James M. Tiedje, Primary Publications (1969-present):
  1. Tiedje, J.M. and M. Alexander. 1969. Enzymatic cleavage of the ether bond of 2,4-D. J. Agr. Food Chem. 17:1080-1084.

  2. Tiedje, J.M., J.M. Duxbury, M. Alexander, and J.E. Dawson. 1969. 2,4-D metabolism: Pathway of degradation of chlorocatechols by Arthrobacter sp. J. Agr. Food Chem. 17:1021-1026.

  3. Duxbury, J.M., J.M. Tiedje, M. Alexander, and J.E. Dawson. 1969. 2,4-D metabolism: Enzymatic conversion of chloromaleylacetic acid to succinic acid. J. Agr. Food Chem. 18:199-201. [PubMed]

  4. Erickson, A.E., J.M. Tiedje, B.G. Ellis, and C.M. Hansen. 1971. A barriered landscape renovation system for removing phosphate and nitrogen from feedlot waste, p. 232-234. In Proc. Int. Symp. Livestock Wastes, Columbus, OH. Special Publ. Amer. Soc. Agr. Engr.

  5. Erickson, A.E., J.M. Tiedje, B.G. Ellis, and C.M. Hansen. 1972. Initial observations of several medium sized barriered landscape water renovation systems for animal wastes, p. 405-410. In Water Management Res., Proc. Cornell Agr. Waste Management Conference.

  6. Caldwell, D.W., S.H. Lai, and J.M. Tiedje 1973. A two-dimensional steady-state diffusion gradient for ecological studies. In T.H. Rosswall (ed.), Modern Methods in the Study of Microbiol Ecology. Bull. Ecol. Res. Comm. (Stockholm) 17:151-158.

  7. Reyes, V.G. and J.M. Tiedje. 1973. Metabolism of 14C uniformly labelled organic material by woodlice (Isopoda: Oniscoidea) and soil microorganisms. Soil Biol. Biochem. 5:603-611.

  8. Tiedje, J.M., S.H. Lai, and A.E. Erickson. 1973. Martian life detection based on in situ soil gas analysis. In T.H. Rosswall (ed.) Modern Methods in the Study of Microbial Ecology. Bull. Ecol. Res. Comm. (Stockholm) 17:489-497.

  9. Tiedje, J.M., B.B. Mason, C.B. Warren, and E.J. Malec. 1973. Metabolism of nitrilotriacetate by cells of Pseudomonas species. Appl. Environ. Microbiol. 25:811-818. [PubMed]

  1. Erickson. A.E., B.G. Ellis, J.M. Tiedje, A.R. Wolcott, C.M. Hansen. F.R. Peabody, E.C. Miller and J.W. Thomas. 1974. Soil modification for denitrification and phosphate reduction of feedlot waste. EPA Rep. No. EPA-660-2-74-057. 118 pp.

  2. Tiedje, J.M., T.P. Duong, and M. Cichowski. 1974. Environmental control of nitrogen fixation in lakes: I. In situ nitrogen fixation by free living blue-green algae and I. Nitrogen fixation by the duckweed-algal association. OWRR Res. Rep. No. A-046MCIH. 34 pp.

  3. Tiedje, J.M., and B.B. Mason. 1974. Biodegradation of nitrilotriacetate (NTA) in soils. Soil Sci. Soc. Amer. Proc. 38:278-283.

  4. Caldwell, D.E., S.J. Caldwell and J.M. Tiedje. 1975. An ecological study of the sulfur-oxidizing bacteria from the littoral ozone of a Michigan lake and a sulfur spring in Florida. Plant and Soil 43:101-114.

  5. Caldwell, D.E. and J.M. Tiedje. 1975. A morphological study of anaerobic bacteria from the hypolimnia of several Michigan lakes. Can. J. Microbiol. 21:377-385. [PubMed]

  6. Caldwell, D.E. and J.M. Tiedje. 1975. The structure of anaerobic bacteria communities in the hypolimnia of several Michigan lakes. Can. J. Microbiol. 21:362-376. [PubMed]

  7. Firestone, M.K. and J.M. Tiedje. 1975. Biodegradation of metal-nitrilotriacetate complexes by a Pseudomonas species: mechanism of reaction. Appl. Environ. Microbiol. 29:758-764. [PubMed]

  8. Tiedje, J.M. 1975. Microbial degradation of ethylene diaminetetracetate in soils and sediments. Appl. Environ. Microbiol. 30:327-329.

  9. Tiedje, J.M. and M.L. Hagedorn. 1975. Degradation of alachlor by a soil fungus, Chaetomium globosum. J. Agr. Food Chem. 23:77-81. [PubMed]

  10. Jacobs. L.W., S.F. Chou and J.M. Tiedje. 1976. Fate of polybrominated biphenyls (PBB's) in soils: Persistence and plant uptake. J. Agr. Food Chem. 24:1198-1201. [PubMed]

  11. Lai, S.-H., J.M. Tiedje, and A.E. Erickson. 1976. In situ measurement of gas diffusion coefficient in soils. Soil Sci. Soc. Amer. Proc. 40:3-6.

  12. Reyes, V.G. and J.M. Tiedje. 1976. Ecology of the gut microbiota of an isopod, Tracheoniscus rathkei Brandt. Pedobiologia 16:67-74.

  13. Reyes, V.G. and J.M. Tiedje. 1976. Metabolism of 14C-labeled plant material by woodlice (Tracheoniscus rathkei Brandt) and soil microorganisms. Soil Biol. Biochem. 8:103-108.

  14. Gamble, T.N., M.R. Betlach, and J.M. Tiedje. 1977. Numerically dominant denitrifying bacteria from world soils. Appl. Environ. Microbiol. 33:926-939. [PubMed]

  15. Tiedje, J.M. 1977. Influence of environmental parameters on EDTA biodegradation in soils and sediments. J. Environ. Qual. 6:21-26.

  16. Chou, S.F., L.W. Jacobs, D. Penner, and J.M. Tiedje. 1978. Absence of plant uptake and translocation of polybrominated biphenyls (PBB's). Environ. Health Perspec. 23:9-12. [PubMed]

  17. Firestone, M.K., S.D. Aust, and J.M. Tiedje. 1978. A nitrilotriacetate monoxygenase with conditional NADH-oxidase activity. Arch. Biochem. 190:617-623. [PubMed]

  18. Firestone, M.K. and J.M. Tiedje. 1978. Pathway of degradation of nitrilotriacetate (NTA) by a Pseudomonas species. Appl. Environ. Microbiol. 35:955-961. [PubMed]

  19. Jacobs, L.W., S.F. Chou, and J.M. Tiedje. 1978. Field concentration and persistence of polybrominated biphenyls (PBB's) in soils and solubility of PBB in natural waters. Environ. Health Perspec. 23:1-8. [PubMed]

  20. McGahen, L.L. and J.M. Tiedje. 1978. Metabolism of two new acylanilide herbicides, Antor herbicide(tm) (H-22234) and Dual TM (metolachlor) by the soil fungus, Chaetomium globosum. J. Agr. Food Chem. 26:414-415.

  21. Smith, M.S., M.K. Firestone and J.M. Tiedje. 1978. The acetylene inhibition method for short-term measurement of denitrification and its evaluation using 13N. Soil Sci. Soc. Amer. J. 42:611-615.

  22. Strayer, R.F. and J.M. Tiedje. 1978. Application of the fluorescent antibody technique to study a methanogenic bacterium in lake sediments. Appl. Environ. Microbiol. 35:192-198. [PubMed]

  23. Strayer, R.F. and J.M. Tiedje. 1978. Kinetic parameters of the conversion of methane precursors to methane in a hypereutrophic lake sediment. Appl. Environ. Microbiol. 36:330-340.

  24. Strayer, R.F. and J.M. Tiedje. 1978. In situ methane production in a small, hypereutrophic, hard water lake: loss of methane from sediments by diffusion and ebullition. Limnol. Oceanogr. 23:1201-1206.

  25. Tiedje, J.M. 1978. Denitrification in soils, p. 362-366. In D. Schlessinger (ed.), Microbiology 1978. Amer. Soc. Microbiol. Washington, DC.

  26. Tiedje, J.M., M.K. Firestone, M.S. Smith, M.R. Betlach, and R.B. Firestone. 1978. Short-term measurement of denitrification rates in soils using 13N and acetylene inhibition methods, p. 132-137. In Proc. Intl. Symp. Microbiol. Ecology, Dunedin, NZ, Aug. 1977. Springer-Verlag.

  1. Caskey, W.H. and J.M. Tiedje. 1979. Nitrate-stimulated mineralization of ammonium in anaerobic soils. Ocealogia 41:339-341.

  2. Caskey, W.H. and J.M. Tiedje. 1979. Evidence for Clostridia agents of dissimilatory reduction of nitrate to ammonium in soils. Soil Sci. Soc. Amer. J. 43:931-936.

  3. Firestone, M.K., R.B. Firestone and J.M. Tiedje. 1979. Nitric oxide as an intermediate in denitrification: evidence from nitrogen-13 isotope exchange. Biochem. Biophys. Res. Commun. 91:10-16. [PubMed]

  4. Firestone, M.K., M.S. Smith, R.B. Firestone, and J.M. Tiedje. 1979. The influence of nitrate, nitrite and oxygen on the composition of the gaseous products of nitrification in soils. Soil Sci. Soc. Amer. J. 43:1140-1144.

  5. Firestone, M.K. and J.M. Tiedje. 1979. Temporal change in nitrous oxide and dinitrogen for denitrification following onset of anaerobiosis. Appl. Environ. Microbiol. 38:673-679.

  6. Smith, M.S. and J.M. Tiedje. 1979. Phases of denitrification following oxygen depletion in soils. Soil Biol. Biochem. 1:261-267.

  7. Smith, M.S. and J.M. Tiedje. 1979. The effects of roots on soil denitrification. Soil Sci. Soc. Amer. J. 43:951-955.

  8. Tiedje, J.M., R.B. Firestone, M.R. Betlach, M.S. Smith, and W.H. Caskey. 1979. Methods for the production and use of nitrogen-13 in studies of denitrification. Soil Sci. Soc. Amer. J. 43:709-715.

  9. Caskey, W.H. and J.M. Tiedje. 1980. The reduction of nitrate to ammonium by a Clostridum spp. isolated from soil. J. Gen. Microbiol. 119:217-223. [PubMed]

  10. Firestone, M.K., R.B. Firestone, and J.M. Tiedje. 1980. Nitrous oxide for soil denitrification: Factors controlling its biological production. Science 208:749-751.

  11. Kaspar, H.F. and J.M. Tiedje. 1980. Response of electron capture detector to H2, O2, N2, CO2, NO and N20. J. Chromatogr. 193:142-147.

  12. Mountfort, D.O., R.A. Asher, E.L. Mays and J.M. Tiedje. 1980. Carbon and electron flow in mud and sand flat international sediments at Delaware Inlet, Nelson, New Zealand. Appl. Environ. Microbiol. 39:686-694.

  13. Smith, M.S. and J.M. Tiedje. 1980. Growth and survival of antibiotic-resistance denitrifier strains in soil. Can J. Microbiol. 26:854-856.

  14. Sorensen, J., J.M. Tiedje, and R.B. Firestone. 1980. Inhibition of nitric and nitrous oxide reduction by denitrifying Pseudomonas fluorescens. Appl. Environ. Microbiol 39:105-108. [PubMed]

  15. Tiedje, J.M. 1980. An attempt at identifying research needs of studies on microbial transformations, pp. 333-334. In I.D. Schlessinger (ed.), Microbiology 1980. ASM Publications, Washington, DC.

  16. Tiedje, J.M. 1980. Nitrilotriacetate: hindsight and gunsight, pp. 114-119. In A.W. Maki, K.L. Dickson and J. Cairns (eds.), Biotransformation and fate of chemicals in the aquatic environment. Amer. Soc. Microbiol., Washington, DC.

  17. Betlach, M.R. and J.M. Tiedje. 1981. Assimilatory nitrate uptake in Pseudomonas fluorescens studied using nitrogen-13. Arch. Microbiol. 129:135-140. [PubMed]

  18. Firestone, R.B., M.R. Betlach, J.M. Tiedje, and M.K. Firestone. 1981. The feasibility of producing 11C, 13N, 15O, and 18F with heavy-ion beams, pp. 251-260. In J.W. Root and K.A. Krohn (eds.), Short-lived Radionuclides in Chemistry and Biology. Adv. Chem. Ser. No. 197, Amer. Chem. Soc., Washington.

  19. Kaspar, H.F. and J.M. Tiedje. 1981. Dissimilatory reduction of nitrate and nitrite in the bovine rumen: Nitrous oxide production and effect of acetylene. Appl. Environ. Microbiol. 41:705-709. [PubMed]

  20. Robinson, J.A., R.F. Strayer, and J.M. Tiedje. 1981. A method for measuring dissolved hydrogen in anaerobic ecosystems: Application to the rumen. Appl. Environ. Microbiol. 41:545-548. [PubMed]

  21. Tiedje, J.M. 1981. Use of nitrogen-13 and nitrogen-15 in studies on the dissimilatory fate of nitrate, pp. 481-497. In J.M. Lyons et al. (eds.), Genetic Engineering of Symbiotic Nitrogen Fixation and Conversation of Fixed Nitrogen. Plenum Publ., New York.

  22. Tiedje, J.M., R.B. Firestone, M.K. Firestone, M.R. Betlach, H.F. Kaspar, and J. Sorensen. 1981. Use of nitrogen-13 in studies of denitrification, pp. 295-317. In J.W. Root and K.A. Krohn (eds.), Short-lived Radionuclides in Chemistry and Biology. Adv. Chem. Ser. No. 197, Amer. Chem. Soc., Washington.

