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National Institute of Environmental Health Sciences

 

Person Details

Superfund Research Program

James M. Tiedje

Michigan State University
Center for Microbial Ecology
1066 Bogue Street, Room 540E
Plant and Soil Sciences Building
East Lansing, MI 48824
Phone: 517-353-9021 x1287
Fax: 517-353-2917
Email:

Projects

Research Briefs

Hazardous Waste Sites

Allied Paper, Inc./Portage Creek/Kalamazoo

  • Michigan State University: Molecular Insight into Polyaromatic Toxicant Degradation by Microbial Communities

HS7 and HS28

  • Michigan State University: Molecular Insight into Polyaromatic Toxicant Degradation by Microbial Communities

Mississinewia River

  • Michigan State University: Molecular Insight into Polyaromatic Toxicant Degradation by Microbial Communities

Picatinny Arsenal (USARMY)

  • Michigan State University: Molecular Insight into Polyaromatic Toxicant Degradation by Microbial Communities

Woods Pond

  • Michigan State University: Molecular Insight into Polyaromatic Toxicant Degradation by Microbial Communities

Publications

2014
  • Cole, James R. and James M. Tiedje. 2014. History and impact of RDP: A legacy from Carl Woese to microbiology. RNA Biology. 11(3):239-243. doi:10.4161/rna.28306  
  • Cole, James R., Qiong Wang, Jordan A. Fish, Benli Chai, Donna M. McGarrell, Yanni Sun, C Titus Brown, Andrea Porras-Alfaro, Cheryl R. Kuske, and James M. Tiedje. 2014. Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Research.   42(D1):D633-D642. doi:10.1093/nar/gkt1244  
2013
  • Fish, Jordan A., Benli Chai, Qiong Wang, Yanni Sun, C Titus Brown, James M. Tiedje, and James R. Cole. 2013. FunGene: The functional gene pipeline and repository. Frontiers in Microbiology. 4:291. doi:10.3389/fmicb.2013.00291  
  • Penton, C Ryan, Timothy A. Johnson, John F. Quensen, Shoko Iwai, James R. Cole, and James M. Tiedje. 2013. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: Primers and processing matter. Frontiers in Microbiology. 4:279. doi:10.3389/fmicb.2013.00279  
2012
  • Baushke, Samuel W., Robert D. Stedtfeld, Dieter M. Tourlousse, Farhan Ahmad, Lukas M. Wick, Erdogan Gulari, James M. Tiedje, and Syed A. Hashsham. 2012. Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves. Journal of Microbiological Methods.   90(1):29-35. doi:10.1016/j.mimet.2012.04.003  
2011
2010
  • Iwai, Shoko, Benli Chai, Woo Jun Sul, James R. Cole, Syed A. Hashsham, and James M. Tiedje. 2010. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. The ISME Journal: Multidisciplinary Journal of Microbial Ecology.   4(2):279-285. doi:10.1038/ismej.2009.104  
  • Parnell, J.Jacob, Vincent J. Denef, Joonhong Park, Tamara V. Tsoi, and James M. Tiedje. 2010. 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.   21(1):147-156. doi:10.1007/s10532-009-9289-4  
2009
  • Sul, Woo Jun, Joonhong Park, John F. Quensen, Jorge M. Rodrigues, Laurie Seliger, Tamara V. Tsoi, Gerben J. Zylstra, and James M. Tiedje. 2009. DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Applied and Environmental Microbiology.   75(17):5501-6. doi:10.1128/AEM.00121-09  
2008
2007
  • Leigh, Mary B., Vivian H. Pellizari, Ondrej Uhlik, Robin Sutka, Jorge M. Rodrigues, Nathaniel Ostrom, Jizhong Zhou, and James M. Tiedje. 2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). The ISME Journal: Multidisciplinary Journal of Microbial Ecology.   1(2):134-48.
2006
