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James Tiedje

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Oligonucleotide Array Sequence Analysis

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Yong-Guan Zhu; Guang-Xia Guo; Syed A Hashsham; Timothy A Johnson; Min Qiao; Robert D Stedtfeld; Jian-Qiang Su; James M Tiedje
Diverse and abundant antibiotic resistance genes in Chinese swine farms.
Jorge L M Rodrigues; James M Tiedje; Siu Mui Tsai; Fabiana S Paula; Vivian H Pellizari; Kyunghwa Baek; Brendan J M Bohannan; Brigitte Feigl; George S Hamaoui; Ederson da C Jesus; Babur Mirza; Rebecca Mueller; Klaus Nüsslein
Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities.
Caio T C C Rachid; Adriana L Santos; James M Tiedje; Fabiano C Balieiro; Heitor L C Coutinho; Raquel S Peixoto; Marisa C Piccolo; Alexandre S Rosado
Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure.

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2013: Yong-Guan Zhu; Guang-Xia Guo; Syed A Hashsham; Timothy A Johnson; Min Qiao; Robert D Stedtfeld; Jian-Qiang Su; James M Tiedje
Diverse and abundant antibiotic resistance genes in Chinese swine farms.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(9):3435-40.
2013: Jorge L M Rodrigues; James M Tiedje; Siu Mui Tsai; Fabiana S Paula; Vivian H Pellizari; Kyunghwa Baek; Brendan J M Bohannan; Brigitte Feigl; George S Hamaoui; Ederson da C Jesus; Babur Mirza; Rebecca Mueller; Klaus Nüsslein
Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(3):988-93.
2013: Caio T C C Rachid; Adriana L Santos; James M Tiedje; Fabiano C Balieiro; Heitor L C Coutinho; Raquel S Peixoto; Marisa C Piccolo; Alexandre S Rosado
Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure.
PloS one 2013;8(3):e59342.
2012: Ernesto Ormeño-Orrillo; Marco A Rogel; James M Tiedje; Ligia Maria Oliveira Chueire; Esperanza Martínez-Romero; Mariangela Hungria
Genome sequences of Burkholderia sp. strains CCGE1002 and H160, isolated from legume nodules in Mexico and Brazil.
Journal of bacteriology 2012;194(24):6927.
2012: S Katharios-Lanwermeyer; M Rakic-Martinez; S Ratani; James M Tiedje; Driss Elhanafi; Sophia Kathariou
Coselection of cadmium and benzalkonium chloride resistance in conjugative transfers from nonpathogenic Listeria spp. to other Listeriae.
Applied and environmental microbiology 2012;78(21):7549-56.
2012: Ruo He; John W Pohlman; John Quensen; James M Tiedje; Matthew J Wooller; Mary Beth Leigh
Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments.
The ISME journal 2012;6(10):1937-48.
2012: Jason Pell; James M Tiedje; Rosangela Canino-Koning; Arend Hintze; Adina Howe; C Titus Brown
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(33):13272-7.
2012: Dieter M Tourlousse; Farhan Ahmad; Gregoire Seyrig; robert stedtfeld; James M Tiedje; Syed A Hashsham
A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification.
Biomedical microdevices 2012;14(4):769-78.
2012: Samuel W Baushke; Erdogan Gulari; Farhan Ahmad; robert stedtfeld; James M Tiedje; Dieter M Tourlousse; Lukas Wick; Syed A Hashsham
Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves.
Journal of microbiological methods 2012;90(1):29-35.
2012: Ruo He; John W Pohlman; John Quensen; James M Tiedje; Matthew J Wooller; Mary Beth Leigh
Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes.
Applied and environmental microbiology 2012;78(13):4715-23.
2012: Ruo He; Catharine Catranis; John W Pohlman; John Quensen; James M Tiedje; Matthew J Wooller; Mary Beth Leigh
Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing.
Environmental microbiology 2012;14(6):1403-19.
2012: robert stedtfeld; Tiffany M Stedtfeld; James M Tiedje; Dieter M Tourlousse; Farhan Ahmad; Erdogan Gulari; Maggie Kronlein; Scott Price; Gregoire Seyrig; Syed A Hashsham
Gene-Z: a device for point of care genetic testing using a smartphone.
Lab on a chip 2012;12(8):1454-62.
2012: Rui Li; James M Tiedje; Chichia Chiu; Robert M Worden
Soluble electron shuttles can mediate energy taxis toward insoluble electron acceptors.
Environmental science & technology 2012;46(5):2813-20.
2012: Alejandro Caro-Quintero; Jie Deng; Manfred Höfle; Jennifer Auchtung; Ingrid Brettar; James M Tiedje; Konstantinos T Konstantinidis
Genome sequencing of five Shewanella baltica strains recovered from the oxic-anoxic interface of the Baltic Sea.
Journal of bacteriology 2012;194(5):1236.
2012: Stefan J Green; Daniela Hubbard; Puja Jasrotia; Will A Overholt; Om Prakash; Christopher Schadt; James M Tiedje; David B Watson; Scott C Brooks; Erick Cardenas; Joel E Kostka
Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.
Applied and environmental microbiology 2012;78(4):1039-47.
2012: Torey Looft; Heather K Allen; David P Alt; Darrell O Bayles; Benli Chai; James R Cole; Syed A Hashsham; Timothy A Johnson; Robert D Stedtfeld; Tiffany M Stedtfeld; Woo Jun Sul; James M Tiedje; Thaddeus B Stanton
In-feed antibiotic effects on the swine intestinal microbiome.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(5):1691-6.
2012: Seungdae Oh; James M Tiedje; Deborah R Yoder-Himes; Sarah Buddenborg; Konstantinos T Konstantinidis
Genomic diversity of Escherichia isolates from diverse habitats.
PloS one 2012;7(10):e47005.
2012: Sang-Hoon Kim; Terence L Marsh; Joan B Broderick; John K Davis; Christina Harzman; Rachel Hutcheson; James M Tiedje
Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction.
BMC microbiology 2012;12():21.
2011: Farhan Ahmad; Gregoire Seyrig; robert stedtfeld; James M Tiedje; Dieter M Tourlousse; Syed A Hashsham
A CCD-based fluorescence imaging system for real-time loop-mediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips.
Biomedical microdevices 2011;13(5):929-37.
2011: Marianna A Patrauchan; James M Tiedje; Christine Florizone; Michael P McLeod; J Jacob Parnell; Lindsay D Eltis
Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400.
Archives of microbiology 2011;193(9):641-50.
2011: Woo Jun Sul; Qiong Wang; James R Cole; Ryan J Farris; Jordan A Fish; Ederson da C Jesus; James M Tiedje
Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(35):14637-42.
2011: Jorge L M Rodrigues; Margrethe H Serres; James M Tiedje
Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level.
Applied and environmental microbiology 2011;77(15):5352-60.
2011: Joy D Van Nostrand; Liyou Wu; Weimin Wu; Zhijian Huang; Terry J Gentry; Ye Deng; Jack Carley; Sue Carroll; Zhili He; Baohua Gu; Jian Luo; Craig S Criddle; David B Watson; Philip M Jardine; Terence L Marsh; James M Tiedje; Terry C Hazen; ali khawwam
Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer.
Applied and environmental microbiology 2011;77(11):3860-9.
2011: Shoko Iwai; Timothy A Johnson; Benli Chai; Syed A Hashsham; James M Tiedje
Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples.
Applied and environmental microbiology 2011;77(11):3551-7.
2011: Tae Kwon Lee; Jaejin Lee; Woo Jun Sul; Shoko Iwai; Benli Chai; James M Tiedje; Joonhong Park
Novel biphenyl-oxidizing bacteria and dioxygenase genes from a korean tidal mudflat.
Applied and environmental microbiology 2011;77(11):3888-91.
2011: Tatiana A Vishnivetskaya; Susan Lucas; Alex Copeland; Alla Lapidus; Tijana Glavina del Rio; E Dalin; Hope Tice; David C Bruce; Lynne A Goodwin; Sam Pitluck; E Saunders; Tom Brettin; Chris Detter; Cliff Han; Frank Larimer; Miriam L Land; Loren J Hauser; Nikos C Kyrpides; Galina Ovchinnikova; Sophia Kathariou; Robert F Ramaley; Debora F Rodrigues; Christie Hendrix; Paul Richardson; James M Tiedje
Complete genome sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b.
Journal of bacteriology 2011;193(11):2880-1.
2011: Pelin Yilmaz; Linda Amaral-Zettler; Manimozhiyan Arumugam; Susanna Assunta-Sansone; Mark Bailey; Laura Baumgartner; Bruce W Birren; Martin J Blaser; Vivien Bonazzi; Tim Booth; Peer Bork; Frederic D Bushman; Pier Luigi Buttigieg; Patrick S G Chain; Emily Charlson; Guy Cochrane; James R Cole; Elizabeth K Costello; Peter Dawyndt; Todd DeSantis; Dawn Field; Noah Fierer; Jed A Fuhrman; Rachel E Gallery; Dirk Gevers; Richard A Gibbs; Jack A Gilbert; Antonio Gonzalez; Jeffrey I Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Christopher Hunter; Heather Huot-Creasy; Janet Jansson; Anjanette Johnston; Ilene Karsch-Mizrachi; Andrew L Kau; Scott T Kelley; Jerry Kennedy; Rob Knight; Dan Knights; Omry Koren; Renzo Kottmann; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L Lauber; Teresa Legg; Ruth E Ley; Catherine A Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn Maguire; Barbara A Methé; Folker Meyer; Norman Morrison; Brian Muegge; Sara Nakielny; Karen E Nelson; Diana Nemergut; Josh D Neufeld; Lindsay K Newbold; Anna E Oliver; Norman R Pace; Giriprakash Palanisamy; Joonhong Park; Jörg Peplies; Joseph Petrosino; Lita Proctor; Elmar Pruesse; Christian Quast; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A Relman; Philippe Rocca-Serra; Inigo San Gil; Patrick D Schloss; Lynn M Schriml; Rohini Sinha; Michelle I Smith; Erica Sodergren; Aymé Spo; Peter Sterk; Jesse Stombaugh; James M Tiedje; Robert Vaughan; Doyle V Ward; George M Weinstock; Doug Wendel; Owen R White; Andrew Whiteley; Andreas Wilke; Jennifer Wortman; Tanya Yatsunenko; Frank Oliver Glöckner
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Nature biotechnology 2011;29(5):415-20.