  23. Tiedje, J.M., J. Sorensen, and Y.-Y.L. Chang. 1981. Assimilatory and dissimilatory nitrate reduction: Perspectives and methodology for simultaneous measurement of several nitrogen cycle processes, p. 331-342. In F.E. Clark and T. Rosswall (eds.), Terrestrial Nitrogen Cycles -- Processes, Ecosystem Strategies and Management Impact. Ecol. Bull. (Stockholm) No. 33.

  24. Betlach, M.R. and J.M. Tiedje. 1981. A kinetic explanation for accumulation of nitrite, nitric oxide, and nitrous oxide during bacterial denitrification. Appl. Environ. Microbiol. 42:1074-1084.

  25. Kaspar, H.F., J.M. Tiedje, and R.B. Firestone. 1981. Denitrification and dissimilatory nitrate reduction to ammonium by digested sludge. Can. J. Microbiol. 27:878-885. [PubMed]

  26. Kaspar, H.F. and J.M. Tiedje. 1982. Anaerobic bacteria and processes. pp. 989-1009. In A.L. Page, R.H. Miller, and D.R. Keeney (eds.), Methods of Soil Analysis, Part 2. Agronomy Monograph No. 9, Amer. Soc. Agron., Madison, WI.

  27. Tiedje, J.M. 1982. Denitrification, pp. 1011-1026. In A.L. Page, R.H. Miller and D.R. Keeney (eds.), Methods of Soil Analysis, Part 2. Agronomy Monograph No. 9., Amer. Soc. Agron., Madison, WI.

  28. Tiedje, J.M. 1982. Soil Microbiology, pp. 177-209. In V.J. Kilmer (ed.), Handbook of Soils and Climate in Agriculture. CRC Press, Boca Raton, FL.

  29. Averill, B.A. and J.M. Tiedje. 1982. The chemical mechanism of microbial denitrification -- a hypothesis. FEBS Letters. 138:8-12. [PubMed]

  30. Horowitz, A., D.R. Shelton, C.P. Cornell, and J.M. Tiedje. 1982. Anaerobic degradation of aromatic compounds in sediments and digested sludge. Dev. Industr. Microbiol. 23:475-484.

  31. Bleakley, B.H. and J.M. Tiedje. 1982. Nitrous oxide production by organism other than nitrifiers and denitrifiers. Appl. Environ. Microbiol. 44:1342-1348.

  32. Robinson, J.A. and J.M. Tiedje. 1982. Kinetics of hydrogen consumption by rumen fluid, anaerobic digestor sludge and sediment. Appl. Environ. Microbiol. 44:1374-1384.

  33. Tiedje, J.M., A.J. Sexstone, D.D. Myrold, and J.A. Robinson. 1982. Denitrification: Ecological niches, competition and survival. Ant. van Leeuwenhoek J. Microbiol. 48:569-583. [PubMed]

  34. Suflita, J.M., A. Horowitz, D.R. Shelton, and J.M. Tiedje. 1982. Dehalogenation: Novel pathway for the anaerobic biodegradation of haloaromatic compounds. Science. 218:1115-1117.

  35. Garcia, J.-L. and J.M. Tiedje. 1982. Denitrification in rice soils, p. 187-208. In Dommergues and H.G. Diem (eds.), Microbiology of Tropical Soils and Plant Productivity. Martinus Nijhoff Publishers, The Hague.

  36. Robinson, J.A. and J.M. Tiedje. 1983. Nonlinear estimation of monod growth kinetic parameters from a single substrate depletion curve. Appl. Environ. Microbiol. 45:1453-1458. [PubMed]

  37. Horowitz, A., J.M. Suflita, and J.M. Tiedje. 1983. Reductive dehalogenation of halobenzoates by anaerobic lake sediment micro-organisms. Appl. Environ. Microbiol. 45:1459-1465.

  38. Suflita, J.M., J.A. Robinson, and J.M. Tiedje. 1983. Kinetics of microbial dehalogenation of haloaromatic substrates in methanogenic environments. Appl. Environ. Microbiol. 45:1466-1473.

  1. Morrissey, D.J., J.A. Nolen, C. Purcell, and J.M. Tiedje. 1984. A gas proportional counter system for the detection of 13N and other beta emitting gases. Nucl. Inst. Meth. Phys. Res. 224:238-242.

  2. Parkin, T.B., H.F. Kaspar, A.J. Sexstone, and J.M. Tiedje. 1984. A gas flow core method to measure field denitrification rates. Soil Biol. Biochem. 16:323-330.

  3. Parkin, T.B. and J.M. Tiedje. 1984. Application of a soil core method to investigate the affect of oxygen concentration on denitrification. Soil. Biol. Biochem. 16:331-334.

  4. Robertson, G.P. and J.M. Tiedje. 1984. Denitrification and nitrous oxide production in successional and old growth Michigan forests. Soil Sci. Soc. Amer. J. 48:383-389.

  5. Shelton, D.R., S.A. Boyd, and J.M. Tiedje. 1984. Anaerobic biodegradation of phthalic acid esters in sludge. Environ. Sci. Technol. 18:93-97.

  6. Shelton, D.R., and J.M. Tiedje. 1984. General method for determining anaerobic biodegradation potential. Appl. Environ. Microbiol. 47:850-857. [PubMed]

  7. Shelton, D.R. and J.M. Tiedje. 1984. Isolation and partial characterization of bacteria in an anaerobic consortium that mineralizes 3-chlorobenzoic acid. Appl. Environ. Microbiol. 48:840-848.

  8. Suflita, J.M., J. Stout, and J.M. Tiedje. 1984. Dechlorination of (2,4,5-trichlorophenoxy) acetic acid by anaerobic microorganisms. J. Agr. Food Chem. 32:218-221.

  9. Tiedje, J.M., A.J. Sexstone, T.B. Parkin, N.P. Revsbech, and D.R. Shelton. 1984. Anaerobic processes in soil. Plant and Soil 76:197-212.

  10. Robinson, J.A. and J.M. Tiedje. 1984. Competition between sulfate-reducing and methanogenic bacteria for H2 under resting and growing conditions. Arch. Microbiol. 137:26-32.

  11. Parkin, T.P., A.J. Sexstone, and J.M. Tiedje. 1985. Comparison of field denitrification rates determined by acetylene-based soil core 15N methods. Soil Sci. Soc. Amer. J. 49:94-99.

  12. Sexstone, A.J., T.P. Parkin, and J.M. Tiedje. 1985. Temporal response of soil denitrification rates to rainfall irrigation. Soil Sci. Soc. Amer. J. 49:99-103.

  13. Sexstone, A.J., N.P. Revsbech, T.P. Parkin, and J.M. Tiedje. 1985. Direct measurement of oxygen profiles and denitrification rates in soil aggregates. Soil Sci. Soc. Amer. J. 49:645-651.

  14. Myrold, D.D. and J.M. Tiedje. 1985. Diffusional constraints on denitrification in soil. Soil Sci. Soc. Amer. J. 49:651-657.

  15. Parkin, T.B., A.J. Sexstone, and J.M. Tiedje. 1985. Adaptation of denitrifying populations to low soil pH. Appl. Environ. Microbiol. 49:1053-1056.

  16. Morrissey, D.J., J.A. Nolen, and J.M. Tiedje. 1985. Radiotracers from heavy-ion fragmentation. Nucl. Instr. Methods in Physics Res. B10/11:963-966.

  17. Myrold, D.D. and J.M. Tiedje. 1985. Establishment of denitrification capacity in soil: effects of carbon, nitrate, and moisture. Soil Biol. Biochem. 17:819-822

  18. Robertson, G.P. and J.M. Tiedje. 1985. An automated technique for sampling the contents of stoppered gas-collection vials. Plant and Soil 83:453-457.

  19. Duong, T.P. and J.M. Tiedje. 1985. Nitrogen fixation by naturally occurring duckweed algae associations. Can J. Microbiol. 31:327-330.

  20. Dwyer, D.F. and J.M. Tiedje. 1986. Metabolism of polyethylene glycol by two anaerobic bacteria, Desulfovibrio desulfuricans and a Bacteroides sp. Appl. Environ. Microbiol. 52:852-856. [PubMed]

  21. Dolfing, J. and J.M. Tiedje. 1986. Hydrogen cycling in a three-tiered food web growing in the methanogenic conversion of 3-chlorobenzoate. FEMS Microbiol. Ecol. 38:293-298.

  22. Aerssens, G., J.M. Tiedje and B.A. Averill. 1986. Isotope labeling studies on the mechanism of N-N bond formation in denitrification. J. Biol. Chem. 261:9652-9656. [PubMed]

  23. Myrold, D.D. and J.M. Tiedje. 1986. Simultaneous estimation of several nitrogen cycle rates using 15N: Theory and application. Soil Biol. Biochem. 18:559-568.

  24. Dwyer, D.F., M.L. Krumme, S.A. Boyd and J.M. Tiedje. 1986. Kinetics of phenol biodegradation by an immobilized methanogenic consortium. Appl. Environ. Microbiol. 52:345-351.

  25. DeWeerd, K.A., J.M. Suflita, T. Linkfield, J.M. Tiedje, and P.H. Pritchard. 1986. The relationship between reductive dehalogenation and other aryl substituent removal reactions catalyzed by anaerobes. FEMS Microbiol. Ecol. 38:331-339.

  26. Robertson, G.P., P.M. Vitousek, P.A. Matson, and J.M. Tiedje. 1987. Denitrification in a clearcut loblolly pine (Pinus taeda L.) plantation in the southeastern U.S.: differences related to harvest intensity site preparation and herbicide treatment. Plant and Soil 97:119-129.

  27. Robertson, G.P. and J.M. Tiedje. 1987. Nitrous oxide sources in aerobic soils: Nitrification, denitrification, and other biological processes. Soil Biol. Biochem. 19:187-193.

  28. Tiedje, J.M. 1987. Environmental monitoring of microorganisms. In Prospects for Physical and Biological Containment of Genetically Engineered Organisms, pp. 115-127. J.W. Gillett (ed.), Ecosyst. Res. Center Rept. No. 114, Cornell University, Ithaca, NY.

  29. Dolfing, J. and J.M. Tiedje. 1987. Growth yield increase linked to reductive dechlorination in a defined 3-chlorobenzoate degrading methanogenic coculture. Arch. Microbiol. 149:102-105. [PubMed]

  30. Tiedje, J.M., S.A. Boyd, and B.Z. Fathepure. 1987. Anaerobic degradation of chlorinated aromatic hydrocarbons. Dev. Indust. Microbiol. 27:117-127.

  31. Fathepure, B.Z., J.M. Tiedje and S.A. Boyd. 1987. Reductive dechlorination of 4-chlororesorcinol by anaerobic microorganisms. Environ. Toxicol. Chem. 6:929-934.

  32. Weeg-Aerssens, E., J.M. Tiedje, and B. Averill. 1987. The mechanism of microbial denitrification. J. Amer. Chem. Soc. 109: 7214-7215.

  33. Groffman, P.M., J.M. Tiedje, G.P. Robertson, and S. Christensen. 1988. Denitrification at different temporal and geographical scales: proximal and distal controls. pp. 174-191. In "Advances in Nitrogen Cycling in Agricultural Ecosystems." J.R. Wilson (ed.), C.A.B. International: Wallingford, U.K.

  34. Christensen, S. and J.M. Tiedje. 1988. Sub-parts-per-billion nitrate method: Use of an N2O producing denitrifier to convert NO3- or 15NO3- to N2O. Appl. Environ. Microbiol. 54:1409-1413.

  35. Dolfing, J. and J.M. Tiedje. 1988. Acetate inhibition of methanogenic, syntrophic benzoate degradation. Appl. Environ. Microbiol. 54:1871-1873.

  36. Holben, W.E. and J.M. Tiedje. 1988. Applications of nucleic acid hybridization in microbial ecology. Ecology 69:561-568.

  37. Holben, W.E., J.K. Jansson, B.K. Chelm, and J.M. Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:703-711.

  38. Robertson, G.P., M.A. Huston, F.C. Evans, and J.M. Tiedje. 1988. Spatial variability in a successional plant community: Patterns of nitrogen mineralization, nitrification, and denitrification. Ecology. 69:1517-1524.

  39. Rice, C.W., P.E. Sierzega, J.M. Tiedje and L.W. Jacobs. 1988. Stimulated denitrification in the microenvironment of a biodegradable organic waste injected into soil. Soil Sci. Soc. Amer. J. 52:102-108.

  40. Tiedje, J.M. and T.O. Stevens. 1988. The ecology of an anaerobic dechlorinating consortium. p. 3-14. In G.S. Omenn, R. Colwell, A. Chakrabarty, M. Levin, P. McCarty (eds), Environmental Biotechnology: Reducing Risks from Environmental Chemicals, Plenum Press, New York. [Review]

  41. Fathepure, B.Z., J.M. Tiedje and S.A. Boyd. 1988. Reductive dechlorination of hexachlorobenzene to tri- and dichlorobenzenes in anaerobic sewage sludge. Appl. Environ. Microbiol. 54:327-330. [PubMed]

  42. Sexstone, A.J., T.B. Parkin, and J.M. Tiedje. 1988. Denitrification response to soil wetting in aggregated and unaggregated soil. Soil Biol. Biochem. 20:767-769.

  43. Tiedje, J.M. 1988. Ecology of denitrification and dissimilatory nitrate reduction to ammonium. p. 179-244. In A.J.B. Zehnder (ed), Environmental Microbiology of Anaerobes. John Wiley and Sons, N.Y.

  44. Christensen, S. and J.M. Tiedje. 1988. Oxygen control prevents denitrifiers and barley plant roots from directly competing for nitrate. FEMS Microbiol. Ecol. 53:217-221.

  45. Groffman, P.M. and J.M. Tiedje. 1988. Denitrification hysteresis during wetting and drying cycles in soil. Soil Sci. Soc. Amer. J. 52:1626-1629.

  46. Dwyer, D.F., Weeg-Aerssens, E., Shelton, D., and J.M. Tiedje. 1988. Bioenergetic conditions of butyrate metabolism by a syntrophic, anaerobic bacterium in coculture with hydrogen-oxidizing methanogenic and sulfidogenic bacteria. Appl. Environ. Microbiol. 54:1354-1359.

