TM Vogel Publications

PUBLICATIONS: Timothy M. VOGEL

BOOKS (or Chapters)

Vogel, T.M. and Walter, M. 2002. Bioaugmentation In: Manual of Environmental Microbiology ASM pp.952-959.

Magar, V.S., Vogel, T.M., Aelion, C.M., et Leeson, A. (editors)2001. Innovative Methods in Support of Bioremediation. Battelle Press.Columbus, OH, USA

Ballerini, D., Gatellier, G., and Vogel,T.M. 1998. L’Etat de l’Art du Traitement Biologique du Sol, ADEME, Angers, France

Adriaens, P. and Vogel, T.M. 1995. Biological treatment of chlorinated organics. In: Microbial Transformation and Degradation of Toxic Organic Chemicals, eds. L.Y. Young and C.E. Cerniglia. Wiley-Liss, New York.

Norris, R.D., Hinchee, R.E., Brown, R., McCarty, P.L., Semprini, L., Wilson, J.T., Kampbell, D.H., Reinhard, M., Bouwer, E.J., Borden, R.C., Vogel, T.M., Thomas, J.M., and Ward, C.H. 1994. Handbook of Bioremediation, Lewis Publishers,

Montgomery, L., Assaf-Anid, N., Nies, L., Anid, P.J. and Vogel, T.M. 1991. Anaerobic biodegradation of chlorinated organic compounds. In: Biodegradation and Bioreclamation Technologies, K.G. Rasul Chaudry (ed.). Dioscordes Publ.

REFEREED ARTICLES

Nemir, A., David, M.M., Perrussel, R., Sapkota, A., Pascal Simonet, P., Jean-Michel Monier, J.M., Vogel, T.M. 2010. Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils. Chemosphere doi:10.1016/j.chemosphere.2010.03.036

Lyon, D., Buret, F., Vogel, TM, Monier JM. 2010. Is resistance futile? Changing external resistance does not improve microbial fuel cell performance, Bioelectrochemistry. 78: 2-7.

Lyon, D. Y., Monier, J-M., Dupraz, S., Freissinet, C., Simonet, P., and Vogel, T.M. 2010. Integrity and biological activity of DNA after UV exposure. Astrobiology, In press.

Larose, C., Sibel Berger, Christophe Ferrari, Elisabeth Navarro, Aurélien Dommergue, Dominique Schneider, Vogel, T.M. 2010. Microbial sequences retrieved from environmental samples from seasonal Arctic snow and meltwater from Svalbard, Norway. Extremophiles. DOI: 10.1007/s00792-009-0299-2

Malandain, C., Fayolle-Guichard, F., Vogel, TM. 2010. Cytochromes P450-mediated degradation of fuel oxygenates by environmental isolates; FEMS Microbial Ecology 10.1111/j.1574-6941.2010.00847.x

Lyon, D. Y., Pivetal, J., Blanchard, L. and Vogel, T. M. 2010. Bioremediation via
In Situ Electrotransformation, Bioremediation Journal, 14: 2, 109-119

Vogel TM, Simonet P, Jansson J, Hirsch PR, Tiedje JM, Van Elsas JD, Bailey MJ, Nalin R and Philippot L. 2009. TerraGenome: a consortium for the sequencing of a soil metagenome. Nat. Rev. Microbiol. 7: 252.

Demanèche, S., Philippot, L., David, M.M., Navarro, E., Vogel, T.M., Simonet, P. 2009. Characterization of Denitrification Gene Clusters of Soil Bacteria via a Metagenomic Approach. Appl. Environ. Microbiol.75: 534-537

Demanèche, S., David, M.M., Navarro, E., Simonet, P., Vogel, T.M. 2009. Evaluation of functional gene enrichment in a soil metagenomic clone library. J. Microbiol. Methods76: 105-107

Poté, J., Mavingui, P., Navarro, E., Rosselli, W., Wildi, W., Simonet, P., M. Vogel, T.M. 2009.
Extracellular Plant DNA in Geneva Groundwater and Traditional Artesian Drinking Water Fountains. Chemosphere, 75: 498-504.