  • Chain, Patrick SG, Vincent J. Denef, Konstantinos T. Konstantinidis, Lisa M. Vergez, Loreine Agullo, Valeria Latorre Reyes, Loren Hauser, Macarena Cordova, Luis Gomez, Myriam Gonzalez, Miriam Land, Victoria Lao, Frank W. Larimer, John J. LiPuma, Eshwar Mahenthiralingam, Stephanie A. Malfatti, Christopher J. Marx, J. Jacob Parnell, Alban Ramette, Paul M. Richardson, Michael Seeger, Daryl Smith, Theodore Spilker, Woo Jun Sul, Tamara V. Tsoi, Luke E. Ulrich, Igor B. Zhulin, and James M. Tiedje. 2006. 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 (PNAS).   103(42):15280-7.
  • Parnell, J.Jacob, Joonhong Park, Vincent J. Denef, Tamara V. Tsoi, Syed A. Hashsham, John F. Quensen, and James M. Tiedje. 2006. Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress. Applied and Environmental Microbiology.   72(10):6607-14.
2004
  • Denef, Vincent J., Joonhong Park, Tamara V. Tsoi, Jean Marie Rouillard, H. Zhang, Jamie A. Wibbenmeyer, Willy Verstraete, Erdogan Gulari, Syed A. Hashsham, and James M. Tiedje. 2004. Biphenyl and benzoate metabolism in a genomic context: Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Applied and Environmental Microbiology.   70(8):4961-4970.
  • Goris, Johan, Paul De Vos, Jesus Caballero-Mellado, Joonhong Park, Enevold Falsen, John F. Quensen, James M. Tiedje, and Peter Vandamme. 2004. Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400(T) and relatives as Burkholderia xenovorans sp nov. International Journal of Systematic and Evolutionary Microbiology.   54(5):1677-1681.
  • Tiedje, James M. and Konstantinos T. Konstantinidis. 2004. 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 (PNAS).   101(9):3160-3165.
2003
  • Denef, Vincent J., Joonhong Park, Jorge M. Rodrigues, Tamara V. Tsoi, Syed A. Hashsham, and James M. Tiedje. 2003. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environmental Microbiology.   5(10):933-943.
  • Park, Joonhong, Hongxia Li, and James M. Tiedje. 2003. Determination of gene-dependent sorption of DNA on clays using a microarray technique. In: Proceedings of the 103rd General Meeting of the American Society for Microbiology, May 18-22. Washington, DC.
  • Park, Joonhong, Andrew Ramsburg, Linda M. Abriola, and James M. Tiedje. 2003. Biofilm-associated utilization of biphenyl on organo-coated sand by Burkholderia sp. LB400. In: Proceedings of the General Meeting, American Society for Microbiology, May 23-27. New Orleans, LA.
  • Tiedje, James M. 2003. Molecular windows into microbial communities. In: Proceedings of the International Meeting of the Federation of Korean Microbiological Societies. October 24-25. College of Science, Yonsei University, Seoul, Korea, Republic Of.
  • Tiedje, James M. 2003. Molecular windows into microbial communities. In: Proceedings of the International Meeting of the Federation of Korean Microbiological Societies. October 24-25. College of Science, Yonsei University, Seoul, Korea, Republic Of.
2002
  • Dybas, Michael J., David W. Hyndman, Robert Heine, James M. Tiedje, Katrina D. Linning, David Wiggert, Thomas C. Voice, Xianda Zhao, Leslie Dybas, and Craig S. Criddle. 2002. Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation. Environmental Science & Technology.   36(16):3635-3644.
2001
  • Rodrigues, Jorge M., Olga V. Maltseva, Tamara V. Tsoi, Rebekah R. Helton, John F. Quensen, Masao Fukuda, and James M. Tiedje. 2001. Development of a Rhodococcus recombinant strain for degradation products from anaerobic dechlorination of PCBs. Environmental Science & Technology.   35(4):663-668.
