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James Fredrickson

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Liang Shi; John M Zachara; Kevin M Rosso; James K Fredrickson
Mtr extracellular electron-transfer pathways in Fe(III)-reducing or Fe(II)-oxidizing bacteria: a genomic perspective.
Bulbul Ahmed; Bin Cao; Alice Dohnalkova; James K Fredrickson; Tuba Ica; Ozlem Istanbullu; Jeffrey S McLean; Akin Paksoy; Haluk Beyenal
Fe(III) reduction and U(VI) immobilization by Paenibacillus sp. strain 300A, isolated from Hanford 300A subsurface sediments.
Bin Cao; James K Fredrickson; Staffan Kjelleberg; Paul D Majors; Ryan S Renslow; Liang Shi; Crystal P Silvia; Bulbul Ahmed; Haluk Beyenal
Biofilm shows spatially stratified metabolic responses to contaminant exposure.

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All Publications

2012: Liang Shi; John M Zachara; Kevin M Rosso; James K Fredrickson
Mtr extracellular electron-transfer pathways in Fe(III)-reducing or Fe(II)-oxidizing bacteria: a genomic perspective.
Biochemical Society transactions 2012;40(6):1261-7.
2012: Bulbul Ahmed; Bin Cao; Alice Dohnalkova; James K Fredrickson; Tuba Ica; Ozlem Istanbullu; Jeffrey S McLean; Akin Paksoy; Haluk Beyenal
Fe(III) reduction and U(VI) immobilization by Paenibacillus sp. strain 300A, isolated from Hanford 300A subsurface sediments.
Applied and environmental microbiology 2012;78(22):8001-9.
2012: Bin Cao; James K Fredrickson; Staffan Kjelleberg; Paul D Majors; Ryan S Renslow; Liang Shi; Crystal P Silvia; Bulbul Ahmed; Haluk Beyenal
Biofilm shows spatially stratified metabolic responses to contaminant exposure.
Environmental microbiology 2012;14(11):2901-10.
2012: James C Stegen; Allan E Konopka; Xueju Lin; James K Fredrickson
Stochastic and deterministic assembly processes in subsurface microbial communities.
The ISME journal 2012;6(9):1653-64.
2012: Ji-Hoon Lee; Xueju Lin; Dean A Moore; Bruce N Bjornstad; Maxim I Boyanov; James K Fredrickson; Kenneth M Kemner; David W Kennedy; Allan E Konopka; Ravi K Kukkadapu; Charles T Resch; Jerry L Phillips
Microbial reductive transformation of phyllosilicate Fe(III) and U(VI) in fluvial subsurface sediments.
Environmental science & technology 2012;46(7):3721-30.
2012: Andrew E Plymale; Charles T Resch; Liang Shi; Zheming Wang; Edgar C Buck; James K Fredrickson; Steve M Heald; Dean A Moore; Vanessa L Bailey; Harvey Bolton
Biotic and abiotic reduction and solubilization of Pu(IV)O₂•xH₂O(am) as affected by anthraquinone-2,6-disulfonate (AQDS) and ethylenediaminetetraacetate (EDTA).
Environmental science & technology 2012;46(4):2132-40.
2012: Liang Shi; John M Zachara; Tomas A Clarke; David J Richardson; Kevin M Rosso; James K Fredrickson
Molecular Underpinnings of Fe(III) Oxide Reduction by Shewanella Oneidensis MR-1.
Frontiers in microbiology 2012;3():50.
2012: Juan Liu; Eric D Merkley; David J Richardson; Kevin M Rosso; Sara M Belchik; Julea N Butt; Marcus J Edwards; James K Fredrickson; David W Kennedy; Mary S Lipton; Chongxuan Liu; Zheming Wang; John M Zachara; Liang Shi
Identification and Characterization of MtoA: A Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-Oxidizing Bacterium Sideroxydans lithotrophicus ES-1.
Frontiers in microbiology 2012;3():37.
2011: Grigoriy E Pinchuk; Jennifer L Reed; Alexander S Beliaev; Oleg V Geydebrekht; Eric A Hill; Allan E Konopka; James K Fredrickson
Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions.
Applied and environmental microbiology 2011;77(23):8234-40.
2011: Ji-Hoon Lee; Dean A Moore; Ponnusamy Nachimuthu; Samantha B Reed; Alice Dohnalkova; David W Kennedy; James K Fredrickson
Manganese sulfide formation via concomitant microbial manganese oxide and thiosulfate reduction.
Environmental microbiology 2011;13(12):3275-88.
