James M. Tiedje, Primary Publications (1994-1998):

  1. Tiedje, J.M., G.B. Smith, S. Simkins, W.E. Holben, C. Finney and D.A. Gilichinsky. 1994. Recovery of DNA, denitrifiers and patterns of antibiotic sensitivity in microorganisms from ancient permafrost soils of Eastern Siberia. pp. 83-98. In D. Gilichinsky (ed), Viable Microorganisms in Permafrost. Russian Academy of Sciences, Pushchino.
  2. Fathepure, B.Z. and J.M. Tiedje. 1994. Reductive dechlorination of tetrachloroethylene by a chlorobenzoate enriched biofilm reactor. Environ. Sci. and Technol. 28:746-752.
  3. Tiedje, J.M. 1994. Denitrifiers. pp 245-267. Methods of Soil Analysis, Part 2. Microbiological and Biochemical Properties. Soil Sci. Soc. Amer., Madison, Wisconsin.
  4. Kasper, H.F. and J.M. Tiedje. 1994. Anaerobic bacteria and processes. pp 223-243. Methods of Soil Analysis, Part 2. Microbiological and Biochemical Properties. Soil Sci. Soc. Amer., Madison, Wisconsin.
  5. Tiedje, J.M., M.R. Fries, J. Chee-Sanford and J. Cole. 1994. Anaerobic degradation of aromatic chlorinated and gasoline compounds in soils and aquifers. Transactions of the 15th World Congress of Soil Science, Int'l. Soc. Soil Sci. Vol. 4a, 364-374.
  6. Ye, R.W., B.A. Averill and J.M. Tiedje. 1994. Denitrification: Production and consumption of nitric oxide. Appl. Environ. Microbiol. 60:1053-1058. [PubMed]
  7. Thiem, S.M., M.L. Krumme, R.L. Smith and J.M. Tiedje. 1994. Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer. Appl. Environ. Microbiol. 60:1059-1067. [PubMed]
  8. Ka, J.O., W.E. Holben and J.M. Tiedje. 1994. Genetic and phenotypic diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria isolated from 2,4-D-treated field soils. Appl. Environ. Microbiol. 60:1106-1115. [PubMed]
  9. Ka, J.O., W.E. Holben and J.M. Tiedje. 1994. Use of gene probes to aid in recovery and identification of functionally dominant 2,4-dichlorophenoxyacetic acid-degrading populations in soil. Appl. Environ. Microbiol. 60:1116-1120. [PubMed]
  10. Ka, J.O., W.E. Holben and J.M. Tiedje. 1994. Analysis of competition in soil among 2,4-dichlorophenoxyacetic acid-degrading bacteria. Appl. Environ. Microbiol. 60:1121-1128. [PubMed]
  11. Ka, J.O. and J.M. Tiedje. 1994. Integration and excision of a 2,4-dichlorophenoxyacetic acid-degradative plasmid in Alcaligenes paradoxus and evidence of its natural intergeneric transfer. J. Bacteriol. 176:5284-5289. [PubMed]
  12. Krumme, M.L., R.L. Smith, S.M. Thiem, J. Egestorff, J.M. Tiedje, K.N. Timmis and D.F. Dwyer. 1994. Behavior of pollutant-degrading organisms in aquifers; predictions for genetically engineered organisms. Environ. Sci. Technol. 28:1134-1138.
  13. Tiedje, J.M., J.F. Quensen, III, J. Chee-Sanford, J.P. Schimel and S.A. Boyd. 1994. Microbial reductive dechlorination of PCBs. Biodegradation 4:231-240.
  14. Fries, M.R., J.Z. Zhou, J.C. Chee-Sanford and J.M. Tiedje. 1994. Isolation, characterization and distribution of denitrifying toluene degraders from a variety of habitats. Appl. Environ. Microbiol. 60:2802-2810. [PubMed]
  15. Cole, J.R., A.L. Cascarelli, W.W. Mohn, and J.M. Tiedje. 1994. Isolation and characterization of a novel bacterium growing via reductive dehalogenation of 2-chlorophenol. Appl. Environ. Microbiol. 60:3536-3542. [PubMed]
  16. Højberg, Revsbach, Tiedje. 1994. Denitrification in Soil Aggregates Analyzed with Microsensors for Nitrous Oxide and Oxygen. Soil Sci. Soc. Am. J. 58:1691-1698.