2000
  • Hyndman, David W., Michael J. Dybas, L. Forney, Robert Heine, T. Mayotte, Mantha S. Phanikumar, G. Tatara, James M. Tiedje, Thomas C. Voice, Roger B. Wallace, David Wiggert, Xueying Zhao, and Craig S. Criddle. 2000. Hydraulic characterization and design of a full-scale biocurtain. Ground Water.   38(3):462-474.
  • Maltseva, Olga V., Jorge M. Rodrigues, John F. Quensen, Tamara V. Tsoi, and James M. Tiedje. 2000. Growth of Burkholderia sp. LB400 and recombinant LH400(ohb) on simulated anaerobic dechlorination products from Aroclor 1242. In: Proceedings of the American Society for Microbiology 100th general meeting. pp.149.
  • Maltseva, Olga V., Tamara V. Tsoi, John F. Quensen, Masao Fukuda, and James M. Tiedje. 2000. Degradation of anaerobic reductive chlorination products of Aroclor 1242 by four aerobic bacteria. Biodegradation.   10:363-371.
  • Quensen, John F., Tamara V. Tsoi, Olga V. Maltseva, Jorge M. Rodrigues, M.J. Zwiernik, and James M. Tiedje. 2000. Strategies for the anaerobic/aerobic biotreatment of polychlorinated biphenyls. In: Proceedings of the Society of Environmental Toxicology and Chemistry, 21st Annual Meeting, 12-16 November. Nashville, TN. pp.56.
  • Rodrigues, Jorge M., M.R. Aiello, Olga V. Maltseva, Tamara V. Tsoi, and James M. Tiedje. 2000. A flourescent PCR-based method to quantify the recombinant Rhodococcus sp. strain RHA1 in soil. In: Proceedings of the American Society for Microbiology, 100th General Meeting, 21-25 May. Los Angeles, CA. pp.170.
  • Tiedje, James M. 2000. Putting novel microbes to work on industry wastes. In: Proceedings of the Symposium for Japan Bioindustry Association. pp.47-54.
  • Tsoi, Tamara V., J.R. Cole, S. Rech, and James M. Tiedje. 2000. Molecular Analysis Implicates Existence Of Two Differing Mechanisms Of Aryl Reductive Ortho-Dehalogenation In Coryneform Bacterium Strain KZ-4. In: Proceedings of the American Society for Microbiology 100th general meeting.
1999
  • Hrywna, Y., Tamara V. Tsoi, Olga V. Maltseva, John F. Quensen, and James M. Tiedje. 1999. Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls. Applied and Environmental Microbiology.   65(5):2163-2169.
  • Tsoi, Tamara V., J.R. Cole, Olga V. Maltseva, S. Rech, John F. Quensen, Jorge M. Rodrigues, J. Spain, and James M. Tiedje. 1999. Promiscuous Dehalogenating Dioxygenase (ISP) From Pseudomonas aeruginosa 142: Evolutionary Model And Metabolic Engineering Tool. In: Proceedings of the International Symposium Pseudomonas. Maui, HI.
  • Tsoi, Tamara V., E.G. Plotnikova, J.R. Cole, W.F. Guerin, M. Bagdasarian, and James M. Tiedje. 1999. Cloning, expression and nucleotide sequence of the Pseudomonas aeruginosa strain 142 ohb genes coding for oxygenolytic ortho-dehalogenation of halobenzoates. Applied and Environmental Microbiology.   65(5):2151-2162.
  • Urbance, J.W., Jerome J. Kukor, and James M. Tiedje. 1999. Analysis of the phylogenetic distribution of biodegradative bacteria. In: Proceedings of the International Symposium Pseudomonas. Maui, HI.
  • Ye, D., John F. Quensen, James M. Tiedje, and Stephen A. Boyd. 1999. 2-Bromoethanesulfonate, sulfate, molybdate, and ethanesulfonate inhibit anaerobic dechlorination of polychlorobiphenyls by pasteurized microorganisms. Applied and Environmental Microbiology.   65:327-329.