2011: Chengwei Luo; Seth T Walk; David M Gordon; Michael Feldgarden; James M Tiedje; Konstantinos T Konstantinidis
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(17):7200-5.
2011: Rui Li; Jennifer M Auchtung; James M Tiedje; Robert M Worden
Shewanella oneidensis MR-1 chemotaxis in a diffusion gradient chamber.
Environmental science & technology 2011;45(3):1014-20.
2011: Adriana L Santos; José F Siqueira; Ederson C Jesus; Isabela N Rôças; Alexandre S Rosado; James M Tiedje
Comparing the bacterial diversity of acute and chronic dental root canal infections.
PloS one 2011;6(11):e28088.
2011: Claribel Cruz-García; Alison E Murray; Jorge L M Rodrigues; Jeffrey A Gralnick; Lee Ann McCue; Margaret F Romine; Frank E Loeffler; James M Tiedje
Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1.
BMC microbiology 2011;11():64.
2011: Henrique Fragoso dos Santos; Juliano Carvalho Cury; Flávia Lima do Carmo; Adriana Lopes dos Santos; James M Tiedje; Jan Dirk van Elsas; Alexandre Soares Rosado; Raquel S Peixoto
Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution.
PloS one 2011;6(3):e16943.
2010: Blaz Stres; Laurent Philippot; Jadran Faganeli; James M Tiedje
Frequent freeze-thaw cycles yield diminished yet resistant and responsive microbial communities in two temperate soils: a laboratory experiment.
FEMS microbiology ecology 2010;74(2):323-35.
2010: Bostjan Murovec; James M Tiedje; Blaz Stres
DNA encoding for an efficient 'Omics processing.
Computer methods and programs in biomedicine 2010;100(2):175-90.
2010: Erick Cardenas; Weimin Wu; Mary Beth Leigh; Jack Carley; Sue Carroll; Terry Gentry; Jian Luo; David Watson; Baohua Gu; Matthew Ginder-Vogel; Peter K Kitanidis; Philip M Jardine; ali khawwam; Craig S Criddle; Terence L Marsh; James M Tiedje
Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.
Applied and environmental microbiology 2010;76(20):6778-86.
2010: Shannon M Hinsa-Leasure; Laya Bhavaraju; Jorge L M Rodrigues; Corien Bakermans; David Gilichinsky; James M Tiedje
Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample.
FEMS microbiology ecology 2010;74(1):103-13.
2010: Lia C R S Teixeira; Raquel S Peixoto; Juliano C Cury; Woo Jun Sul; Vivian H Pellizari; James M Tiedje; Alexandre S Rosado
Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica.
The ISME journal 2010;4(8):989-1001.
2010: Meiying Xu; Weimin Wu; Liyou Wu; Zhili He; Joy D Van Nostrand; Ye Deng; Jian Luo; Jack Carley; Matthew Ginder-Vogel; Terry J Gentry; Baouhua Gu; David Watson; Philip M Jardine; Terence L Marsh; James M Tiedje; Terry Hazen; Craig S Criddle; Jizhong Zhou
Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation.
The ISME journal 2010;4(8):1060-70.
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: Seungdae Oh; Deborah R Yoder-Himes; James M Tiedje; Joonhong Park; Konstantinos T Konstantinidis
Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain.
Applied and environmental microbiology 2010;76(9):2980-8.
2010: Christopher L Hemme; Ye Deng; Terry J Gentry; matthew w fields; Liyou Wu; Soumitra Barua; Kerrie Barry; Susannah G Tringe; David B Watson; Zhili He; Terry C Hazen; James M Tiedje; Edward M Rubin; ali khawwam
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community.
The ISME journal 2010;4(5):660-72.
2010: Héctor L Ayala-del-Río; Patrick S Chain; Joseph J Grzymski; Monica A Ponder; Natalia Ivanova; Peter W Bergholz; Genevive Di Bartolo; Loren Hauser; Miriam Land; Corien Bakermans; Debora Rodrigues; Joel Klappenbach; Dan Zarka; Frank Larimer; Paul Richardson; Alison Murray; Michael Thomashow; James M Tiedje
The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth.
Applied and environmental microbiology 2010;76(7):2304-12.
2010: Shoko Iwai; Benli Chai; Woo Jun Sul; James R Cole; Syed A Hashsham; James M Tiedje
Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.
The ISME journal 2010;4(2):279-85.
2010: Jacob Parnell; Vincent J Denef; Joonhong Park; Tamara V Tsoi; James M Tiedje
Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400.
Biodegradation 2010;21(1):147-56.
2010: Jack A Gilbert; Folker Meyer; Janet Jansson; Jeff Gordon; Norman Pace; James M Tiedje; Ruth Ley; Noah Fierer; Dawn Field; Nikos Kyrpides; Frank Oliver Glöckner; Hans-Peter Klenk; K Eric Wommack; Elizabeth Glass; Kathryn Docherty; Rachel Gallery; Rick Stevens; Rob Knight
The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.
Standards in genomic sciences 2010;3(3):249-53.
2010: Deborah R Yoder-Himes; Konstantinos T Konstantinidis; James M Tiedje
Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics.
PloS one 2010;5(1):e8724.
2009: P S G Chain; D V Grafham; R S Fulton; M G Fitzgerald; J Hostetler; D Muzny; J Ali; B Birren; D C Bruce; C Buhay; J R Cole; Y Ding; S Dugan; D Field; George M Garrity; R Gibbs; T Graves; C S Han; S H Harrison; S Highlander; P Hugenholtz; H M Khouri; C D Kodira; E Kolker; Nikos Kyrpides; D Lang; A Lapidus; S A Malfatti; V Markowitz; T Metha; K E Nelson; J Parkhill; S Pitluck; X Qin; T D Read; J Schmutz; S Sozhamannan; P Sterk; R L Strausberg; G Sutton; N R Thomson; James M Tiedje; G Weinstock; A Wollam; J C Detter
Genomics. Genome project standards in a new era of sequencing.
Science (New York, N.Y.) 2009;326(5950):236-7.
2009: Seth T Walk; Elizabeth Alm; David M Gordon; Jeffrey L Ram; Gary A Toranzos; James M Tiedje; Thomas S Whittam
Cryptic lineages of the genus Escherichia.
Applied and environmental microbiology 2009;75(20):6534-44.
2009: Joy D Van Nostrand; Weimin Wu; Liyou Wu; Ye Deng; Jack Carley; Sue Carroll; Zhili He; Baohua Gu; Jian Luo; Craig S Criddle; David B Watson; Philip M Jardine; Terence L Marsh; James M Tiedje; Terry C Hazen; ali khawwam
GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer.
Environmental microbiology 2009;11(10):2611-26.
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: Woo Jun Sul; Joonhong Park; John F Quensen; Jorge L M Rodrigues; Laurie Seliger; Tamara V Tsoi; Gerben J Zylstra; James M Tiedje
DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment.
Applied and environmental microbiology 2009;75(17):5501-6.
2009: Ederson da C Jesus; Terence L Marsh; James M Tiedje; Fatima M de S Moreira
Changes in land use alter the structure of bacterial communities in Western Amazon soils.
The ISME journal 2009;3(9):1004-11.
2009: Carlos M Rodríguez-Minguela; Juha H A Apajalahti; Benli Chai; James R Cole; James M Tiedje
Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact.
Applied and environmental microbiology 2009;75(15):5100-10.
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: Blaz Stres; James M Tiedje; Bostjan Murovec
BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer-enzyme-sequence databases.
Bioinformatics (Oxford, England) 2009;25(12):1556-8.
2009: Debora F Rodrigues; Ederson da C Jesus; Héctor L Ayala-del-Río; Vivian H Pellizari; David Gilichinsky; Lycely Sepulveda-Torres; James M Tiedje
Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium.
The ISME journal 2009;3(6):658-65.
2009: Tatiana A Vishnivetskaya; Sophia Kathariou; James M Tiedje
The Exiguobacterium genus: biodiversity and biogeography.
Extremophiles : life under extreme conditions 2009;13(3):541-55.
2009: Peter W Bergholz; Corien Bakermans; James M Tiedje
Psychrobacter arcticus 273-4 uses resource efficiency and molecular motion adaptations for subzero temperature growth.
Journal of bacteriology 2009;191(7):2340-52.
2009: D R Yoder-Himes; Patrick S G Chain; Y Zhu; O Wurtzel; E M Rubin; James M Tiedje; R Sorek
Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(10):3976-81.
2009: A Ramette; James M Tiedje; Antje Boetius
Impact of space, time and complex environments on microbial communities.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2009;15 Suppl 1():60-2.
2009: J R Cole; Q Wang; E Cardenas; J Fish; B Chai; R J Farris; A S Kulam-Syed-Mohideen; Donna McGarrell; T Marsh; George M Garrity; James M Tiedje
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
Nucleic acids research 2009;37(Database issue):D141-5.
2009: Corien Bakermans; Rudolph E Sloup; Daniel G Zarka; James M Tiedje; Michael F Thomashow
Development and use of genetic system to identify genes required for efficient low-temperature growth of Psychrobacter arcticus 273-4.
Extremophiles : life under extreme conditions 2009;13(1):21-30.
2008: Erick Cardenas; James M Tiedje
New tools for discovering and characterizing microbial diversity.
Current opinion in biotechnology 2008;19(6):544-9.
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: Liyou Wu; Laurie Kellogg; Allan H Devol; James M Tiedje; ali khawwam
Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico.
Applied and environmental microbiology 2008;74(14):4516-29.
2008: Monica A Ponder; Michael F Thomashow; James M Tiedje
Metabolic activity of Siberian permafrost isolates, Psychrobacter arcticus and Exiguobacterium sibiricum, at low water activities.
Extremophiles : life under extreme conditions 2008;12(4):481-90.