  47. Quensen, J.F., J.M. Tiedje, and S.A. Boyd. 1988. Reductive dechlorination of polychlorinated biphenyls by anaerobic microorganisms from sediments. Science 242:752-754.

  48. Hulse, C.L. J.M. Tiedje and B.A. Averill. 1988. A spectrophotometric assay for dissimilatory nitrite reductases. Anal. Biochem. 172:420-426. [PubMed]

  49. Weeg-Aerssens, E., J.M. Tiedje, and B.A. Averill. 1988. Evidence from isotope labelling studies for a sequential mechanism for dissimilatory nitrite reduction. J. Amer. Chem. Soc. 110:6851-6856.

  50. Stevens, T.O., T.G. Linkfield, and J.M. Tiedje. 1988. Physiological characterization of strain DCB-1, a unique dehalogenating sulfidogenic bacterium. Appl. Environ. Microbiol. 54:2938-2943. [PubMed]

  51. Stevens, T.O. and J.M. Tiedje. 1988. Carbon dioxide fixation and mixotrophic metabolism by strain DCB-1, a dehalogenating anaerobic bacterium. Appl. Environ. Microbiol. 54:2944-2948. [PubMed]

  52. Robertson, G.P. and J.M. Tiedje. 1988. Deforestation alters denitrification in a lowland tropical rain forest. Nature 336:756-759.

  1. Rice, C.W. and J.M. Tiedje. 1989. Regulation of nitrate assimilation by ammonium in soils and in isolated soil microorganisms. Soil Biol. Biochem. 21:597-602.

  2. Groffman, P.M. and J.M. Tiedje. 1989. Denitrification in north temperate forest soils: relationships between denitrification and environmental factors at the landscape scale. Soil Biol. Biochem. 21:621-626.

  3. Groffman, P.M. and J.M. Tiedje. 1989. Denitrification in north temperate forest soils: spatial and temporal patterns at the landscape and seasonal scales. Soil Biol. Biochem. 21:613-620.

  4. Coyne, M.S., A. Arunakumari, B.A. Averill, and J.M. Tiedje. 1989. Immunological identification and distribution of dissimilatory heme cd1 and nonheme copper nitrite reductases in denitrifying bacteria. Appl. Environ. Microbiol. 55:2924-2931. [PubMed]

  5. Jansson, J.K., W.E. Holben, and J.M.Tiedje. 1989. Detection in soil of a deletion in an engineered DNA sequence by using DNA probes. Appl. Environ. Microbiol. 55:3022-3025. [PubMed]

  6. Linkfield, T.G., J.M. Sulfita, and J.M. Tiedje. 1989. Characterization of the acclimation period before anaerobic dehalogenation of halobenzoates. Appl. Environ. Microbiol. 55:2773-2778. [PubMed]

  7. Tiedje, J.M., S. Simkins, and P.M. Groffman. 1989. Perspectives on measurement of denitrification in the field including recommended protocols for acetylene based methods. Plant and Soil 115:261-284.

  8. Tiedje, J.M., R.K. Colwell, Y.L. Grossman, R.E. Hodson, R.E. Lenski, R.N. Mack, and P.J. Regal. 1989. The planned introduction of genetically engineered organisms: ecological considerations and recommendations. Ecology 70:297-315.

  9. Hulse, C.L., J.M. Tiedje, and B.A. Averill. 1989. Evidence for a copper-nitrosyl intermediate in denitrification by the copper-containing nitrite reductase of Achromobacter cycloclastes. J. Am. Chem. Soc. 111:2322.

  10. Zak, D.R., P.M. Groffman, K.S. Pregitzer, S. Christensen, and J.M. Tiedje. 1990. The vernal dam:plant-microbe competition for nitrogen in northern hardwood forests. Ecology 71:651-656.

  11. Linkfield, T.G. and J.M. Tiedje. 1990. Characterization of the requirements and substrate for reductive dehalogenation by strain DCB-1. J. Indust. Microbiol. 5:9-15. [PubMed]

  12. Coyne, M.S. and J.M. Tiedje. 1990. Induction of denitrifying enzymes in oxygen-limited Achromobacter cycloclastes in continuous culture. FEMS Microbial Ecology 73:263-270.

  13. Mohn, W.W. and J.M. Tiedje. 1990. Strain DCB-1 conserves energy for growth from reductive dechlorination coupled to formate oxidation. Arch. Microbiol. 153:267-271. [PubMed]

  14. Mohn, W.W., T.G. Linkfield, H.S. Pankratz, and J.M.Tiedje. 1990. Involvement of a cellular structure in polar growth and cell division of strain DCB-1. Appl. Environ. Microbiol. 56:1206-1211.

  15. Mohn, W.W. and J.M. Tiedje. 1990. Catabolic thiosulfate disproportionation and carbon dioxide reduction by strain DCB-1, the reductively dechlorinating anaerobe. J. Bacteriol. 172:2065-2070. [PubMed]

  16. Coyne, M.S. and J.M. Tiedje. 1990. Distribution and diversity of dissimilatory NO2- reductases in dentrifying bacteria. In Denitrification in Soil and Sediment. J. Sorensen and N.P. Revsbech, ed., Plenum Press, N.Y. p. 21-35.

  17. Coyne, M.S., A. Arunakamari, H.S. Pankratz, and J. M. Tiedje. 1990. Localization of the cytochrome cd1 copper nitrite reductases in denitrifying bacteria. J. Bacteriol. 172:2558-2562. [PubMed]

  18. Christensen, S. and J.M. Tiedje. 1990. Brief and vigorous N2O production by soil at spring thaw. J. Soil Sci. 41:1-4.

  19. Tiedje, J.M. 1990. Ecological principles and experiences in the environmental release of genetically engineered organisms. In Advances in Biotechnology. Proceedings of Int'l Conf., Swedish Council for Forestry and Agricultural Research and Swedish Recombinant DNA Advisory Comm., pp. 115-130, SJFR, Stockholm.

  20. Quensen, J.F. III, S.A. Boyd and J.M. Tiedje. 1990. Dechlorination of four commercial polychlorinated biphenyl mixtures (Aroclors) by anaerobic microorganisms from sediments. Appl. Environ. Microbiol. 56:2360-2369.

  21. Christensen, S., S. Simkins and J.M. Tiedje. 1990. Spatial variation in soil denitrification: occurrence of activity centers (hot spots) as influenced by the soil environment. Soil Sci. Soc. Am. J. 54:1608-1618.

  22. Christensen, S., S. Simkins and J.M. Tiedje. 1990. Temporal patterns of soil denitrification: their stability and causes. Soil Sci. Soc. Am. J. 54:1614-1618.

  23. Hasebe, A., W.E. Holben, and J.M. Tiedje. 1990. Effect of percolation on vertical movements of the inoculated bacteria in soil. Soil Microorganisms 35:31-34 (In Japanese).

  24. Tiedje, J.M., W.E. Holben, W.W. Mohn, and J.F. Quensen III. 1990. Role of microorganisms in the protection of the environment. (Plenary lecture). Transact. 14th Int'l Congress of Soil Science, Kyoto, Japan; Int'l Soc. Soil Sci, VIII, 3-14.

  25. Dolfing, J., and J.M. Tiedje. 1991. Influence of substituents on reductive dehalogenation of 3-chlorobenzoate analogs. Appl. Environ. Microbiol. 57:820-824.

  26. Groffman, P., and J.M. Tiedje. 1991. Relationships between denitrification, CO2 production and air-filled porosity in soils of different texture and drainage. Soil Biol. Biochem. 23:229-302.

  27. Weeg-Aerssens, E., W. Wu, R.W. Ye, J.M. Tiedje, and C.K. Chang. 1991. Purification of cytochrome cd1 nitrite reductase from Pseudomonas stutzeri JM300 and reconstitution with native and synthetic heme d1. J. Biol. Chem. 266:7496-7502. [PubMed]

  28. Ye, R.W., I. Toro-Suarez, J.M. Tiedje, and B.A. Averill. 1991. H218O isotope exchange studies on the mechanism of reduction of nitric oxide and nitrite to nitrous oxide by denitrifying bacteria: evidence for an electrophilic nitrosyl during reduction of nitric oxide. J. Biol. Chem. 266:12848-12851. [PubMed]

  29. Knight, I.T., W.E. Holben, J.M. Tiedje, and R.R. Colwell. 1991. Nucleic acid hybridization techniques for detection, identification and enumeration of microorganisms in the environment, p. 65-91. In M.A. Levin, R.J. Seidler and M. Rogal (eds.), Microbial Ecology: Principles, Methods and Applications, McGraw-Hill, Inc., New York, NY.

  30. Dolfing, J., and J.M. Tiedje. 1991. Acetate as a source of reducing equivalents in the reductive dechlorination of 2,5-dichlorobenzoate. Arch. Microbiol. 156:356-361.

  31. Dolfing, J., and J.M. Tiedje. 1991. Kinetics of two complementary hydrogen sink reactions in a defined 3-chlorobenzoate degrading methano-genic co-culture. FEMS Microbiol. Ecol. 86:25-32.

  32. Tiedje, J.M., J.F. Quensen, III, W.W. Mohn, J.P. Schimel, J.A. Cole, and S.A. Boyd. 1991. Reductive dechlorination of chlorinated aromatic pollutants, p. 292-307. In: R.W. Rossmoore (ed.), Biodeterioration and Biodegradation 8, Elsevier Applied Science, New York, NY.

  33. Jackson, M.A., J.M. Tiedje, and B.A. Averill. 1991. Evidence for an NO-rebound mechanism for production of N2O from nitrite by the copper-containing nitrite reductase from Achromobacter cycloclastes. FEBS Letters 291:41-44. [PubMed]

  34. Mohn, W.W., and J.M. Tiedje. 1991. Evidence for chemiosmotic coupling of reductive dechlorination and ATP synthesis in Desulfomonile tiedjei. Arch. Microbiol. 157:1-6.

  35. Tiedje, J.M., J.K. Jansson, W.W. Mohn, W.E. Holben, and J.F. Quensen, III. 1991. Biotechnology for biodegradation and reductive dechlorination and nucleic acid probe tracking methods, 84-106. In L. Golovleva (ed.), Microbial degradation of xenobiotics. USSR Academy of Sciences, Pushchino, Russia.

  36. Groffman, P.M., J.M. Tiedje, D.L. Mokma, and S. Simkins. 1992. Regional scale analysis of denitrification in north temperate forest soils. Landscape Ecol. 7:45-53.

  37. Smith, G.B., and J.M. Tiedje. 1992. Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria. Appl. Environ. Microbiol. 58:376-384. [PubMed]

  38. Griffith, G.D., J.R. Cole, J.F. Quensen, III, and J.M. Tiedje. 1992. Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O. Appl. Environ. Microbiol. 58:409-411. [PubMed]

  39. Ye, D., J.F. Quensen, III, J.M. Tiedje, and S.A. Boyd. 1992. Anaerobic dechlorination of PCBs (Aroclor 1242) by pasteurized and ethanol treated microorganisms from sediments. Appl. Environ. Microbiol. 58:1110-1114. [PubMed]

  40. Ye, R.W., A. Arunakumari, B.A. Averill, and J.M. Tiedje. 1992. Mutants of Pseudomonas fluorescens deficient in dissimilatory nitrite reduction are also altered in nitric oxide reduction. J. Bacteriol. 174:2560-2564. [PubMed]

  41. Mohn, W.W. and J.M. Tiedje. 1992. Microbial reductive dehalogenation. Microbiol. Reviews, 56:482-507. [PubMed]

  42. Ye, R.W., B.A. Averill, and J.M. Tiedje. 1992. Characterization of Tn5 mutants deficient in dissimilatory nitrite reduction in Pseudomonas sp. strain G-179, which contains a copper nitrite reductase. J. Bacteriol. 174:6653-6658. [PubMed]

  43. Morris, P.J., W.W. Mohn, J.F. Quensen, III, J.M. Tiedje and S.A. Boyd. 1992. Establishment of a polychlorinated biphenyl-degrading enrichment culture with predominantly meta dechlorination. Appl Environ. Microbiol. 58:3088-3094. [PubMed]

  44. Morris, P.J., J.F. Quensen, III, J.M. Tiedje and S.A. Boyd. 1992. Reductive debromination of the commercial polybrominated biphenyl mixture firemaster BP6 by anaerobic microorganisms from sediments. Appl. Environ. Microbiol. 58:3249-3256. [PubMed]

  45. Holben, W.E., B.M. Schroeter, V.G.M. Calabrese, R.H. Olsen, J.K. Kukor, V.O. Biederbeck, A.E. Smith and J.M. Tiedje. 1992. Gene probe analysis of soil microbial populations selected by amendment with 2,4-dichlorophenoxyacetic acid (2,4-D). Appl. Environ. Microbiol. 58:3941-3948. [PubMed]

  46. Sanford, R.A. and J.M. Tiedje. 1992. Biodegradation of 2,4-D and chlorophenols under denitrifying conditions in soil column, microaerobic and anoxic enrichments, 543-548. In Soil Decontamination Using Biological Processes: International Symposium, Karlsruhe, Germany, DECHEMA, Frankfurt am Main.

  47. Quensen III, J.F., J.M. Tiedje, S.A. Boyd, C. Enke, R. Lopshire, J. Giesy, M. Mora, R. Crawford, and D. Tillitt. 1992. Evaluation of the suitability of reductive dechlorination for the bioremediation of pcb-contaminated soils and sediments, 91-100. In Soil Decontamination Using Biological Processes: International Symposium, Karlsruhe, Germany, DECHEMA, Frankfurt am Main.