2011: Semen A Leyn; Xiaoqing Li; Pavel Novichkov; Andrei L Osterman; Samantha Reed; Margaret F Romine; Chen Yang; Qingxiang Zheng; James K Fredrickson; Dmitry A Rodionov
Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis.
The Journal of biological chemistry 2011;286(41):35782-94.
2011: Haizhen Zhang; Eric D Merkley; Roslyn N Brown; James K Fredrickson; Eric E Merkley; Matthew Monroe; Ronald J Moore; Jea H Park; Ljiljana Paša-Tolić; Samuel O Purvine; Wei-Jun Qian; Liang Shi; Richard D Smith; Yuexi Wang; Feng Yang; Mary S Lipton
Identification of c-type heme-containing peptides using nonactivated immobilized metal affinity chromatography resin enrichment and higher-energy collisional dissociation.
Analytical chemistry 2011;83(19):7260-8.
2011: Liang Shi; Thomas C Squier; Kateryna Sybirna; John M Zachara; Sara M Belchik; Hervé Bottin; Alice Dohnalkova; Steve M Heald; Andrew E Plymale; James K Fredrickson
Purification and characterization of the [NiFe]-hydrogenase of Shewanella oneidensis MR-1.
Applied and environmental microbiology 2011;77(16):5584-90.
2011: Liang Shi; Zheming Wang; John M Zachara; Sara M Belchik; Alice Dohnalkova; David W Kennedy; Matthew J Marshall; James K Fredrickson
Identification and characterization of UndAHRCR-6, an outer membrane endecaheme c-type cytochrome of Shewanella sp. strain HRCR-6.
Applied and environmental microbiology 2011;77(15):5521-3.
2011: Sara M Belchik; Alice C Dohnalkova; James K Fredrickson; David W Kennedy; Yuehe Lin; H Peter Lu; Papatya C Sevinc; Yuanmin Wang; Hong Wu; Liang Shi
Extracellular reduction of hexavalent chromium by cytochromes MtrC and OmcA of Shewanella oneidensis MR-1.
Applied and environmental microbiology 2011;77(12):4035-41.
2011: Andrew E Plymale; James K Fredrickson; John M Zachara; Alice C Dohnalkova; Steve M Heald; Dean A Moore; David W Kennedy; Matthew J Marshall; Chongmin Wang; Charles T Resch; Ponnusamy Nachimuthu
Competitive reduction of pertechnetate (99TcO4-) by dissimilatory metal reducing bacteria and biogenic Fe(II).
Environmental science & technology 2011;45(3):951-7.
2011: Dmitry A Rodionov; Irina A Rodionova; Margaret F Romine; Elena D Stavrovskaya; Adam P Arkin; Inna Dubchak; James K Fredrickson; Anna V Gerasimova; Alexey E Kazakov; Marat D Kazanov; Galina Yu Kovaleva; Olga N Laikova; Xiaoqing Li; Pavel Novichkov; Andrei Osterman; Ross Overbeek; Elizaveta A Permina; Dmitry A Ravcheev; Mikhail S Gelfand
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.
BMC genomics 2011;12 Suppl 1():S3.
2010: Haichun Gao; Soumitra Barua; Yili Liang; Lin Wu; Yangyang Dong; Samantha Reed; Jingrong Chen; Dave Culley; David Kennedy; Yunfeng Yang; Zhili He; Kenneth H Nealson; James K Fredrickson; James M Tiedje; Margaret Romine; ali khawwam
Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration.
Microbial biotechnology 2010;3(4):455-66.
2010: Haizhen Zhang; Roslyn N Brown; Wei-Jun Qian; Matthew Monroe; Samuel O Purvine; Ronald J Moore; Marina A Gritsenko; Liang Shi; Margaret F Romine; James K Fredrickson; Ljiljana Pasa-Tolić; Richard D Smith; Mary S Lipton
Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling.
Journal of proteome research 2010;9(5):2160-9.
2010: C L Reardon; Alice Dohnalkova; P Nachimuthu; David W Kennedy; Daad A Saffarini; B W Arey; Liang Shi; Zheming Wang; D Moore; Jeffrey S McLean; Dianne Moyles; Matthew J Marshall; John M Zachara; James K Fredrickson; Alexander S Beliaev
Role of outer-membrane cytochromes MtrC and OmcA in the biomineralization of ferrihydrite by Shewanella oneidensis MR-1.
Geobiology 2010;8(1):56-68.
2009: Shenghua Jiang; Ji-Hoon Lee; Min-Gyu Kim; Nosang V Myung; James K Fredrickson; Michael J Sadowsky; Hor-Gil Hur
Biogenic formation of As-S nanotubes by diverse Shewanella strains.