2008: Erick Cardenas; Weimin Wu; Mary Beth Leigh; Jack Carley; Sue Carroll; Terry Gentry; Jian Luo; David Watson; Baohua Gu; Matthew Ginder-Vogel; Peter K Kitanidis; Philip M Jardine; ali khawwam; Craig S Criddle; Terence L Marsh; James M Tiedje
Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels.
Applied and environmental microbiology 2008;74(12):3718-29.
2008: robert stedtfeld; Samuel W Baushke; Dieter M Tourlousse; Sarah M Miller; Tiffany M Stedtfeld; Erdogan Gulari; James M Tiedje; Syed A Hashsham
Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform.
Applied and environmental microbiology 2008;74(12):3831-8.
2008: Liyou Wu; Xueduan Liu; matthew w fields; Dorothea K Thompson; Christopher E Bagwell; James M Tiedje; Terry C Hazen; ali khawwam
Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness.
The ISME journal 2008;2(6):642-55.
2008: James M Tiedje; Timothy Donohue
Microbes in the energy grid.
Science (New York, N.Y.) 2008;320(5879):985.
2008: Sarah M Miller; Dieter M Tourlousse; robert stedtfeld; Samuel W Baushke; Amanda B Herzog; Lukas Wick; Jean-Marie Rouillard; Erdogan Gulari; James M Tiedje; Syed A Hashsham
In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water.
Applied and environmental microbiology 2008;74(7):2200-9.
2008: Debora Frigi Rodrigues; James M Tiedje
Coping with our cold planet.
Applied and environmental microbiology 2008;74(6):1677-86.
2008: Debora F Rodrigues; Natalia Ivanova; Zhili He; Marianne Huebner; ali khawwam; James M Tiedje
Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach.
BMC genomics 2008;9():547.
2007: Aviaja A Hansen; Rodney A Herbert; Karina Mikkelsen; Lars Liengård Jensen; Tommy Kristoffersen; James M Tiedje; Bente Aa Lomstein; Kai Finster
Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway.
Environmental microbiology 2007;9(11):2870-84.
2007: Konstantinos T Konstantinidis; James M Tiedje
Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead.
Current opinion in microbiology 2007;10(5):504-9.
2007: Daryl J Smith; Joonhong Park; James M Tiedje; William W Mohn
A large gene cluster in Burkholderia xenovorans encoding abietane diterpenoid catabolism.
Journal of bacteriology 2007;189(17):6195-204.
2007: Weimin Wu; Jack Carley; Jian Luo; Matthew A Ginder-Vogel; Erick Cardenas; Mary Beth Leigh; Chiachi Hwang; Shelly D Kelly; Chuanmin Ruan; Liyou Wu; Joy Van Nostrand; Terry Gentry; Kenneth Lowe; Tonia L Mehlhorn; Sue Carroll; Wensui Luo; matthew w fields; Baohua Gu; David Watson; Kenneth M Kemner; Terence L Marsh; James M Tiedje; ali khawwam; Scott Fendorf; Peter K Kitanidis; Philip M Jardine; Craig S Criddle
In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen.
Environmental science & technology 2007;41(16):5716-23.
2007: Qiong Wang; George M Garrity; James M Tiedje; James R Cole
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Applied and environmental microbiology 2007;73(16):5261-7.
2007: Mary Beth Leigh; Vivian H Pellizari; Ondrej Uhlík; Robin Sutka; Jorge Rodrigues; Nathaniel E Ostrom; ali khawwam; James M Tiedje
Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs).
The ISME journal 2007;1(2):134-48.
2007: David Gilichinsky; G S Wilson; E Imre Friedmann; Christopher P McKay; R S Sletten; Elizaveta Rivkina; Tatiana A Vishnivetskaya; LG Erokhina; NE Ivanushkina; GA Kochkina; Viktoria Shcherbakova; Vera S Soina; Elena V Spirina; E A Vorobyova; D G Fyodorov-Davydov; B Hallet; SM Ozerskaya; V A Sorokovikov; K S Laurinavichyus; AV Shatilovich; J P Chanton; V E Ostroumov; James M Tiedje
Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology.
Astrobiology 2007;7(2):275-311.
2007: Tatiana A Vishnivetskaya; Robin Siletzky; Natalie Jefferies; James M Tiedje; Sophia Kathariou
Effect of low temperature and culture media on the growth and freeze-thawing tolerance of Exiguobacterium strains.
Cryobiology 2007;54(2):234-40.
2007: Louise A O'Sullivan; Andrew J Weightman; T Hefin Jones; Angela M Marchbank; James M Tiedje; Eshwar Mahenthiralingam
Identifying the genetic basis of ecologically and biotechnologically useful functions of the bacterium Burkholderia vietnamiensis.
Environmental microbiology 2007;9(4):1017-34.
2007: Corien Bakermans; Sandra L Tollaksen; Carol S Giometti; Curtis G Wilkerson; James M Tiedje; Michael F Thomashow
Proteomic analysis of Psychrobacter cryohalolentis K5 during growth at subzero temperatures.
Extremophiles : life under extreme conditions 2007;11(2):343-54.
2007: Alban Ramette; James M Tiedje
Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(8):2761-6.
2007: Jill C Tarter; Peter R Backus; Rocco L Mancinelli; Jonathan M Aurnou; Dana E Backman; Gibor S Basri; Alan P Boss; Andrew Clarke; Drake Deming; Laurance R Doyle; Eric D Feigelson; Friedmann Freund; David H Grinspoon; Robert M Haberle; Steven A Hauck; Martin J Heath; Todd J Henry; Jeffery L Hollingsworth; Manoj M Joshi; Steven Kilston; Michael C Liu; Eric Meikle; I Neill Reid; Lynn J Rothschild; John Scalo; Antigona Segura; Carol M Tang; James M Tiedje; Margaret C Turnbull; Lucianne M Walkowicz; Arthur L Weber; Richard E Young
A reappraisal of the habitability of planets around M dwarf stars.
Astrobiology 2007;7(1):30-65.
2007: Suping Zheng; Monica A Ponder; Janice Yang Jen Shih; James M Tiedje; Michael F Thomashow; David M Lubman
A proteomic analysis of Psychrobacter articus 273-4 adaptation to low temperature and salinity using a 2-D liquid mapping approach.
Electrophoresis 2007;28(3):467-88.
2007: Debora Frigi Rodrigues; James M Tiedje
Multi-locus real-time PCR for quantitation of bacteria in the environment reveals Exiguobacterium to be prevalent in permafrost.
FEMS microbiology ecology 2007;59(2):489-99.
2007: Alban Ramette; James M Tiedje
Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution.
Microbial ecology 2007;53(2):197-207.
2007: Johan Goris; Konstantinos T Konstantinidis; Joel A Klappenbach; Tom Coenye; Peter Vandamme; James M Tiedje
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.
International journal of systematic and evolutionary microbiology 2007;57(Pt 1):81-91.
2007: robert stedtfeld; Lukas Wick; Samuel W Baushke; Dieter M Tourlousse; Amanda B Herzog; Yongmei Xia; Jean-Marie Rouillard; Joel A Klappenbach; James R Cole; Erdogan Gulari; James M Tiedje; Syed A Hashsham
Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays.
Applied and environmental microbiology 2007;73(2):380-9.
2007: Claribel Cruz-García; Alison E Murray; Joel A Klappenbach; Valley Stewart; James M Tiedje
Respiratory nitrate ammonification by Shewanella oneidensis MR-1.
Journal of bacteriology 2007;189(2):656-62.
2007: James R Cole; Benli Chai; RJ Farris; Qiong Wang; A S Kulam-Syed-Mohideen; Donna McGarrell; A M Bandela; E Cardenas; George M Garrity; James M Tiedje
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.
Nucleic acids research 2007;35(Database issue):D169-72.
2006: Konstantinos T Konstantinidis; Alban Ramette; James M Tiedje
The bacterial species definition in the genomic era.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1475):1929-40.
2006: Konstantinos T Konstantinidis; Alban Ramette; James M Tiedje
Toward a more robust assessment of intraspecies diversity, using fewer genetic markers.
Applied and environmental microbiology 2006;72(11):7286-93.
2006: Patrick S G Chain; Vincent J Denef; Konstantinos T Konstantinidis; Lisa M Vergez; Loreine Agulló; Valeria Latorre Reyes; Loren Hauser; Macarena Córdova; Luis Gómez; Myriam González; Miriam Land; Victoria Lao; Frank W Larimer; John J LiPuma; Eshwar Mahenthiralingam; Stephanie Malfatti; Christopher J Marx; Jacob Parnell; Alban Ramette; Paul Richardson; Michael Seeger; Daryl Smith; Theodore Spilker; Woo Jun Sul; Tamara V Tsoi; Luke E Ulrich; Igor B Zhulin; James M Tiedje
Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(42):15280-7.
2006: C Ryan Penton; Allan H Devol; James M Tiedje
Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments.
Applied and environmental microbiology 2006;72(10):6829-32.
2006: Jacob Parnell; Joonhong Park; Vincent J Denef; Tamara V Tsoi; Syed A Hashsham; John F Quensen; James M Tiedje
Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress.
Applied and environmental microbiology 2006;72(10):6607-14.
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: Debora Frigi Rodrigues; Johan Goris; Tatiana A Vishnivetskaya; David Gilichinsky; Michael F Thomashow; James M Tiedje
Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov.
Extremophiles : life under extreme conditions 2006;10(4):285-94.
2006: Tatiana A Vishnivetskaya; Maya A Petrova; John Urbance; Monica A Ponder; Craig L Moyer; David Gilichinsky; James M Tiedje
Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods.
Astrobiology 2006;6(3):400-14.
2006: Corien Bakermans; Héctor L Ayala-del-Río; Monica A Ponder; Tatiana A Vishnivetskaya; David Gilichinsky; Michael F Thomashow; James M Tiedje
Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost.
International journal of systematic and evolutionary microbiology 2006;56(Pt 6):1285-91.
2006: George W Payne; Alban Ramette; Helen L Rose; Andrew J Weightman; T Hefin Jones; James M Tiedje; Eshwar Mahenthiralingam
Application of a recA gene-based identification approach to the maize rhizosphere reveals novel diversity in Burkholderia species.