Pontiroli A, Rizzi A, Simonet P, Daffonchio D, Vogel TM and Monier JM. 2009. Visual evidence of horizontal gene transfer between plant and bacteria in the phytosphere of transplastomic tobacco. Appl. Environ. Microbiol. 75: 3314-3322.

Poté J, Ceccherini MT, Rosselli W, Wildi W, Simonet P and Vogel TM. 2009. Leaching and transformability of transgenic DNA in unsaturated soil columns. Ecotoxicology and Environmental Safety (in press).

van Elsas, J.D., Costa, R., Jansson, J., Sjöling, S., Bailey, M., Nalin, R., Vogel, T.M. and van Overbeek, L. 2008. The metagenomics of disease suppressive soils – experiences from the METACONTROL project. Trends in Biotechnol. doi:10.1016/j.tibtech.2008.07.004

Smalla, K., Tebbe, C.C., van Elsas, J.D., Vogel, T.M. 2008. Microbial community networks. FEMS Microbial Ecology.DOI: 10.1111/j.1574-6941.2008.00596.x

David M, Sapkota AR, Simonet P, Vogel T.M. 2008. A novel and rapid method for synthesizing positive controls or standards for quantitative PCR. J. Microbiol. Methods. 73:73-77.

Demanèche S, Sanguin H, Poté J, Navarro E, Bernillon D, Mavingui P, Wildi W, Vogel T.M. and Simonet P. 2008 Antibiotic resistant soil bacteria in transgenic plant fields. Proc Natl Acad. Sci. (USA) PNAS. 105:3957-3962.

Lefevre F, Robe P, Jarrin C, Ginolhac A, Zago C, Auriol D, Vogel T.M., Simonet P and Nalin R. Drugs from hidden bugs: Discovery from untapped resources. Res. Microbiol. 159:153-161.

Rizzi A, Pontiroli A, Brusetti L, Borin S, Sorlini C, Abruzzes Ae, Sacchi GA, Vogel T.M., Simonet P, Bazzicalupo M, Nielsen KM, Monier J.M and Daffonchio D. 2008. Strategy for In Situ Detection of Natural Transformation-Based Horizontal Gene Transfer Events. Appl. Environ. Microbiol. 74: 1250-1254.

Ceccherini, M.T., Ascher, J., Pietramellara, G., Vogel, T.M. and Nannipieri, P. 2007. Vertical advection of extracellular DNA by water capillarity in soil columns Soil Biology and Biochemistry, 39:158-163

Mercier, A., E. Kay, T. M. Vogel and P. Simonet. 2007. Gene flow in the rhizosphere. In Pinton, R., Z. Varaniniand P. Nannipieri (ed.), The Rhizosphere, Biochemistry and Organic Substances at the Soil-Plant Interface. CRC Press, Boca Raton, FL.

Fall S, Mercier A, Bertolla F, Calteau A, Gueguen L, Perrière G, Vogel T.M. and P. Simonet . 2007. Horizontal Gene Transfer Regulation in Bacteria as a "Spandrel" of DNA Repair Mechanisms. PLoS ONE 2(10): e1055. doi:10.1371/journal.pone.0001055.

Pontiroli A, Simonet P, Frostegard A, Vogel T.M. and JM Monier. 2007. Fate of transgenic plant DNA in the environment. Environ Biosafety Res. January-June; 6(1-2):15-35. Epub 2007 Oct 26

Monier JM, Bernillon D, Kay E, Faugier A, Rybalka O, Dessaux Y, Simonet P and T.M. Vogel. 2007. Detection of potential transgenic plant DNA recipients among soil bacteria. Environ Biosafety Res. January-June; 6(1-2):71-83. Epub 2007 Oct 26.

Boubakri, H, Beuf, M., Simonet, P., Vogel, T.M., 2006. Development of metagenomic DNA shuffling for the construction of a xenobiotic gene, Gene, 375: 87-94.

