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Person Details: James M. Tiedje

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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, Michigan 48824
Phone: 517-353-9021 x1287
Fax: 517-353-2917


Research Briefs

Hazardous Waste Sites

Allied Paper, Inc./Portage Creek/Kalamazoo

  • Invalid project

HS7 and HS28

  • Invalid project

Mississinewia River

  • Invalid project

Picatinny Arsenal (USARMY)

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Woods Pond

  • Invalid project




  • Chai B, Tsoi TV, Sallach JB, Liu C, Landgraf J, Bezdek M, Zylstra GJ, Li H, Johnston CT, Teppen BJ, Cole JR, Boyd SA, Tiedje JM. 2020. Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression. Sci Total Environ 712:135525. doi:10.1016/j.scitotenv.2019.135525 PMID:32050392



  • Stedtfeld RD, Guo X, Stedtfeld TM, Sheng H, Williams MR, Hauschild K, Gunturu S, Tift L, Wang F, Howe A, Chai B, Yin D, Cole JR, Tiedje JM, Hashsham SA. 2018. Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements. FEMS Microbiol Ecol 94(9):8. doi:10.1093/femsec/fiy130 PMID:52926
  • Zhang Y, Boyd SA, Teppen BJ, Tiedje JM, Zhang W, Zhu D, Li H. 2018. Bioavailability of tetracycline to antibiotic resistant Escherichia coli in water-clay systems. Environ Pollut 243(PtB):1078-1086. doi:10.1016/j.envpol.2018.09.059 PMID:30253298


  • Ahmad F, Stedtfeld RD, Waseem H, Williams MR, Cupples AM, Tiedje JM, Hashsham SA. 2017. Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in <25min. J Microbiol Methods 132:27-33. doi:10.1016/j.mimet.2016.11.010 PMID:27856278 PMCID:PMC5195917
  • Munir A, Waseem H, Williams MR, Stedtfeld RD, Gulari E, Tiedje JM, Hashsham SA. 2017. Modeling hybridization kinetics of gene probes in a DNA biochip using FEMLAB. Microarrays (Basel) 6(2):9. doi:10.3390/microarrays6020009 PMID:28555058 PMCID:PMC5487956
  • Srinivasan V, Stedtfeld RD, Tourlousse DM, Baushke SW, Xin Y, Miller SM, Pham T, Rouillard JM, Gulari E, Tiedje JM, Hashsham SA. 2017. Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner. J Microbiol Methods 139:15-21. doi:10.1016/j.mimet.2017.04.009 PMID:28438642 PMCID:PMC5491306
  • Stedtfeld RD, Chai B, Crawford RB, Stedtfeld TM, Williams MR, Xiangwen S, Kuwahara T, Cole JR, Kaminski NE, Tiedje JM, Hashsham SA. 2017. Modulatory influence of segmented filamentous bacteria on transcriptomic response of gnotobiotic mice exposed to TCDD. Front Microbiol 8:12. doi:10.3389/fmicb.2017.01708 PMID:28936204 PMCID:PMC5594080
  • Stedtfeld RD, Sallach JB, Crawford RB, Stedtfeld TM, Williams MR, Waseem H, Johnston CT, Li H, Teppen BJ, Kaminski NE, Boyd SA, Tiedje JM, Hashsham SA. 2017. TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal. Appl Microbiol Biotechnol 101:7409-7415. doi:10.1007/s00253-017-8460-9 PMID:28812142
  • Stedtfeld RD, Stedtfeld TM, Fader KA, Williams MR, Bhaduri P, Quensen JF, Zacharewski TR, Tiedje JM, Hashsham SA. 2017. TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome. FEMS Microbiol Ecol 93:8. doi:10.1093/femsec/fix058 PMID:28475713 PMCID:PMC5458050
  • Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae J, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, Tiedje JM, Upham BL, Hashsham SA. 2017. Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. J Environ Manage 198:213-220. doi:10.1016/j.jenvman.2017.04.079 PMID:28460328
  • Waseem H, Williams MR, Stedtfeld TM, Chai B, Stedtfeld RD, Cole JR, Tiedje JM, Hashsham SA. 2017. Virulence factor activity relationships (VFARs): a bioinformatics perspective. Environ Sci Process Impacts 19(3):247-260. doi:10.1039/c6em00689b PMID:28261716 PMCID:PMC5897045
  • Williams MR, Stedtfeld RD, Stedtfeld TM, Tiedje JM, Hashsham SA. 2017. Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device. Biomed Microdevices 19:45. doi:10.1007/s10544-017-0191-2 PMID:28536858
  • Williams MR, Stedtfeld RD, Tiedje JM, Hashsham SA. 2017. MicroRNAs-based inter-domain communication between the host and members of the gut microbiome. Front Microbiol 8:10. doi:10.3389/fmicb.2017.01896 PMID:29021788 PMCID:PMC5624305
  • Williams MR, Stedtfeld RD, Waseem H, Stedtfeld TM, Upham BL, Khalife WT, Etchebarne B, Hughes M, Tiedje JM, Hashsham SA. 2017. Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices. Analytical Methods 9:1229-1241. doi:10.1039/C6AY03405E PMID:29657581 PMCID:PMC5898395