Applied and environmental microbiology 2009;75(21):6896-9.
2009: Konstantinos T Konstantinidis; Margrethe H Serres; Margaret F Romine; Jorge L M Rodrigues; Jennifer Auchtung; Lee-Ann McCue; Mary S Lipton; Anna Obraztsova; Carol S Giometti; Kenneth H Nealson; James K Fredrickson; James M Tiedje
Comparative systems biology across an evolutionary gradient within the Shewanella genus.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(37):15909-14.
2009: Haichun Gao; Zamin K Yang; Soumitra Barua; Samantha B Reed; Margaret F Romine; Kenneth H Nealson; James K Fredrickson; James M Tiedje; ali khawwam
Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA.
The ISME journal 2009;3(8):966-76.
2009: Chongxuan Liu; John M Zachara; Lirong Zhong; Steve M Heald; Zheming Wang; Byong-Hun Jeon; James K Fredrickson
Microbial reduction of intragrain U(VI) in contaminated sediment.
Environmental science & technology 2009;43(13):4928-33.
2009: M A Charania; K L Brockman; Y Zhang; A Banerjee; G E Pinchuk; James K Fredrickson; Alexander S Beliaev; Daad A Saffarini
Involvement of a membrane-bound class III adenylate cyclase in regulation of anaerobic respiration in Shewanella oneidensis MR-1.
Journal of bacteriology 2009;191(13):4298-306.
2009: Grigory E Pinchuk; Dmitry A Rodionov; Chen Yang; Xiaoqing Li; Andrei Osterman; Etienne Dervyn; Oleg V Geydebrekht; Samantha B Reed; Margaret F Romine; Frank R Collart; James H Scott; James K Fredrickson; Alexander S Beliaev
Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(8):2874-9.
2009: Matthew J Marshall; Alice Dohnalkova; David W Kennedy; Andrew E Plymale; Sara H Thomas; Frank E Loeffler; Robert A Sanford; John M Zachara; James K Fredrickson; Alexander S Beliaev
Electron donor-dependent radionuclide reduction and nanoparticle formation by Anaeromyxobacter dehalogenans strain 2CP-C.
Environmental microbiology 2009;11(2):534-43.
2008: James K Fredrickson; Margaret F Romine; Alexander S Beliaev; Jennifer M Auchtung; Michael E Driscoll; Timothy S Gardner; Kenneth H Nealson; Andrei L Osterman; Grigoriy Pinchuk; Jennifer L Reed; Dmitry A Rodionov; Jorge L M Rodrigues; Daad A Saffarini; Margrethe H Serres; Alfred M Spormann; Igor B Zhulin; James M Tiedje
Towards environmental systems biology of Shewanella.
Nature reviews. Microbiology 2008;6(8):592-603.
2008: Liang Shi; Shuang Deng; Matthew J Marshall; Zheming Wang; David W Kennedy; Alice C Dohnalkova; Heather M Mottaz; Eric A Hill; Yuri A Gorby; Alexander S Beliaev; David J Richardson; John M Zachara; James K Fredrickson
Direct involvement of type II secretion system in extracellular translocation of Shewanella oneidensis outer membrane cytochromes MtrC and OmcA.
Journal of bacteriology 2008;190(15):5512-6.
2008: Jeffrey S McLean; Paul D Majors; Catherine L Reardon; Christina L Bilskis; Samantha B Reed; Margaret F Romine; James K Fredrickson
Investigations of structure and metabolism within Shewanella oneidensis MR-1 biofilms.
Journal of microbiological methods 2008;74(1):47-56.
2008: Jeffrey S McLean; G E Pinchuk; O V Geydebrekht; C L Bilskis; B A Zakrajsek; E A Hill; Daad A Saffarini; Margaret F Romine; Y A Gorby; James K Fredrickson; Alexander S Beliaev
Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1.
Environmental microbiology 2008;10(7):1861-76.
2008: James K Fredrickson; John M Zachara
Electron transfer at the microbe-mineral interface: a grand challenge in biogeochemistry.
Geobiology 2008;6(3):245-53.
2008: Haizhen Zhang; Xiaoting Tang; Gerhard R Munske; Natalia Zakharova; Li Yang; Chunxiang Zheng; Megan A Wolff; Nikola Tolic; Gordon A Anderson; Liang Shi; Matthew J Marshall; James K Fredrickson; James E Bruce
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 2008;7(4):1712-20.
