James M. Tiedje, Primary Publications (2004-2008):

  1. Stres, B., I. Mahne, G. Avgustin and J.M. Tiedje. 2004. Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils. Appl. Environ. Microbiol. 70:301-309. [PubMed]

  2. Konstantinidis, K.T. and J.M. Tiedje. 2004. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc. Natl. Acad. Sci. 101:3160-3165. [PubMed]

  3. Zhou, J., B. Xia, H. Huang, A.V. Palumbo and J.M. Tiedje. 2004. Microbial diversity and heterogeneity in sandy subsurface soils. Appl. Environ. Microbiol. 70:1723-1734. [PubMed]

  4. Rivkina, E., K. Laurinavichius, J. McGrath and J. Tiedje, V. Shcherbakova and D. Gilichinsky. 2004. Microbial life in permafrost. Advances in Space Research 33:1215-1221. [PubMed]

  5. Griffin, B.M., J.M. Tiedje and F.E. Loffler. 2004. Anaerobic microbial reductive dechlorination of tetrachloroethene (PCE) to predominately trans-1,2-Dichloroethene (trans-DCE).   Environ. Sci. Technol. 38:4300-4303. [PubMed]

  6. Ayala-del-Rio, H.L., S.J. Callister, C.S. Criddle and J.M. Tiedje. 2004. Correspondence between community structure and function during succession in phenol- and phenol-plus-trichloroethene-fed sequencing batch reactors. Appl. Environ. Microbiol. 70:4950-4960. [PubMed]

  7. Denef, V.J., J. Park, T.V. Tsoi, J.M. Rouillard, H. Zhang, J.A. Wibbenmeyer, W. Verstraete, E. Gulari, S.A. Hashsham and J.M. Tiedje. 2004. Biphenyl and benzoate metabolism in a genomic context: Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl. Environ. Microbiol. 70:4961-4970. [PubMed]

  8. Ponder, M., T. Vishnivetskaya, J. McGrath and J. Tiedje. 2004. Microbial life in permafrost: extended times in extreme conditions. pp. 151-169.   in B.J. Fuller, N. Lane, E.E. Benson (Eds.), Life in the Frozen State, CRC Press. [book info]

  9. Qiu, X.Y., R.A. Hurt, L.Y. Wu, C.H. Chen, J.M. Tiedje and J.Z. Zhou. 2004. Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR. J. Microbiol. Methods 59:199-210. [PubMed]

  10. Goris, J., P. DeVos, J. Caballero-Mellado, J. Park, E. Falsen, J.F. Quensen, III, J.M. Tiedje and P. Vandamme. 2004. Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov. Int. J. Syst. Evol. Microbiol. 54:1677-1681. [PubMed]

  11. Qiu, X., G.W. Sundin, B. Chai and J.M. Tiedje. 2004. Survival of Shewanella oneidensis MR-1 after UV radiation exposure.   Appl. Environ. Microbiol. 70:6435-6443. [PubMed]

  12. Wu, L., D.K. Thompson, X. Liu, M.W. Fields, C.E. Bagwell, J.M. Tiedje and J. Zhou. 2004. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications.   Environ. Sci. Technol. 38:6775-6782. [PubMed]

  13. Hashsham, S.A., L.M. Wick, J.-M. Rouillard, E. Gulari and J.M. Tiedje. 2004. Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs. Biosens. Bioelectron. 20:668-683. [PubMed]

  14. Kolker, E., A.F. Picone, M.Y. Galperin, M.F. Romine and J.M. Tiedje (with 35 authors). 2005. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. PNAS, 102:2099-2104. [PubMed]

  15. Konstantinidis, K. and J.M. Tiedje. 2005. Genomic insights that advance the species definition for prokaryotes. PNAS, 102:2567-2572. [PubMed]

  16. Qiu, X., G.W. Sundin, L. Wu, J. Zhou and J.M. Tiedje. 2005. Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB and UVA radiation. J. Bacteriol. 187:3556-3564. [PubMed]

  17. Ramette, A., J.J. LiPuma and J.M. Tiedje. 2005. Species abundance and diversity of Burkholderia cepacia complex in the environment. Appl. Environ. Microbiol. 71:1193-1201. [PubMed]

  18. Cole, J.R., Chai, B., Farris. R.J., Wang. Q., Kulam, S.A., McGarrell, D.M., Garrity, G.M., and Tiedje, J.M. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33:D294-D296. [PubMed]