FEMS microbiology letters 2006;259(1):126-32.
2006: Jorge L M Rodrigues; C Alan Kachel; Michael R Aiello; John F Quensen; Olga V Maltseva; Tamara V Tsoi; James M Tiedje
Degradation of aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp. strain RHA1(fcb).
Applied and environmental microbiology 2006;72(4):2476-82.
2006: Xiaoyun Qiu; Michael J Daly; Alexander Vasilenko; Marina V Omelchenko; Elena K Gaidamakova; Liyou Wu; ali khawwam; George W Sundin; James M Tiedje
Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation.
Journal of bacteriology 2006;188(3):1199-204.
2006: Lukas Wick; Jean-Marie Rouillard; Thomas S Whittam; Erdogan Gulari; James M Tiedje; Syed A Hashsham
On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes.
Nucleic acids research 2006;34(3):e26.
2006: Vincent J Denef; J A Klappenbach; Marianna A Patrauchan; Christine Florizone; Jorge L M Rodrigues; Tamara V Tsoi; W Verstraete; Lindsay D Eltis; James M Tiedje
Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400.
Applied and environmental microbiology 2006;72(1):585-95.
2005: Vincent J Denef; Marianna A Patrauchan; Christine Florizone; Joonhong Park; Tamara V Tsoi; W Verstraete; James M Tiedje; Lindsay D Eltis
Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400.
Journal of bacteriology 2005;187(23):7996-8005.
2005: Xiaoyun Qiu; James M Tiedje; George W Sundin
Genome-wide examination of the natural solar radiation response in Shewanella oneidensis MR-1.
Photochemistry and photobiology 2005;81(6):1559-68.
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: Konstantinos T Konstantinidis; James M Tiedje
Towards a genome-based taxonomy for prokaryotes.
Journal of bacteriology 2005;187(18):6258-64.
2005: Claudia Etchebehere; James M Tiedje
Presence of two different active nirS nitrite reductase genes in a denitrifying Thauera sp. from a high-nitrate-removal-rate reactor.
Applied and environmental microbiology 2005;71(9):5642-5.
2005: David Gilichinsky; Elizaveta Rivkina; Corien Bakermans; Viktoria Shcherbakova; Lada Petrovskaya; Svetlana Ozerskaya; Natalia Ivanushkina; Galina Kochkina; Kyastus Laurinavichuis; Svetlana Pecheritsina; Rushania Fattakhova; James M Tiedje
Biodiversity of cryopegs in permafrost.
FEMS microbiology ecology 2005;53(1):117-28.
2005: Monica A Ponder; Sarah J Gilmour; Peter W Bergholz; Carol A Mindock; Rawle Hollingsworth; Michael F Thomashow; James M Tiedje
Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria.
FEMS microbiology ecology 2005;53(1):103-15.
2005: Xiaoyun Qiu; George W Sundin; Liyou Wu; ali khawwam; James M Tiedje
Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation.
Journal of bacteriology 2005;187(10):3556-64.
2005: Alban Ramette; John J LiPuma; James M Tiedje
Species abundance and diversity of Burkholderia cepacia complex in the environment.
Applied and environmental microbiology 2005;71(3):1193-201.
2005: Konstantinos T Konstantinidis; James M Tiedje
Genomic insights that advance the species definition for prokaryotes.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(7):2567-72.
2005: Eugene Kolker; Alex F Picone; Michael Galperin; Margaret F Romine; Roger Higdon; Kira S Makarova; Natali Kolker; Gordon A Anderson; Xiaoyun Qiu; Kenneth J Auberry; Gyorgy Babnigg; Alex S Beliaev; Paul Edlefsen; Dwayne A Elias; Yuri A Gorby; Ted Holzman; Joel A Klappenbach; Konstantinos T Konstantinidis; Miriam L Land; Mary S Lipton; Lee-Ann McCue; Matthew Monroe; Ljiljana Pasa-Tolic; Grigoriy Pinchuk; Samuel Purvine; Margrethe H Serres; Sasha Tsapin; Brian A Zakrajsek; Wenhong Zhu; Jizhong Zhou; Frank W Larimer; Charles E Lawrence; Monica Riley; Frank R Collart; John R Yates; Richard D Smith; Carol S Giometti; Kenneth H Nealson; James K Fredrickson; James M Tiedje
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 2005;102(6):2099-104.
2005: James R Cole; Benli Chai; RJ Farris; Qiong Wang; S A Kulam; Donna McGarrell; George M Garrity; James M Tiedje
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.
Nucleic acids research 2005;33(Database issue):D294-6.
2004: Liyou Wu; Dorothea K Thompson; Xueduan Liu; matthew w fields; Christopher E Bagwell; James M Tiedje; ali khawwam
Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications.
Environmental science & technology 2004;38(24):6775-82.
2004: Xiaoyun Qiu; George W Sundin; Benli Chai; James M Tiedje
Survival of Shewanella oneidensis MR-1 after UV radiation exposure.
Applied and environmental microbiology 2004;70(11):6435-43.
2004: Syed A Hashsham; Lukas Wick; Jean-Marie Rouillard; Erdogan Gulari; James M Tiedje
Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs.
Biosensors & bioelectronics 2004;20(4):668-83.
2004: X-Y Qiu; R A Hurt; L-Y Wu; Chung-Hsuan Chen; James M Tiedje; JZ Zhou
Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR.
Journal of microbiological methods 2004;59(2):199-210.
2004: Johan Goris; Paul De Vos; Jesús Caballero-Mellado; Joonhong Park; Enevold Falsen; John F Quensen; James M Tiedje; Peter Vandamme
Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov.
International journal of systematic and evolutionary microbiology 2004;54(Pt 5):1677-81.
2004: Benjamin M Griffin; James M Tiedje; Frank E Loeffler
Anaerobic microbial reductive dechlorination of tetrachloroethene to predominately trans-1,2-dichloroethene.
Environmental science & technology 2004;38(16):4300-3.
2004: Vincent J Denef; Joonhong Park; Tamara V Tsoi; Jean-Marie Rouillard; H Zhang; J A Wibbenmeyer; W Verstraete; Erdogan Gulari; Syed A Hashsham; James M Tiedje
Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400.
Applied and environmental microbiology 2004;70(8):4961-70.
2004: Héctor L Ayala-del-Río; Stephen J Callister; Craig S Criddle; James M Tiedje
Correspondence between community structure and function during succession in phenol- and phenol-plus-trichloroethene-fed sequencing batch reactors.
Applied and environmental microbiology 2004;70(8):4950-60.
2004: Konstantinos T Konstantinidis; James M Tiedje
Trends between gene content and genome size in prokaryotic species with larger genomes.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(9):3160-5.
2004: ali khawwam; Beicheng Xia; Heshu Huang; Anthony V Palumbo; James M Tiedje
Microbial diversity and heterogeneity in sandy subsurface soils.
Applied and environmental microbiology 2004;70(3):1723-34.
2004: Elizaveta Rivkina; K Laurinavichius; J McGrath; James M Tiedje; Viktoria Shcherbakova; David Gilichinsky
Microbial life in permafrost.
Advances in space research : the official journal of the Committee on Space Research (COSPAR) 2004;33(8):1215-21.
2004: Blaz Stres; Ivan Mahne; Gorazd Avgustin; James M Tiedje
Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils.
Applied and environmental microbiology 2004;70(1):301-9.
2003: Vincent J Denef; Joonhong Park; Jorge L M Rodrigues; Tamara V Tsoi; Syed A Hashsham; James M Tiedje
Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities.
Environmental microbiology 2003;5(10):933-43.
2003: Lubov V Dorofeeva; Valentina I Krausova; Lyudmila I Evtushenko; James M Tiedje
Agromyces albus sp. nov., isolated from a plant (Androsace sp.).
International journal of systematic and evolutionary microbiology 2003;53(Pt 5):1435-8.
2003: SL Dollhopf; M L Pariseau; Syed A Hashsham; James M Tiedje
Competitive and interactions affecting a fermentative spirochete in anaerobic chemostats.
Microbial ecology 2003;46(1):1-11.
2003: Xueduan Liu; Sonia M Tiquia; Gina Holguin; Liyou Wu; Stephen C Nold; Allan H Devol; Kuan Luo; Anthony V Palumbo; James M Tiedje; ali khawwam
Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico.
Applied and environmental microbiology 2003;69(6):3549-60.
2003: Gesche Braker; James M Tiedje
Nitric oxide reductase (norB) genes from pure cultures and environmental samples.
Applied and environmental microbiology 2003;69(6):3476-83.
2003: Youlboong Sung; Kirsti M Ritalahti; Robert A Sanford; John W Urbance; Shannon J Flynn; James M Tiedje; Frank E Loeffler
Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp. nov.
Applied and environmental microbiology 2003;69(5):2964-74.
2003: David Gilichinsky; Elizaveta Rivkina; Viktoria Shcherbakova; K Laurinavichuis; James M Tiedje
Supercooled water brines within permafrost-an unknown ecological niche for microorganisms: a model for astrobiology.
Astrobiology 2003;3(2):331-41.
2003: Tingfen Yan; matthew w fields; Liyou Wu; Yuangang Zu; James M Tiedje; ali khawwam
Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater.
Environmental microbiology 2003;5(1):13-24.
2003: James R Cole; Benli Chai; Terence L Marsh; RJ Farris; Qiong Wang; S A Kulam; S Chandra; Donna McGarrell; Thomas M Schmidt; George M Garrity; James M Tiedje
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.
Nucleic acids research 2003;31(1):442-3.
2003: John W Urbance; James Cole; Paul Saxman; James M Tiedje
BSD: the Biodegradative Strain Database.
Nucleic acids research 2003;31(1):152-5.
2003: D S Treves; B Xia; ali khawwam; James M Tiedje
A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil.
Microbial ecology 2003;45(1):20-8.
2002: Lubov V Dorofeeva; Lyudmila I Evtushenko; Valentina I Krausova; Alexander V Karpov; Sergey A Subbotin; James M Tiedje
Rathayibacter caricis sp. nov. and Rathayibacter festucae sp. nov., isolated from the phyllosphere of Carex sp. and the leaf gall induced by the nematode Anguina graminis on Festuca rubra L., respectively.