Sanguin H., Herrera A., Oger-Desfeux C., Dechesne A., Simonet P., Navarro E., Vogel T.M., Moënne-Loccoz Y., Nesme X., Grundmann G.L. 2006. Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ. Microbiol. 70 :6342-6346.

Cérémonie, H., Boubakri, H., Mavingui, P., Simonet, P. Vogel, T.M. 2006. Plasmid-Encoded Gamma-Hexachlorocyclohexane degradation genes and insertion sequences in Sphingobium francense (ex-Sphingomonas paucimobilis Sp+) FEMS Microbiol. Lett. 257:243-252.

Sanguin, H., Remenant, B., Dechesne, A., Thioulouse, J., Vogel, T.M., Nesme, X., Moënne-Loccoz, Y., Grundmann, G.L. 2006. Potential of a 16S rRNA-based taxonomic microarray for analyzing maize rhizosphere effect on Agrobacterium and bacterial communities. Appl Environ Microbiol 72 :4302-4312.

Nex, F.,Schäfer, G., Côme, J.-M., Vogel, T.M. 2006. A novel approach for modelling the biodegradation of chlorinated volatile organic compounds in porous aquifers | [Une approche innovante pour modéliser la biodégradation des composés organochlorés volatils en aquifères poreux], Comptes Rendus - Geoscience 338:297-306

Cérémonie, H.,Buret, F., Simonet, P., Vogel, T.M. 2006. Natural electrotransformation of lightning-competent Pseudomonas sp. strain N3 in artificial soil microcosms. Appl Environ Microbiol 72: 2385-2389

Boubakri, H., H. Ceremonie, D. Bernillon, P. Simonet and T. M. Vogel. 2005. Compréhension de la structure mosaïque d'un gène: linA. Les actes du BRG 5:497-509.

Hery M, Herrera A, Vogel, TM., Normand P., Navarro E. 2005. Effect of carbon and nitrogen input on the bacterial community structure of Neocaledonian nickel mine soils. FEMS Microbial Ecology. 51: 333-340

Ginolhac A., Jarrin C., Robe P., Perrière G., Vogel T. M. , Simonet P. Nalin R. 2005. Type I PKS may have evolved through horizontal gene transfer. Journal of Molecular Evolution. 60:716-725.

Bertrand H., Poly F., Van T. V., Lombard N., Nalin R., Vogel T.M. Simonet P. 2005. Improved quality of DNA extracted from soil suitable for metagenomic library construction. J. Microb. Methods 62 :1-11.

Ginolhac, A., Jarrin, C., Gillet, B., Robe, P., Pujic, P., Tuphile, K.,Bertrand, H., Vogel,T.M., Perrière, G., Simonet, P., Nalin, R. 2004. Phylogenetic Analysis of Polyketide Synthase I Domains from Soil Metagenomic Libraries Allows Selection of Promising Clones. Applied Environmental Microbiology.70:5522-5527.

Cérémonie H., Buret F., Simonet P. Vogel T. M. 2004. Isolation of lightning-competent soil bacteria. Appl. Environ. Microbiol., 70: 6342-6346.

Poté, J. Ceccherini, MT., Van Tran, V., Rosselli, W., Wildi, W., Simonet, P., Vogel, T.M. 2003 Fate and transport of antibiotic resistance genes in saturated soil columns. European Journal of Soil Biology, 39:65-72.

Robe, P., Nalin, R., Capellano, C., Vogel, T.M., Simonet, P. 2003. Extraction of DNA from soil, European Journal of Soil Biology, 39:183-190.

Dechesne, A., Pallud, C., Debouzie, D., Flandrois, J.P., Vogel, T.M., Gaudet, J.P. Grundmann, G.L. 2003. A novel method for characterizing the microscale 3D spatial distribution of bacteria in soil, Soil Biology and Biochemistry, 35:1537-1546

Kay, E., Chabrillat G., Vogel T. M. and Simonet P. 2003. Intergeneric Transfer of Chromosomal and Conjugative Plasmid Genes Between Ralstonia solanacearum and Acinetobacter sp. BD413. Mol Plant Microbe Interactions 2003, Vol - Issue : 16 1 pp: 74 - 82

Ceccherini, MT., Poté, J., Kay, E., Tran Van, V., Maréchal, J., Pietramellara, G., Nannipieri, P., Vogel, T.M., Simonet, P. 2003. Degradation and transformability of DNA from transgenic plants. Applied Environmental Microbiology 69:673-678.