  • Chai B, Tsoi TV, Iwai S, Liu C, Fish JA, Gu C, Johnson TA, Zylstra GJ, Teppen BJ, Li H, Hashsham SA, Boyd SA, Cole JR, Tiedje JM. 2016. Sphingomonas wittichii strain RW1 genome-wide gene expression shifts in response to dioxins and clay. PLoS One 11(6):e0157008. doi:10.1371/journal.pone.0157008 PMID:27309357 PMCID:PMC4911050
  • Stedtfeld RD, Williams M, Fakher U, Johnson TA, Stedtfeld TM, Wang F, Khalife WT, Hughes M, Etchebarne B, Tiedje JM, Hashsham SA. 2016. Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol Ecol 92(3):doi:10.1093/femsec/fiw020 PMID:26850162
  • Wang F, Stedtfeld RD, Kim O, Chai B, Yang L, Stedtfeld TM, Hong SG, Kim D, Lim HS, Hashsham SA, Tiedje JM, Sul WJ. 2016. Influence of soil characteristics and proximity to Antarctic research stations on abundance of antibiotic resistance genes in soils. Environ Sci Technol 50(23):12621-12629. doi:10.1021/acs.est.6b02863 PMID:27797533


  • Stedtfeld RD, Liu Y, Stedtfeld TM, Kostic T, Kronlein M, Srivannavit O, Khalife WT, Tiedje JM, Gulari E, Hughes M, Etchebarne B, Hashsham SA. 2015. Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens. Biomed Microdevices 17(5):89. doi:10.1007/s10544-015-9994-1 PMID:26260693 PMCID:PMC4531140
  • Wang Q, Fish JA, Gilman M, Sun Y, Brown C, Tiedje JM, Cole JR. 2015. Xander: employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome 3:32. doi:10.1186/s40168-015-0093-6 PMID:26246894 PMCID:PMC4526283




  • Baushke SW, Stedtfeld RD, Tourlousse DM, Ahmad F, Wick LM, Gulari E, Tiedje JM, Hashsham SA. 2012. Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves. J Microbiol Methods 90(1):29-35. doi:10.1016/j.mimet.2012.04.003 PMID:22537822 PMCID:PMC3366151



  • Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM. 2010. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J 4(2):279-285. doi:10.1038/ismej.2009.104 PMID:19776767 PMCID:PMC2808446
  • Parnell JJ, Denef VJ, Park J, Tsoi TV, Tiedje JM. 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 PMID:19672561


  • Sul WJ, Park J, Quensen JF, Rodrigues JM, Seliger L, Tsoi TV, Zylstra GJ, Tiedje JM. 2009. DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75(17):5501-5506. doi:10.1128/AEM.00121-09 PMID:19648381 PMCID:PMC2737913