International journal of systematic and evolutionary microbiology 2002;52(Pt 6):1917-23.
2002: Baolin Sun; Benjamin M Griffin; Héctor L Ayala-del-Río; Syed A Hashsham; James M Tiedje
Microbial dehalorespiration with 1,1,1-trichloroethane.
Science (New York, N.Y.) 2002;298(5595):1023-5.
2002: James M Tiedje
Shewanella--the environmentally versatile genome.
Nature biotechnology 2002;20(11):1093-4.
2002: Jorge L M Rodrigues; Michael R Aiello; John W Urbance; Tamara V Tsoi; James M Tiedje
Use of both 16S rRNA and engineered functional genes with real-time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil.
Journal of microbiological methods 2002;51(2):181-9.
2002: Jianzhong He; Youlboong Sung; Mike E Dollhopf; Babu Z Fathepure; James M Tiedje; Frank E Loeffler
Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene-contaminated sites.
Environmental science & technology 2002;36(18):3945-52.
2002: Michael J Dybas; David W Hyndman; Robert Heine; James M Tiedje; Katrina Linning; David Wiggert; Thomas C Voice; Xianda Zhao; Leslie Dybas; Craig S Criddle
Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation.
Environmental science & technology 2002;36(16):3635-44.
2002: Kazuhito Itoh; Rie Kanda; Yoko Sumita; Hongik Kim; Yoichi Kamagata; Kousuke Suyama; Hiroki Yamamoto; Robert P Hausinger; James M Tiedje
tfdA-like genes in 2,4-dichlorophenoxyacetic acid-degrading bacteria belonging to the Bradyrhizobium-Agromonas-Nitrobacter-Afipia cluster in alpha-Proteobacteria.
Applied and environmental microbiology 2002;68(7):3449-54.
2002: Anders Priemé; Gesche Braker; James M Tiedje
Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils.
Applied and environmental microbiology 2002;68(4):1893-900.
2002: Jae-Chang Cho; James M Tiedje
Quantitative detection of microbial genes by using DNA microarrays.
Applied and environmental microbiology 2002;68(3):1425-30.
2002: Robert A Sanford; James R Cole; James M Tiedje
Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium.
Applied and environmental microbiology 2002;68(2):893-900.
2002: Dorothea K Thompson; Alex S Beliaev; Carol S Giometti; Sandra L Tollaksen; Tripti Khare; Douglas P Lies; Kenneth H Nealson; Hanjo Lim; John Yates; Craig C Brandt; James M Tiedje; ali khawwam
Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress.
Applied and environmental microbiology 2002;68(2):881-92.
2002: Alex S Beliaev; Dorothea K Thompson; Tripti Khare; Hanjo Lim; Craig C Brandt; Guangshan Li; Alison E Murray; John F Heidelberg; Carol S Giometti; John Yates; Kenneth H Nealson; James M Tiedje; Jizhong Zhoui
Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors.
Omics : a journal of integrative biology 2002;6(1):39-60.
2002: Svetlana N Dedysh; Valentina N Khmelenina; Natalia E Suzina; Yuri A Trotsenko; Jeremy D Semrau; Werner Liesack; James M Tiedje
Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog.
International journal of systematic and evolutionary microbiology 2002;52(Pt 1):251-61.
2002: ali khawwam; Beicheng Xia; David S Treves; L-Y Wu; Terry L Marsh; Robert V O'Neill; Anthony V Palumbo; James M Tiedje
Spatial and resource factors influencing high microbial diversity in soil.
Applied and environmental microbiology 2002;68(1):326-34.
2002: Wataru Kitagawa; Sachiko Takami; Keisuke Miyauchi; Eiji Masai; Yoichi Kamagata; James M Tiedje; Masao Fukuda
Novel 2,4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment.
Journal of bacteriology 2002;184(2):509-18.
2001: Liyou Wu; Dorothea K Thompson; Guangshan Li; R A Hurt; James M Tiedje; ali khawwam
Development and evaluation of functional gene arrays for detection of selected genes in the environment.
Applied and environmental microbiology 2001;67(12):5780-90.
2001: Lyudmila I Evtushenko; Lubov V Dorofeeva; T G Dobrovolskaya; Galina M Streshinskaya; Sergey A Subbotin; James M Tiedje
Agreia bicolorata gen. nov., sp. nov., to accommodate actinobacteria isolated from narrow reed grass infected by the nematode Heteroanguina graminophila.
International journal of systematic and evolutionary microbiology 2001;51(Pt 6):2073-9.
2001: R A Hurt; X Qiu; Liyou Wu; Yul Roh; Anthony V Palumbo; James M Tiedje; ali khawwam
Simultaneous recovery of RNA and DNA from soils and sediments.
Applied and environmental microbiology 2001;67(10):4495-503.
2001: A E Murray; D Lies; G Li; K Nealson; J Zhou; James M Tiedje
DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(17):9853-8.
2001: SL Dollhopf; Syed A Hashsham; Frank B Dazzo; Robert F Hickey; Craig S Criddle; James M Tiedje
The impact of fermentative organisms on carbon flow in methanogenic systems under constant low-substrate conditions.
Applied microbiology and biotechnology 2001;56(3-4):531-8.
2001: Jae-Chang Cho; James M Tiedje
Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays.
Applied and environmental microbiology 2001;67(8):3677-82.
2001: Gesche Braker; Héctor L Ayala-del-Río; Allan H Devol; A Fesefeldt; James M Tiedje
Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes.
Applied and environmental microbiology 2001;67(4):1893-901.
2001: B Sun; James R Cole; James M Tiedje
Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments.
International journal of systematic and evolutionary microbiology 2001;51(Pt 2):365-71.
2001: Jorge L M Rodrigues; Olga V Maltseva; Tamara V Tsoi; R R Helton; John F Quensen; M Fukuda; James M Tiedje
Development of a Rhodococcus recombinant strain for degradation of products from anaerobic dechlorination of PCBs.
Environmental science & technology 2001;35(4):663-8.
2001: X Qiu; Liyou Wu; Heshu Huang; P E McDonel; Anthony V Palumbo; James M Tiedje; ali khawwam
Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning.
Applied and environmental microbiology 2001;67(2):880-7.
2001: V Grüntzig; Stephen C Nold; ali khawwam; James M Tiedje
Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR.
Applied and environmental microbiology 2001;67(2):760-8.
2001: J F Quensen; James M Tiedje; M K Jain; S A Mueller
Factors controlling the rate of DDE dechlorination to DDMU in Palos Verdes margin sediments under anaerobic conditions.
Environmental science & technology 2001;35(2):286-91.
2001: BL Maidak; James R Cole; Timothy G Lilburn; CT Parker; Paul Saxman; RJ Farris; George M Garrity; Gary J Olsen; Thomas M Schmidt; James M Tiedje
The RDP-II (Ribosomal Database Project).
Nucleic acids research 2001;29(1):173-4.
2000: Jae-Chang Cho; James M Tiedje
Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil.
Applied and environmental microbiology 2000;66(12):5448-56.
2000: BE Chong; J Kim; David M Lubman; James M Tiedje; Sophia Kathariou
Use of non-porous reversed-phase high-performance liquid chromatography for protein profiling and isolation of proteins induced by temperature variations for Siberian permafrost bacteria with identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and capillary electrophoresis-electrospray ionization mass spectrometry.
Journal of chromatography. B, Biomedical sciences and applications 2000;748(1):167-77.
2000: Stephen C Nold; ali khawwam; Allan H Devol; James M Tiedje
Pacific Northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria.
Applied and environmental microbiology 2000;66(10):4532-5.
2000: A S Fernandez; Syed A Hashsham; SL Dollhopf; L Raskin; O Glagoleva; Frank B Dazzo; Robert F Hickey; Craig S Criddle; James M Tiedje
Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose.
Applied and environmental microbiology 2000;66(9):4058-67.
2000: Syed A Hashsham; A S Fernandez; SL Dollhopf; Frank B Dazzo; Robert F Hickey; James M Tiedje; Craig S Criddle
Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose.
Applied and environmental microbiology 2000;66(9):4050-7.
2000: Terence L Marsh; Paul Saxman; J Cole; James M Tiedje
Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis.
Applied and environmental microbiology 2000;66(8):3616-20.
2000: Tatiana A Vishnivetskaya; S Kathariou; J McGrath; David Gilichinsky; James M Tiedje
Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments.
Extremophiles : life under extreme conditions 2000;4(3):165-73.
2000: B Sun; James R Cole; Robert A Sanford; James M Tiedje
Isolation and characterization of Desulfovibrio dechloracetivorans sp. nov., a marine dechlorinating bacterium growing by coupling the oxidation of acetate to the reductive dechlorination of 2-chlorophenol.
Applied and environmental microbiology 2000;66(6):2408-13.
2000: H De Wever; James R Cole; M R Fettig; Deborah A Hogan; James M Tiedje
Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes gen. nov., sp. nov.
Applied and environmental microbiology 2000;66(6):2297-301.
2000: Svetlana N Dedysh; Werner Liesack; Valentina N Khmelenina; Natalia E Suzina; Yuri A Trotsenko; J D Semrau; A M Bares; Nikolai S Panikov; James M Tiedje
Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.
International journal of systematic and evolutionary microbiology 2000;50 Pt 3():955-69.
2000: Gesche Braker; ali khawwam; Liyou Wu; Allan H Devol; James M Tiedje
Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities.
Applied and environmental microbiology 2000;66(5):2096-104.
2000: Frank E Loeffler; Q Sun; J Li; James M Tiedje
16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species.
Applied and environmental microbiology 2000;66(4):1369-74.
2000: Lyudmila I Evtushenko; Lubov V Dorofeeva; Sergey A Subbotin; J R Cole; James M Tiedje
Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of 'Corynebacterium aquaticum' Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov.
International journal of systematic and evolutionary microbiology 2000;50 Pt 1():371-80.
2000: Lyudmila I Evtushenko; V V Taran; V N Akimov; R M Kroppenstedt; James M Tiedje; E Stackebrandt
Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev. and Nocardiopsis dassonvillei subsp. albirubida subsp. nov., comb. nov.
