmcALiang Shi
Microbiology Group, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
J Bacteriol 190:5512-6. 2008.... - Kinetics of reduction of Fe(III) complexes by outer membrane cytochromes MtrC and OmcA of Shewanella oneidensis MR-1Zheming Wang
Pacific Northwest National Laboratory, Richland, WA 99352, USA
Appl Environ Microbiol 74:6746-55. 2008..The results demonstrate that ligand complexation plays an important role in microbial dissimilatory reduction and mineral transformation of iron, as well as other redox-sensitive metal species in nature... - Imaging hydrated microbial extracellular polymers: comparative analysis by electron microscopyAlice C Dohnalkova
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, USA
Appl Environ Microbiol 77:1254-62. 2011..Dehydration-induced polymer collapse can lead to inaccurate spatial relationships and hence could subsequently affect conclusions regarding the nature of interactions between microbial extracellular polymers and their environment... - High-affinity binding and direct electron transfer to solid metals by the Shewanella oneidensis MR-1 outer membrane c-type cytochrome OmcAYijia Xiong
Division of Biological Sciences and Environmental Molecular Science Laboratory, Biogeochemistry Grand Challenge Program, Pacific Northwest National Laboratory, Richland, WA 99352, USA
J Am Chem Soc 128:13978-9. 2006.... - Microbial reduction of intragrain U(VI) in contaminated sedimentChongxuan Liu
Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Environ Sci Technol 43:4928-33. 2009.... - Isolation of a high-affinity functional protein complex between OmcA and MtrC: Two outer membrane decaheme c-type cytochromes of Shewanella oneidensis MR-1Liang Shi
Microbiology Group, Pacific Northwest National Laboratory, 902 Battelle Blvd, P O Box 999, MSIN P7 50, Richland, WA 99354, USA
J Bacteriol 188:4705-14. 2006..oneidensis MR-1... - Modeling the inhibition of the bacteral reduction of U(VI) by beta-MnO2(s)Chongxuan Liu
Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Environ Sci Technol 36:1452-9. 2002..The coupled model that was modified to account for the "effective" contact surface area between UO2(s) and beta-MnO2(s) significantly improved the simulation of microbial reduction of U(VI) in the presence of beta-MnO2(s)... - Biogeochemical processes and microbial characteristics across groundwater-surface water boundaries of the Hanford Reach of the Columbia RiverDuane P Moser
Pacific Northwest National Laboratory, P O Box 999, Richland, Washington 99352, USA
Environ Sci Technol 37:5127-34. 2003..Although freezing modestly diminished recovery of viable bacteria, freeze core techniques proved reliable for the collection of intact hyporheic sediments... - Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199M F Romine
Pacific Northwest National Laboratory, Richland, Washington 99352, USA
J Bacteriol 181:1585-602. 1999..was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes... - NMR methods for in situ biofilm metabolism studiesPaul D Majors
Pacific Northwest National Laboratory, MSIN: K8-98, Richland, WA 99352, USA
J Microbiol Methods 62:337-44. 2005..These results represent progress toward our ultimate goal of correlating time- and depth-resolved metabolism and mass transport with gene expression in live in situ biofilms using combined NMR/optical microscopy techniques... - Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomicsDwayne A Elias
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Proteomics 5:3120-30. 2005..These results demonstrate the utility of the AMT tag methodology for comprehensive profiling of the microbial proteome while confirming the expression of a large number of hypothetical genes... - Microbial Diversity and Biogeochemical Function of the Phototrophic Microbial Mats of Epsomitic Hot Lake, WAS R Lindemann
Microbiology, Pacific Northwest National Laboratory, Richland, WA
Microsc Microanal 18:10-1. 2012..Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 - August 2, 2012... - Desulfotomaculum and Methanobacterium spp. dominate a 4- to 5-kilometer-deep faultDuane P Moser
Environmental Microbiology Group, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Appl Environ Microbiol 71:8773-83. 2005..The geochemical setting and microbial communities described here are notably different from microbial ecosystems reported for shallower continental subsurface environments... - Investigations of structure and metabolism within Shewanella oneidensis MR-1 biofilmsJeffrey S McLean
Pacific Northwest National Laboratory, MSIN P7 50, Richland, WA 99354, United States
J Microbiol Methods 74:47-56. 2008.... - Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1Dwayne A Elias
Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
J Microbiol Methods 66:223-33. 2006..Our results indicate that 399 proteins can now be upgraded from "conserved hypothetical protein" to "expressed protein in Shewanella," 19 of which appeared to be expressed under specific culture conditions... - Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labelingHaizhen Zhang
Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
J Proteome Res 9:2160-9. 2010.... - Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific OceanHaichun Gao
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