  48. Tiedje, J.M., J.F. Quensen III, J. Chee-Sanford, J.P. Schimel, and S.A. Boyd. 1993. Microbial reductive dechlorination of PCBs. Biodegradation 4:231-240. [PubMed]

  49. Ye, R.W., M.R. Fries, S.B. Bezborodnikov, B.A. Averill and J.M. Tiedje. 1993. Characterization of the structural gene for a copper containing nitrite reductase and its homology to other denitrifiers. Appl. Environ. Microbiol. 59:250-254. [PubMed]

  50. Groffman, P.M., D.R. Zak, S. Christensen, A. Mosier and J.M. Tiedje. 1993. Early spring nitrogen dynamics in a temperate forest landscape. Ecology. 74(5):1579-1585.

  51. Groffman, P.M., C.W. Rice, J.M. Tiedje. 1993. Denitrification in a tallgrass prairie landscape. Ecology 74(3):855-862.

  52. Jordan, D., C.W. Rice, J.M. Tiedje. 1993. The effect of suppression treatments on the uptake of 15N by intercropped corn from labeled alfalfa (Medicago sativa). Biol. Fertil. Soils 16:221-226.

  53. Jorgensen, K.S. and J.M. Tiedje. 1993. Survival of denitrifiers in nitrate-free, anaerobic environments. Appl. Environ. Microbiol. 59:3297-3305.

  54. Morris, P.J., J.F. Quensen, III, J.M. Tiedje and S.A. Boyd. 1993. An assessment of the reductive debromination of polybrominated biphenyls in the Pine River Reservoir. Environ. Sci. Technol. 27:1580-1586.

  55. Tiedje, J.M. 1993. Bioremediation from an ecological perspective. p. 110-120. In In situ Bioremediation: when does it work? National Academy Press, Washington, D.C.

  56. Tiedje, J.M. 1993. (Editor) Environmental biotechnology issue, Current Opinion in Biotechnology, 4(3):273-362.

  57. Tiedje, J.M., M. Fries and J. Chee-Sanford. 1993. Is bioremediation of BTEX contaminated soils and aquifers possible under anaerobic conditions. Sec II, In Pacific Basin Conference on Hazardous Wastes, 1993 Proceedings, East-West Center, Honolulu, Hawaii.

  58. Holben, W.E., V.G.M. Calabrese, D. Harris, J.O. Ka and J.M. Tiedje. 1993. Analysis of structure and selection in microbial communities by molecular methods. pp. 367-370. In R. Guerrero and C. Pedros-Alio (eds.), Trends in Microbial Ecology, Spanish Society for Microbiology, Barcelona, Spain.

  59. Klug, M.J. and J.M. Tiedje. 1993. Response of microbial communities to changing environmental conditions: chemical and physiological approaches. pp. 371-374. In R. Guerrero and C. Pedros-Alio (eds.), Trends in Microbial Ecology, Spanish Society for Microbiology, Barcelona, Spain.

  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]
  1. Maidak, B.L., J.R. Cole, C.T. Parker, Jr., G.M. Garrity, N. Larsen, B. Li, T.G. Lilburn, M.J. McCaughey, G.J. Olsen, R. Overbeek, S. Pramanik, T.M. Schmidt, J.M. Tiedje and C.R. Woese. 1999. A new version of the RDP (Ribosomal Database Project). Nucl. Acids Res., 27:171-173. [PubMed]

  2. Ye, D., J.F. Quensen, III, J.M. Tiedje and S.A. Boyd. 1999. 2-Bromoethanesulfonate, sulfate, molybdate, and ethanesulfonate inhibit anaerobic dechlorination of polychlorobiphenyls by pasteurized microorganisms. Appl. Environ. Microbiol. 65:327-329. [PubMed]

  3. Tiedje, J.M. and J.L. Stein. 1999. Microbial Biodiversity: Strategies for its recovery. pp.682-692. In A.L. Demain and J. Davies (eds.). Manual of Industrial Microbiology and Biotechnology. Amer. Soc. Microbiol., Washington, DC.

  4. Tsoi, T.V., E.G. Plotnikova, J.R. Cole, W.F. Guerin, M. Bagdasarian and J.M. Tiedje. 1999. Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates. Appl. Environ. Microbiol. 65:2151-2162. [PubMed]

  5. Hrywna, Y., T.V. Tsoi, O.V. Maltseva, J.F. Quensen, III and J.M. Tiedje. 1999. Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls. Appl. Environ. Microbiol. 65:2163-2169. [PubMed]

  6. Tiedje, J.M., S. Asuming-Brempong, K. Nusslein, T.L. Marsh and S.J. Flynn. 1999. Opening the black box of soil microbial diversity. Appl. Soil Ecology 13:109-122. [ASE Abstract]

  7. Nüsslein, K. and J.M. Tiedje. 1999. Soil bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil. Appl. Environ. Microbiol. 65:3622-3626. [PubMed]

  8. Fernandez, A., S. Huang, S. Seston, J. Xing, R. Hickey, C. Criddle and J. Tiedje. 1999. How stable is stable? Function versus community composition. Appl. Environ. Microbiol. 65:3697-3704. [PubMed]

  9. Löffler, F.E., J.M. Tiedje and R.A. Sanford. 1999. Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology. Appl. Environ. Microbiol. 65:4049-4056. [PubMed]

  10. Fathepure, B.Z. and J.M. Tiedje. 1999. Anaerobic bioremediation: Microbiology, principles, and applications. pp. 339-396. In D.C. Adriano, J.M. Bollag, W.T. Frankenberger, Jr. and R.C. Sims (eds.). Bioremediation of Contaminated Soils, Agronomy Monograph no. 37. Soil Science Society of America, Madison, WI.

  11. Song, B., M.M. Haggblom, J. Zhou, J.M. Tiedje and N.J. Palleroni. 1999. Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp. nov. and Azoarcus toluclasticus sp. nov. Int'l. J. Syst. Bacteriol. 49:1129-1140. [PubMed]

  12. Boutonnet, J.C., P. Bingham, D. Calamari, C. de Rooij, J. Franklin, T. Kawano, J.M. Libre, A. McCulloch, G. Malinverno, J.M. Odom, G.M. Rusch, K. Smythe, I. Sobolev, R. Thompson and J.M. Tiedje. 1999. Environmental risk assessment of trifluoroacetic acid. Hum. Ecol. Risk Assess. 5:59-124.

  13. Tiedje, J.M. 1999. Exploring microbial life in Lake Vostok. p. 19-21. In R.E. Bell and D.M. Karl (eds.), Lake Vostok Workshop: Final Report. Lamont-Doherty of Columbia Univ., Palisades, NY.

  14. Maltseva, O.V., T.V. Tsoi, J.F. Quensen, III, M. Fukuda and J.M. Tiedje. 1999. Degradation of anaerobic reductive dechlorination products of Aroclor 1242 by four aerobic bacteria. Biodegradation 10:363-371. [PubMed]

  15. Tiedje, J.M. 2000. 20 years since Dunedin: The past and future of microbial ecology. pp. 933-939. In C.R. Bell, M. Brylinsky, P. Johnson-Green (eds.). Microbial Biosystems: New Frontiers.

  16. Dedysh, S.N., W. Liesack, V.N. Khmelenina, N.E. Suzina, Y.A. Trotsenko, J.D. Semrau, A.M. Bares, N.S. Panikov and J.M. Tiedje. 2000. Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int'l. J. Syst. Evol. Microbiol. 50:955-969. [PubMed]

  17. Evtushenko, L.I., V.V. Taran, V.N. Akimov, R.M. Kroppenstedt, J.M. Tiedje and E. Stackebrandt. 2000. Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev., and Nocardiopsis dassonvillei subsp. albirubida subsp. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 50:73-81. [PubMed]

  18. Evtushenko, L.I., L.V. Dorofeeva, S.A. Subbotin, J.R. Cole and J.M. Tiedje. 2000. Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of 'Corynebacterium aquaticum' Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 50:371-380. [PubMed]

  19. Flynn, S.J., F.E. Loffler and J.M. Tiedje. 2000. Microbial community changes associated with a shift from reductive dechlorination of PCE to reductive dechlorination of cis-DCE and VC. Environ. Sci and Technol. 34:1056-1061.

  20. Maidak, B.L., J.R. Cole, T.G. Lilburn, C.T. Parker, Jr., P.R. Saxman, J.M. Stredwick, G.M. Garrity, B. Li, G.J. Olsen, S. Pramanik, T.M. Schmidt and J.M. Tiedje. 2000. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28:173-174. [PubMed]

  21. Vishnivetskaya, T., S. Kathariou, J. McGrath, D. Gilichinsky and J.M. Tiedje. 2000. Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments. Extremophiles. 4:165-173. [PubMed]

  22. Löffler, F.E., Q. Sun, J. Li and J.M. Tiedje. 2000. 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Appl. Environ. Microbiol. 66:1369-1374. [PubMed]

  23. Braker, G., J. Zhou, L. Wu, A.H. Devol and J.M. Tiedje. 2000. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities. Appl. Environ. Microbiol. 66:2096-2104. [PubMed]

  24. DeWever, H., J.R. Cole, M.R. Fettig, D.A. Hogan and J.M. Tiedje. 2000. Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes, gen. nov., sp. nov. Appl. Environ. Microbiol. 66:2297-2301. [PubMed]

  25. Sun, B., J.R. Cole, R.A. Sanford and J.M. Tiedje. 2000. Isolation and characterization of Desulfovibrio dechloracetivorans sp. nov., a marine dechlorinating bacterium growing by coupling the oxidation of acetate to the reductive dechlorination of 2-chlorophenol. Appl. Environ. Microbiol. 66:2408-2413. [PubMed]

  26. Marsh, T.L., P. Saxman, J. Cole and J. Tiedje. 2000. Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl. Environ. Microbiol. 66:3616-3620. [PubMed]

  27. Hashsham, S.A., A.S. Fernandez, S.L. Dollhopf, F.B. Dazzo, R.F. Hickey, J.M. Tiedje and C.S. Criddle. 2000. Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose. Appl. Environ. Microbiol. 66:4050-4057. [PubMed]

  28. Fernandez, A.S., S.A. Hashsham, S.L. Dollhopf, L. Raskin, O. Glagoleva, F.B. Dazzo, R.F. Hickey, C.S. Criddle and J.M. Tiedje. 2000. Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Appl. Environ. Microbiol. 66:4058-4067. [PubMed]

  29. Nold, S.C., J. Zhou, A.H. Devol and J.M. Tiedje. 2000. Pacific northwest marine sediments contain ammonia-oxidizing bacteria in the ( subdivision of the Proteobacteria. Appl. Environ. Microbiol. 66:4532-4535. [PubMed]

  30. Cho, J.C. and J.M. Tiedje. 2000. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66:5448-5456. [PubMed]

  31. Hyndman, D.W., M.J. Dybas, D. Wiggert, X. Zhao, R. Wallace, T. Voice, A. Chan, M.S. Phanikumar and C.S. Criddle. 2000. Hydraulic characterization and design of a full-scale biocurtain. Ground Water, 38:462-474.

  32. Reichardt, W., K. Inubushi and J. Tiedje. 2000. Microbial processes in C and N dynamics. In G.J.D. Kirk and D.C. Olk (eds.), Carbon and Nitrogen Dynamics in Flodded Soils, International Rice Research Institute (IRRI), Los Baños, The Philippines.

  33. Tiedje, J.M. 2000. Putting novel microbes to work on industry wastes. pp. 47-54, In BioJapan 2000 Symposium Proceedings, Tokyo, Sept. 26-28. Japan Bioindustry Association, Tokyo.

  34. Hooper, D.U., D.E. Bignell, V.K. Brown, L. Brussaard, J.M. Dangerfield, D.H. Wall, D.A. Wardle, D.C. Coleman, K.E. Giller, P. Lavelle, W.H. Van Der Putten, P.C. De Ruiter, J. Rusek, W.L. Silver, J.M. Tiedje and V. Wolters. 2000. Interactions between aboveground and belowground biodiversity in terrestrial ecosystems: patterns, mechanisms, and feedbacks. BioScience 50:1049-1061. [request PDF]

  35. Rodrigues, J.L.M., O.V. Maltseva, T.V. Tsoi, R.R. Helton, J.F. Quensen, III, M. Fukuda and J.M. Tiedje. 2001. Development of a Rhodococcus recombinant strain for degradation of products from anaerobic dechlorination of PCBs. Environ. Sci. and Technol. 35:663-668. [PubMed]

  36. Quensen, III, J.F., J.M. Tiedje, M.K. Jain and S.A. Mueller. 2001. Factors controlling the rate of DDE dechlorination to DDMU in Palos Verdes margin sediments under anaerobic conditions. Environ. Sci. and Technol. 35:286-291. [PubMed]

  37. Tiedje, J.M., J.C. Cho, A. Murray, D. Treves, B. Xia and J. Zhou. 2001. Soil teeming with life: new frontiers for soil science. pp. 393-412. In R.M. Rees, B.C. Ball, C.D. Campbell and C.A. Watson (eds.), Sustainable Management of Soil Organic Matter. CABI Int'l, Wallingford, U.K.