  19. Etchebehere, C. and J.M. Tiedje. 2005. Presence of two different active nirS nitrite reductase genes in a denitrifying Thauera sp. from a high-nitrate-removal-rate reactor. Appl. Environ. Microbiol. 71:5642-5645. [PubMed]

  20. Snow, A.A., D.A. Andow, P. Gepts, E.M. Hallerman, A. Power, J.M. Tiedje and L.L. Wolfenbarger. 2005. Genetically engineered organisms and the environment: Current status and recommendations. Ecological Applications 15:377-404. [abstract | article]

  21. Ponder, M.A., S.J. Gilmour, P.W. Bergholz, C.A. Mindock, R. Hollingsworth, M.F. Thomashow and J.M. Tiedje. 2005. Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria. FEMS Microbiol. Ecol. 53:103-115. [PubMed]

  22. Qiu, X., J.M. Tiedje and G.W. Sundin. 2005. Genome-wide examination of the natural solar radiation response in Shewanella oneidensis MR-1. Photochem & Photobiol. 81:1559-1568. [PubMed]

  23. Konstantinidis, K.T. and J.M. Tiedje. 2005. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 187:6258-6264. [PubMed]

  24. Beliaev, A.S., D.M. Klingeman, J.A. Klappenbach, L. Wu, M.F. Romine, J.M. Tiedje, K.H. Nealson, J.K. Fredrickson and J. Zhou. 2005. Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors. J. Bacteriol. 187:7138-7145. [PubMed]

  25. Denef V.J., M.A. Patrauchan, C. Florizone, J. Park, T.V. Tsoi, W. Verstraete, J.M. Tiedje and L.D. Eltis. 2005. Growth substrate and phase specific expression of biphenyl, benzoate and C1 metabolic pathways in Burkholderia xenovorans LB400. J. Bacteriol. 187:7996-8005. [PubMed]

  26. Tiedje, J.M., T.V. Tsoi, K.D. Pennell, L.D. Hansen, A. Wani and D.P. Howell. 2005. Enhancing PCB bioremediation. pp. 147-214. In J.W. Talley (Ed.), Bioremediation of Recalcitrant Compounds, Taylor & Francis Group. [book info]

  27. Ramette, A. and J.M. Tiedje. 2007. Biogeography: An emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microbial Ecol. 53:197-207; doi: 10.1007/s00248-005-5010-2. [PubMed]

  28. Denef, V.J., J.A. Klappenbach, M.A. Patrauchan, C. Florizone, J.L.M. Rodrigues, T.V. Tsoi, W. Verstraete, L.D. Eltis and J.M. Tiedje. 2006. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl. Environ. Microbiol. 72:585-595. [PubMed]

  29. Qiu, X., M.J. Daly, A. Vasilenko, M.V. Omelchenko, E.K. Gaidamakova, L. Wu, J, Zhou, G.W. Sundin and J.M. Tiedje. 2006. Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation. J. Bacteriol. 188:1199-1204. [PubMed]

  30. Wick, L.M., J.M. Rouillard, T.S. Whittam, E. Gulari, J.M. Tiedje and S.A. Hashsham. 2006. On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Res. 34:e26. [PubMed]

  31. Vishnivetskaya, T.A., M.A. Petrova, J. Urbance, M. Ponder, C.L. Moyer, D.A. Gilichinsky, J.M. Tiedje. 2006. Bacterial Community in Ancient Siberian Permafrost as Characterized by Culture and Culture-Independent Methods. Astrobiology 6:400-414. [PubMed]

  32. Stres, B. and J.M. Tiedje. 2006. New frontiers in soil microbiology: how to link structure and function of microbial communities? pp. 1-22. In P. Nannipieri, K. Smalla (Eds.), Nucleic Acids and Proteins in Soil, Soil Biology, Volume 8, Springer-Verlag Berlin Heidelberg. [book info]

  33. Gao, H., A. Obraztova, N. Stewart, R. Popa, J.K. Fredrickson, J.M. Tiedje, K.H. Nealson and J. Zhou. 2006. Shewanella loihica sp. nov. isolated from iron-rich microbial mats in the Pacific Ocean. Int'l J. Syst. Evol. Microbiol. 56:1911-1916. [PubMed]

  34. Rodrigues, J.L.M., C.A. Kachel, M.R. Aiello, J.F. Quensen, O.V. Maltseva, T.V. Tsoi and J.M. Tiedje. 2006. Degradation of Aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400 (ohb) and Rhodococcus sp. strain RHA1 (fcb). Appl. Environ. Microbiol. 72:2476-2482. [PubMed]