  17. Massol-Deyá, A., R. Hickey, and J.M. Tiedje. 1994. Microbial biofilm communities in biological activated carbon fluidized bed reactors for treatment of groundwater contaminated with aromatic hydrocarbons, pp.164-169. In E.J. Macari, J.D. Frost, L.F. Pumarada (eds.). Geo-Environmental Issues Facing the Americas.
  18. Massol-Deyá, A.A., J. Whallon, R.F. Hickey, and J.M. Tiedje. 1995. Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater. Appl. Environ. Microbiol. 61:769-777. [PubMed]
  19. Tiedje, J.M. 1995. Approaches to the comprehensive evaluation of prokaryote diversity of a habitat. pp.73-87. In D. Allsopp, D.L. Hawksworth and R.R. Colwell (eds), CAB International, Microbial Diversity and Ecosystem Function.
  20. Cole, J.R., B.Z. Fathepure, and J.M. Tiedje. 1995. Tetrachloroethylene and 3-chlorobenzoate dechlorination activities are co-induced in Desulfomonile tiedjei DCB-1. Biodegradation 6:167-172. [PubMed]
  21. Yadav, J.S., J.F. Quensen III, J.M. Tiedje, and C.A. Reddy. 1995. Degradation of polychlorinated biphenyl mixtures (aroclors 1242, 1254, and 1260) by the white rot fungus Phanerochaete chrysosporium as evidenced by congener-specific analysis. Appl. Environ. Microbiol. 61:2560-2565. [PubMed]
  22. Mahne, I. and J.M. Tiedje. 1995. Criteria and methodology for identifying respiratory denitrifiers. Appl. Environ. Microbiol. 61:1110-1115.
  23. Ye, R.W., D. Haas, J.-O. Ka, V. Krishnapillai, A. Zimmermann, C. Baird, and J.M. Tiedje. 1995. Anaerobic activation of the entire denitrification pathway in Pseudomonas aeruginosa requires ANR, an analog of FNR. J. Bacteriol. 177:3606-3609. [PubMed]
  24. Massol-Deyá, A.A., D.A. Odelson, R.F. Hickey, and J.M. Tiedje. 1995. Bacterial community fingerprinting of amplified 16S and 16-23S ribosomal DNA gene sequences and restriction endonuclease analysis (ARDRA). pp. 1-8 In Molecular Microbial Ecology Manual. Kluwer Acad, Pub., Dordrecht.
  25. Zhou, J., M.R. Fries, J.C. Chee-Sanford, and J.M. Tiedje. 1995. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene and description of Azoarcus tolulyticus sp. nov. Int'l. J. Syst. Bacteriol. 45:500-506. [PubMed]
  26. Ka, J.O., P. Burauel, J.A. Bronson, W.E. Holben, and J.M. Tiedje. 1995. DNA probe analysis of the microbial community selected in the field by long-term 2,4-D application. Soil Sci. Soc. Amer. 59:1581-1587.
  27. Zhou, J. and J.M. Tiedje. 1995. Development of phylogenetic probes specific to Burkholderia cepacia G4. pp 65-75. In Monitoring and verification of bioremediation, R.E. Hinchee, G.S. Douglas, and S.K. Ong (ed.), Battelle Press, Columbus, OH.
  28. Zhou, J.-Z. and J.M. Tiedje. 1995. Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium. Molec. Ecol. 4:613-618. [PubMed]
  29. Tiedje, J.M., S.M. Thiem, A. Massol-Deyá, J.O. Ka and M.R. Fries. 1995. Tracking microbial populations effective in reducing exposure. Environ. Health Perspect. 103 (Suppl 5):117-120. [PubMed]
  30. Tiedje, J.M., R.A. Sanford, and A.A. Massol-Deyá. 1995. Advantages and disadvantages of consortia in bioremediation. pp. 357-367 In Bioremediation: The Tokyo '94 Workshop, OECD, Paris.
  31. Tiedje, J.M. 1995. New advances and challenges for bioremediation. pp. 81-87 In Bioremediation: The Tokyo '94 Workshop, OECD, Paris.
  32. Fulthorpe, R.R., C. McGowan, O.V. Maltseva, W.E. Holben, and J.M. Tiedje. 1995. 2,4-dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes. Appl. Environ. Microbiol. 61:3274-3281. [PubMed]
  33. Ye, D., J.F. Quensen III, J.M. Tiedje, and S.A. Boyd. 1995. Evidence for para dechlorination of polychlorobiphenyls (PCBs) by methanogenic bacteria. Appl. Environ. Microbiol. 61:2166-2171.