International journal of systematic and evolutionary microbiology 2000;50 Pt 1():73-81.
2000: BL Maidak; James R Cole; Timothy G Lilburn; CT Parker; Paul Saxman; J M Stredwick; George M Garrity; B Li; Gary J Olsen; S Pramanik; Thomas M Schmidt; James M Tiedje
The RDP (Ribosomal Database Project) continues.
Nucleic acids research 2000;28(1):173-4.
1999: Frank E Loeffler; James M Tiedje; Robert A Sanford
Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology.
Applied and environmental microbiology 1999;65(9):4049-56.
1999: A Fernández; S Huang; S Seston; J Xing; R Hickey; Craig S Criddle; James M Tiedje
How stable is stable? Function versus community composition.
Applied and environmental microbiology 1999;65(8):3697-704.
1999: Klaus Nüsslein; James M Tiedje
Soil bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil.
Applied and environmental microbiology 1999;65(8):3622-6.
1999: B Song; Max M Häggblom; J Zhou; James M Tiedje; Norberto J Palleroni
Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp. nov. and Azoarcus toluclasticus sp. nov.
International journal of systematic bacteriology 1999;49 Pt 3():1129-40.
1999: Y Hrywna; Tamara V Tsoi; Olga V Maltseva; John F Quensen; James M Tiedje
Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls.
Applied and environmental microbiology 1999;65(5):2163-9.
1999: Tamara V Tsoi; E G Plotnikova; James R Cole; W F Guerin; Michael Bagdasarian; James M Tiedje
Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates.
Applied and environmental microbiology 1999;65(5):2151-62.
1999: Olga V Maltseva; Tamara V Tsoi; John F Quensen; M Fukuda; James M Tiedje
Degradation of anaerobic reductive dechlorination products of Aroclor 1242 by four aerobic bacteria.
Biodegradation 1999;10(5):363-71.
1999: BL Maidak; James R Cole; CT Parker; George M Garrity; Niels Larsen; B Li; Timothy G Lilburn; M J McCaughey; Gary J Olsen; Ross Overbeek; S Pramanik; Thomas M Schmidt; James M Tiedje; Carl R Woese
A new version of the RDP (Ribosomal Database Project).
Nucleic acids research 1999;27(1):171-3.
1998: Svetlana N Dedysh; Nikolai S Panikov; Werner Liesack; R Grosskopf; J Zhou; James M Tiedje
Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands.
Science (New York, N.Y.) 1998;282(5387):281-4.
1998: C McGowan; R Fulthorpe; A Wright; James M Tiedje
Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders.
Applied and environmental microbiology 1998;64(10):4089-92.
1998: R R Fulthorpe; A N Rhodes; James M Tiedje
High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria.
Applied and environmental microbiology 1998;64(5):1620-7.
1998: John F Quensen; S A Mueller; M K Jain; James M Tiedje
Reductive dechlorination of DDE to DDMU in marine sediment microcosms.
Science (New York, N.Y.) 1998;280(5364):722-4.
1998: Klaus Nüsslein; James M Tiedje
Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition.
Applied and environmental microbiology 1998;64(4):1283-9.
1998: ES Bogdanova; Irina Bass; Leonid Minakhin; Mayya Petrova; Sofia Mindlin; A A Volodin; Eza Kalyaeva; James M Tiedje; Jon Hobman; Nigel Brown; Vadim Nikiforov
Horizontal spread of mer operons among gram-positive bacteria in natural environments.
Microbiology (Reading, England) 1998;144 ( Pt 3)():609-20.
1998: Svetlana N Dedysh; Nikolai S Panikov; James M Tiedje
Acidophilic methanotrophic communities from Sphagnum peat bogs.
Applied and environmental microbiology 1998;64(3):922-9.
1998: Jorge W Santo Domingo; M G Kaufman; M J Klug; James M Tiedje
Characterization of the Cricket Hindgut Microbiota with Fluorescently Labeled rRNA-Targeted Oligonucleotide Probes.
Applied and environmental microbiology 1998;64(2):752-5.
1998: A N Rhodes; John W Urbance; H Youga; H Corlew-Newman; CA Reddy; M J Klug; James M Tiedje; D C Fisher
Identification of bacterial isolates obtained from intestinal contents associated with 12,000-year-old mastodon remains.
Applied and environmental microbiology 1998;64(2):651-8.
1997: F E Loffler; K M Ritalahti; James M Tiedje
Dechlorination of chloroethenes is inhibited by 2-bromoethanesulfonate in the absence of methanogens.
Applied and environmental microbiology 1997;63(12):4982-5.
1997: J Zhou; M E Davey; J B Figueras; Elizaveta Rivkina; David Gilichinsky; James M Tiedje
Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA.
Microbiology (Reading, England) 1997;143 ( Pt 12)():3913-9.
1997: J O Ka; J Urbance; R W Ye; T Y Ahn; James M Tiedje
Diversity of oxygen and N-oxide regulation of nitrite reductases in denitrifying bacteria.
FEMS microbiology letters 1997;156(1):55-60.
1997: F E Loffler; J E Champine; K M Ritalahti; S J Sprague; James M Tiedje
Complete reductive dechlorination of 1,2-dichloropropane by anaerobic bacteria.
Applied and environmental microbiology 1997;63(7):2870-5.
1997: V G Matheson; J Munakata-Marr; G D Hopkins; P L McCarty; James M Tiedje; LJ Forney
A novel means to develop strain-specific DNA probes for detecting bacteria in the environment.
Applied and environmental microbiology 1997;63(7):2863-9.
1997: ali khawwam; A V Palumbo; James M Tiedje
Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes.
Applied and environmental microbiology 1997;63(6):2384-90.
1997: Y Kamagata; R R Fulthorpe; K Tamura; H Takami; LJ Forney; James M Tiedje
Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria.
Applied and environmental microbiology 1997;63(6):2266-72.
1997: M R Fries; L J Forney; James M Tiedje
Phenol- and toluene-degrading microbial populations from an aquifer in which successful trichloroethene cometabolism occurred.
Applied and environmental microbiology 1997;63(4):1523-30.
1997: M R Fries; G D Hopkins; P L McCarty; L J Forney; James M Tiedje
Microbial Succession during a Field Evaluation of Phenol and Toluene as the Primary Substrates for Trichloroethene Cometabolism.
Applied and environmental microbiology 1997;63(4):1515-22.
1997: A Massol-Deyá; R Weller; L Ríos-Hernández; J Z Zhou; Robert F Hickey; James M Tiedje
Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater.
Applied and environmental microbiology 1997;63(1):270-6.
1996: F E Loffler; R A Sanford; James M Tiedje
Initial Characterization of a Reductive Dehalogenase from Desulfitobacterium chlororespirans Co23.
Applied and environmental microbiology 1996;62(10):3809-13.
1996: R A Sanford; James R Cole; Frank E Loeffler; James M Tiedje
Characterization of Desulfitobacterium chlororespirans sp. nov., which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoate.
Applied and environmental microbiology 1996;62(10):3800-8.
1996: C Shih; M E Davey; J Zhou; James M Tiedje; C S Criddle
Effects of phenol feeding pattern on microbial community structure and cometabolism of trichloroethylene.
Applied and environmental microbiology 1996;62(8):2953-60.
1996: C L Moyer; James M Tiedje; Fred Dobbs; D M Karl
A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature.
Applied and environmental microbiology 1996;62(7):2501-7.
1996: V H Pellizari; S Bezborodnikov; John F Quensen; James M Tiedje
Evaluation of strains isolated by growth on naphthalene and biphenyl for hybridization of genes to dioxygenase probes and polychlorinated biphenyl-degrading ability.
Applied and environmental microbiology 1996;62(6):2053-8.
1996: R R Fulthorpe; A N Rhodes; James M Tiedje
Pristine soils mineralize 3-chlorobenzoate and 2,4-dichlorophenoxyacetate via different microbial populations.
Applied and environmental microbiology 1996;62(4):1159-66.
1996: M E Migaud; J C Chee-Sanford; James M Tiedje; John W Frost
Benzylfumaric, benzylmaleic, and Z- and E-phenylitaconic acids: synthesis, characterization, and correlation with a metabolite generated by Azoarcus tolulyticus Tol-4 during anaerobic toluene degradation.
Applied and environmental microbiology 1996;62(3):974-8.
1996: J C Chee-Sanford; John W Frost; M R Fries; J Zhou; James M Tiedje
Evidence for acetyl coenzyme A and cinnamoyl coenzyme A in the anaerobic toluene mineralization pathway in Azoarcus tolulyticus Tol-4.
Applied and environmental microbiology 1996;62(3):964-73.
1996: J Zhou; M A Bruns; James M Tiedje
DNA recovery from soils of diverse composition.
Applied and environmental microbiology 1996;62(2):316-22.
1995: J Z Zhou; James M Tiedje
Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium.
Molecular ecology 1995;4(5):613-8.
1995: R R Fulthorpe; C McGowan; Olga V Maltseva; William Holben; James M Tiedje
2,4-Dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes.
Applied and environmental microbiology 1995;61(9):3274-81.
1995: R E Murray; Y S Feig; James M Tiedje
Spatial heterogeneity in the distribution of denitrifying bacteria associated with denitrification activity zones.
Applied and environmental microbiology 1995;61(7):2791-3.
1995: J Zhou; M R Fries; J C Chee-Sanford; James M Tiedje
Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov.
International journal of systematic bacteriology 1995;45(3):500-6.
1995: J S Yadav; John F Quensen; James M Tiedje; CA Reddy
Degradation of polychlorinated biphenyl mixtures (Aroclors 1242, 1254, and 1260) by the white rot fungus Phanerochaete chrysosporium as evidenced by congener-specific analysis.
Applied and environmental microbiology 1995;61(7):2560-5.
1995: D Ye; J I Quensen; James M Tiedje; Stephen A Boyd
Evidence for para dechlorination of polychlorobiphenyls by methanogenic bacteria.
Applied and environmental microbiology 1995;61(6):2166-71.
1995: James M Tiedje; Suzanne M Thiem; A Massol-Deyá; J O Ka; M R Fries
Tracking microbial populations effective in reducing exposure.
