Environmental Microbial Genomics Group

Logos GenomEnviron and Ampere
Laboratoire Ampere
Ecole Centrale de Lyon . France
(33) 472 18 60 92
Sequences from publications can be found at ftp://ftp-adn.ec-lyon.fr/



McCarty, P.L., Criddle, C.S., and Vogel, T.M. 2020. Retroperspectives on microbial transformations of chlorinated organics. Environ. Sci.: Processes Impacts, 2020, 22, 512

Beaulne J.-S., Mishra S.R., Suar M., Panda A.N., Rastogi G., Pattnaik A.K.,
Raina V. & Vogel T.M., Spatial Analysis of Bacteria in Brackish Lake Sediment, International Journal of Sediment Research, https://doi.org/10.1016/j.ijsrc.2020.01.003.


Bergk Pinto B, Maccario L, Dommergue A, Vogel TM and Larose C (2019) Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow? Front. Microbiol. 10:2492. doi: 10.3389/fmicb.2019.02492

Nicol, G.W., Hink, L, Gubry-Rangin, C., Prosser, J.I., and Lehtovirta-Morley, L.E. (2019) The genome sequence of “Candidatus Nitrosocosmicus franklandus” C13, a terrestrial ammonia oxidising archaeon with a high tolerance to ammonium. Microbiology Resource Announcements. 40: e00435-19

Wu X, Wang Y, Zhu Y, Tian H, Qin X,Cui C, Zhao L, Simonet P, Zhang X. 2019.Variability in the response of bacterial community assembly to environmental selection and biotic factors depends on the immigrated bacteria, as revealed by a soil microcosm experiment. mSystems4:e00496-19.https://doi.org/10.1128/mSystems.00496-19.

Els, N., Larose, C., Baumann-Stanzer, K. Tignat-Perrier, R., Keuschnig, C., Vogel, T.M., Larose, C. 2019. Microbial composition in seasonal time series of free tropospheric air and precipitation reveals community separation. Aerobiologia 35, 671–701 doi:10.1007/s10453-019-09606-x

Prosser, J.I., Hink, L., Gubry-Rangin, C., and Nicol, G.W. (2019) Nitrous oxide production by ammonia oxidisers: community composition matters. Global Change Biology. 26: 103-118.

Tignat-Perrier, R., Dommergue, A., Thollot, A., Christoph Keuschnig, Olivier Magand, Timothy M. Vogel & Catherine Larose. 2019. Global airborne microbial communities controlled by surrounding landscapes and wind conditions. Sci Rep 9, 14441 doi:10.1038/s41598-019-51073-4

Hoyos-Hernandez, Caroline, Christelle Courbert, Caroline Simonucci, Sebastien David, Timothy M Vogel, Catherine Larose. 2019. Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima, FEMS Microbiology Letters, 366:180, https://doi.org/10.1093/femsle/fnz180

Wang, Z., Cao, Y., Zhu-Barker, X., Nicol, G.W., Wright, A.L., Jia, Z., and Jiang, X. (2019) Comammox Nitrospira clade B contributes to nitrification in soil. Soil Biology and Biochemistry. 135: 392-395.

Baloh P, Els N, David RO, Larose C, Whitmore K, Sattler B and Grothe H (2019) Assessment of Artificial and Natural Transport Mechanisms of Ice Nucleating Particles in an Alpine Ski Resort in Obergurgl, Austria. Front. Microbiol. 10:2278. doi: 10.3389/fmicb.2019.02278

Sekkour, Sonia; Bekki, Abdelkader; Bouchiba, Zoulikha; Vogel, Timothy M; Navarro, Elisabeth. 2019. The diversity of cultivable hydrocarbon-degrading bacteria isolated from crude oil contaminated soil and sludge from Arzew refinery in Algeria, The Journal of Microbiology, Biotechnology and Food Sciences, 9: 70. DOI:10.15414/jmbfs.2019.9.1.70-77

Maccario, L., Carpenter, S.D., Deming, J.W. Vogel, T.M., Larose, C. 2019. Sources and selection of snow-specific microbial communities in a Greenlandic sea ice snow cover. Sci Rep 9, 2290  doi:10.1038/s41598-019-38744-y

Schostag, M.D., Muhammad Zohaib Anwar, Carsten Suhr Jacobsen, Catherine Larose, Timothy M. Vogel, Lorrie Maccario, Samuel Jacquiod, Samuel Faucherre, Anders Priemé 2019. Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome. bioRxiv, doi: http://dx.doi.org/10.1101/599233.