  35. Payne, G.W., A. Ramette, H.L. Rose, A.J. Weightman, T. Hefin Jones, J.M. Tiedje and E. Mahenthiralingam. 2006. Application of a recA gene-based identification approach to the maize rhizosphere reveals novel diversity in Burkholderia species. FEMS Microbiol. Lett. 259:126-132. [PubMed]

  36. Penton, C. Ryan, A.H. Devol and J.M. Tiedje. 2006. Molecular evidence for the broad distribution of anammox in freshwater and marine sediments. Appl. Environ. Microbiol. 72:6829-6832. [PubMed]

  37. Konstantinidis, K.T., A. Ramette and J.M. Tiedje. 2006. The bacterial species definition in the genomic era. Philosophical transactions of the Royal Society B: Biol. Sci. 361:1929-1940. [PubMed]

  38. Konstantinidis, K.T., A. Ramette and J.M. Tiedje. 2006. Towards a more robust assessment of intra-species diversity using fewer genetic markers. Appl. Environ. Microbiol. 72:7286-7293. [PubMed]

  39. Bakermans, C., H.L. Ayala-del-Rio, M.A. Ponder, T. Vishnivetskaya, D. Gilichinsky, M.F. Thomashow and J.M. Tiedje. 2006. Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov. isolated from Siberian permafrost. Int'l J. Syst. Evol. Microbiol. 56:1285-1291. [PubMed]

  40. Rodrigues, D.F., J. Goris, T. Vishnivetskaya, D. Gilichinsky, M.F. Thomashow and J.M. Tiedje. 2006. Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov. Extremophiles. 10:285-294. [PubMed]

  41. Parnell, J., J. Park, V. Denef, T. Tsoi, S. Hashsham, J. Quensen, III and J.M. Tiedje. 2006. Coping with PCB toxicity: The physiological and genome-wide response of Burkholderia xenovorans LB400 to PCB (polychlorinated biphenyl)-mediated stress. Appl. Environ. Microbiol. 72:6607-14. [PubMed]

  42. Chain, P.S.G., V.J. Denef, K. Konstantinidis, L.M. Vergez, L. Agullo, V. Latorre Reyes, L. Hauser, M. Cordova, L. Gomez, M. Gonzalez, M. Land, V. Lao, F. Larimer, J.J. LiPuma, E. Mahenthiralingam, S.A. Malfatti, C.J. Marx, J. J. Parnell, A. Ramette, P. Richardson, M. Seeger, D. Smith, T. Spilker, W.J. Sul, T.V. Tsoi, L.E. Ulrich, I.B. Zhulin and J.M. Tiedje. 2006. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73 M bp genome shaped for versatility. PNAS, 103:15280-15287. [PubMed]

  43. Zheng, S., M.A. Ponder, J.M. Tiedje, M.F. Thomashow and D.M. Lubman. 2007. How psychrobacter survive in permafrost: a proteomic perspective. Electrophoresis 28:467-488. [PubMed]

  44. Goris, J., K.T. Konstantinidis, J.A. Klappenbach, T. Coenye, P. Vandamme and J.M. Tiedje. 2007. DNA-DNA hybridization values and their relation to whole genome sequence similarities. Int'l J. Syst. Evol. Microbiol. 57:81-91. [PubMed]

  45. Tarter, J.C., P.R. Backus, R.L. Mancinelli, J.M. Aurnou, D.E. Backman, G.S. Basri, A.P. Boss, A. Clarke, D. Deming, L.R. Doyle, E.D. Feigelson, F. Freund, D.H. Grinspoon, R.M. Haberle, S.A. Hauck, II, M.J. Heath, T.J. Henry, J.L. Hollingsworth, M.M. Joshi, S. Kilston, M.C. Liu, E.Meikle, I.N. Reid, L.J. Rothschile, J.M. Scalo, A. Segura, C.M. Tang, J.M. Tiedje, M.C. Turnbull, L.M. Walkowicz, A.L. Weber and R.E. Young.   2007.   Special paper: A re-appraisal of the habitability of planets around M dwarf stars.   Astrobiology 7:30-65. doi: 10.1089/ast.2006.0124. [abstract]

  46. Rodrigues, D.F. and J.M. Tiedje.  2007.  Multi-locus real-time PCR for quantitation of bacteria in the environment reveals Exiguobacterium to be prevalent in permafrost.  FEMS Microbiol. Ecol. 59:489-499. [PubMed]