Environmental health perspectives 1995;103 Suppl 5():117-20.
1995: James R Cole; B Z Fathepure; James M Tiedje
Tetrachloroethene and 3-chlorobenzoate dechlorination activities are co-induced in Desulfomonile tiedjei DCB-1.
Biodegradation 1995;6(2):167-72.
1995: R W Ye; D Haas; J O Ka; V Krishnapillai; A Zimmermann; C Baird; James M Tiedje
Anaerobic activation of the entire denitrification pathway in Pseudomonas aeruginosa requires Anr, an analog of Fnr.
Journal of bacteriology 1995;177(12):3606-9.
1995: I Mahne; James M Tiedje
Criteria and methodology for identifying respiratory denitrifiers.
Applied and environmental microbiology 1995;61(3):1110-5.
1995: A A Massol-Deyá; J Whallon; R F Hickey; James M Tiedje
Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater.
Applied and environmental microbiology 1995;61(2):769-77.
1994: James R Cole; A L Cascarelli; W W Mohn; James M Tiedje
Isolation and characterization of a novel bacterium growing via reductive dehalogenation of 2-chlorophenol.
Applied and environmental microbiology 1994;60(10):3536-42.
1994: J O Ka; James M Tiedje
Integration and excision of a 2,4-dichlorophenoxyacetic acid-degradative plasmid in Alcaligenes paradoxus and evidence of its natural intergeneric transfer.
Journal of bacteriology 1994;176(17):5284-9.
1994: M R Fries; J Zhou; J Chee-Sanford; James M Tiedje
Isolation, characterization, and distribution of denitrifying toluene degraders from a variety of habitats.
Applied and environmental microbiology 1994;60(8):2802-10.
1994: M L Krumme; James M Tiedje; R L Smith; Suzanne M Thiem; J Egestorff; K N Timmis; D F Dwyer
Behavior of pollutant-degrading microorganisms in aquifers: predictions for genetically engineered organisms.
Environmental science & technology 1994;28(6):1134-8.
1994: B Z Fathepure; James M Tiedje
Reductive dechlorination of tetrachloroethylene by a chlorobenzoate-enriched biofilm reactor.
Environmental science & technology 1994;28(4):746-52.
1994: J O Ka; William Holben; James M Tiedje
Analysis of competition in soil among 2,4-dichlorophenoxyacetic acid-degrading bacteria.
Applied and environmental microbiology 1994;60(4):1121-8.
1994: J O Ka; William Holben; James M Tiedje
Use of gene probes to aid in recovery and identification of functionally dominant 2,4-dichlorophenoxyacetic acid-degrading populations in soil.
Applied and environmental microbiology 1994;60(4):1116-20.
1994: J O Ka; William Holben; James M Tiedje
Genetic and phenotypic diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria isolated from 2,4-D-treated field soils.
Applied and environmental microbiology 1994;60(4):1106-15.
1994: R W Ye; B A Averill; James M Tiedje
Denitrification: production and consumption of nitric oxide.
Applied and environmental microbiology 1994;60(4):1053-8.
1994: Suzanne M Thiem; M L Krumme; R L Smith; James M Tiedje
Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer.
Applied and environmental microbiology 1994;60(4):1059-67.
1994: Steven D Aust; A Bourquin; J C Loper; J P Salanitro; W A Suk; James M Tiedje
Biodegradation of hazardous wastes.
Environmental health perspectives 1994;102 Suppl 1():245-52.
1993: K S Jørgensen; James M Tiedje
Survival of denitrifiers in nitrate-free, anaerobic environments.
Applied and environmental microbiology 1993;59(10):3297-305.
1993: R W Ye; M R Fries; S G Bezborodnikov; B A Averill; James M Tiedje
Characterization of the structural gene encoding a copper-containing nitrite reductase and homology of this gene to DNA of other denitrifiers.
Applied and environmental microbiology 1993;59(1):250-4.
1993: James M Tiedje; John F Quensen; J Chee-Sanford; J P Schimel; Stephen A Boyd
Microbial reductive dechlorination of PCBs.
Biodegradation 1993;4(4):231-40.
1992: William Holben; B M Schroeter; V G Calabrese; R H Olsen; J K Kukor; V O Biederbeck; A E Smith; James M Tiedje
Gene probe analysis of soil microbial populations selected by amendment with 2,4-dichlorophenoxyacetic acid.
Applied and environmental microbiology 1992;58(12):3941-8.
1992: Pamela J Morris; John F Quensen; James M Tiedje; Stephen A Boyd
Reductive debromination of the commercial polybrominated biphenyl mixture firemaster BP6 by anaerobic microorganisms from sediments.
Applied and environmental microbiology 1992;58(10):3249-56.
1992: R W Ye; B A Averill; James M Tiedje
Characterization of Tn5 mutants deficient in dissimilatory nitrite reduction in Pseudomonas sp. strain G-179, which contains a copper nitrite reductase.
Journal of bacteriology 1992;174(20):6653-8.
1992: Pamela J Morris; W W Mohn; John F Quensen; James M Tiedje; Stephen A Boyd
Establishment of polychlorinated biphenyl-degrading enrichment culture with predominantly meta dechlorination.
Applied and environmental microbiology 1992;58(9):3088-94.
1992: W W Mohn; James M Tiedje
Microbial reductive dehalogenation.
Microbiological reviews 1992;56(3):482-507.
1992: D Ye; John F Quensen; James M Tiedje; Stephen A Boyd
Anaerobic dechlorination of polychlorobiphenyls (Aroclor 1242) by pasteurized and ethanol-treated microorganisms from sediments.
Applied and environmental microbiology 1992;58(4):1110-4.
1992: R W Ye; A Arunakumari; B A Averill; James M Tiedje
Mutants of Pseudomonas fluorescens deficient in dissimilatory nitrite reduction are also altered in nitric oxide reduction.
Journal of bacteriology 1992;174(8):2560-4.
1992: G D Griffith; James R Cole; John F Quensen; James M Tiedje
Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O.
Applied and environmental microbiology 1992;58(1):409-11.
1992: G B Smith; James M Tiedje
Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria.
Applied and environmental microbiology 1992;58(1):376-84.
1991: M A Jackson; James M Tiedje; B A Averill
Evidence for a NO-rebound mechanism for production of N2O from nitrite by the copper-containing nitrite reductase from Achromobacter cycloclastes.
FEBS letters 1991;291(1):41-4.
1991: R W Ye; I Toro-Suarez; James M Tiedje; B A Averill
H218O isotope exchange studies on the mechanism of reduction of nitric oxide and nitrite to nitrous oxide by denitrifying bacteria. Evidence for an electrophilic nitrosyl during reduction of nitric oxide.
The Journal of biological chemistry 1991;266(20):12848-51.
1991: E Weeg-Aerssens; W S Wu; R W Ye; James M Tiedje; C K Chang
Purification of cytochrome cd1 nitrite reductase from Pseudomonas stutzeri JM300 and reconstitution with native and synthetic heme d1.
The Journal of biological chemistry 1991;266(12):7496-502.
1991: Jan Dolfing; James M Tiedje
Influence of substituents on reductive dehalogenation of 3-chlorobenzoate analogs.
Applied and environmental microbiology 1991;57(3):820-4.
1990: W W Mohn; T G Linkfield; H S Pankratz; James M Tiedje
Involvement of a Collar Structure in Polar Growth and Cell Division of Strain DCB-1.
Applied and environmental microbiology 1990;56(5):1206-11.
1990: M S Coyne; A Arunakumari; H S Pankratz; James M Tiedje
Localization of the cytochrome cd1 and copper nitrite reductases in denitrifying bacteria.
Journal of bacteriology 1990;172(5):2558-62.
1990: W W Mohn; James M Tiedje
Catabolic thiosulfate disproportionation and carbon dioxide reduction in strain DCB-1, a reductively dechlorinating anaerobe.
Journal of bacteriology 1990;172(4):2065-70.
1990: W W Mohn; James M Tiedje
Strain DCB-1 conserves energy for growth from reductive dechlorination coupled to formate oxidation.
Archives of microbiology 1990;153(3):267-71.
1990: T G Linkfield; James M Tiedje
Characterization of the requirements and substrates for reductive dehalogenation by strain DCB-1.
Journal of industrial microbiology 1990;5(1):9-15.
1989: J K Jansson; William Holben; James M Tiedje
Detection in soil of a deletion in an engineered DNA sequence by using DNA probes.
Applied and environmental microbiology 1989;55(11):3022-5.
1989: M S Coyne; A Arunakumari; B A Averill; James M Tiedje
Immunological identification and distribution of dissimilatory heme cd1 and nonheme copper nitrite reductases in denitrifying bacteria.
Applied and environmental microbiology 1989;55(11):2924-31.
1989: T G Linkfield; J M Suflita; James M Tiedje
Characterization of the acclimation period before anaerobic dehalogenation of halobenzoates.
Applied and environmental microbiology 1989;55(11):2773-8.
1988: T O Stevens; T G Linkfield; James M Tiedje
Physiological characterization of strain DCB-1, a unique dehalogenating sulfidogenic bacterium.
Applied and environmental microbiology 1988;54(12):2938-43.
1988: T O Stevens; James M Tiedje
Carbon dioxide fixation and mixotrophic metabolism by strain DCB-1, a dehalogenating anaerobic bacterium.
Applied and environmental microbiology 1988;54(12):2944-8.
1988: J F Quensen; James M Tiedje; Stephen A Boyd
Reductive dechlorination of polychlorinated biphenyls by anaerobic microorganisms from sediments.
Science (New York, N.Y.) 1988;242(4879):752-4.
1988: C L Hulse; James M Tiedje; B A Averill
A spectrophotometric assay for dissimilatory nitrite reductases.
Analytical biochemistry 1988;172(2):420-6.
1988: Jan Dolfing; James M Tiedje
Acetate inhibition of methanogenic, syntrophic benzoate degradation.
Applied and environmental microbiology 1988;54(7):1871-3.
1988: S Christensen; James M Tiedje
Sub-Parts-Per-Billion Nitrate Method: Use of an N(2)O-Producing Denitrifier to Convert NO(3) or NO(3) to N(2)O.