2008: James K Fredrickson; Shu-Mei W Li; Elena K Gaidamakova; Vera Y Matrosova; Min Zhai; Heather M Sulloway; Johannes Scholten; Mindy G Brown; David L Balkwill; Michael J Daly
Protein oxidation: key to bacterial desiccation resistance?
The ISME journal 2008;2(4):393-403.
2008: Dwayne A Elias; Sandra L Tollaksen; David W Kennedy; Heather M Mottaz; Carol S Giometti; Jeffrey S McLean; Eric A Hill; Grigoriy E Pinchuk; Mary S Lipton; James K Fredrickson; Yuri A Gorby
The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression.
Archives of microbiology 2008;189(4):313-24.
2008: Grigoriy E Pinchuk; Christine Ammons; David E Culley; Shu-Mei W Li; Jeffrey S McLean; Margaret F Romine; Kenneth H Nealson; James K Fredrickson; Alexander S Beliaev
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 2008;74(4):1198-208.
2008: Matthew J Marshall; Andrew E Plymale; David W Kennedy; Liang Shi; Zheming Wang; Samantha B Reed; Alice Dohnalkova; Cody J Simonson; Chongxuan Liu; Daad A Saffarini; Margaret F Romine; John M Zachara; Alexander S Beliaev; James K Fredrickson
Hydrogenase- and outer membrane c-type cytochrome-facilitated reduction of technetium(VII) by Shewanella oneidensis MR-1.
Environmental microbiology 2008;10(1):125-36.
2007: Ji-Hoon Lee; Min-Gyu Kim; Bongyoung Yoo; Nosang V Myung; Jongsun Maeng; Takhee Lee; Alice Dohnalkova; James K Fredrickson; Michael J Sadowsky; Hor-Gil Hur
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 2007;104(51):20410-5.
2007: Orianna Bretschger; Anna Obraztsova; Carter A Sturm; In Seop Chang; Yuri A Gorby; Samantha B Reed; David E Culley; Catherine L Reardon; Soumitra Barua; Margaret F Romine; Jizhong Zhou; Alexander S Beliaev; Rachida Bouhenni; Daad A Saffarini; Florian Mansfeld; Byung-Hong Kim; James K Fredrickson; Kenneth H Nealson
Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants.
Applied and environmental microbiology 2007;73(21):7003-12.
2007: Liang Shi; Thomas C Squier; John M Zachara; James K Fredrickson
Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes.
Molecular microbiology 2007;65(1):12-20.
2007: Michael J Daly; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Richard Leapman; Barry Lai; Bruce Ravel; Shu-Mei W Li; Kenneth M Kemner; James K Fredrickson
Protein oxidation implicated as the primary determinant of bacterial radioresistance.
PLoS biology 2007;5(4):e92.
2007: Mary F Deflaun; James K Fredrickson; H Dong; Susan M Pfiffner; Tullis C Onstott; David L Balkwill; Sheryl H Streger; E Stackebrandt; S Knoessen; Esta Van Heerden
Isolation and characterization of a Geobacillus thermoleovorans strain from an ultra-deep South African gold mine.
Systematic and applied microbiology 2007;30(2):152-64.
2007: Vasudevanpillai Biju; Duohai Pan; Yuri A Gorby; James K Fredrickson; Jeff McLean; Daad A Saffarini; H Peter Lu
Combined spectroscopic and topographic characterization of nanoscale domains and their distributions of a redox protein on bacterial cell surfaces.
Langmuir : the ACS journal of surfaces and colloids 2007;23(3):1333-8.
2007: Kira S Makarova; Marina V Omelchenko; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Alla Lapidus; Alex Copeland; Edwin Kim; Miriam Land; Konstantinos Mavrommatis; Samuel Pitluck; Paul M Richardson; Chris Detter; Thomas S Brettin; Elizabeth Saunders; Barry Lai; Bruce Ravel; Kenneth M Kemner; Yuri I Wolf; Alexei Sorokin; Anna V Gerasimova; Mikhail S Gelfand; James K Fredrickson; Eugene V Koonin; Michael J Daly
Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.
PloS one 2007;2(9):e955.
2006: Yijia Xiong; Liang Shi; Baowei Chen; Uljana Mayer; Brian H Lower; Yuri Londer; Saumyaditya Bose; Michael F Hochella; James K Fredrickson; Thomas C Squier
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 2006;128(43):13978-9.
2006: Chongxuan Liu; Byong-Hun Jeon; John M Zachara; Zheming Wang; Alice Dohnalkova; James K Fredrickson
Kinetics of microbial reduction of Solid phase U(VI).
Environmental science & technology 2006;40(20):6290-6.