  38. Qiu, X., L. Wu, H. Huang, P.E. McDonel, A.V. Palumbo, J.M. Tiedje and J.Z. Zhou. 2001. Evaluation of PCR-generated chimeras, mutations and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 67:880-887. [PubMed]

  39. Maidak, B.L., J.R. Cole, T.G. Lilburn, C.T. Parker, Jr., P.R. Saxman, R.J. Farris, G.M. Garrity, G.J. Olsen, T.M. Schmidt and J.M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173-174. [PubMed]

  40. Grüntzig, V., S.C. Nold, J. Zhou and J.M. Tiedje. 2001. Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR. Appl. Environ. Microbiol. 67:760-768. [PubMed]

  41. Braker, G., H.L. Ayala-del Rio, A.H. Devol, A. Fesefeldt and J.M. Tiedje. 2001. Community structure of denitrifiers, Bacteria, and Archaea along redox gradients in Pacific Northwest marine sediments by Terminal Restriction Fragment Length Polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl. Environ. Microbiol. 67:1893-1901. [PubMed]

  42. Dollhopf, S.L., S.A. Hashsham, F.B. Dazzo, R.F. Hickey, C.S. Criddle and J.M. Tiedje. 2001. The impact of fermentative organisms on carbon flow in methanogenic systems under constant low-substrate conditions. Appl. Microbiol. Biotechnol. 56:531-538. [PubMed]

  43. Sun, B., J.R. Cole and J.M. Tiedje. 2001. Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments. Int'l. J. Syst. Evol. Microbiol. 51:365-371. [PubMed]

  44. Dollhopf, S.L., S.A. Hashsham and J.M. Tiedje. 2001. Interpreting 16S rDNA T-RFLP data: Application of self-organizing maps and principle component analysis to describe community dynamics and convergence. Microb. Ecol. 42:495-505. [PubMed]

  45. Cho, J.C. and J.M. Tiedje. 2001. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl. Environ. Microbiol. 67:3677-3682. [PubMed]

  46. Evtushenko, L.I., L.V. Dorofeeva, T.G. Dobrovolskaya, G.M. Streshinskaya, S.A. Subbotin and J.M. Tiedje. 2001. Agreia bicolorata gen. nov., sp. nov. to accommodate actinobacteria isolated from narrow reed grass infected by nematode Heteroanguina graminophila. Int'l J. Syst. Evol. Microbiol. 51:2073-2079. [PubMed]

  47. Murray, A.E., D. Lies, G. Li, K. Nealson, J. Zhou and J.M. Tiedje. 2001. DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. PNAS 98:9853-9858. [PubMed]

  48. Hurt, R.A., X. Qiu, L. Wu, Y. Roh, A.V. Palumbo, J.M. Tiedje and J. Zhou. 2001. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67:4495-4503. [PubMed]

  49. Wu, L., D.K. Thompson, G. Li, R.A. Hurt, J.M. Tiedje and J. Zhou. 2001. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67:5780-5790. [PubMed]

  50. Tiedje, J., A. Fernandez, S. Hashsham, S. Dollhopf, F. Dazzo, R. Hickey and C. Criddle. 2001. Stability, persistence and resilience in anaerobic reactors: a community unveiled. In Advances in Water and Wastewater Treatment Technology, (eds) Matsuo, Hanaki, Takizawa, Satoh; Elsevier, Amsterdam.

  51. Hashsham, S.A., T.L. Marsh, S.L. Dollhopf, A.S. Fernandez, F.B. Dazzo, R.F. Hickey, C.S. Criddle and J.M. Tiedje. 2001. Relating function and community structure of complex microbial systems using neural networks. In Advances in Water and Wastewater Treatment Technology, (eds) Matsuo, Hanaki, Takizawa, Satoh; Elsevier, Amsterdam.

  52. Kitagawa, W., S. Takami, K. Miyauchi, E. Masai, Y. Kamagata, J.M. Tiedje and M. Fukuda. 2002. Novel 2,4-Dichlorophenoxyacetic acid degradation genes from an oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment. J. Bacteriol. 184:509-518. [PubMed]

  53. Beliaev, A.S., D.K. Thompson, C.S. Giometti, C.C. Brandt, G. Li, J. Yates III, K.H. Nealson, J.M. Tiedje, A.E. Murray, J.F. Heidelberg and J. Zhou. 2001. Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors. OMICS 6(1):39-60; errata in OMICS 7:138-139. [PubMed]

  54. Sanford, R.A., J.R. Cole and J.M. Tiedje. 2002. Characterization and description of Anaeromyxobacter dehalogenans gen. nov. sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl. Environ. Microbiol. 68:893-900. [PubMed]

  55. Dedysh, S.N., V.N. Khmelenina, N.E. Suzina, Y.A. Trotsenko, J.D. Semrau, W. Liesack and J.M. Tiedje. 2002. Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. Int'l J. Syst. Evol. Microbiol. 52:251-261. [PubMed]

  56. Zhou, J., B. Xia, D.S. Treves, L.Y. Wu, T.L. Marsh, R.V. O'Neill, A.V. Palumbo and J.M. Tiedje. 2002. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68:326-334. [PubMed]

  57. Thompson, D.K., A.S. Beliaev, C.S. Giometti, D. Lies, K.H. Nealson, H. Lim, J. Yates III, C.C. Brandt, J.M. Tiedje and J. Zhou. 2002. Transcription and proteomic analysis of a ferric uptake regulator (Fur) mutant of Shewanella oneidensis: Possible involvement of Fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl. Environ. Microbiol. 68:881-892. [PubMed]

  58. Cho, J.-C., J.M. Tiedje. 2002. Quantitative detection of microbial genes by using DNA microarrays. Appl. Environ. Microbiol. 68:1425-1430. [PubMed]

  59. Prieme, A., G. Braker and J.M. Tiedje. 2002. Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl. Environ. Microbiol. 68:1893-1900. [PubMed]

  60. Dybas, M.J., D.W. Hyndman, R. Heine, J. Tiedje, K. Linning, D. Wiggert, T. Voice, X. Zhao, L. Dybas and C.S. Criddle. 2002. Development, operation and long-term performance of a full-scale biocurtain utilizing bioaugmentation. Environ. Sci. and Technol. 36:3635-3644. [PubMed]

  61. He, J., Y. Sung, M.E. Dollhopf, B.Z. Fathepure, J.M. Tiedje and F.E. Löffler. 2002. Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene-contaminated sites. Environ. Sci. and Technol. 36:3945-3952. [PubMed]

  62. Itoh, K., R. Kanda, Y. Sumita, H. Kim, Y. Kamagata, K. Suyama, H. Yamamoto, R.P. Hausinger and J.M. Tiedje. 2002. tfdA-like genes in 2,4-dichlorophenoxyacetic acid-degrading bacteria belonging to the Bradyrhizobium-Agromonas-Nitrobacter-Afipia cluster in µ-Proteobacteria. Appl. Environ. Microbiol. 68:3449-3454. [PubMed]

  63. Rodrigues, J.L.M., M.R. Aiello, J.W. Urbance, T.V. Tsoi and J.M. Tiedje. 2002. Use of both 16S rRNA and engineered functional genes with real-time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil. J. Microbiol. Methods 51:181-189. [PubMed]

  64. Sun, B., B.M. Griffin, H.L. Ayala-del-Rio, S.A. Hashsham and J.M. Tiedje. 2002. Microbial dehalorespiration with 1,1,1-trichloroethane. Science. 298:1023-1025. [PubMed]

  65. Tiedje, J.M. 2002. Shewanella - the environmentally versatile genome. Nature Biotechnol. 20:1093-1094. [PubMed]

  66. Dorofeeva, L.V., L.I. Evtushenko, V.I. Krausova, A.V. Karpov, S.A. Subbotin and J.M. Tiedje. 2002. Rathayibacter caricis sp. nov. and Rathayibacter festucae sp. nov., isolated from the phyllosphere of Carex sp. and the leaf gall induced by the nematode Anguina graminis on Festuca rubra L., respectively. Int'l J. Syst. Evol. Microbiol 52:1917-1923. [PubMed]

  67. Zhou, J.-Z. and J.M. Tiedje. 2002. New DOE program expands dramatically beyond microbial genomics. ASM News: 68:110-111.

  68. Dollhopf, S.L., M.L. Pariseau, S.A. Hashsham and J.M. Tiedje. 2003. Competitive and cooperative interactions affecting a fermentative spirochete in anaerobic chemostats. Microb. Ecol. 46:1-11. [PubMed]

  69. Yan, T.-F., M.W. Fields, L.-Y. Wu, Y.-G. Zu, J.M. Tiedje and J.-Z. Zhou. 2003. Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ. Microbiol. 5:13-24. [PubMed]

  70. Liu, X.L., S.M. Tiquia, G. Holguin, L. Wu, S.C. Nold, A.H. Devol, K. Luo, A.V. Palumbo, J.M. Tiedje and J.-Z. Zhou. 2003. Molecular diversity of denitrifying genes in continental margin sediments within the oxygen deficient zone of the Pacific Coast of Mexico. Appl. Environ. Microbiol. 69:3549-3560. [PubMed]

  71. Lendvay, J.M., F.E. Loffler, M. Dollhopf, M.R. Aiello, G. Daniels, B.Z. Fathepure, M. Gebhard, R. Heine, R. Helton, J. Shi, R. Krajmalnik-Brown, C.L. Major, Jr., M.J. Barcelona, E. Petrovskis, R. Hickey, J.M. Tiedje and P. Adriaens. 2003. Bioreactive barriers: A comparison of bioaugmentation and biostimulation for chlorinated solvent remediation. Environ. Sci. Technol. 37:1422-1431. [EST Abstract]

  72. Sung, Y., K.M. Ritalahti, R.A. Sanford, J.W. Urbance, S.J. Flynn, J.M. Tiedje and F.E. Löffler. 2003. Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria, and their description as Desulfuromonas michiganensis sp. nov. Appl. Environ. Microbiol. 69:2964-2974. [PubMed]

  73. Braker, G. and J.M. Tiedje. 2003. Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Appl. Environ. Microbiol. 69:3476-3483. [PubMed]

  74. Zhou, J.-Z., B. Xia, H. Huang, D.S. Treves, L.J. Hauser, R.J. Mural, A.V. Palumbo and J.M.Tiedje. 2003. Bacterial phylogenetic diversity and a novel candidate division of two humid region sandy surface soils. Soil Biol. Biochem. 35:915-924.

  75. Löffler, F.E., J.R. Cole, K.M. Ritalahti and J.M. Tiedje. 2003. Diversity of dechlorinating bacteria. pp. 53-87. In Dehalogenation: Microbial Processes and Environmental Applications, (eds) Haggblom and Boussert; Kluwer Academic Publishers.

  76. Dorofeeva, L.V., V.I. Krausova, L.I. Evtushenko and J.M. Tiedje. 2003. Agromyces albus sp. nov., isolated from a plant (Androsace sp.). Int'l J. Syst. Evol. Microbiol. 53:1435-1438. [PubMed]

  77. Treves, D.S., B. Xia, J. Zhou and J.M. Tiedje. 2003. A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil. Microb. Ecol. 45:20-28. [PubMed]

  78. Urbance, J.W., J. Cole, P. Saxman and J.M. Tiedje. 2003. BSD: The biodegradative strain database. Nucleic Acids Res. 31:152-155. [PubMed]

  79. Cole, J.R., B. Chai, T.L. Marsh, R.J. Farris, Q. Wang, S.A. Kulam, S. Chandra, D.M. McGarrell, T.M. Schmidt, G.M. Garrity and J.M. Tiedje. 2003. The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31:442-443. [PubMed]

  80. Denef, V.J., J. Park, J.L.M. Rodrigues, T.V. Tsoi, S.A. Hashsham and J.M. Tiedje. 2003. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ. Microbiol. 5:933-943. [PubMed]

  81. Gilichinsky, D., E. Rivkina, V. Shcherbakova, K. Laurinavichuis and J. Tiedje. 2003. Supercooled water brines within permafrost-an unknown ecological niche for microorganisms: a model for astrobiology. Astrobiology 3:331-341. [Pubmed]
  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]

  1. Cole, J.R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R.J. Farris, A.S. Kulam-Syed-Mohideen, D.M. McGarrell, T. Marsh, G.M. Garrity and J.M. Tiedje. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. (Database issue) 37:D141-D145; doi: 10.1093/nar/gkn879. [PubMed]

  2. Bakermans, C., R.E. Sloup, D.G. Zarka, J.M. Tiedje and M.F. Thomashow. 2008. Development and use of genetic system to identify genes required for efficient low-temperature growth of Psychrobacter arcticus 273-4. Extremophiles 13:21-30; doi: 10.1007/s00792-008-0193-3. [PubMed]

  3. Ramette A., J.M. Tiedje and A. Boetius. 2009. Impact of space, time and complex environments on microbial communities. Clin. Microbiol. Infection 15(s1):60-62; doi: 10.11141/j.169-0691.2008.02692.x. [PubMed]

  4. 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 106:3976-3981; doi: 10.1073/pnas.0813403106 [PubMed]

  5. Bergholz, P.W., C. Bakermans and J.M. Tiedje. 2009. Psychrobacter arcticus 273-4 uses resource efficiency and molecular motin adaptations for subzero temperature growth. J. Bacteriol. 191:2340-2352; doi: 10.1128/JB.01377-08. [PubMed]

  6. Rodrigues, D.F., E.C. Jesus, H.L. Ayala-del-Río, V.H. Pellizari, D. Gilichinsky, L. Sepulveda-Torres and J.M. Tiedje. 2009. Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium. ISME Journal 3:658-665; doi: 10.1038/ismej.2009.25. [PubMed]

  7. Gao, H., Z.K. Yang, S. Barua, S.B. Reed, M.F. Romine, K.H. Nealson, J.K. Fredrickson, J.M. Tiedje and J. Zhou. 2009. Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA and NapA. ISME Journal, 3:1-11; doi: 10.1038/ismej.2009.40. [PubMed]

  8. Cardenas, E., J.R. Cole, J.M. Tiedje and J. Park. 2009. Microbial community analysis using RDPII (Ribosomal Database Project II): Methods, tools and new advances. Environ. Engr. Res., 14:3-9; doi: 10.4491/eer.2009.14.1.003. [pdf]

  9. Vishnivetskaya, T.A., S. Kathariou and J.M. Tiedje. 2009. The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 13:541-555; doi: 10.1007/s00792-009-0243-5. [PubMed]

  10. Rodríguez-Minguela, C.M., J.H.A. 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. 75:5100-5110; doi: 10.1128/AEM.00133-09. [PubMed]

  11. Jesus, E.C., T.L. Marsh, J.M. Tiedje and F.M. de S Moreira. 2009. Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME Journal 3:1004-1011; doi: 10.1038/ismej.2009.47. [PubMed]

  12. 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 sediments. Appl. Environ. Microbiol. 75:5501-5506; doi: 10.1128/AEM.00121-09. [PubMed]