Els N, Baumann-Stanzer K, Larose C, Vogel TM, Sattler B. Beyond the planetary boundary layer: Bacterial and fungal vertical biogeography at Mount Sonnblick, Austria. Geo: Geography and Environment. 2019;e00069. https://doi.org/10.1002/geo2.69

Dommergue A, Amato P, Tignat-Perrier R, Magand O, Thollot A, Joly M, Bouvier L, Sellegri K, Vogel T, Sonke JE, Jaffrezo J-L, Andrade M, Moreno I, Labuschagne C, Martin L, Zhang Q and Larose C (2019) Methods to Investigate the Global Atmospheric Microbiome. Front. Microbiol. 10:243. doi: 10.3389/fmicb.2019.00243


Zhu, Yong-Guan; Gillings, Michael; Simonet, Pascal; Stekel, Dov; Banwart, Steven; Penuelas, Josep 2018. Human dissemination of genes and microorganisms in Earth's Critical Zone Global Change Biology, vol. 24, issue 4, pp. 1488-1499 doi:10.1111/gcb.14003

Vasileiadis, S., Puglisi, E., Papadopoulou, E. S., Pertile, G., Suciu N., Pappolla, R. A., Tourna, M., Karas, P. A., Papadimitriou, F., Kasiotakis, A., Ipsilanti, N., Ferrarini, A., Sułowicz, S., Fornasier, F., Menkissoglu-Spiroudi, U., Nicol, G. W., Trevisan, M., and Karpouzas, D. G. 2018. Blame it on the metabolite: 3,5-dichloraniline rather than the parent compound is responsible for decreasing diversity and function of soil microorganisms. Applied and Environmental Microbiology. 84: e01536-18.

Lu, X., Nicol, G.W., and Neufeld, J.D. (2018). Differential responses of soil ammonia-oxidizing archaea and bacteria to temperature and depth under two different land uses in Ontario. Soil Biology and Biochemistry. In press.

Stein, L.Y., and Nicol, G.W. (2018). Nitrification. eLS. In press.

Hink, L., Gubry-Rangin, C., Nicol, G.W., and Prosser, J.I. (2018). The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions. The ISME Journal. In press.

Li, Y., Chapman, S.J., Nicol, G.W., and Yao, H. (2018) Nitrification and nitrifiers in acidic soils. Soil Biology and Biochemistry 116: 290–301.

Hily, J. M., S. Demaneche, N. Poulicard, M. Tannieres, S. Djennane, M. Beuve, E. Vigne, G. Demangeat, V. Komar, C. Gertz, A. Marmonier, C. Hemmer, S. Vigneron, A. Marais, T. Candresse, P. Simonet and O. Lemaire. 2018. Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome. Plant. Biotechnol. J. 16:208-220.

Hazard C, Johnson D. 2018. Does genotypic and species diversity of mycorrhizal plants and fungi affect ecosystem function? New Phytologist DOI:10.1111/nph.15010

Djeran-Maigrea, I., Dubujet, P., Vogel, T.M. 2018. Variation over time of excavated soil properties treated with surfactants. Environmental Earth Sciences, in press.


Zhu YG, Gillings M, Simonet P, Stekel D, Banwart S and Penuelas J. 2017. Microbial mass movements. Science 357:1099-1100.

Ramirez K, Knight C […] Thion C, van der Heijden M & de Vries F. Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology, doi:10.1038/s41564-017-0062-x

Nicol, G.W. (2017) Archaea and the Nitrogen Cycle. Microbiology Today. 44:106-109.

Nielsen, T.K., Rasmussen, M., Sandrine Demaneche, S., Cecillon, S., Vogel, T.M. and Hansen, L.H.2017. Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH. Genome Biology and Evolution 9(9):2477–2490.

Hink, L., Lycus, P., Gubry‐Rangin, C., Frostegård, A., Nicol, G.W., Prosser, J.I., Bakken, L.R. (2017) Kinetics of NH3‐oxidation, NO‐turnover, N2O‐production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers. Environmental Microbiology. 19: 4882-4896.