2006: Matthew J Marshall; Alexander S Beliaev; Alice Dohnalkova; David W Kennedy; Liang Shi; Zheming Wang; Maxim I Boyanov; Barry Lai; Kenneth M Kemner; Jeffrey S McLean; Samantha B Reed; David E Culley; Vanessa L Bailey; Cody J Simonson; Daad A Saffarini; Margaret F Romine; John M Zachara; James K Fredrickson
c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis.
PLoS biology 2006;4(9):e268.
2006: Scott D Harvey; Gary M Mong; Richard M Ozanich; Jeffrey S McLean; Shannon M Goodwin; Nancy B Valentine; James K Fredrickson
Preparation and evaluation of spore-specific affinity-augmented bio-imprinted beads.
Analytical and bioanalytical chemistry 2006;386(2):211-9.
2006: Haichun Gao; Anna Obraztova; Nathan Stewart; Radu Popa; James K Fredrickson; James M Tiedje; Kenneth H Nealson; ali khawwam
Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean.
International journal of systematic and evolutionary microbiology 2006;56(Pt 8):1911-6.
2006: Hassan Brim; Jeffrey P Osborne; Heather M Kostandarithes; James K Fredrickson; Lawrence P Wackett; Michael J Daly
Deinococcus radiodurans engineered for complete toluene degradation facilitates Cr(VI) reduction.
Microbiology (Reading, England) 2006;152(Pt 8):2469-77.
2006: Dwayne A Elias; Matthew Monroe; Richard D Smith; James K Fredrickson; Mary S Lipton
Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1.
Journal of microbiological methods 2006;66(2):223-33.
2006: Yuri A Gorby; Svetlana Yanina; Jeffrey S McLean; Kevin M Rosso; Dianne Moyles; Alice Dohnalkova; Terry J Beveridge; In Seop Chang; Byung Hong Kim; Kyung Shik Kim; David E Culley; Samantha B Reed; Margaret F Romine; Daad A Saffarini; Eric A Hill; Liang Shi; Dwayne A Elias; David W Kennedy; Grigoriy Pinchuk; Kazuya Watanabe; Shunichi Ishii; Bruce Logan; Kenneth H Nealson; James K Fredrickson
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 2006;103(30):11358-63.
2006: Liang Shi; Baowei Chen; Zheming Wang; Dwayne A Elias; Uljana Mayer; Yuri A Gorby; Shuison Ni; Brian H Lower; David W Kennedy; David S Wunschel; Heather M Mottaz; Matthew J Marshall; Eric A Hill; Alexander S Beliaev; John M Zachara; James K Fredrickson; Thomas C Squier
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 2006;188(13):4705-14.
2006: Yul Roh; Haichun Gao; Hojatollah Vali; David W Kennedy; Zamin K Yang; Weimin Gao; Alice Dohnalkova; Raymond D Stapleton; Ji-Won Moon; Tommy J Phelps; James K Fredrickson; ali khawwam
Metal reduction and iron biomineralization by a psychrotolerant Fe(III)-reducing bacterium, Shewanella sp. strain PV-4.
Applied and environmental microbiology 2006;72(5):3236-44.
2006: Ruihua Fang; Dwayne A Elias; Matthew Monroe; Yufeng Shen; Martin McIntosh; Pei Wang; Carrie D Goddard; Stephen J Callister; Ronald J Moore; Yuri A Gorby; Joshua N Adkins; James K Fredrickson; Mary S Lipton; Richard D Smith
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 2006;5(4):714-25.
2006: Mary S Lipton; Margaret F Romine; Matthew Monroe; Dwayne A Elias; Ljiljana Pasa-Tolic; Gordon A Anderson; David J Anderson; James K Fredrickson; Kim K Hixson; Christophe Masselon; Heather M Mottaz; Nikola Tolic; Richard D Smith
AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis.
Methods of biochemical analysis 2006;49():113-34.
2006: William P Kovacik; Ken Takai; Melanie R Mormile; James P McKinley; Fred J Brockman; James K Fredrickson; William Holben
Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S(zero)-reducing bacteria in a sulfate-rich environment.
Environmental microbiology 2006;8(1):141-55.
2005: Duane P Moser; Thomas M Gihring; Fred J Brockman; James K Fredrickson; David L Balkwill; Michael E Dollhopf; Barbara Sherwood Lollar; Lisa M Pratt; Erik Boice; Gordon Southam; Greg Wanger; Brett Baker; Susan M Pfiffner; Li-Hung Lin; Tullis C Onstott
Desulfotomaculum and Methanobacterium spp. dominate a 4- to 5-kilometer-deep fault.
Applied and environmental microbiology 2005;71(12):8773-83.