  47. Cruz-Garcia, C. A.E. Murray, J.A. Klappenbach, V. Stewart and J.M. Tiedje.  2007.  Respiratory nitrate ammonification by Shewanella oneidensis MR-1. J. Bacteriol. 189:656-662. [PubMed]

  48. Bakermans, C., S.L. Tollaksen, C.S. Giometti, C. Wilkerson, J.M. Tiedje and M.F. Thomashow.  2007.  Proteomic analysis of Psychrobacter cryohalolentis K5 during growth at subzero temperatures.  Extremophiles 11: 343-354. [PubMed]

  49. Stedtfeld, R.D., L. Wick, S.W. Baushke, D. Tourlousse, A. Herzog, Y. Xia, J.M. Rouillard, J. Klappenbach, J.R.Cole, E. Gulari, J.M. Tiedje and S.A. Hashsham.  2007.  Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays.  Appl. Environ. Microbiol.  73:380-389. [PubMed]

  50. Cole, J.R., B. Chai, R.J. Farris, Q. Wang, A.S. Kulam-Syed-Mohideen, D.M. McGarrell, A.M. Bandela, E. Cardenas, G.M. Garrity and J.M. Tiedje.  2007.  The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.  Nucl. Acids. Res. Database issue 37:D169-D172, doi: 10.1093/nar/gkl889. [PubMed]

  51. O’Sullivan, L.A., A.J. Weightman, T.H. Jones, A.M. Marchbank, J.M. Tiedje and E. Mahenthiralingam.  2007.  Identifying the genetic basis of ecologically and biotechnologically useful functions of the bacterium Burkholderia vietnamiensis.  Environ. Microbiol. 9:1017-1034. [PubMed]

  52. Ramette, A. and J.M. Tiedje.  2007.  Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem.  PNAS 104:2761-2766. [PubMed]

  53. Vishnivetskaya, T.A., R. Siletzky, N. Jefferies, J.M. Tiedje and S. Kathariou.  2007.  Effect of low temperature and culture media on the growth and freeze-thawing tolerance of Exiguobacterium strains.  Cryobiology 54:234-240. [PubMed]

  54. Gilichinsky, D.A., G.S. Wilson, E.I. Friedmann, C.P. McKay, R.S. Sletten, E.M. Rivkina, T.A. Vishnivetskaya, L.G. Erokhina, N.E. Ivanushkina, G.A. Kochkina, V.A. Shcherbakova, V.S. Soina, E.V. Spirina, E.A. Vorobyova, D.G. Fyodorov-Davydov, B. Hallet, S.M. Ozerskaya, V.A. Sorokovikov, K.S. Laurinavichyus, A.V. Shatilovich, J.P. Chanton, V.E. Ostroumov and J.M. Tiedje.  2007.  Research Paper: Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology.  Astrobiology 7:275-311. [PubMed]

  55. Wang, Q., G.M. Garrity, J.M. Tiedje and J.R. Cole.  2007.  A naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.  Appl. Environ. Microbiol. 73:5261-5267. [PubMed]

  56. Leigh, M.B., V.H. Pellizari, O. Uhlik, R. Sutka, J. Rodrigues, N.E. Ostrom, J. Zhou and J.M. Tiedje.  2007.  Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs).  ISME Journal 1:134-148. [abstract|article]

  57. Smith, D.J., J. Park, J.M. Tiedje and W.W. Mohn.  2007.  A large gene cluster in Burkholderia xenovorans encoding abietane diterpenoid catabolism.  J. Bacteriol. 189:6195-6204. [PubMed]

  58. Hansen. A.A., R.A. Herbert, K. Mikkelsen, L.L. Jensen, T. Kristoffersen, J.M. Tiedje, B.A. Lomstein and K.W. Finster.  2007.  Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway.  Environ. Microbiol. 9:2870-2884. doi: 10.1111/j.1462-2920.2007.01403.x. [PubMed]

  59. Griffin, B.M. and J.M. Tiedje.  2007.  Microbial reductive dehalogenation in Antarctic melt pond sediments.  Antarctic Sci. 19:1-6. [abstract]