  34. Zhou. J., M.A. Bruns, and J.M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322. [PubMed]
  35. Chee-Sanford, J.C., J.W. Frost, M.R. Fries, J.-Z. Zhou, and J.M. Tiedje. 1996. Evidence for acetyl-CoA and cinnamoyl-CoA in the anaerobic toluene mineralization pathway in Azoarcus tolutyticus strain Tol-4. Appl. Environ. Microbiol. 62:964-973. [PubMed]
  36. Migaud, M.E., J.C. Chee-Sanford, J.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. Appl. Environ. Microbiol. 62:974-978. [PubMed]
  37. Fulthorpe, R.R., A.N. Rhodes and J.M. Tiedje. 1996. Pristine soils mineralize 3-chlorobenzoate and 2,4-dichlorophenoxyacetate via different microbial populations. Appl. Environ. Microbiol. 62:1159-1166. [PubMed]
  38. Pellizari, V.H., S. Bezborodnikov, J.F. Quensen, III, and J.M. Tiedje. 1996. Evaluation of strains isolated by growth on naphthalene and biphenyl for hybridization of genes to dioxygenase probes and polychlorinated biphenyl-degrading ability. Appl. Environ. Microbiol. 62:2053-2058. [PubMed]
  39. Moyer, C.L., J.M. Tiedje, F.C. Dobbs, and D.M. Karl. 1996. 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. Appl. Environ. Microbiol. 62:2501-2507. [PubMed]
  40. Shih, C.-C., M.E. Davey, J. Zhou, J.M. Tiedje, and C.S. Criddle. 1996. Effects of phenol feeding pattern on microbial community structure and cometabolism of trichloroethylene. Appl. Environ. Microbiol. 62:2953-2960.
  41. Sanford, R.A., J.R. Cole, F.E. Löffler, and J.M. Tiedje. 1996. Characterization of Desulfitobacterium chlororespirans sp. nov., which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoate. Appl. Environ. Microbiol. 62:3800-3808. [PubMed]
  42. Löffler, F.E., R.A. Sanford, and J.M. Tiedje. 1996. Initial characterization of a reductive dehalogenase from Desulfitobacterium chlororespirans strain Co23. Appl. Environ. Microbiol. 62:3809-3813.
  43. Tiedje, J., J. Urbance, N. Larsen, T. Schmidt, O. Strunk, S. Pramanik, R. Overbeek, R. Martin and J. Holt. 1996. Towards an integrated microbial database. pp. 63-68. In: Culture collections to improve the quality of life; R.A. Samson, J.A. Stalpers, D. van der Mei, and A.H. Stouthamer (eds.), CBS Publishing, Baarn, The Netherlands.
  44. Tiedje, J.M. and J. Zhou. 1996. Analysis of non-culturable bacteria. pp. 53-65. In Methods for the examination of organismal diversity in soils and sediments. Geoffrey S. Hall (ed)., CAB International.
  45. Massol-Deyá, A., R. Weller, L. Ríos-Hernández, J.-Z. Zhou, R.F. Hickey, and J.M. Tiedje. 1997. Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl. Environ. Microbiol. 63:270-276. [PubMed]
  46. Sanford, R.A. and J.M. Tiedje. 1997. Chlorophenol dechlorination and subsequent degradation in denitrifying microcosms fed low concentrations of nitrate. Biodegradation 7:425-434.
  47. Fries, M.R., G.D. Hopkins, P.L. McCarty, L.J. Forney, and J.M. Tiedje. 1997. Microbial succession during a field evaluation of phenol and toluene as the primary substrates for trichloroethene cometabolism. Appl. Environ. Microbiol. 63:1515-1522.
  48. Fries, M.R., L.J. Forney, and J.M. Tiedje. 1997. Phenol- and toluene-degrading microbial populations from an aquifer in which successful trichloroethene cometabolism occurred. Appl. Environ. Microbiol. 63:1523-1530.
  49. Quensen III, J.F. and J.M. Tiedje. 1997. Methods for evaluation of PCB dechlorination in sediments. pp. 241-253. In: Methods in Biotechnology, Vol. 2: Bioremediation Protocols. Edited by: D. Sheehan. Humana Press Inc., Totowa, NJ.