Kay E., Bertolla F. Vogel T.M and Simonet P. 2002. Opportunistic colonization of Ralstonia solanacearum-infected plants by Acinetobacter sp. and its natural competence development. Microbiol.Ecol.43:291-297.

Kay E., Vogel T. M., Bertolla F., Nalin R. and Simonet P. 2002. In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria Applied Environmental Microbiology 68: 3345-3351.

Amellal, N., Portal, J.-M., Vogel, T.M., Berthelin, J. 2001. Distribution and location of polycyclic aromatic hydrocarbons (PAHs) and PAH-degrading bacteria within polluted soil aggregates. Biodegradation , 12:49-57.

Demanèche S., Bertolla F., Buret F., Nalin R., Sailland A., Auriol P., Vogel T.M. and Simonet P. 2001. Laboratory-scale evidence for lightning-mediated gene transfer in soil. Applied Environmental Microbiology 67: 3440-3444.

Nalin, R., Simonet, P., Vogel, T.M., et Normand, P. 1999. Rhodanobacter lindaniclasticus gen. Nov., sp. Nov., a lindane-degrading bacterium. International Journal of Systematic Bacteriology , 49 :19-23.

Richard, J-Y, et Vogel, T.M. 1999. Characterization of a soil bacterial consortium capable of degrading diesel fuel. International Biodeterioration & Biodegradation . 44 :93-100.

Ganaye, V.A., Keiding, K.K., Vogel, T.M., Viriot, M.-L. et Block, J.-C. 1997. Evaluation of soil organic matter polarity by pyrene fluorescence spectrum variations. Environmental Science and Technology 31:2701-2706.

Vogel, T.M. 1996. Bioaugmentation as a bioremediation approach. Current Opinions in Biotechnology 7:311-316.

Thomas, J.-C., Berger, F., Jacquier, M., Bernillon, D., Baud-Grasset, F. Truffaut, N., Normand, P., Vogel, T.M., et Simonet, P. 1996. Isolation and characterization of a novel gamma-hexachlorocyclohexane-degrading bacterium. J. Bacteriology 178:6049-6055.

Alvarez, P.J.J. et Vogel, T.M. 1995. Degradation of BTEX and their aerobic metabolites by indigenous microorganisms under nitrate reducing conditions. Water Science and Technology; 31:15-28.

Petrovskis, E.A., Vogel, T.M., et Adriaens, P. 1994. Effects of electron donors and acceptors on carbon tetrachloride transformation by Shewanella putrefaciens. FEMS Microbiology Letters . 121:357-364.

Alvarez, P.J.J., Anid, P.J. et Vogel, T.M. 1994. Kinetics of toluene degradation by denitrifying aquifer microorganisms. ASCE J. Environmental Engineering ; 120: 1327-1336.

Anid, P.J., Alvarez, P.J.J. et Vogel, T.M. 1993. Biodegradation of monoaromatic hydrocarbons in aquifer columns amended with hydrogen peroxide and nitrate. Water Research . 27:685-691.

Assaf-Anid, N., Hayes, K.F., et Vogel, T.M. 1993. Effect of redox potential and pH on the reductive dechlorination of carbon tetrachloride by cyanocobalamin (II). Environmental Science and Technology , 28:246-252.

Anid, P.J., Ravest-Webster, B.P., et Vogel, T.M. 1993. Effect of hydrogen peroxide on the biodegradation of PCBs in anaerobically dechlorinated river sediments. Biodegradation , 4:241-248.

Montgomery, L. et Vogel, T.M. 1992. Dechlorination of 2,3,5,6-tetrachlorobiphenyl by a phototrophic enrichment culture. FEMS Microbiology Letters , 94:247-250.