  13. 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; doi: 10.1073/pnas.0902000106. [PubMed]

  14. 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; doi: 10.1128/AEM.01262-09. [PubMed]

  15. Parnell, J.J., V.J. Denef, J.Park, T. Tsoi and J.M. Tiedje. 2009. 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 21:147-156; doi: 10.1007/s10532-009-9289-4. [PubMed]

  16. 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; doi: 10.1038/ismej.2009.104. [PubMed]

  17. Van Nostrand, Joy D., W-M Wu, L. Wu, Y. Deng, J. Carley, S. Carroll, Z. He, B. Gu, J. Luo, C.S. Criddle, D.B. Watson, P.M. Jardine, T.L. Marsh, J.M. Tiedje, T.C. Hazen and J. Zhou. 2009. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ. Microbiol. 11:2611-2626; doi: 10.1111/j.1462-2920.2009.01986.x. [PubMed]

  18. Cole, J.R., K. Konstantidindis, R.J. Farris and J.M. Tiedje. 2010. Microbial diversity and phylogeny: Extending from rRNAs to genomes. pp. 1-19. In W-T Liu and J.K. Jansson (eds), Environmental Molecular Microbiology, Caister Academic Press. [book link]

  19. Yoder-Himes, D., K.T. Konstantinidis and J.M. Tiedje. 2010. Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS One 5(1):1-11 (e8724); doi: 10.1371/journal.pone.0008724. [PubMed]

  20. Ayala-del-Río, H., P.S. Chain, J.J. Grzymski, M.A. Ponder, N. Ivanova, P.W. Bergholz, G. Di Bartolo, L. Hauser, M. Land, C. Bakermans, D. Rodrigues, J. Klappenbach, D. Zarka, F. Larimer, P. Richardson, A. Murray, M. Thomashow and J.M. Tiedje. 2010. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl. Environ. Microbiol. 76:2304-2312; doi: 10.1128/AEM.02101-09. [PubMed]

  21. Oh, S., D.R. Yoder-Himes, J. Tiedje, J. Park and K.T. Konstantinidis. 2010. Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain. Appl. Environ. Microbiol. 76:2890-2988; doi: 10.1128/AEM.02826-09. [PubMed]

  22. Hemme, C., Y. Deng, T.J. Gentry, M.W. Fields, L. Wu, S. Barua, K. Barry, S.G. Tringe, D.B. Watson, Z. He, T.C. Hazen, J.M. Tiedje, E.M. Rubin and J. Zhou. 2010. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME Journal 4:660-672; doi: 10.1038/ismej.2009.154. [PubMed]

  23. Jesus, E., E. Susilawati, 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.

  24. Stres, B., L. Philippot, J. Faganeli and J.M. Tiedje, 2010. Frequent freeze-thaw cycles yield diminished yet resistant and responsive microbial communities in two temperate soils: a laboratory experiment. FEMS Microbiol Ecol. 74:323-335; doi: 10.1111/j.1574-6941.2010.00951.x. [PubMed]

  25. 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. 2010. A combined massively parallel sequencing-indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities. Appl. Environ. Microbiol. 76:6778-6786; doi: 10.1128/AEM.01097-10. [PubMed]

  26. Hinsa-Leasure, S., L. Bhavaraju, J. Rodrigues, C. Bakermans, D. Gilichinsky and J. Tiedje. 2010. Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample. FEMS Microbiol Ecol. 74:103-113; doi: 10.1111/j.1574-6941.2010.00945.x. [PubMed]

  27. Gao, H., S. Barua, Y. Liang, L. Wu, Y. Dong, S. Reed, J. Chen, D. Culley, D. Kennedy, Y. Yang, Z. He, K.H. Nealson, J.K. Fredrickson, J.M. Tiedje, M. Romine and J. Zhou. 2010. Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration. Microbiol Biotechnol. 3:455-466; doi: 10.1111/j.1751-7915.2010.00181.x. [PubMed]

  28. Teixeira, L., R.S. Peixoto1, J.C. Cury, W.J. Sul, V.H. Pellizari, J.Tiedje and A.S. Rosado. 2010. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME Journal 4:989-1001; doi: 10.1038/ismej.2010.35. [PubMed]

  29. Xu, M., W-M. Wu, L. Wu, Z. He, J.D. Van Nostrand, Y. Deng, J. Luo, J. Carley, M. Ginder-Vogel, T.J. Gentry, B. Gu,. D. Watson, P.M. Jardine, T.L. Marsh, J.M. Tiedje, T. Hazen, C.S. Criddle and J. Zhou. 2010. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME Journal 4:1060-1070; doi: 10.1038/ismej.2010.31. [PubMed]

  30. Cole, J.R., D.D. Myrold, C.H. Nakatsu, P.R. Owens, G. Kowalchuk, C. Tebbe and J.M. Tiedje. 2010. Development of Soil Metadata Standards for International DNA Sequence Databases. Proceedings, 19th World Congress of Soil Science, Brisbane, Australia, http://www.iuss.org/19th WCSS/WCSS_Main_Page.html. [pdf]

  31. Iwai, S., B. Chai, E. da C. Jesus, C.R. Penton, T.K. Lee, J.R. Cole and J.M. Tiedje.. 2011. Gene-targeted-metagenomics (GT-metagenomics) to explore the extensive diversity of genes of interest in microbial communities. pp. In Frans J. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. J. Wiley & Sons Press, Hoboken, NJ. [book link]

  32. Cole, James R., Qiong Wang, Benli Chai and James M. Tiedje. 2011. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. pp. In Frans J. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. J. Wiley & Sons Press, Hoboken, NJ. [book link]

  33. Brown, C.T. and J.M. Tiedje. 2011 Metagenomics: the paths forward. pp. In Frans J. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. J. Wiley & Sons Press, Hoboken, NJ. [book link]

  34. Wu, W-M., J. Carley, D. Watson, B. Gu, S. Brooks, S.S. Kelly, K. Kemner, J.D. van Nostrand, L. Wu, M. Xu, J. Zhou, J. Luo, E. Cardenas, C. Hwang, M.W. Fields, T.L. Marsh, J.M. Tiedje, S.J. Green, J.E. Kostka, P.K. Kitanidis, P.M. Jardine and C.S. Criddle. 2011. Bioreduction and immobilization of uranium in situ: a case study at USA DOE Oak Ridge site, Tennessee. Acta Scientiae Circumstaniae (in Chinese) 31(3). [Abstract]

  35. Li, R. J.M. Auchtung, J.M. Tiedje and R.M. Worden. 2011. Shewanella oneidensis MR-1 chemotaxis in a diffusion gradient chamber. Environ. Sci. Technol. 45:1014-1020; doi: 10.1021/es102425p. [PubMed]

  36. Santos, H.F., J. Cury, F. Lima Carmo, A. Lopes Santos, J. Tiedje, J.D. van Elsas, A. Soares Rosado and R. Silva Peixoto. 2011. Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: Bacterial proxies for oil pollution. PLoS One 6(3):e16943; doi: 10.1371/journal.pone.0016943. [PubMed]

  37. 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; doi: 10.1073/pnas.1015622108. [PubMed]

  38. 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; doi: 10.1128/AEM.00331-11. [PubMed]

  39. Cruz-García, Clarible, Alison E. Murray, Jorge L.M. Rodrigues, Jeffrey A. Gralnick, Lee Ann McCue, Margaret F. Romine, Frank E. Löffler and James M. Tiedje. 2011. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1. BMC Microbiology 11:64; doi: 10.1186/1471-2180-11-64. [PubMed]

  40. Patrauchan, M.A., J.J. Parnell, M.P. McLeod, C. Florizone, J.M. Tiedje and L.D. Eltis. 2011. Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400. Arch. Microbiol. (ePub ahead of print 26 Apr 11); doi: 10.1007/s00203-011-0705-x. [PubMed].

  41. Lee, T.K., J. Lee, W.J. Sul, S. Iwai, B. Chai, J.M. Tiedje, J. Park. 2011. Novel biphenyl oxidizing bacteria and dioxygenase genes from a Korean tidal mudflat. Appl. Environ. Microbiol. 77:3888-3891; doi: 10.1128/AEM.00023-11. [PubMed]

  42. Vishnivetskaya, T.A., S. Lucas, A. Copeland, A. Lapidus, T. Glavina del Rio, S. Kathariou, R.F. Ramaley, D.F. Rodrigues, C. Hendrix, P. Richardson and J.M. Tiedje. 2011. Complete genome sequence of the thermophilic bacterium Exiguobacterium sp. AT1b. J. Bacteriol. 193: 2880-2881; doi: 10.1128/JB.00303-11. [PubMed]

  43. 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. (ePub ahead of print 3 Jun 11.) doi: 10.1128/AEM.00097-1. [PubMed]

  44. Sul, Woo Jun, James R Cole, Ederson da C Jesus, Qiong Wang, Ryan J Farris, Jordan A Fish and James M Tiedje. 2011. Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering. PNAS 108:14637-14642; doi: 10.1073/pnas.1111435108. [PubMed]

  45. Ahmad, Farhan, Gregoire Seyrig, Dieter M. Tourlousse, Robert D. Stedtfeld, James M. Tiedje and Syed A. Hashsham. 2011. A CCD-based fluorescence imaging system for real-time loop-mediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips, Biomed. Microdevices 13:929-937; doi: 10.1007/s10544-011-9562-2.

  46. Santos, Adriana L, Jose F. Siqueira Jr., Isabela N. Rocas, Ederson C. Jesus, Alexandre S. Rosado, James M. Tiedje. 2011. Comparing the bacterial diversity of acute and chronic dental root canal infections. PLoS One 6(11):e28088; doi: 10.1371/journal.pone.0028088 [PubMed]

  47. Van Nostrand J.D., L. Wu, W.M. Wu, Z. Huang, T.J.Gentry, Y. Deng, J. Carley, S. Carroll, Z. He, B. Gu, J. Luo, C.S. Criddle, D.B. Watson, P.M. Jardine, T.L. Marsh, J.M. Tiedje, T.C. Hazen, J. Zhou. 2011. Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer. Appl Environ Microbiol. 77:3860-3869; doi: 10.1128/AEM.01981-10. [PubMed]

  48. Bakermans, C., P.W. Bergholz, D.F. Rodrigues, T.A. Vishnivetskaya, H.L. Ayala-del-Río and J.M. Tiedje. 2012. Genomic and expression analyses of cold-adapted microorganisms (Chapter 6). In Lyle Whyte and Robert Miller (Eds), Polar Microbiology: Life in a Deepfreeze. ASM Press, Washington. [book link]

  49. Liang, Chao, Ederson da C. Jesus, David S. Duncan, Randall D. Jackson, James M. Tiedje, Teri C. Balser. 2012. Soil microbial communities under model biofuel cropping systems in southern Wisconsin, USA: Impact of crop species and soil properties. Applied Soil Ecology 54:24-31; doi: 10.1016/j.apsoil.2011.11.015.

  50. Green, Stephan, Om Prakash, Puja Jasrotia, Will Overholt, Erick Cardenas, Daniela Hubbard, James Tiedje, David Watson, Christopher Schadt, Scott Brooks and Joel Kostka. 2012. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site. Appl Environ. Microbiol. 78(4):1039-1047; doi: 10.1128/AEM.06435-11. [PubMed]

  51. Caro-Quintero, Alejandro, Jennifer Auchtung, Jie Deng, Ingrid Brettar, Manfred Höfle, James M. Tiedje and Konstantinos T. Konstantinidis.. 2012. Genome sequencing of five Shewanella baltica strains recovered from the oxic-anoxic Interface of the Baltic Sea. J. Bacteriol. 194(5):1236 doi: 10.1128/JB.06468-11. [PubMed]

  52. Kim, Sang-Hoon, Christina Harzman, John K. Davis, Rachel Hutcheson, Joan B. Broderick, Terence L. Marsh, James M. Tiedje. 2012. Genome sequence of Desulfitobacterium hafniense DCB-2, a gram-positive anaerobe capable of dehalogenation and metal reduction. BMC Microbiology 12:21 doi: 10.1186/1471-2180-12-21. [PubMed]

  53. 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; doi: 10.1073/pnas.1120238109. [PubMed]

  54. He, Ruo, Matthew J. Wooller, John W. Pohlman, Catharine Catranis, John Quensen, James M. Tiedje, Mary Beth Leigh. 2012. Identification of functionally active aerobic methanotrophs in sediments from an Arctic lake using stable isotope probing. Environ. Microbiol. 14(6):1403-19; doi: 10.1111/j.1462-2920.2012.02725.x. [PubMed]

  55. Stedtfeld, Robert D., Dieter M. Tourlousse, Gregoire Seyrig, Tiffany M. Stedtfeld, Maggie Kronlein, Scott Price, Farhan Ahmad, Erdogan Gulari, James M. Tiedje, Syed A. Hashsham. 2012. Gene-Z: A device for point of care genetic testing using a Smartphone. Lab on a Chip 12(8):1454-1462; doi: 10.1039/C2LC21226A.

  56. Li, Rui, James M. Tiedje, Chichia Chiu and Robert M. Worden. 2012. Soluble electron shuttles can mediate energy taxis toward insoluble electron acceptors. Environ Sci and Technol. 46:2813-2820; doi: 10.1021/es204302w.