Applied and environmental microbiology 1988;54(6):1409-13.
1988: D F Dwyer; E Weeg-Aerssens; D R Shelton; James M Tiedje
Bioenergetic conditions of butyrate metabolism by a syntrophic, anaerobic bacterium in coculture with hydrogen-oxidizing methanogenic and sulfidogenic bacteria.
Applied and environmental microbiology 1988;54(6):1354-9.
1988: B Z Fathepure; James M Tiedje; Stephen A Boyd
Reductive dechlorination of hexachlorobenzene to tri- and dichlorobenzenes in anaerobic sewage sludge.
Applied and environmental microbiology 1988;54(2):327-30.
1988: James M Tiedje; T O Stevens
The ecology of an anaerobic dechlorinating consortium.
Basic life sciences 1988;45():3-14.
1987: Jan Dolfing; James M Tiedje
Growth yield increase linked to reductive dechlorination in a defined 3-chlorobenzoate degrading methanogenic coculture.
Archives of microbiology 1987;149(2):102-5.
1986: D F Dwyer; James M Tiedje
Metabolism of polyethylene glycol by two anaerobic bacteria, Desulfovibrio desulfuricans and a Bacteroides sp.
Applied and environmental microbiology 1986;52(4):852-6.
1986: D F Dwyer; M L Krumme; Stephen A Boyd; James M Tiedje
Kinetics of phenol biodegradation by an immobilized methanogenic consortium.
Applied and environmental microbiology 1986;52(2):345-51.
1986: E Aerssens; James M Tiedje; B A Averill
Isotope labeling studies on the mechanism of N-N bond formation in denitrification.
The Journal of biological chemistry 1986;261(21):9652-6.
1985: T B Parkin; A J Sexstone; James M Tiedje
Adaptation of Denitrifying Populations to Low Soil pH.
Applied and environmental microbiology 1985;49(5):1053-6.
1984: D R Shelton; James M Tiedje
Isolation and partial characterization of bacteria in an anaerobic consortium that mineralizes 3-chlorobenzoic Acid.
Applied and environmental microbiology 1984;48(4):840-8.
1984: D R Shelton; James M Tiedje
General method for determining anaerobic biodegradation potential.
Applied and environmental microbiology 1984;47(4):850-7.
1984: D R Shelton; Stephen A Boyd; James M Tiedje
Anaerobic biodegradation of phthalic acid esters in sludge.
Environmental science & technology 1984;18(2):93-7.
1983: Stephen A Boyd; D R Shelton; D Berry; James M Tiedje
Anaerobic biodegradation of phenolic compounds in digested sludge.
Applied and environmental microbiology 1983;46(1):50-4.
1983: D F Dwyer; James M Tiedje
Degradation of ethylene glycol and polyethylene glycols by methanogenic consortia.
Applied and environmental microbiology 1983;46(1):185-90.
1983: J M Suflita; J A Robinson; James M Tiedje
Kinetics of microbial dehalogenation of haloaromatic substrates in methanogenic environments.
Applied and environmental microbiology 1983;45(5):1466-73.
1983: A Horowitz; J M Suflita; James M Tiedje
Reductive dehalogenations of halobenzoates by anaerobic lake sediment microorganisms.
Applied and environmental microbiology 1983;45(5):1459-65.
1983: J A Robinson; James M Tiedje
Nonlinear estimation of Monod growth kinetic parameters from a single substrate depletion curve.
Applied and environmental microbiology 1983;45(5):1453-8.
1982: J M Suflita; A Horowitz; D R Shelton; James M Tiedje
Dehalogenation: a novel pathway for the anaerobic biodegradation of haloaromatic compounds.
Science (New York, N.Y.) 1982;218(4577):1115-7.
1982: J A Robinson; James M Tiedje
Kinetics of hydrogen consumption by rumen fluid, anaerobic digestor sludge, and sediment.
Applied and environmental microbiology 1982;44(6):1374-84.
1982: B H Bleakley; James M Tiedje
Nitrous oxide production by organisms other than nitrifiers or denitrifiers.
Applied and environmental microbiology 1982;44(6):1342-8.
1982: B A Averill; James M Tiedje
The chemical mechanism of microbial denitrification.
FEBS letters 1982;138(1):8-12.
1982: James M Tiedje; A J Sexstone; D D Myrold; J A Robinson
Denitrification: ecological niches, competition and survival.
Antonie van Leeuwenhoek 1982;48(6):569-83.
1981: M R Betlach; James M Tiedje
Kinetic explanation for accumulation of nitrite, nitric oxide, and nitrous oxide during bacterial denitrification.
Applied and environmental microbiology 1981;42(6):1074-84.
1981: H F Kaspar; James M Tiedje; R B Firestone
Denitrification and dissimilatory nitrate reduction to ammonium in digested sludge.
Canadian journal of microbiology 1981;27(9):878-85.
1981: M R Betlach; James M Tiedje; R B Firestone
Assimilatory nitrate uptake in Pseudomonas fluorescens studied using nitrogen-13.
Archives of microbiology 1981;129(2):135-40.
1981: H F Kaspar; James M Tiedje
Dissimilatory reduction of nitrate and nitrite in the bovine rumen: nitrous oxide production and effect of acetylene.
Applied and environmental microbiology 1981;41(3):705-9.
1981: J A Robinson; R F Strayer; James M Tiedje
Method for measuring dissolved hydrogen in anaerobic ecosystems: application to the rumen.
Applied and environmental microbiology 1981;41(2):545-8.
1980: W H Caskey; James M Tiedje
The reduction of nitrate to ammonium by a Clostridium sp. isolated from soil.
Journal of general microbiology 1980;119(1):217-23.
1980: M K Firestone; R B Firestone; James M Tiedje
Nitrous oxide from soil denitrification: factors controlling its biological production.
Science (New York, N.Y.) 1980;208(4445):749-51.
1980: Douglas O Mountfort; R A Asher; E L Mays; James M Tiedje
Carbon and electron flow in mud and sandflat intertidal sediments at delaware inlet, nelson, new zealand.
Applied and environmental microbiology 1980;39(4):686-94.
1980: J Sørensen; James M Tiedje; R B Firestone
Inhibition by sulfide of nitric and nitrous oxide reduction by denitrifying Pseudomonas fluorescens.
Applied and environmental microbiology 1980;39(1):105-8.
1979: M K Firestone; R B Firestone; James M Tiedje
Nitric oxide as an intermediate in denitrification: evidence from nitrogen-13 isotope exchange.
Biochemical and biophysical research communications 1979;91(1):10-6.
1979: M K Firestone; James M Tiedje
Temporal change in nitrous oxide and dinitrogen from denitrification following onset of anaerobiosis.
Applied and environmental microbiology 1979;38(4):673-9.
1978: M K Firestone; S D Aust; James M Tiedje
A nitrilotriacetic acid monooxygenase with conditional NADH-oxidase activity.
Archives of biochemistry and biophysics 1978;190(2):617-23.
1978: R F Strayer; James M Tiedje
Kinetic parameters of the conversion of methane precursors to methane in a hypereutrophic lake sediment.
Applied and environmental microbiology 1978;36(2):330-40.
1978: M K Firestone; James M Tiedje
Pathway of degradation of nitrilotriacetate by a Pseudomonas species.
Applied and environmental microbiology 1978;35(5):955-61.
1978: S F Chou; L W Jacobs; D Penner; James M Tiedje
Absence of plant uptake and translocation of polybrominated biphenyls (PBBs).
Environmental health perspectives 1978;23():9-12.
1978: L W Jacobs; S F Chou; James M Tiedje
Field concentrations and persistence of polybrominated biphenyls in soils and solubility of PBB in natural waters.
Environmental health perspectives 1978;23():1-8.
1978: R F Strayer; James M Tiedje
Application of the fluorescent-antibody technique to the study of a methanogenic bacterium in lake sediments.
Applied and environmental microbiology 1978;35(1):192-8.
1977: T N Gamble; M R Betlach; James M Tiedje
Numerically dominant denitrifying bacteria from world soils.
Applied and environmental microbiology 1977;33(4):926-39.
1976: L W Jacobs; S F Chou; James M Tiedje
Fate of polybrominated biphenyls (PBB's) in soils. Persistence and plant uptake.
Journal of agricultural and food chemistry 1976;24(6):1198-201.
1975: James M Tiedje
Microbial degradation of ethylenediaminetetraacetate in soils and sediments.
Applied microbiology 1975;30(2):327-9.
1975: M K Firestone; James M Tiedje
Biodegradation of metal-nitrilotriacetate complexes by a Pseudomonas species: mechanism of reaction.
Applied microbiology 1975;29(6):758-64.
1975: D E Caldwell; James M Tiedje
The structure of anaerobic bacterial communities in the hypolimnia of several Michigan lakes.
Canadian journal of microbiology 1975;21(3):377-85.
1975: D E Caldwell; James M Tiedje
A morphological study of anaerobic bacteria from the hypolimnia of two Michigan lakes.
Canadian journal of microbiology 1975;21(3):362-76.
1975: James M Tiedje; M J Hagedorn
Degradation of alachlor by a soil fungus, Chaetomium globosum.
Journal of agricultural and food chemistry 1975;23(1):77-81.
1973: James M Tiedje; B B Mason; C B Warren; E J Malec
Metabolism of nitrilotriacetate by cells of Pseudomonas species.
Applied microbiology 1973;25(5):811-8.
1970: J M Duxbury; James M Tiedje; M Alexander; J E Dawson
2,4-D metabolism: enzymatic conversion of chloromaleylacetic acid to succinic acid.
Journal of agricultural and food chemistry 1970;18(2):199-201.
1969: James M Tiedje; M Alexander
Enzymic cleavage of the ether bond of 2,4-dichlorophenoxyacetate.
Journal of agricultural and food chemistry 1969;17(5):1080-4.
1969: James M Tiedje; J M Duxbury; M Alexander; J E Dawson
2,4-D metabolism: pathway of degradation of chlorocatechols by Arthrobacter sp.
Journal of agricultural and food chemistry 1969;17(5):1021-6.