Int J Syst Evol Microbiol 56:1911-6. 2006..nov. is proposed. The type strain is PV-4(T) (=ATCC BAA-1088(T)=DSM 17748(T))... - Deinococcus radiodurans engineered for complete toluene degradation facilitates Cr(VI) reductionHassan Brim
Department of Microbiology and Cancer Center, Howard University, 2041 Georgia Avenue N W, Washington, DC 20060, USA
Microbiology 152:2469-77. 2006..As such, the Tod/Xyl strain could provide a model for examining the reduction of metals coupled to organic contaminant oxidation in aerobic radionuclide-contaminated sediments... - Engineering Deinococcus geothermalis for bioremediation of high-temperature radioactive waste environmentsHassan Brim
Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
Appl Environ Microbiol 69:4575-82. 2003..These characteristics support the prospective development of this thermophilic radiophile for bioremediation of radioactive mixed waste environments with temperatures as high as 55 degrees C... - Metal reduction and iron biomineralization by a psychrotolerant Fe(III)-reducing bacterium, Shewanella sp. strain PV-4Yul Roh
Institute for Environmental Genomics, and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
Appl Environ Microbiol 72:3236-44. 2006..The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation... - Isolation of Halobacterium salinarum retrieved directly from halite brine inclusionsMelanie R Mormile
Department of Biological Sciences, University of Missouri Rolla, Rolla, MO 65401, USA
Environ Microbiol 5:1094-102. 2003..The described method of retrieving particle-containing brine from fluid inclusions offers a robust approach for assessing the antiquity of microorganisms associated with evaporites... - Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutantsOrianna Bretschger
Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA
Appl Environ Microbiol 73:7003-12. 2007..Overall, these data suggest a very complex picture of electron transfer to solid and soluble substrates by S. oneidensis MR-1... - In vivo identification of the outer membrane protein OmcA-MtrC interaction network in Shewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkersHaizhen Zhang
Department of Chemistry, Washington State University, Pullman, Washington, USA
J Proteome Res 7:1712-20. 2008.... - Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S(zero)-reducing bacteria in a sulfate-rich environmentWilliam P Kovacik
Microbial Ecology Program, Division of Biological Sciences, The University of Montana, Missoula, 59812, USA
Environ Microbiol 8:141-55. 2006..The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale... - The influence of cultivation methods on Shewanella oneidensis physiology and proteome expressionDwayne A Elias
Department of Biochemistry, University of Missouri Columbia, Columbia, MO 65211, USA
Arch Microbiol 189:313-24. 2008..By decreasing cell to cell variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research... - Protein oxidation implicated as the primary determinant of bacterial radioresistanceMichael J Daly
Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
PLoS Biol 5:e92. 2007..We present the case that protein, rather than DNA, is the principal target of the biological action of IR in sensitive bacteria, and extreme resistance in Mn-accumulating bacteria is based on protein protection... - Inhibition of bacterial U(VI) reduction by calciumScott C Brooks
Environmental Sciences Division, P O Box 2008, MS 6038, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 6038, USA
Environ Sci Technol 37:1850-8. 2003..The results do not support Ca inhibition caused by direct interactions with the cells or with the electron donor as the reduction of fumarate or Tc(VII)O4- under identical conditions was unaffected by the presence of Ca... - Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotationsEugene Kolker
BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
Proc Natl Acad Sci U S A 102:2099-104. 2005..We propose that this integrative approach offers a valuable means to undertake the enormous challenge of characterizing the rapidly growing number of hypothetical proteins with each newly sequenced genome... - Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinksKira S Makarova
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
PLoS ONE 2:e955. 2007.... - How radiation kills cells: survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stressDebabrota Ghosal
Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
FEMS Microbiol Rev 29:361-75. 2005.... - Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profilingMichael E Driscoll
Boston University, St Boston, MA 02215, USA
Genome Inform 18:287-98. 2007..In sum, these results indicate that S. oneidensis possesses a broader capacity for carbon utilization than previously reported, a view with implications for optimizing its role in microbial fuel cell and bioremediative applications... - Biogenic formation of photoactive arsenic-sulfide nanotubes by Shewanella sp. strain HN-41Ji Hoon Lee
Department of Environmental Science and Engineering and International Environmental Research Center, Gwangju Institute of Science and Technology, Gwangju 500 712, Republic of Korea
Proc Natl Acad Sci U S A 104:20410-5. 2007..The As-S nanotubes produced by Shewanella may provide useful materials for novel nano- and opto-electronic devices...