  • Zhou, Jizhong and James M. Tiedje. 1999. Development of phylogenetic probes specific to Burkholderia cepacia G4. In: Proceedings of the International In Situ and On-site Bioreclamation Symposium. San Diego, CA. pp.65-75.
1998
  • Dybas, Michael J., Michael Joseph Barcelona, S. Bezborodnikov, S. Davies, L. Forney, O. Kawka, T. Mayotte, Lycely del C Sepulveda-Torres, K. Smalla, M. Sneathen, James M. Tiedje, Thomas C. Voice, David Wiggert, Michael E. Witt, and Craig S. Criddle. 1998. Pilot-scale evaluation of bioaugmentation for in situ remediation of a carbon tetrachloride-contaminated aquifer. Environmental Science & Technology.   32(22):3598-3611.
  • Maltseva, Olga V., John F. Quensen, Tamara V. Tsoi, and James M. Tiedje. 1998. Intermediate products recently discovered to accumulate during the aerobic degradation of PCB congeners formed from anaerobic dechlorination of Aroclor 1242. In: Proceedings Superfund Basic Research Program: A Decade of Improving Health through Multi-Disciplinary Research. Chapel Hill, NC. pp.92.
1997
  • Massol-Deya, A., R. Weller, L. Rios-Hernandez, Jizhong Zhou, R.F. Hickey, and James M. Tiedje. 1997. Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Applied and Environmental Microbiology.   63(1):270-276.
  • Quensen, John F. and James M. Tiedje. 1997. Evaluation of PCB Dechlorination in Sediments. In: Methods in Biotechnology, V. 2: Bioremediation Protocols. Humana Press Inc, Totowa, NJ.
  • Zhou, J., A.V. Palumbo, and James M. Tiedje. 1997. Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes. Applied and Environmental Microbiology.   63(6):2384-2390.
1996
  • Chee-Sanford, J.C., J.W. Frost, M.R. Fries, Jizhong Zhou, and James M. Tiedje. 1996. Evidence for acetyl coenzyme A and cinnamoyl coenzyme A in the anaerobic toluene mineralization pathway in Azoarcus tolulyticus Tol-4. Applied and Environmental Microbiology.   62(3):964-973.
  • Migaud, M.E., J.C. Chee-Sanford, James M. Tiedje, and J.W. Frost. 1996. Benzylfumaric, benzylmaleic, Z- and E-phenylitaconic acids: synthesis, characterization and correlation with a metabolite generated by Azoarcus tolulyticus strain Tol-4 during anaerobic toluene degradation. Applied and Environmental Microbiology.   62(3):974-978.
  • Zhou, Jizhong, Mary Ann Bruns, and James M. Tiedje. 1996. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology.   62:316-322.
1995
  • Tiedje, James M. 1995. New advances and challenges for bioremediation. In: Proceedings of Bioremediation: The Tokyo 1994 Workshop, OECD (Organisation for Economic Co-Operation and Development). Paris, France. pp.81-87.
  • Tiedje, James M., R.A. Sanford, and A. Massol-Deya. 1995. Advantages and disadvantages of consortia in bioremediation. In: Proceedings of Bioremediation: The Tokyo 1994 Workshop, OECD (Organisation for Economic Co-Operation and Development). Paris, France. pp.357-367.
  • Tiedje, James M., S.M. Thiem, A. Massol-Deya, J.O. Ka, and M.R. Fries. 1995. Tracking microbial populations effective in reducing exposure. Environmental Health Perspectives. 103(supp.5):117-120.
  • Zhou, Jizhong, M.R. Fries, J.C. Chee-Sanford, and James M. Tiedje. 1995. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov. International Journal of Systemic Bacteriology.   45(3):500-506.
  • Zhou, Jizhong and James M. Tiedje. 1995. Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium. Molecular Ecology.   4(5):613-618.

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