2005: Alexander S Beliaev; D M Klingeman; J A Klappenbach; L Wu; Margaret F Romine; James M Tiedje; Kenneth H Nealson; James K Fredrickson; J Zhou
Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors.
Journal of bacteriology 2005;187(20):7138-45.
2005: Paul D Majors; Jeffrey S McLean; Grigoriy E Pinchuk; James K Fredrickson; Yuri A Gorby; Kevin R Minard; Robert A Wind
NMR methods for in situ biofilm metabolism studies.
Journal of microbiological methods 2005;62(3):337-44.
2005: Dwayne A Elias; Matthew Monroe; Matthew J Marshall; Margaret F Romine; Alexander S Belieav; James K Fredrickson; Gordon A Anderson; Richard D Smith; Mary S Lipton
Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics.
Proteomics 2005;5(12):3120-30.
2005: James K Fredrickson; Margaret F Romine
Genome-assisted analysis of dissimilatory metal-reducing bacteria.
Current opinion in biotechnology 2005;16(3):269-74.
2005: James K Fredrickson
Crystal ball. Between a rock and a hard place: geomicrobial electron transfer.
Environmental microbiology 2005;7(4):475-6.
2005: Debabrota Ghosal; Marina V Omelchenko; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Amudhan Venkateswaran; Min Zhai; Heather M Kostandarithes; Hassan Brim; Kira S Makarova; Lawrence P Wackett; James K Fredrickson; Michael J Daly
How radiation kills cells: survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress.
FEMS microbiology reviews 2005;29(2):361-75.
2004: Michael J Daly; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Amudhan Venkateswaran; M Hess; Marina V Omelchenko; Heather M Kostandarithes; Kira S Makarova; Lawrence P Wackett; James K Fredrickson; Debabrota Ghosal
Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance.
Science (New York, N.Y.) 2004;306(5698):1025-8.
2004: James K Fredrickson; John M Zachara; David L Balkwill; David Kennedy; Shu-Mei W Li; Heather M Kostandarithes; Michael J Daly; Margaret F Romine; Fred J Brockman
Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington state.
Applied and environmental microbiology 2004;70(7):4230-41.
2004: David L Balkwill; Thomas L Kieft; T Tsukuda; Heather M Kostandarithes; Tullis C Onstott; S Macnaughton; J Bownas; James K Fredrickson
Identification of iron-reducing Thermus strains as Thermus scotoductus.
Extremophiles : life under extreme conditions 2004;8(1):37-44.
2004: Margaret F Romine; Dwayne A Elias; Matthew Monroe; Kenneth J Auberry; Ruihua Fang; James K Fredrickson; Gordon A Anderson; Richard D Smith; Mary S Lipton
Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis.
Omics : a journal of integrative biology 2004;8(3):239-54.
2003: Duane P Moser; James K Fredrickson; David R Geist; Evan V Arntzen; Aaron D Peacock; Shu-Mei W Li; Tina Spadoni; James P McKinley
Biogeochemical processes and microbial characteristics across groundwater-surface water boundaries of the Hanford Reach of the Columbia River.
Environmental science & technology 2003;37(22):5127-34.
2003: Tullis C Onstott; Duane P Moser; Susan M Pfiffner; James K Fredrickson; Fred J Brockman; Tommy J Phelps; David C White; Aaron Peacock; David L Balkwill; R Hoover; Lee R Krumholz; M Borscik; Thomas L Kieft; R Wilson
Indigenous and contaminant microbes in ultradeep mines.
Environmental microbiology 2003;5(11):1168-91.
2003: Melanie R Mormile; Michelle A Biesen; M Carmen Gutierrez; Antonio Ventosa; Justin B Pavlovich; Tullis C Onstott; James K Fredrickson
Isolation of Halobacterium salinarum retrieved directly from halite brine inclusions.
Environmental microbiology 2003;5(11):1094-102.
2003: Hassan Brim; Amudhan Venkateswaran; Heather M Kostandarithes; James K Fredrickson; Michael J Daly
Engineering Deinococcus geothermalis for bioremediation of high-temperature radioactive waste environments.
Applied and environmental microbiology 2003;69(8):4575-82.
2003: Scott C Brooks; James K Fredrickson; Sue L Carroll; David W Kennedy; John M Zachara; Andrew E Plymale; Shelly D Kelly; Kenneth M Kemner; Scott Fendorf
Inhibition of bacterial U(VI) reduction by calcium.
Environmental science & technology 2003;37(9):1850-8.