  • Leigh MB, Pellizari VH, Uhlik O, Sutka R, Rodrigues JM, Ostrom N, Zhou J, Tiedje JM. 2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J 1(2):134-148. doi:10.1038/ismej.2007.26 PMID:18043623


  • Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, Reyes VL, Hauser L, Cordova M, Gomez L, Gonzalez M, Land M, Lao V, Larimer FW, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson PM, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM. 2006. Burkholderia xenovorans LB400 harbors a multi-replicon, 973-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A 103(42):15280-15287. doi:10.1073/pnas.0606924103 PMID:17030797 PMCID:PMC1622818
  • Denef VJ, Klappenbach JA, Patrauchan MA, Florizone C, Rodrigues JM, Tsoi TV, Verstraete W, Tiedje JM, Eltis LD. 2006. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl Environ Microbiol 72(1):585-595. doi:10.1128/AEM.72.1.585-595.2006 PMID:16391095 PMCID:PMC1352278
  • Parnell JJ, Park J, Denef VJ, Tsoi TV, Hashsham SA, Quensen JF, Tiedje JM. 2006. Coping with polychlorinated biphenyl (PCB) toxicity: physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress. Appl Environ Microbiol 72(10):6607-14. PMID:17021212


  • Denef VJ, Park J, Tsoi TV, Rouillard JM, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM. 2004. Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl Environ Microbiol 70(8):4961-4970. PMID:15294836
  • Goris J, De Vos P, Caballero-Mellado J, Park J, Falsen E, Quensen JF, Tiedje JM, Vandamme P. 2004. Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400(T) and relatives as Burkholderia xenovorans sp nov. Int J Syst Evol Microbiol 54(5):1677-1681.
  • Tiedje JM, Konstantinidis KT. 2004. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci U S A 101(9):3160-3165. PMID:14973198


  • Denef VJ, Park J, Rodrigues JM, Tsoi TV, Hashsham SA, Tiedje JM. 2003. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol 5(10):933-943. PMID:14510847
  • Park J, Li H, Tiedje JM. 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 J, Ramsburg A, Abriola LM, Tiedje JM. 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 JM. 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 JM. 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.


  • Dybas MJ, Hyndman DW, Heine R, Tiedje JM, Linning KD, Wiggert D, Voice TC, Zhao X, Dybas L, Criddle CS. 2002. Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation. Environ Sci Technol 36(16):3635-3644. PMID:12214659


  • Rodrigues JM, Maltseva OV, Tsoi TV, Helton RR, Quensen JF, Fukuda M, Tiedje JM. 2001. Development of a Rhodococcus recombinant strain for degradation products from anaerobic dechlorination of PCBs. Environ Sci Technol 35(4):663-668. PMID:11349275


  • Hyndman DW, Dybas MJ, Forney L, Heine R, Mayotte T, Phanikumar MS, Tatara G, Tiedje JM, Voice TC, Wallace RB, Wiggert D, Zhao X, Criddle CS. 2000. Hydraulic characterization and design of a full-scale biocurtain. Ground Water 38(3):462-474.
  • Maltseva OV, Rodrigues JM, Quensen JF, Tsoi TV, Tiedje JM. 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.
  • Quensen JF, Tsoi TV, Maltseva OV, Rodrigues JM, Zwiernik MJ, Tiedje JM. 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 JM, Aiello MR, Maltseva OV, Tsoi TV, Tiedje JM. 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 JM. 2000. Putting novel microbes to work on industry wastes. In: Proceedings of the Symposium for Japan Bioindustry Association. pp.47-54.
  • Tsoi TV, Cole JR, Rech S, Tiedje JM. 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.