Hink, L., Nicol, G.W., and Prosser, J.I. (2016). Archaea produce lower yields of N2O than bacteria during aerobic ammonia oxidation in soil. Environmental Microbiology.19: 4829-4837.

Hazard C, Kruitbos L, Davidson H, Mbow FT, Taylor AFS, Johnson D. 2017. Strain identity of the ectomycorrhizal fungus Laccaria bicolor is more important than richness in regulating plant and fungal performance under nutrient rich conditions. Frontiers in Microbiology 8: 1874. 

Catão E, Thion C, Krüger R & Prosser JI (2017). Ammonia oxidizers in a non-nitrifying Brazilian savanna soil. FEMS Microbiology Ecology, 93(11).

Demanèche S, Schauser L, Dawson L, Franqueville L, Simonet P. 2017. Microbial soil community analyses for forensic science: Application to a blind test. Forensic Science International 270 :153–158.

Blanchard LS, Monin A, Ouertani H, Touaibia L, Michel E, Buret F, Simonet P, Morris CE and Demanèche S. 2017. Survival and electrotransformation of Pseudomonas syringae strains under simulated cloud-like conditions. FEMS Microb. Ecol. (in press).

Hily JM, Demanèche S, Poulicard N, Tannières M, Djennane S, Beuve M, Vigne E, Demangeat G, Komar V, Marmonier A, Hemmer C, Vigneron S, Marais A, Candresse T, Simonet P and Lemaire O. 2017. Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome. Plant Biotechnol J (in press).

Simonet P. 2017. Fiche thématique n°7, Apport de la metagénomique pour évaluer la capacité d’adaptation du microbiote du sol aux changements environnementaux, notamment climatiques. Fiches thématiques Partie 1 « Les mécanismes biologiques d’adaptation aux changements climatiques », 3 - Ecosystèmes, Dans Institut de France. Rapport de l’Académie des Sciences : « Les mécanismes d’adaptation de la biodiversité aux changements climatiques et leurs limites » (87-91). (In press).

Royet D, Hériveaux Y, Marchalot J, Scorretti R, Dias A, Dempsey NM, Bonfim M, Simonet P and Frénéa-Robin M. Using injection molding and reversible bonding for easy fabrication of magnetic cell trapping and sorting devices. J. Magn. Magn. Mater. (in press).

Zhu YG, Gillings M, Simonet P, Stekel D, Banwart S and Penuelas J. 2017. Increased abundance of antibiotic resistance in Earth’s Critical Zone: A paradigm for human dissemination of genes and microorganisms. Global Change Biology (in press).

Hazard C, Kruitbos L, Davidson H, Mbow FT, Taylor AFS, Johnson D. 2017. Strain identity of the ectomycorrhizal fungus Laccaria bicolor is more important than richness in regulating plant and fungal performance under nutrient rich conditions. Frontiers in Microbiology. 8: doi: 10.3389/fmicb.2017.01874

Hazard C, Kruitbos L, Davidson H, Taylor AFS, Johnson D. 2017. Contrasting effects of intra- and interspecific identity and richness of ectomycorrhizal fungi on host plants, nutrient retention and multifunctionality. New Phytologist 213: 852-86

Herbold, C.W., Lehtovirta‐Morley, L.E., Jung, M.-Y., Jehmlich, N., Hausmann, B., Han, P., Loy, A., Pester, M., Sayavedra‐Soto, L.A., Rhee, S.-K., Prosser, J.I., Nicol, G.W., Wagner, M., Gubry‐Rangin, C. (2017) Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics. Environmental Microbiology. 19: 4939-4952.

Gubry-Rangin, C., Novotnik, B., Mandič-Mulec, I., Graeme W. Nicol, J. I. Prosser. 2017. Temperature responses of soil ammonia-oxidising archaea depend on pH.  Soil Biology and Biochemistry, 106: 61-68.

Habtom H, Demanèche S, Dawson L, Azulay C, Matan O, Robe P, Gafny R, Simonet P, Jurkevitch E and Z Pasternak. 2017. Soil characterisation by bacterial community analysis for forensic application: a quantitative comparison of environmental technologies. Forensic Sci. Int. 26:21-29.