2003: James K Fredrickson; Sreenivas Kota; Ravi K Kukkadapu; Chongxuan Liu; John M Zachara
Influence of electron donor/acceptor concentrations on hydrous ferric oxide (HFO) bioreduction.
Biodegradation 2003;14(2):91-103.
2003: Ken Takai; Melanie R Mormile; James P McKinley; Fred J Brockman; William Holben; William P Kovacik; James K Fredrickson
Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock.
Environmental microbiology 2003;5(4):309-20.
2003: Brett Baker; Duane P Moser; Barbara J MacGregor; Susan Fishbain; Michael Wagner; Norman K Fry; Brad Jackson; Nico Speolstra; Steffen Loos; Ken Takai; Barbara Sherwood Lollar; James K Fredrickson; David L Balkwill; Tullis C Onstott; Charles F Wimpee; David A Stahl
Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State.
Environmental microbiology 2003;5(4):267-77.
2002: Chongxuan Liu; Yuri A Gorby; John M Zachara; James K Fredrickson; Christopher F Brown
Reduction kinetics of Fe(III), Co(III), U(VI), Cr(VI), and Tc(VII) in cultures of dissimilatory metal-reducing bacteria.
Biotechnology and bioengineering 2002;80(6):637-49.
2002: Mary S Lipton; Ljiljana Pasa-Tolic'; Gordon A Anderson; David J Anderson; Deanna L Auberry; John R Battista; Michael J Daly; James K Fredrickson; Kim K Hixson; Heather M Kostandarithes; Christophe Masselon; Lye Meng Markillie; Ronald J Moore; Margaret F Romine; Yufeng Shen; Eric Stritmatter; Nikola Tolic'; Harold R Udseth; Amudhan Venkateswaran; Kwong-Kwok Wong; Rui Zhao; Richard D Smith
Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(17):11049-54.
2002: Chongxuan Liu; John M Zachara; James K Fredrickson; David W Kennedy; Alice Dohnalkova
Modeling the inhibition of the bacteral reduction of U(VI) by beta-MnO2(s).
Environmental science & technology 2002;36(7):1452-9.
2001: Ken Takai; Duane P Moser; Mary F Deflaun; Tullis C Onstott; James K Fredrickson
Archaeal diversity in waters from deep South African gold mines.
Applied and environmental microbiology 2001;67(12):5750-60.
2001: Ken Takai; Duane P Moser; Tullis C Onstott; N Spoelstra; Susan M Pfiffner; Alice Dohnalkova; James K Fredrickson
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 2001;51(Pt 4):1245-56.
2001: Chongxuan Liu; S Kota; John M Zachara; James K Fredrickson; C K Brinkman
Kinetic analysis of the bacterial reduction of goethite.
Environmental science & technology 2001;35(12):2482-90.
2001: T Shi; James K Fredrickson; David L Balkwill
Biodegradation of polycyclic aromatic hydrocarbons by Sphingomonas strains isolated from the terrestrial subsurface.
Journal of industrial microbiology & biotechnology 2001;26(5):283-9.
2001: James K Fredrickson; John M Zachara; Ravi K Kukkadapu; Yuri A Gorby; S C Smith; Christopher F Brown
Biotransformation of Ni-substituted hydrous ferric oxide by an Fe(III)-reducing bacterium.
Environmental science & technology 2001;35(4):703-12.
2000: Mark E Fuller; Sheryl H Streger; Randi K Rothmel; Brian J Mailloux; James A Hall; Tullis C Onstott; James K Fredrickson; David L Balkwill; Mary F Deflaun
Development of a vital fluorescent staining method for monitoring bacterial transport in subsurface environments.
Applied and environmental microbiology 2000;66(10):4486-96.
2000: FH Crocker; James K Fredrickson; David C White; DB Ringelberg; David L Balkwill
Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments.
Microbiology (Reading, England) 2000;146 ( Pt 6)():1295-310.
2000: R E Wildung; Yuri A Gorby; K M Krupka; N J Hess; SW Li; Andrew E Plymale; James P McKinley; James K Fredrickson
Effect of electron donor and solution chemistry on products of dissimilatory reduction of technetium by Shewanella putrefaciens.
Applied and environmental microbiology 2000;66(6):2451-60.
2000: James K Fredrickson; Heather M Kostandarithes; SW Li; Andrew E Plymale; Michael J Daly
Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1.
Applied and environmental microbiology 2000;66(5):2006-11.
2000: Hassan Brim; S C McFarlan; James K Fredrickson; KW Minton; Min Zhai; Lawrence P Wackett; Michael J Daly
Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments.
Nature biotechnology 2000;18(1):85-90.