  57. He, Ruo, Matthew J. Wooller, John W. Quensen, James M. Tiedje, Mary Beth Leigh. 2012. Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments. ISMEJ 6(10):1937-1948; doi: 10.1038/ismej.2012.34. [PubMed]

  58. He, Ruo, Matthew Wooller, John Pohlman, John Quensen, James Tiedje and Mary Leigh. 2012. Shifts in identity and activity of methanotrophs in Arctic lake sediments in response to temperature changes. Appl Environ. Microbiol ePub 20 April; doi: 10.1128/AEM.00853-12. [PubMed]

  59. Pell, Jason, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje and C. Titus Brown. 2012. Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. PNAS 109:13272-13277; doi: 10.1073/pnas.1121464109. [PubMed]

  60. Katharios-Lanwermeyer. S, M. Rakic-Martinez, S. Ratani, D. Elhanafi, J. M. Tiedje and S. Kathariou. 2012. Co-selection of cadmium and benzalkonium chloride resistance in conjugative transfer from non-pathogenic Listeria spp. to other listeriae. Appl Environ Microbiol. 8(21):7549-7556; doi: 10.1128/AEM.02245-12. [PubMed]

  61. Liang, Chao, David S. Duncan, Teri C. Balser, James M. Tiedje and Randall D. Jackson. 2012. Soil microbial residue storage linked to soil legacy under biofuel cropping systems in southern Wisconsin, USA. Soil Biol Biochem. 57:939-942; doi: 10.1016/j.soilbio.2012.09.006.

  62. Oh, Seungdae, Sarah Buddenborg, Deborah R. Yoder-Himes, James Tiedje and Konstantinos T. Konstantinidis. 2012. Genomic diversity of Escherichia isolates from diverse habitats. PLoS One 7(10):e47005; doi: 10.1371/journal.pone.0047005. [PubMed]

  63. Penton, Christopher R., Jonathan L. Deenik, Brian N. Popp, Greg L. Bruland, Pia Engstrom, Derek St. Louis and, James Tiedje. 2012. Importance of sub-surface rhizosphere-mediatedcoupled nitrification- denitrification in a flooded agroecosystem in Hawaii. Soil Biol Biochem. 57:362-373; doi: 10.1016/j.soilbio.2012.10.018.

  64. Rodrigues, Jorge L. M.; Vivian Pellizari, Rebecca Mueller, Kyunghwa Baek, Ederson da C. Jesus, Fabiana Paula, Babur Mirza, George Hamaoui, Siu Mui Tsai, Brigitte Feigl, James M. Tiedje, Brendan J.M. Bohannan and Klaus NĂĽsslein. 2013. Conversion of the Amazon Rainforest to agriculture results in biotic homogenization of soil bacterial communities. PNAS 110:988-993; doi: 10.1073/pnas.1220608110. [PubMed]

  65. Tourlousse, Dieter M., Farhan Ahmad, Robert D. Stedtfeld, Gregoire Seyrig, James M. Tiedje and Syed A. Hashsham. 2012. A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomed. Devices. 14:769-778; doi: 10.1007/s10544-012-9658-3.

  66. Vital, Marius, Christopher R. Penton, Qiong Wang, Vincent B. Young, Dion A. Antonopoulos, Mitchell L. Sogin, Hilary G. Morrison, Laura Raffals, Eugene B. Chang, Gary B. Huffnagle, Thomas M. Schmidt, James R. Cole and James M. Tiedje. 2013. A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. BMC Microbiome 1:8; doi: 10.1186/2049-2618-1-8.

  67. Young, Vincent B., Laura H. Raffals, Susan M. Huse, Marius Vital, Dongjuan Dai, Patrick D. Schloss, Jennifer M. Brulc, Dionysios A. Antonopoulos, Rose L. Arrieta, John H. Kwon, K. Gautham Reddy, Nathaniel A. Hubert, Sharon L. Grimm, Joseph H. Vineis, Sushila Dalal, Hilary G. Morrison, A. Murat Eren, Folker Meyer, Thomas M. Schmidt, James M. Tiedje, Eugene B. Chang and Mitchell L. Sogin. 2013. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. BMC Microbiome 1:9; doi: 10.1186/2049-2618-1-9

  68. Zhu, Yong-Guan, 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; doi: 10.1073/pnas.1222743110 [PubMed]

  69. Rachid, Caio T. C. C., Adriana L. Santos, Marisa C. Piccolo, Fabiano C. Balieiro, Heitor L. C. Coutinho, Raquel S. Peixoto, James M. Tiedje and Alexandre S. Rosado. 2013. Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure. PLoS ONE 8:e59342; doi: 10.1371/journal.pone.0059342 [PubMed]

  70. Hinsa-Leasure, Shannon, Cassandra Koid, James M. Tiedje and Janna N. Schultzhaus. 2013. Biofilm formation by Psychrobacter arcticus and the role of a large adhesin in attachment to surfaces. Appl Environ Microbiol. 79:967-3973; doi: 10.1128/AEM.00867-13 PubMed]

  71. Sul, Woo Jun, Stella Asuming-Brempong, Qiong Wang. Dieter M. Tourlousse, C. Ryan Penton, Ye Deng, Jorge L. M. Rodrigues, Samuel G.K. Adiku, James W. Jones, Jizhong Zhou, James R. Cole and James M. Tiedje. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biol Biochem. 65:33-38; doi: 10.1016/j.soilbio.2013.05.007

  72. Wang, Q., J.F. Quensen III, J.A. Fish, T.K. Lee, Y. Sun, J.M. Tiedje and J.R. Cole. 2013. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. mBio 4:e00592-13; doi: 10.1128/mBio.00592-13 [PubMed]

  73. Penton C.P., T.A. Johnson, J.F. Quensen III, S. Iwai, J.R. Cole and J.M. Tiedje. 2013. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. Front Microbiol. 4:279, doi: 10.3389/fmicb.2013.00279 [PubMed]

  74. Fish, J.A., B. Chai, Q.Wang, Y. Sun, C.T. Brown, J.M. Tiedje and J.R. Cole. 2013. Functional gene pipeline and repository: tools for functional gene analysis. Front Microbiol. 4:291, doi: 10.3389/fmicb.2013.00291 [PubMed]

  75. Stres, B., W-J.Sul, B. Murovec and J.M. Tiedje. 2013. Recently deglaciated high-altitude soils of the Himalaya: diverse environments, heterogenous bacterial communities and long-range dust inputs from the upper troposphere. PLoS One. 8:e76440. doi: 10.1371/journal.pone.0076440 [PubMed]

  76. Rhodes, Albert N., Roberta R. Fulthorpe and James M. Tiedje. 2013. Probing functional diversity of global pristine soil communities with 3-chlorobenzoate reveals communities of generalists dominate catabolic degradation capacities. Appl Environ Microbiol. 79:6932-6940. doi: 10.1128/AEM.01905-13 [PubMed]

  77. Jin, Mingjie, William Bothfeld, Samantha Austin, Trey K. Sato, Alex La Reau, John F. Quensen, James M. Tiedje, Daniel R. Noguera, Bruce E. Dale, Robert Landick, Yaoping Zhang and Venkatesh Balan. 2013. Effect of storage conditions on the stability and fermentability of lignocellulosic hydrolysate. Bioresource Technol. 47:212-220. [PubMed]

  78. Penton, C.P., D. St. Louis, J.R. Cole, Y. Luo, L.Wu, E.A.G Schuur, J-Z. Zhou, J.M.Tiedje. 2013. Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions. Appl Environ Microbiol. 79:7063-7072; doi: 10.1128/AEM.01702-13 [PubMed]

  79. Yang, Yu, John Quensen, Jacques Mathieu, Qiong Wang, Jing Wang, Mengyan Li, James M. Tiedje, Pedro J.J. Alvarez. 2013. Pyrosequencing reveals higher impact of silver nanoparticles than Ag+ on the microbial community structure of activated sludge. Water Research 48:317-325; doi: 10.1016/j.watres.2013.09.046 [PubMed]

  1. Cole, J.R.., Q. Wang, J.A. Fish, B. Chai, D.M. McGarrell, Y. Sun, C.T. Brown, A. Porras- Alfaro, C.R. Kuske and J.M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucl Acids Res. 42, Database issue:D633-D642; doi: 10.1093/nar/gkt1244 [PubMed]

  2. Deng, J., I. Brettar, C. Luo, J. Auchtung, K.T. Konstantinidis, J.L. Rodrigues, M. Höfle and J.M. Tiedje. 2014. Stability, genotypic and phenotypic diversity of the Shewanella baltica population in the redox transition zone of the Baltic Sea. Environ Microbiol. 16(6):1854-1866; doi: 10.1111/1462-2920.12344 [PubMed]

  3. Yang, Y., J. Quensen, J. Mathieu, Q. Wang, J. Wang, M. Li, J.M. Tiedje and P.J. Alvarez. 2014. Pyrosequencing reveals higher impact of silver nanoparticles than Ag+ on the microbial community structure of activated sludge. Water Res. 48:317-325; doi: 10.1016/j.watres.2013.09.046 [PubMed]

  4. Zhang, Y., S.A. Boyd, B.J. Teppen, J.M. Tiedje and H. Li. 2014. Organic acids enhance bioavailability of tetracycline in water to Escherichia coli for uptake and expression of antibiotic resistance. Water Res. 65:98-106; doi: 10.1016/j.watres.2014.07.021 [PubMed]

  5. Penton, C.R., V.V. Gupta, J.M. Tiedje, S.M. Neate, K. Ophel-Keller, M. Gillings, P. Harvey, A. Pham and D.K. Roget. 2014. Fungal Community Structure in Disease Suppressive Soils Assessed by 28S LSU Gene Sequencing. PLoS ONE 09(4):e93893; doi: 10.1371/journal.pone.0093893 [PubMed]

  6. Smalla, K. and J.M. Tiedje. 2014. Editorial overview: Ecology and industrial microbiology. Curr Opin Microbiol. 19:v-vii; doi: 10.1016/j.mib.2014.06.011 [PubMed]

  7. Siles, J.A., C.T. Rachid, I. Sampedro, I. GarcĂ­a-Romera and J.M. Tiedje. 2014. Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment. PLoS One 9(7):e103035; doi: 10.1371/journal.pone.0103035 [PubMed]

  8. Luo, C., R.L.M. Rodriguez., E. Johnston, L. Wu, L. Cheng, K. Xue, Q. Tu, Y. Deng, Z. He, Z. Shi, M. Yuan, S. Rebecca, D. Li, Y. Luo, E.A.G. Schuur, P. Chain, J. Tiedje, J. Zhou and K. Konstantinidis. 2014. Soil microbial community responses to a decade of warming as revealed by comparative Metagenomics. Appl Environ Microbiol. 80:1777-1786. doi: 10.1128/AEM.03712-13 [PubMed]

  9. Vital, M., C.R. Penton, Q. Wang, V.B. Young, D.A. Antonopoulo, M.L. Sogin, H.G. Morrison, L. Raffals, E.B. Chang, G.B. Huffnagle, T.M. Schmidt, J.R. Cole and J.M. Tiedje. 2014. A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome. 2013 Mar 4;1(1):8; doi: 10.1186/2049-2618-1-8 [PubMed]

  10. Young, V.B., L.H. Raffals, S.M. Huse, M. Vital, D. Dai, P.D. Schloss, J.M. Brulc, D.A. Antonopoulos, R.L. Arrieta, J.H. Kwon, K.G. Reddy, N.A. Hubert, S.L. Grim, J.H. Vineis, S. Dalal, H.G. Morrison, A.M. Eren, F. Meyer, T.M. Schmidt, J.M. Tiedje, E.B. Chang and M.L. Sogin. 2014. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome. 1(1):9; doi: 10.1186/2049-2618-1-9 [PubMed]

  11. Zhou, J.Z., Y. Deng, P. Zhang, K. Xue, Y. Liang, J.D. Van Nostrand, Y. Yang, Z. He, L. Wu, D.A. Stahl, T.C. Hazen, J.M. Tiedje and A.P. Arkin. 2014. Stochasticity, succession and environmental perturbations in a fluidic ecosystem. PNAS 111(9):E836-E845; doi: 10.1073/pnas.1324044111 [PubMed]

  12. Penton, C.R., J.L. Deenik, B.N. Popp, G.L. Bruland, P. Engstrom, J. Mueller, A. Worden and J.M. Tiedje. 2014. Assessing nitrogen transformations in a flooded agroecosystem using the isotope pairing technique and nitrogen functional gene abundances. Soil Sci. 179(1):2-10; doi: 10.1097/SS.0000000000000038

  13. Zhang, Y., S.A. Boyd, B.J. Teppen, J. M Tiedje and H. Li. 2014. Role of Tetracycline Speciation in the Bioavailability to a Bioreporter for Uptake and Expression of Antibiotic Resistance. Environ. Sci. Technol. 48(9):4893-4900; doi: 10.1021/es5003428 [PubMed]

  14. Howe, A.C., J.K. Jansson, S.A. Malfatti, S.G. Tringe, J.M. Tiedje and C.T. Brown. 2014. Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A. 111(13):4904-4909; doi: 10.1073/pnas.1402564111 [PubMed]

  15. Vital, M., A.C. Howe and J.M. Tiedje. 2014. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. MBio. 5(2):e00889. doi: 10.1128/mBio.00889-14 [PubMed] PMC3994512

  16. Kyrpides, N.C., P. Hugenholtz, J.A. Eisen, T. Woyke, M. Göker, C.T. Parker, R. Amann, B.J. Beck, P.S.G. Chain, J. Chun, R.R. Colwell, A. Danchin, P. Dawyndt, T. Dedeurwaerdere, E.F. DeLong, J.C. Detter, P. De Vos, T. J. Donohue, X-Z. Dong, D.S. Ehrlich, C. Fraser, R. Gibbs, J. Gilbert, P. Gilna, F.O. Glöckner, J.K. Jansson, J.D. Keasling, R. Knight, D. Labeda, A. Lapidus, J-S. Lee, W-J. Li, J. MA, V. Markowitz, E.R.B. Moore, M. Morrison, F. Meyer, K.E. Nelson, M. Ohkuma, C.A. Ouzounis, N. Pace, J. Parkhill, N. Qin, R. Rossello-Mora, J. Sikorski, D. Smith, M. Sogin, R. Stevens, U. Stingl, K. Suzuki, D. Taylor, J.M. Tiedje, B. Tindall, M. Wagner, G. Weinstock, J. Weissenbach, O. White, J. Wang, L. Zhang, Y-G. Zhou, D. Field, W.B. Whitman, G.M. Garrity, H-P. Klenk. 2014. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains. PLoS Biol. 12(8): e1001920; doi: 10.1371/journal.pbio.1001920 [PubMed]