Nacke, H., Schöning, I., Schindler, M., Schrumpf, M., Daniel, R., Nicol, G.W., and Prosser, J.I. (2017) Links between seawater flooding, soil ammonia oxidiser communities and their response to changes in salinity. FEMS Microbiology Ecology. 93: fix14

Müller, J. B., Ramos, D. T., Larose, C., Fernandes, M., Lazzarin, H. S.C., Vogel, T. M., Corseuil, H. X. 2017. Combined iron and sulfate reduction biostimulation as a novel approach to enhance BTEX and PAH source-zone biodegradation in biodiesel blend-contaminated groundwater. Journal of Hazardous Materials. 326: 229-236.

Paitier, A., Godain, A., Lyon, D., Haddour, N., Vogel, T.M., Monier, JM. 2017 Microbial fuel cell anodic microbial population dynamics during MFC start-up, Biosensors and Bioelectronics, ISSN 0956-5663, http://dx.doi.org/10.1016/j.bios.2016.10.096.

Elling, F.J., Könneke, M., Nicol, G.W., Stieglmeier, M., Bayer, B., Spieck, E., de la Torre, J.R., Becker, K.W., Thomm, M., Prosser, J.I., Herndl, G.J., Schleper, C. and Hinrichs, K.-U. (2017) Chemotaxonomic characterization of the thaumarchaeal lipidome. Environmental Microbiology. 19: 2681–2700

Fedrizzi, F., Ramos, D.T., Lazzarin, H.S.C.,  Fernandes., Larose, C., Vogel, T.M., Corseuil, H.X. 2017. A Modified Approach for in Situ Chemical Oxidation Coupled to Biodegradation Enhances Light Nonaqueous Phase Liquid Source-Zone Remediation. Environ. Sci. Technol. 51:463–472.

Simonet P and A Maître. 2017. De la santé de l’environnement à la santé humaine. Les Big Data à découvert In Bouzeghour, M. and R. Mosseri (ed.), Les Big Data à découvert. CNRS Editions, Paris, France (202-203).

Alizon S, F Angelier, G Bécard, L Bézin, F Courchamp, S. Dutreuil, L Guidi, U Hibner, M Jebbar, O Klatz, F Heullier, O Loudet, P Simonet, J Tost, N Vergnolle. 2017. L’être vivant dans son environnement.  pour les sciences de la vie du XXIème siècle . In Jessus, C. (ed.), Etonnant vivant. Découvertes et promesses du XXIème siècle (Livre blanc). CNRS Editions, Paris, France (183-241).



Ramos, D. T., H. S. Lazzarin, P. J. Alvarez, T. M. Vogel, M. Fernandes, M. Do Rosario and H. X. Corseuil. 2016. Biodiesel presence in the source zone hinders aromatic hydrocarbons attenuation in a B20-contaminated groundwater. J. Contam. Hydrol. 193:48-53.

Ufarte, L, S Bozonnet, E Laville, D A Cecchini, S Pizzut-Serin, S Jacquiod, S Demaneche, P Simonet, L Franqueville and G Potocki-Veronese. 2016. Functional Metagenomics: Construction and High- Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes. In Martin, F and S Uroz (ed.), Microbial Environmental Genomics (MEG). Springer Science + Business Media, New York.

Subirats J, A Sànchez-Melsió, CM Borrego, JL Balcázar and P Simonet. 2016. Metagenomic analysis reveals bacteriophages are reservoirs for antibiotic resistance genes. Int. J. Antimicrob. Agents:  48:163-167.

Pylro VS, Mui TS, Rodrigues JLM, Andreote FD, Roesch LFW and the Working Group supporting the INCT Microbiome (P Simonet, T.M. Vogel members of the working group). 2016. A step forward to empower global microbiome research through local leaderships. Trends Microbiol. 24:767-771.

Smalla K, P Simonet, J Tiedje and E Topp. 2016. Opinion Paper/Editorial. Co-editors, Special section of FEMS Microbiology Ecology on the environmental dimension of antibiotic resistance. FEMS Microbiol. Ecol. 92: fiw17.

Masy, T., Demanèche, S., Tromme O, Thonart P, JacquesP, Hiligsmann S, Vogel, T.M. 2016. Hydrocarbon biostimulation and bioaugmentation in organic carbon
and clay-rich soils.
Soil Biology & Biochemistry 99: 66-74.