1999: K J Tobin; Tullis C Onstott; Mary F Deflaun; F S Colwell; James K Fredrickson
In situ imaging of microorganisms in geologic material.
Journal of microbiological methods 1999;37(3):201-13.
1999: Hailiang Dong; Tullis C Onstott; Mary F Deflaun; Mark E Fuller; K M Gillespie; James K Fredrickson
Development of radiographic and microscopic techniques for the characterization of bacterial transport in intact sediment cores from Oyster, Virginia.
Journal of microbiological methods 1999;37(2):139-54.
1999: Thomas L Kieft; James K Fredrickson; Tullis C Onstott; Yuri A Gorby; Heather M Kostandarithes; T J Bailey; David W Kennedy; SW Li; Andrew E Plymale; C M Spadoni; M S Gray
Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate.
Applied and environmental microbiology 1999;65(3):1214-21.
1999: Margaret F Romine; L C Stillwell; K K Wong; SJ Thurston; E C Sisk; Christoph Wilhelm Sensen; T Gaasterland; James K Fredrickson; JD Saffer
Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199.
Journal of bacteriology 1999;181(5):1585-602.
1997: Darrell P Chandler; James K Fredrickson; Fred J Brockman
Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries.
Molecular ecology 1997;6(5):475-82.
1997: N K Fry; James K Fredrickson; Susan Fishbain; Michael Wagner; David A Stahl
Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers.
Applied and environmental microbiology 1997;63(4):1498-504.
1997: David L Balkwill; Gwendolyn R Drake; R H Reeves; James K Fredrickson; David C White; DB Ringelberg; Darrell P Chandler; Margaret F Romine; D W Kennedy; C M Spadoni
Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.
International journal of systematic bacteriology 1997;47(1):191-201.
1995: L C Stillwell; S J Thurston; R P Schneider; Margaret F Romine; James K Fredrickson; JD Saffer
Physical mapping and characterization of a catabolic plasmid from the deep-subsurface bacterium Sphingomonas sp. strain F199.
Journal of bacteriology 1995;177(15):4537-9.
1995: James K Fredrickson; David L Balkwill; Gwendolyn R Drake; Margaret F Romine; D B Ringelberg; D C White
Aromatic-degrading Sphingomonas isolates from the deep subsurface.
Applied and environmental microbiology 1995;61(5):1917-22.
1995: Andrew Ogram; W Sun; F J Brockman; James K Fredrickson
Isolation and characterization of RNA from low-biomass deep-subsurface sediments.
Applied and environmental microbiology 1995;61(2):763-8.
1992: M J Truex; F J Brockman; D L Johnstone; James K Fredrickson
Effect of starvation on induction of quinoline degradation for a subsurface bacterium in a continuous-flow column.
Applied and environmental microbiology 1992;58(8):2386-92.
1991: James K Fredrickson; Fred J Brockman; D J Workman; S W Li; T O Stevens
Isolation and characterization of a subsurface bacterium capable of growth on toluene, naphthalene, and other aromatic compounds.
Applied and environmental microbiology 1991;57(3):796-803.
1991: James K Fredrickson; David L Balkwill; J M Zachara; S M Li; Fred J Brockman; M A Simmons
Physiological diversity and distributions of heterotrophic bacteria in deep cretaceous sediments of the atlantic coastal plain.
Applied and environmental microbiology 1991;57(2):402-11.
1989: David L Balkwill; James K Fredrickson; J M Thomas
Vertical and horizontal variations in the physiological diversity of the aerobic chemoheterotrophic bacterial microflora in deep southeast coastal plain subsurface sediments.
Applied and environmental microbiology 1989;55(5):1058-65.
1989: F J Brockman; B A Denovan; R J Hicks; James K Fredrickson
Isolation and characterization of quinoline-degrading bacteria from subsurface sediments.
Applied and environmental microbiology 1989;55(4):1029-32.
1989: S A Bentjen; James K Fredrickson; P Van Voris; S W Li
Intact soil-core microcosms for evaluating the fate and ecological impact of the release of genetically engineered microorganisms.
Applied and environmental microbiology 1989;55(1):198-202.
1988: James K Fredrickson; R J Hicks; S W Li; Fred J Brockman
Plasmid incidence in bacteria from deep subsurface sediments.
Applied and environmental microbiology 1988;54(12):2916-23.
1988: James K Fredrickson; D F Bezdicek; F J Brockman; S W Li
Enumeration of Tn5 mutant bacteria in soil by using a most- probable-number-DNA hybridization procedure and antibiotic resistance.
Applied and environmental microbiology 1988;54(2):446-53.