  60. Wu, W.M., J. Carley, J. Luo, M.A. Ginder-Vogel, E. Cardenas, M.B. Leigh, C. Hwang, S.D. Kelly, C. Ruan, L. Wu, J. Van Nostrand, T. Gentry, K. Lowe, T. Mehlhorn, S. Carroll, W. Luo, M.W. Fields, B. Gu, D. Watson, K.M. Kemner, T. Marsh, J. Tiedje, J. Zhou, S. Fendorf, P.K. Kitanidis, P.M. Jardine and C.S. Criddle.  2007.  in situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen.  Environ. Sci. Technol. 41:5716-5723. [PubMed]

  61. Konstantinidis, K.T. and J.M. Tiedje.  2007.  Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead.  Curr. Opin. Microbiol. 10:1-6. [PubMed]

  62. Hashsham, S.A., E. Gulari and J.M. Tiedje.  2007.  Microfluidic systems being adapted for microbial, molecular biological analyses.  Microbe 2:531-536. [pdf]

  63. Rodrigues, D.F. and J.M. Tiedje.  2008.  Minireview: Coping with our cold planet.  Appl. Environ. Microbiol. 74:1677-1686. [PubMed]

  64. Miller, S.M., D.M. Tourlousse, R.D. Stedtfeld, S.W. Baushke, A.B. Herzog, L.M. Wick, J.M. Rouillard, E. Gulari, J.M. Tiedje and S.A. Hashsham.  2008.  in situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water.  Appl. Environ. Microbiol. 74:2200-2209. [PubMed]

  65. Cardenas, E., W.M. Wu, M.B. Leigh, J. Carley, S. Carroll, T. Gentry, J. Luo, D. Watson, B. Gu, M. Ginder-Vogel, P.K. Kitanidis, P.M. Jardine, J. Zhou, C.S. Criddle, T.L. Marsh and J.M. Tiedje.  2008.  Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels.  Appl. Environ. Microbiol. 74:3718-3729. [PubMed]

  66. Stedtfeld, R.D., S.W. Baushke, D.M. Tourlousse, S.M. Miller, T.M. Stedtfeld, E. Gulari, J.M. Tiedje and S.A. Hashsham.  2008.  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.  Appl. Environ. Microbiol. 74:3831-3838. [PubMed]

  67. Wu. L., L. Kellogg, A.H. Devol, J.M. Tiedje and J. Zhou.  2008.  Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico.  Appl. Environ. Microbiol. 74:4516-4529. [PubMed]

  68. Bakermans, C., P.W. Bergholz, H. Ayala-del-Rio and J.M. Tiedje.  2008.  Genomic insights into cold adaptation and permafrost bacteria.  pp. 159-168. In R. Margesin (Ed.), Permafrost Soils, Soil Biology 16, Springer-Verlag Berlin Heidelberg 2009. doi: 10.1007/978-3-540-69371-0 [Chapter]

  69. Fredrickson, J.K., M.F. Romine, A.S. Beliaev, J.M. Auchtung, M.E. Driscoll, T.S. Gardner, K.H. Nealson, A.L. Osterman, G. Pinchuk, J.L. Reed, D.A. Rodionov, J.L.M. Rodrigues, D.A. Saffarini, M.H. Serres, A.M. Spormann, I.B. Zhulin and J.M. Tiedje.  2008.  Towards environmental systems biology of Shewanella.  Nature Reviews - Microbiology 6:592-603. [PubMed]

  70. Wu, L., X. Liu, M.W. Fields, D.K. Thompson, C.E. Bagwell, J.M. Tiedje, T.C. Hazen and J.-Z. Zhou.  2008.  Microarray-based whole-genome hybridization as a tool for determining prokaryotic species relatedness. The ISME J. 2:642-655; doi: 10.1038/ismej.2008.23 [Article]

  71. Rodrigues, D.F., N. Ivannova, Z. He, M. Huebner, J. Zhou and J.M. Tiedje.  2008.  Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics 9:547; doi: 10.1186/1471-2164-9-547. [PubMed]

  72. Cardenas, E. and J.M. Tiedje.  2008.  New Tools for discovering and characterizing microbial diversity.  Curr. Opin. Biotechnol.  19:544-549. [PubMed]

  73. Asuming-Brempong, S., S. Gantner, S.G.K. Adiku, G. Archer, V. Edusei and J.M. Tiedje.  2008.  Changes in the biodiversity of microbial populations in tropical soils under different fallow treatments. Soil Biol. Biochem. 40:2811-2818. [Article]

  74. Tiedje, J. and T. Donohue.  2008.  Microbes in the Energy Grid. Science Editorial, 320:985. [PubMed]