Nesme, Joseph, WafaAchouak, SpirosN.Agathos, MarkBailey, PetrBaldrian, Dominique Brunel, ÅsaFrostegård, ThierryHeulin, JanetK.Jansson, Edouard Jurkevitch , KristiinaL.Kruus, GeorgeA.Kowalchuk, AntonioLagares, HilaryM.Lappin-Scott, PhilippeLemanceau, DenisLePaslier, InesMandic-Mulec, J. ColinMurrell , DavidD.Myrold, RenaudNalin, PaoloNannipieri, Josh D.Neufeld, FergalO’Gara, JohnJ.Parnell, AlfredPühler, VictorPylro, Juan L.Ramos, LuizF.W.Roesch, MichaelSchloter, ChristaSchleper , Alexander Sczyrba, AngelaSessitsch , SaraSjöling, JanSørensen,
Søren J.Sørensen, ChristophC.Tebbe, EdwardTopp, GeorgeTsiamis , Jan DirkvanElsas , GeertjevanKeulen, FrancoWidmer, MichaelWagner, TongZhang, XiaojunZhang, LipingZhao, Yong-GuanZhu, Timothy M.Vogel and Pascal Simonet. 2016. Back to the future of metagenomics. Frontiers in Microbiology. 7 doi: 10.3389/fmicb.2016.00073

Lehtovirta-Morley, L.E., Sayavedra-Soto, L.A., Gallois, N., Schouten, S., Stein, L.Y., Prosser, J.I., and Nicol, G.W. (2016) Identifying potential mechanisms enabling acidophily in the ammonia-oxidising archaeon ‘Candidatus Nitrosotalea devanaterra’. Applied and Environmental Microbiology. 82:2608-2619.

Lehtovirta-Morley, L.E., Ross, J., Hink, L, Weber, E.B., Gubry-Rangin, C., Thion, C., Prosser, J.I., and Nicol, G.W. (2016) Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiology Ecology. 92: fiw057.

Bao, Q., Huang, Y., Wang, F., Nie, S., Nicol, G.W., Yao, H., and Ding, L. (2016) Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil. Applied Microbiology and Biotechnology. 100: 5989–5998.

Ighilhariz S., de Lajudie P., Bekki A., Ighilhariz Z., Duponnois R., Reboulet J., Navarro E. (2016). Effect of anthropisation and revegetation efforts on soil bacterial community structure in Terga sandpit, Algeria. J.Biodiv. Environ.Sci. (JBES) 9: 283-296.

Nicol, G.W., and Prosser, J.I. (2016). Ecology of Archaea. Oxford Bibliographies. Oxford University Press. DOI: 10.1093/obo/9780199363445-0041.

Prosser, J.I. and Nicol, G.W. (2016) Candidatus Nitrosotaleales. Bergey’s Manual of Systematics of Archaea and Bacteria. Editor Whitman, P.W.B. Wiley-Blackwell.

Prosser, J.I. and Nicol, G.W. (2016) Candidatus Nitrosotaleaceae. Bergey’s Manual of Systematics of Archaea and Bacteria. Editor Whitman, P.W.B. Wiley-Blackwell.

Prosser, J.I. and Nicol, G.W. (2016) Candidatus Nitrosotalea. Bergey’s Manual of Systematics of Archaea and Bacteria. Editor Whitman, P.W.B. Wiley-Blackwell.


David MM, Cecillon S, Warne BM, Prestat E, Jansson JK, Vogel TM. Microbial ecology of chlorinated solvent biodegradation. Environ Microbiol. (2015) 17(12), 4835–4850

Maccario LSanguino LVogel TMLarose C., 2015. Snow and ice ecosystems: not so extreme. Res Microbiol.:166(10):782-95. doi: 10.1016/j.resmic.2015.09.002. 

Zhu, C. Delmont, TO. Vogel, T M. Bromberg, Y. 2015. Functional Basis of Microorganism Classification. PLoS Computational Biology. 11: e1004472. DOI:10.1371/journal.pcbi.100447

O. Fabrègue, E. Navarro, R. Scorretti, J. Reboulet, P. Simonet, L. Dawson and S. Demanèche. (2015) A software to align fluorescent data between Agilent 2100 Bioanalyzer arrays: application to soil microbial community analysis. BioTechniques, BT-S-15-00117, revision.

