James M. Tiedje

University Distinguished Professor and Director - Molecular microbial community ecology, genomics and metagenomics of soil, the rhizosphere, bioremediation and climate change.

James M. Tiedje


Plant and Soil Science Building
1066 Bogue St., Room 540
East Lansing, MI 48824

Phone: (517) 353-9021x1

Tiedje Lab Website

Click here to see a list of James M. Tiedje's publications on Google Scholar.


BS, Iowa State University, Agronomy
MS., Ph.D Cornell University, Soil microbiology and biochemistry

General areas of expertise:

Microbial ecology, metagenomics, soil microbiology, denitrification, biodegradation, bioremediation, permafrost microbiology, anaerobic processes, antibiotic resistance gene ecology



Tiedje, James and Timothy Donohue.  2008.  Microbes in the Energy Grid. Science - Editorial, 320: 985

Yoder-Himes, D, P.S. Chain, Y. Zhu, O. Wurtzel, E.M. Rubin, J.M. Tiedje, R Sorek. 2009. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. PNAS  106:3976-81.

Rodríguez-Minguela, Carlos. M, J. H. Apajalahti, B. Chai, J. R. Cole and J. M. Tiedje. 2009. Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact. Appl Environ. Microbiol. 75:5100-10.

Jesus, Ederson da C, T. L. Marsh, J. M. Tiedje and Fatima M. de S Moreira. 2009. Changes in land use alter the structure     of bacterial communities in Western Amazon soils. ISME J. 3:1004-10

Konstantinidis, K.I., M.H. Serres, M.F. Romine, J. L.M.Rodrigues, J. Auchtung, L.A. McCue, M.S. Lipton, A. Obraztsova, C.S. Giometti, K.H. Nealson, J.K. Fredrickson, and J.M. Tiedje. 2009. Comparative systems biology across an evolutionary gradient within the Shewanella genus. PNAS 106:15909-15914.

Bergholz, P.W., C. Bakermans and J.M. Tiedje.  2009.  Psychrobacter arcticus 273-4 uses resource efficiency and molecular motion adaptations for subzero temperature growth. J. Bacteriol. 191:2340-2352.

Sul, W.J., J-H. Park, J.F. Quensen III, J.L.M. Rodrigues, L. Seliger, T.V. Tsoi, G.J. Zylstra and J.M. Tiedje.  2009.  DNA-Stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment.  Appl. Environ. Microbiol. 75:5501-5506

Walk, S.T., E.W. Alm, D.M. Gordon, J.L. Ram, G.A. Toranzos, J.M. Tiedje, and T.S. Whittam.  2009.  Cryptic lineages of the Escherichia genus.  Appl. Environ. Microbiol. 75-6534-6544.

Iwai, S., B. Chai, W.J. Sul, J.R. Cole, S.A. Hashsham and J.M. Tiedje.  2009.  Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.  ISME Journal 4:279-285.

    Jesus, Ederson da, E. Susilawat, S. L. Smith, Q. Wang, B. Chai, R. Farris, J. L. M. Rodrigues, K.D. Thelen and J. M. Tiedje. 2010. Bacterial communities in the rhizosphere of biofuel crops grown on marginal lands as evaluated by 16S rRNA gene pyrosequences. Bioenerg. Res. 3:20-27. DOI 10.1007/s12155-009-9073-7.

   Luo, C, S. Walk, D. M. Gordon, M. Feldgarden, J. Tiedje and K. T. Konstantinidis. 2011. Genome sequencing of environmental E. coli expands understanding of the ecology and speciation of the model bacterial species. PNAS 108:7200-7205.

   Iwai S, T. A. Johnson, B. Chai, S. A. Hashsham, and J. M. Tiedje. 2011. Comparison of the specificity and efficacy of primers for aromatic dioxygenase gene analysis of environmental samples. Minireview. Appl. Environ. Microbiol. 77: 3551-3557.

   Rodrigues, J. L. M., M. H. Serres, and J. M. Tiedje. 2011. Large scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at genus level. Appl. Environ. Microbiol. DOI 10.1128/AEM.01097-11.

  Looft T, T. A. Johnson, H.K. Allen, D.O. Bayles, D.P. Alt, R.D. Stedtfeld, W.J. Sul, T.M. Stedtfeld, B. Chai B, J. R. Cole, S.A. Hashsham, J.M.Tiedje and T.B. Stanton. 2012. In-feed antibiotic effects on the swine intestinal microbiome. PNAS 109 (5) 1691-1696.

  Pell, J., A. Hintze, R. Canino-Koning, A. Howe, J. M. Tiedje and C. T. Brown. 2012. Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. PNAS 109:13272-13277.

  Penton, C. R., J. L. Deenik, B. N. Popp, G. L. Bruland, P. Engstrom, D. St. Louis, G. A. Brown and, J. Tiedje. 2012. Importance of sub-surface rhizosphere-mediated coupled nitrification-denitrification in a flooded agroecosystem in Hawaii. Soil Biol Biochem. 57:362-373.

  Rodrigues, J. L. M.; V. Pellizari, R. Mueller, K-H, Baek, E. C Jesus, F. Paula, B. Mirza, G. Hamaoui, S.M. Tsai, B. Feigl, J. M. Tiedje, Brendan J.M. Bohannan and Klaus Nüsslein. 2012. Conversion of the Amazon Rainforest to agriculture results in biotic homogenization of soil bacterial communities. PNAS 110:988-993

  Zhu, Yongguan, Timothy A. Johnson, Jian-Qiang Su, Min Qiao, Guang-Xia Guo, Robert D. Stedtfeld, Syed A. Hashsham, and James M. Tiedje, 2013. Diverse and abundant antibiotic resistance genes in Chinese swine farms, PNAS 110:3435-3440


Courses Taught:

CSS 360, Soil Biology
CSS 455, Fate of Pollutants in the environment (1/3)
MMG 801, Integrative Microbial Biology (lectures)

Websites of Interest:

Tiedje Lab Website 

Former Students:  

Past graduate students, post-docs and visiting scholars, over 100.