  50. Quensen III, J.F. and J.M. Tiedje. 1997. Evaluation of PCB dechlorination in sediments. pp. 257-273. In: Methods in Biotechnology, Vol. 2: Bioremediation Protocols. Edited by: D. Sheehan. Humana Press Inc., Totowa, NJ.
  51. Zhou, J., A.V. Palumbo and J.M. Tiedje. 1997. Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes. Appl. Environ. Microbiol. 63:2384-2390. [PubMed]
  52. Averill, B.A., Y. Wang, J.O. Ka, I.N. Roublevskaia, and J.M. Tiedje. 1997. The chemistry of biological denitrification: spectroscopic studies provide insights into the mechanism of dissimilatory heme Cd1 and copper-containing nitrite reductases. Proc. NATO/ESF Advanced Research Workshop on Biological Electron Transfer Chains: Genetics, Composition and Mode of Operation, Tomar, Portugal, May 3-7, 1997. E. Vijgenboom and G.W. Canters, eds., Kluwer Academic Publishers, Dordrecht.
  53. Kamagata, Y., R.R. Fulthorpe, K. Tamura, H. Takami, L.J. Forney and J.M. Tiedje. 1997. Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria. Appl. Environ. Microbiol. 63:2266-2272. [PubMed]
  54. Matheson, V.G., J. Munakata-Marr, G.D. Hopkins, P.L. McCarty, J.M. Tiedje and L.J. Forney. 1997. A novel means to develop strain-specific DNA probes for detecting bacteria in the environment. Appl. Environ. Microbiol. 63:2863-2869. [PubMed]
  55. Löffler, F.E., J.E. Champine, K.M. Ritalahti, S.J. Sprague and J.M. Tiedje. 1997. Complete reductive dechlorination of 1,2-dichloropropane by anaerobic bacteria. Appl. Environ. Microbiol. 63:2870-2875.
  56. Larsen, N., R. Overbeek, S. Pramanik, T.M. Schmidt, E.E. Selkov, O. Strunk, J.M. Tiedje and J.W. Urbance. 1997. Towards microbial data integration. J. Indust. Microbiol. 18:68-72.
  57. Staley, J.T., R.W. Castenholz, R.R. Colwell, J.G. Holt, M.D. Kane, N.R. Pace, A.A. Salyers and J.M. Tiedje. 1997. The microbial world: Foundation of the biosphere. Amer. Acad. Microbiol., Washington, D.C., 32 pp.
  58. Munakata-Marr, J., V.G. Matheson, L.J. Forney, J.M. Tiedje and P.L. McCarty. 1997. Long-term biodegradation of trichloroethylene influenced by bioaugmentation and dissolved oxygen in aquifer microcosms. Environ. Sci. Technol. 31:786-791.
  59. Ka, J.-O., J. Urbance, R.W. Ye, T.-Y. Ahn and J.M. Tiedje. 1997. Diversity of oxygen and N-oxide regulation of nitrite reductases in denitrifying bacteria. FEMS Microbiol. Letters 156:55-60. [PubMed]
  60. Löffler, F.E., K.M. Ritalahti, and J.M. Tiedje. 1997. Dechlorination of chloroethenes is inhibited by 2-bromoethanesulfonate in the absence of methanogens. Appl. Environ. Microbiol. 63:4982-4985.
  61. Tiedje, J.M., J.-Z. Zhou, K. Nüsslein, C.L. Moyer and R.R. Fulthorpe. 1997. Extent and patterns of soil microbial diversity. pp. 35-41. In: Martins, M.T. et, al. (eds.). Progress in Microbial Ecology, Brazilian Society for Microbiology, Sao Paulo.
  62. Tiedje, J.M., R. Fulthorpe, Y. Kamagata, C. McGowan, A. Rhodes and H. Takami. 1997. What is the global pattern of chloroaromatic degrading microbial populations? pp. 65-74. In Horikoshi, K. et. al., (eds). Microbial Diversity and Genetics of Biodegradation. S. Karger AG, Basel.
  63. Zhou, J., M.E. Davey, J.B. Figueras, E. Rivkina, D. Gilichinsky and J.M. Tiedje. 1997. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:3913-3919. [PubMed]
  64. Brussaard, L., V.M. Behan-Pelletier, D.E. Bignell, V.K. Brown, W.A.M. Didden, P.I. Folgarait, C. Fragoso, D.W. Freckman, V.V.S.R. Gupta, T. Hattori, D. Hawksworth, C. Klopatek, P. Lavelle, D. Malloch, J. Rusek, B. Soderstrom, J.M. Tiedje and R.A. Virginia. 1997. Biodiversity and ecosystem functioning in soil. Ambio 26:563-570.