Sanguino, L. Franqueville, L., Vogel, TM., Larose, C. 2015. Linking environmental prokaryotic viruses and their host through CRISPRs. FEMS Microbial. Ecol. 91: 10.1093/femsec/fiv046

Delmont, TO. Eren, AM. Maccario, L. Prestat, E. Esen, OC. Pelletier, E. Le Paslier, D. Simonet, P. Vogel, TM 2015. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. FRONTIERS IN MICROBIOLOGY 6: 

Oton, E.V., Quince, C., Nicol, G.W., Prosser, J.I. and Gubry-Rangin, C. (2015) Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. The ISME Journal. In press.

Elisabeth Navarro, Olivier Fabrègue, Riccardo Scorretti, Jérémy Reboulet, Pascal Simonet, Lorna Dawson and Sandrine Demanèche. 2015. RisaAligner software to align fluorescent data between Agilent 2100 Bioanalyzer chips;application to soil microbial community analysis.


Maccario L, Vogel T.M. and Larose C 2014 Potential drivers of microbial community structure and function in Arctic spring snow. Front. Microbiol. 5:413. doi: 10.3389/fmicb.2014.00413

Nesme J and Simonet P 2014. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ. Microbiol. (in press). doi: 10.1111/1462-2920.12631

Mathieu A, Vogel TM and Simonet P. 2014. The Future of Skin Metagenomics. Res Mic. 165:69-76. doi: 10.1016/j.resmic.2013.12.002

Pivetal J, Royet D, Ciuta G, Frenéa-Robin M, Haddour N, Dempsey NM, Dumas-Bouchiat F Simonet P. 2014. Selective micro-patterning of microbial cells upon micro-magnet arrays for single cell analysis. J. Magn. Magn. Mater. (in press)

Pivetal J, Ciuta G, Frenéa-Robin M, Haddour N, Dempsey NM, Dumas-Bouchiat F and Simonet P. 2014. Magnetic nanoparticle DNA labeling for individual bacterial cell detection and recovery.  J. Microbiol. Methods (in press). doi: 10.1016/j.mimet.2014.09.006.

Pivetal J, Toru S, Frénéa-Robin M, Haddour N, Cecillon S, Dempsey NM, Dumas-Bouchiat F and Simonet P. 2014. Selective isolation of bacterial cells within a microfluidic device using magnetic probe-based cell fishing. Sensors and Actuators B: Chemical 195: 581–589.

Le Digabel, Y., Demanèche, S., Benoit, Y., Fayolle-Guichard, F., and Vogel, T.M. 2014. Ethyl tert-butyl ether (ETBE)-degrading microbial communities in enrichments from polluted environments. Journal of Hazardous Materials, 279 :502-510.

Nesme, J., Cécillon, S., Delmont, T.O., Monier, J-M., Vogel, T.M., Simonet, P. 2014. Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment Current Biology 24, 1–5, http://dx.doi.org/10.1016/j.cub.2014.03.036

Delmont, T.O., Francioli, D., Jacquesson, S., Laoudi, S., Mathieu, A., Nesme, J., Ceccherini, M.T., Nannipieri, P., Simonet, P., Vogel, T.M. 2014. Microbial community and unseen diversity development in inoculated sterile soil, Biology and Fertility of Soil, DOI: 10.1007/s00374-014-0925-8

Jacquiod S, Demanèche S, Delmont TO, Ausec L, Dunon V, Franqueville L, Mandic-Mulec I, Springael D, Vogel TM and Simonet P. 2014. Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library. J. Biotechnol. 190:18-29.  doi: 10.1016/j.jbiotec.2014.03.036.


Delmont, T.O., Simonet, P., Vogel, T.M. Mastering methodological pitfalls for surviving the metagenomic jungle.. BioEssays, 2013, 35 (8), pp. 744-54. <http://dx.doi.org/10.1002/bies.201200155>

Mathieu, A. Tom Delmont, T.O., Vogel, T.M., Patrick Robe, P., Nalin, R., Simonet, P. Life on Human Surfaces: Skin Metagenomics. PLoS ONE, 2013, 8 (6), pp. e65288. <http://dx.doi.org/10.1371/journal.pone.0065288>

Simonet, P. 2013. Évolution de l’antibiorésistance dans le sol. ANSES: Les cahiers de la Recherche: Santé, Environnement, Travail. Octobre 2013 :42-44.