Chen, Y.M., Abriola, L.M., Alvarez, P.J.J., Anid, P.J., et Vogel, T.M. 1992. Biodegradation and transport of benzene and toluene in sandy aquifer material. Water Resources Research.28:1833-1847.

Shreve, G.S. et Vogel, T.M. 1992.Comparison of substrate utilization and growth kinetics between immobilized and suspended Pseudomonas cells. Biotechnology and Bioengineering , 41:370-379.

Shreve, G., Olsen, R. et Vogel, T.M. 1991. Development of pure culture biofilms of P. putida on solid supports. Biotechnology and Bioengineering , 37:512-518.

Nies, L. et Vogel, T.M. 1991. Identification of the proton source for the microbial reductive dechlorination of a chlorinated aromatic compound (2,3,4,5,6 penta chlorobiphenyl PCB). Applied and Environmental Microbiology , 57:2771-2774.

Alvarez, P.J.J., Anid, P.J., et Vogel, T.M. 1991. Kinetics of aerobic biodegradation of benzene and toluene in sandy aquifer material. Biodegradation , 2:43-51.

Alvarez, P.J.J., et Vogel, T.M. 1991. Substrate interactions of benzene, toluene, and para-xylene during microbial mixed culture aquifer slurries. Applied and Environmental Microbiology , 57:2981-2985.

Fathepure, B.Z. et Vogel, T.M. 1991. Complete degradation of polychlorinated hydrocarbons by a two-stage biofilm reactor. Applied and Environmental Microbiology ( IF=3.35, 57:3418-3422.

Assaf-Anid, N., Nies, L., et Vogel, T.M. 1991. Reductive dechlorination of a PCB congener and hexachlorobenzene by vitamin B12. Applied and Environmental Microbiology . 58:1057-1060.

Nies, L. et Vogel, T.M. 1990. Effects of organic substrates on dechlorination of Aroclor 1242 in anaerobic sediments. Applied and Environmental Microbiology , 56:2612-2617.

Vogel, T.M. et McCarty, P.L. 1987. Rate of abiotic formation of 1,1-dichloroethylene from 1,1,1-trichloroethane in groundwater. Journal of Contaminant Hydrology, 1:299-308.

Grbi-Gali, D. et Vogel, T.M. 1987. Transformation of toluene and benzene by mixed methanogenic cultures. Applied and Environmental Microbiology , 53:254-260.

Vogel, T.M., Criddle, C.S. et McCarty, P.L. 1987. Transformations of halogenated aliphatic compounds. Environmental Science and Technology , 21:722-736.

Vogel, T.M. et McCarty, P.L. 1987. Abiotic and biotic transformations of 1,1,1-trichloroethane under methanogenic conditions. Environmental Science and Technology , 21:1208-1213.

Vogel, T.M. et Grbi-Gali, D. 1986. Incorporation of oxygen from water into toluene and benzene during methanogenic transformation. Applied and Environmental Microbiology , 52:200-202.

Vogel, T.M. et Reinhard, M. 1986. Reaction products and rates of disappearance of simple bromoalkanes, 1,2-dibromopropane, and 1,2-dibromoethane in water. Environmental Science and Technology , 20:992-997.

Vogel, T.M. et McCarty, P.L. 1985. Biotransformation of tetrachloroethylene to trichloroethylene, dichloroethylene, vinyl chloride, and carbon dioxide under methanogenic conditions. Applied and Environmental Microbiology , 49:1080-1083.

Vogel, T.M., Oremland, R.S., et Kvenvolden, K.A. 1982. Low temperature formation of C1 - C4 alkanes in an estuarine sediment. Chemical Geology , 37:289-298.

Kvenvolden, K.A., Vogel, T.M., et Gardner, J.V. 1981. Geo-chemical prospecting for hydrocarbons in the outer continental shelf, Southern Bering Sea, Alaska. Journal of Geochemical Exploration, 14:209-219.