  65. Bogdanova, E.S., I.A. Bass, L.S. Minakhin, M.A. Petrova, S.Z. Mindlin, A.A. Volodin, E.S. Kalyaeva, J.M. Tiedje, J.L. Hobman, N.L. Brown and V.G. Nikiforov. 1998. Horizontal spread of mer operons among Gram-positive bacteria in natural environments. Microbiology 144:609-620. [PubMed]
  66. Dedysh, S.N., N.S. Panikov, J.M. Tiedje. 1998. Acidophilic methanotrophic communities from sphagnum peat bogs. Appl. Environ. Microbiol. 64:922-929. [PubMed]
  67. Moyer, C.L., J.M. Tiedje, F.C. Dobbs and D.M. Karl. 1998. Diversity of deep-sea hydrothermal vent Archaea at from Loihi Seamount, Hawaii. Deep Sea Res. 45:303-317.
  68. Santo Domingo, J.W., M.G. Kaufman, M.J. Klug and J.M. Tiedje. 1998. Characterization of the cricket hindgut microbiota with fluorescently labeled rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64:752-755.
  69. Rhodes, A.N., J.W. Urbance, H. Youga, H. Corlew-Newman, C.A. Reddy, M.J. Klug, J.M. Tiedje and D.C. Fisher. 1998. Identification of bacterial isolates obtained from intestinal contents associated with 12,000 year old mastodon remains. Appl. Environ. Microbiol. 64:651-658. [PubMed]
  70. Rivkina, E., S. Wagener, J. McGrath, D. Gilichinsky and J. Tiedje. 1998. Biogeochemical activity of anaerobic microorganisms from buried permafrost sediments. Geomicrobiology. 15:187-193.
  71. Santo Domingo, J.W., M.G. Kaufman, M.J. Klug, W.E. Holben, D. Harris, J.M. Tiedje. 1998. Influence of diet on the structure and function of the bacterial hindgut community of crickets. Mol. Ecol. 7:761-767.
  72. Nüsslein, K and J.M. Tiedje. 1998. Characterization of a young Hawaiian soil bacterial community for its dominant and rare members using small subunit rDNA amplified from DNA fractionated by its guanine and cytosine composition. Appl. Environ. Microbiol. 64:1283-1289. [PubMed]
  73. Fulthorpe, R.R., A.N. Rhodes and J.M. Tiedje. 1998. High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria. Appl. Environ. Microbiol. 64:1620-1627. [PubMed]
  74. Quensen III, J.F., S.A. Mueller, M.K. Jain, and J.M. Tiedje. 1998. Reductive dechlorination of DDE to DDMU in marine sediment microcosms. Science 280:722-724. [PubMed]
  75. Dedysh, S.N., N.S. Panikov, W. Liesack, R. Gro(kopf, J. Zhou and J.M. Tiedje. 1998. Isolation of acidophilic methane-oxidizing bacteria from Northern peat wetlands. Science 282:281-284. [PubMed]
  76. McGowan, C., R. Fulthorpe, A. Wright and J.M. Tiedje. 1998. Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders. Appl. Environ. Microbiol. 64:4089-4092. [PubMed]
  77. Princic, A., I. Mahne, F. Megusar, E.A. Paul and J.M. Tiedje. 1998. Effects of pH and oxygen and ammonium concentrations on the community structure of nitrifying bacteria from wastewater. Appl. Environ. Microbiol. 64:3584-3590. [PubMed]
  78. Dybas, M.J., M. Barcelona, S. Bezborodnikov, S. Davies, L. Forney, H. Heuer, O. Kawka, T. Mayotte, L. Sepulveda-Torres, K. Smalla, M. Sneathen, J. Tiedje, T. Voice, D.C. Wiggert, M.E. Witt and C.S. Criddle. 1998. Pilot-scale evaluation of bioaugmentation for in-situ remediation of a carbon tetrachloride-contaminated aquifer. Environ. Sci. Technol. 32:3598-3611.
  79. Bruns, M.A., M.A. Fries, J.M. Tiedje and E.A. Paul. 1998. Functional gene hybridization patterns of terrestrial ammonia-oxidizing bacteria. Microbial Ecology 36:293-302. [PubMed]