  17. Paula F.S., J.L.M. Rodrigues, J. Zhou, L. Wu, R.C. Mueller, B.S. Mirza, B.J.M. Bohannan, K. Nuesslein, Y. Deng, J.M. Tiedje and V.H. Pellizari. 2014. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities. Mol Ecol. 23(12):2988-2999; doi: 10.1111/mec.12786 [PubMed]

  18. Cole, J.R. and J.M. Tiedje. 2014. History and impact of RDP: A legacy from Carl Woese to microbiology. RNA Biol. 11(3):239-243; doi: 10.4161/rna.28306 [PubMed]

  19. Siles, J.A., C.T.C.C. Rachid, I. Sampedro, I. GarcĂ­a-Romera and J.M Tiedje. 2014. Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment. PLoS ONE 9(7):e103035; doi: 10.1371/journal.pone.0103035 [PubMed]

  20. Liang, J., D. Li, Z. Shi, J.M. Tiedje, J. Zhou, E.A.G. Schuur, K.T. Konstantinidis and Y.i Luo. 2014. Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation. Soil Biol Biochem. 80:127-135; doi: 10.1016/j.soilbio.2014.10.005

  21. Zaborin, A., D. Smith, K. Garfield, J. Quensen, B. Shakhsheer, M. Kade, M. Tirrell, J. Tiedje, J.A. Gilbert, O. Zaborina and J.C. Alverdy. 2014. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. MBio 5(5):e01361-14; doi: 10.1128/mBio.01361-14 [PubMed]

  22. Vital, M., B. Chai, B. Ostman, J. Cole, K.T. Konstantinidis and J.M. Tiedje. 2014. Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. ISME J. 9:1130-1140; doi: 10.1038/ismej.2014.204 [PubMed]

  23. Vital, M., J. Gao, M. Rizzo, T. Harrison and J.M. Tiedje. 2014. Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia. ISME J. 9:832-833; doi: 10.1038/ismej.2014.179 [PubMed]

  24. Zhang, Y., S.A. Boyd, B.J. Teppen, J.M. Tiedje and H. Li. 2014. Organic acids enhance bioavailability of tetracycline in water to Escherichia coli for uptake and expression of antibiotic resistance. Water Res. 65:98-106; doi: 10.1016/j.watres.2014.07.021 [PubMed]

  25. Su, J.Q., L.J. Ding, K. Xue, H.Y. Yao, J. Quensen, S.J. Bai, W.X. Wei, J.S. Wu, J. Zhou, J.M. Tiedje and Y.G. Zhu. 2015. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Mol Ecol. 24(1):136-150; doi: 10.1111/mec.13010 [PubMed]

  26. Deng, J., Y. Gu, J. Zhang, K. Xue, Y. Qin, M. Yuan, H. Yin, Z. He, L. Wu, E.A. Schuur, J.M. Tiedje and J. Zhou. 2015. Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska. Mol Ecol. 24(1):222-234; doi: 10.1111/mec.13015 [PubMed]

  27. Gillings, M.R., W.H. Gaze, A. Pruden, K. Smalla, J.M. Tiedje and Y-G. Zhu. 2014. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J. 9(6):1269–1279; doi: 10.1038/ismej.2014.226 [PubMed]

  28. Vital, M., J.R. Harkema, M. Rizzo, J. Tiedje and C. Brandenberger. 2015. Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease. J Immunology Res 2015, Article ID 892568:1-8; doi: 10.1155/2015/892568 [PubMed]

  29. He, R., M.J. Wooller, J.W. Pohlman, J.M. Tiedje and M.B. Leigh. 2015. Methane-derived carbon flow through microbial communities in arctic lake sediments. 2015. Environ Microbio. 17(9):3233-3250; doi: 10.1111/1462-2920.12773 [PubMed]

  30. Rachid, C., F.C. Balieiro, E.S. Fonseca, R.S. Peixoto, G.M. Chaer, J.M. Tiedje and A.S. Rosado. 2015. Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations. PLoS ONE 10(2):e011851; doi: 10.1371/journal.pone.0118515 [PubMed]

  31. Zhang, P., W-M. Wu, J.D. Van Nostrand, Y. Deng, Z. He, T. Gihring, G. Zhang, C.W. Schadt, D. Watson, P. Jardine, C.S. Criddle, S. Brooks, T.L. Marsh, J.M. Tiedje, A.P. Arkin and J. Zhou. 2015. Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction. Appl Environ Microbiol. 81(12):4164-4172; doi: 10.1128/AEM.00043-15 [PubMed]

  32. Li, B., Y. Yang, L. Ma, F. Ju, F. Guo, J.M. Tiedje and T. Zhang. 2015. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J Advance 9(11):2490-2502; doi: 10.1038/ismej.2015.59 [PubMed]

  33. Zhang, B., C.R. Penton, C. Xue, Q. Wang, T. Zheng and J.M. Tiedje. 2015. Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH. Appl Environ Microbiol. 81(13):4536-4545; doi: 10.1128/AEM.00111-15 [PubMed]

  34. Leigh, M.B., W-M. Wu, E. Cardenas, O. Uhlik, S. Carroll, T. Gentry, T.L. Marsh, J. Zhou, P. Jardine, C.S. Criddle and J.M. Tiedje. 2015. Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing. Front of Environ Sci Engin 9(3):453-464; doi: 10.1007/s11783-014-0721-6

  35. Penton, C.R., D. St. Louis, A. Pham, J.R. Cole, L. Wu, Y. Luo, E.A.G. Schuur, J. Zhou, and J.M. Tiedje. 2015. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils. Front Microbiology 21 July 2015; doi: 10.3389/fmicb.2015.00746 [PubMed]

  36. Singh, P., T.K. Teal, T.L. Marsh, J.M. Tiedje, R. Mosci, K. Jernigan, A. Zell, D.W. Newton, H. Salimnia, P. Lephart, D. Sundin, W. Khalife, R.A. Britton, J.T. Rudrik and S.D. Manning. 2015. Intestinal microbial communities associated with acute enteric infections and disease recovery. Microbiome 3:45; doi: 10.1186/s40168-015-0109-2 [PubMed]

  37. Wang, Q., J. A. Fish, M. Gilman, Y. Sun, C. T. Brown, J. M Tiedje and J. R Cole. 2015. Xander: employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome 3:32; doi: 10.1186/s40168-015-0093-6 [PubMed]

  38. Stedtfeld, R.D., Y.C. Liu, T.M. Stedtfeld, T. Kostic, M. Kronlein, O. Srivannavit, W.T. Khalife, J.M. Tiedje, E. Gulari, M. Hughes, B. Etchebarne and S.A. Hashsham. 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):9994; doi: 10.1007/s10544-015-9994-1 [PubMed]

  39. Hemme, C.L., Q. Tu, Z. Shi, Y. Qin, W. Gao, Y. Deng, J.D. Van Nostrand, L. Wu, Z. He, P.S.G. Chain, S.G. Tringe, M.W. Fields, E.M. Rubin, J.M. Tiedje, T.C. Hazen, A.P. Arkin and J. Zhou. 2015. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front. Microbiol. 6:1205; doi: 10.3389/fmicb.2015.01205 [PubMed]

  40. Navarrete, A.A., A.M. Venturini, K.M. Meyer, A.M. Klein, J.M. Tiedje, B.J.M. Bohannan, K. NĂĽsslein, S.M. Tsai and J.L.M. Rodrigues. 2015. Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon. Front. Microbiol. 6:1443; doi: 10.3389/fmicb.2015.01443 [PubMed]

  41. Seyrig, G., R.D. Stedtfelda, D.M. Tourloussea, F. Ahmada, K. Towerya, A.M. Cupples, J.M. Tiedje and Syed A. Hashsham. 2015. Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. J Microbiological Methods 119:223–227; doi: 10.1016/j.mimet.2015.11.004 [PubMed]

  42. Jesus, E. da C., C. Liang, J.F. Quensen, E. Susilawati, R.D. Jackson, T.C. Balser and J.M. Tiedje. 2015. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States. ePub ahead of print 26 Dec 2015. GCB Bioenergy 8(2): 481-494; doi: 10.1111/gcbb.12289

  43. Xue, C.. C.R. Penton, B. Zhang, M. Zhao, D.E. Rothstein, D.J. Mladenoff, J.A. Forrester, Q. Shen and J.M. Tiedje. 2016. Soil fungal and bacterial responses to conversion of open land to short rotation woody biomass crops. GCB Bioenergy 8(4):723–736; doi: 10.1111/gcbb.12303

  44. Ma, L., Y. Xia, B. Li, Y. Yang, L-G. Li, J.M. Tiedje and T. Zhang. 2016. Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces. Environ. Sci. Technol. 50(1):420–427; doi: 10.1021/acs.est.5b03522 [PubMed]

  45. Guo, J., J.R. Cole, Q. Zhang, C.T. Brown and J.M. Tiedje. 2016. Microbial community analysis with ribosomal gene fragments from shotgun metagenomes. Appl Environ Microbiol. 82(1):157-166; doi: 10.1128/AEM.02772-15 [PubMed]

  46. Liang, C., E.daC. Jesus, D.S. Duncan, J.F. Quensen, R.D. Jackson, T.C. Balser and J.M. Tiedje. 2016. Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA. Soil Biology and Biochem 94:173-180; doi: 10.1016/j.soilbio.2015.11.020 [PubMed]

  47. Karkman, A., T. Johnson, C. Lyra, R. Stedtfeld, M. Tamminen, J.M. Tiedje and M. Virta. 2016. High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. FEMS Microbiol Ecol.  Jan 31 pii: fiw014. First published online; doi: 10.1093/femsec/fiw014 [PubMed].

  48. Stedtfeld, R., M. Williams, U. Fakhera, T. Johnson, T. Stedtfeld, F. Wang, W. Khalife, M. Hughes, B. Etchebarne, J.M. Tiedje, and S. Hashsham. 2016. Antimicrobial resistance (AR) dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol Ecol. Feb 4 pii: fiw020First published online; doi: 10.1093/femsec/fiw020 [PubMed]

  49. Penton, C.R., V.V. Gupta, J. Yu, J.M. Tiedje. 2016. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons. Front Microbiol. 7:824.; doi: 10.3389/fmicb.2016.00824 [PubMed]

  50. Johnson, T.A., R.D. Stedtfeld, Q. Wang, J.R. Cole, S.A. Hashsham, T. Looft, Y-G. Zhu, and J.M. Tiedje. 2016. Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture. mBio 7(2):e02214-15; doi: 10.1128/mBio.02214-15 [PubMed]

  51. de Carvalho, T. S., E. d. C. Jesus. ,J. Barlow, T.A. Gardner, I.C. Soares, J.M. Tiedje, and F. M. d. S.Moreira. 2016. Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria. Ecology 97(10):2760–2771; doi: 10.1002/ecy.1513

  52. Xue, K., M.M. Yuan, J. Xie, D. Li, Y. Qin, L.E. Hale, L. Wu, Y. Deng, Z. He, J.D. Van Nostrand, Y. Luo, J.M. Tiedje, and J. Zhou. 2016. Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming. mBio 7(5): e00976-16; doi: 10.1128/mBio.00976-16 [PubMed]

  53. Hambright, W.S., J. Deng, J.M. Tiedje, I. Brettar, and J.L.M. Rodrigues. 2016. Shewanella baltica Ecotypes Have Wide Transcriptional Variation under the Same Growth Conditions. mSphere 1(5), pii: e00158-16; doi: 10.1128/mSphere.00158-16 [PubMed]

  54. Smalla, K., P. Simonet, J. Tiedje, and E. Topp. 2016. Emergence of Antibiotic Resistant Pathogens and One Health--Editorial and Opinion: Special section of FEMS Microbiology Ecology on the environmental dimension of antibiotic resistance. FEMS Microbiol Ecol: first published online Sept 2016; doi: 10.1093/femsec/fiw172

  55. Wang, F., R.D. Stedtfeld, O-S. Kim, B. Chai, L. Yang, T.M. Stedtfeld, S.G. Hong, D. Kim, H.S. Lim, S.A. Hashsham, J.M. Tiedje, and W.J. Sul. 2016. Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils. Environ Sci Technol. (ePub before print, October 2016); doi: 10.1021/acs.est.6b02863

  56. Hamaoui, Jr., G.S., J.L.M. Rodrigues, B.J.M. Bohannan, J.M. Tiedje, and K. NĂĽsslein. 2016. Land-use change drives abundance and community structure alterations of thaumarchaeal ammonia oxidizers in tropical rainforest soils in RondĂ´nia, Brazil. Appl Soil Ecol 107: 48-56; doi: 10.1016/j.apsoil.2016.05.012

  57. Garoutte, A., E. Cardenas, J. Tiedje, and A. Howe. 2016. Methodologies for probing the metatranscriptome of grassland soil. J Microbiol Methods 131: 122–129; doi: 10.1016/j.mimet.2016.10.018 [PubMed]

  58. Penton, C.R., C. Yang, L. Wu, Q. Wang, J. Zhang, F. Liu, Y. Qin, Y. Deng, C. L. Hemme, T. Zheng, E.A.G. Schuur, J. Tiedje, and J. Zhou. 2016. NifH-Harboring Bacterial Community Composition Across an Alaskan Permafrost Thaw Gradient. Front Microbiol 7:1894 (e42149); doi: 10.3389/fmicb.2016.01894 [PubMed]

  59. Choi, J., F. Yang, R. Stepanauskas, E. Cardenas, A. Garoutte, R. Williams, J. Flater, J.M. Tiedje, K.S. Hofmockel, B. Gelder, and A. Howe. 2016. Strategies to improve reference databases for soil microbiomes. ISME J, December 9 Epub ahead of print; doi: 10.1038/ismej.2016.168 [PubMed]