  • Hrywna Y, Tsoi TV, Maltseva OV, Quensen JF, Tiedje JM. 1999. Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls. Appl Environ Microbiol 65(5):2163-2169. PMID:10224015
  • Maltseva OV, Tsoi TV, Quensen JF, Fukuda M, Tiedje JM. 1999. Degradation of anaerobic reductive dechlorination products of Aroclor 1242 by four aerobic bacteria. Biodegradation 10(5):363-371. PMID:10870552
  • Tsoi TV, Cole JR, Maltseva OV, Rech S, Quensen JF, Rodrigues JM, Spain J, Tiedje JM. 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 TV, Plotnikova EG, Cole JR, Guerin WF, Bagdasarian M, Tiedje JM. 1999. Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates. Appl Environ Microbiol 65(5):2151-2162. PMID:10224014 PMCID:PMC91311
  • Urbance JW, Kukor JJ, Tiedje JM. 1999. Analysis of the phylogenetic distribution of biodegradative bacteria. In: Proceedings of the International Symposium Pseudomonas. Maui, HI.
  • Ye D, Quensen JF, Tiedje JM, Boyd SA. 1999. 2-Bromoethanesulfonate, sulfate, molybdate, and ethanesulfonate inhibit anaerobic dechlorination of polychlorobiphenyls by pasteurized microorganisms. Appl Environ Microbiol 65:327-329. PMID:9872802
  • Zhou J, Tiedje JM. 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.


  • Dybas MJ, Barcelona MJ, Bezborodnikov S, Davies S, Forney L, Kawka O, Mayotte T, Sepulveda-Torres Ld, Smalla K, Sneathen M, Tiedje JM, Voice TC, Wiggert D, Witt ME, Criddle CS. 1998. Pilot-scale evaluation of bioaugmentation for in situ remediation of a carbon tetrachloride-contaminated aquifer. Environ Sci Technol 32(22):3598-3611.
  • Maltseva OV, Quensen JF, Tsoi TV, Tiedje JM. 1998. Intermediate products recently discovered to accumulate during the aerobic degradation of PCB congeners formed from anaerobic dechlorination of Aroclor 1242. In: Proceedings of the Superfund Basic Research Program: A Decade of Improving Health through Multi-Disciplinary Research. Chapel Hill, NC. pp.92.


  • Massol-Deya A, Weller R, Rios-Hernandez L, Zhou J, Hickey RF, Tiedje JM. 1997. Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl Environ Microbiol 63(1):270-276. PMID:8979355
  • Quensen JF, Tiedje JM. 1997. Evaluation of PCB Dechlorination in Sediments. In: Methods in Biotechnology, V. 2: Bioremediation Protocols. Humana Press Inc, Totowa, NJ.
  • Zhou J, Palumbo AV, Tiedje JM. 1997. Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes. Appl Environ Microbiol 63(6):2384-2390. PMID:9172359 PMCID:PMC168532


  • Chee-Sanford JC, Frost JW, Fries MR, Zhou J, Tiedje JM. 1996. Evidence for acetyl coenzyme A and cinnamoyl coenzyme A in the anaerobic toluene mineralization pathway in Azoarcus tolulyticus Tol-4. Appl Environ Microbiol 62(3):964-973. PMID:8975623
  • Migaud ME, Chee-Sanford JC, Tiedje JM, Frost JW. 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. Appl Environ Microbiol 62(3):974-978. PMID:8975624
  • Zhou J, Bruns MA, Tiedje JM. 1996. DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316-322. PMID:8593035


  • Tiedje JM. 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 JM, Sanford RA, Massol-Deya A. 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 JM, Thiem SM, Massol-Deya A, Ka JO, Fries MR. 1995. Tracking microbial populations effective in reducing exposure. Environ Health Perspect 103(supp.5):117-120. PMID:8565898
  • Zhou J, Fries MR, Chee-Sanford JC, Tiedje JM. 1995. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp nov. Int J Syst Bacteriol 45(3):500-506. doi:10.1099/00207713-45-3-500 PMID:8590677
  • Zhou J, Tiedje JM. 1995. Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium. Microb Ecol 4(5):613-618. PMID:7582169


  • Smith GB, Tiedje JM. 1992. Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria. Appl Environ Microbiol 58(1):376-384. PMID:1539983 PMCID:PMC195218
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