Le Digabel, Y., Demanèche, S., Benoit, Y., Vogel, T.M., and Fayolle-Guichard, F. 2013. Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer. Applied Microbiology and Biotechnology, 97:10531-10539

Bowman, J. S., C. Larose, T. M. Vogel and J. W. Deming. 2013. Selective occurrence of Rhizobiales in frost flowers on the surface of young sea ice near Barrow, Alaska and distribution in the polar marine rare biosphere. Environ. Microbiol. Reports 5:575-582.

Jacquiod, S., Franqueville, L., Cecillon, S., Vogel, T.M., Simonet, P. 2013. Soil Bacterial Community Shifts after Chitin Enrichment: An Integrative Metagenomic Approach. PLoS ONE 8: doi:10.1371/journal.pone.0079699

Larose, C., Dommergue, A., Vogel, T.M. The Dynamic Arctic Snow Pack: An Unexplored Environment for Microbial Diversity and Activity. Biology, 2013, 2 (1), pp. 317-330. <http://dx.doi.org/10.3390/biology2010317>

Gaze WH, Krone SM, Larsson DGJ, Li X-Z, Robinson J, Simonet P, Smalla K, Timinouni M, Topp E, Wellington EM, Wright GD, Zhu Y-G. 2013. The impact of humans on the evolution and mobilization of the environmental antibiotic resistome. Environmental Health Perspectives 19 : doi: 10.3201/eid1907.120871.



Delmont, T.O., Simonet, P., Vogel, T.M. 2012. Describing microbial communities and performing global comparisons in the ‘omic era. ISME Journal 6: 1625-1628.

Zhang X, Nesme J, Simonet P, Frostegård Å. 2012 Fate of invading bacteria in soil and survival of transformants after simulated uptake of transgenes, as evaluated by a model system based on lindane degradation.  Res. Microbiol. 163: 200-210.

Delmont, T.O., Prestat,E., Keegan,K.P., Faubladier,M., Robe,P., Clark,I.M., Pelletier, E., Hirsch,P.R., Meyer,F., Gilbert,J.A., Le Paslier, D., Simonet, P., Vogel, T.M. 2012. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME Journal 6: 1677-1687.

Douglas, T.A., Lisa Loseto, Robie Macdonald, Peter Outridge, Aurélien Dommergue, Alexandre Poulain, Marc Amyot, Tamar Barkay, Torunn Berg, John Chételat, Philippe Constant, Marlene Evans, Christophe Ferrari, Nikolaus Gantner, Matthew Johnson, Jane Kirk, Niels Kroer, Catherine Larose, David Lean, Torkel Nielsen, Laurier Poissant, Sigurd Rognerud, Henrik Skov, Søren Sørensen, Feiuye Wang, Simon Wilson, Christian Zdanowicz. The fate of mercury in Arctic terrestrial and aquatic ecosystems, a review. Environmental Chemistry, 2012, 9 (4), pp. 321-355. <http://dx.doi.org/10.1071/EN11140>

Castro, L., A. Dommerguet, C. Larose, C. Ferrari, L. Maron. A Theoretical Study of Abiotic Methylation Reactions of Gaseous Elemental Mercury by Halogen-Containing Molecules. Journal of Physical Chemistry A, 2012, 115 (22), pp. 5602-5608. <http://dx.doi.org/10.1021/jp200643n>

Eric Dugat-Bony, Corinne Biderre-Petit, Faouzi JAZIRI, Maude David, Jérémie Denonfoux, Delina Lyon, Jean-Yves Richard, Cyrille Curvers, Delphine Boucher, Timothy Vogel, Eric Peyretaillade, Pierre Peyret. In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes. Microbial biotechnology, 2012, 5 (5 SI), pp. 642-653. <http://dx.doi.org/10.1111/j.1751-7915.2012.00339.x>


Delmont, T.O. Cedric Malandain, C., Prestat, E. Catherine Larose, C. Monier, J-M., Simonet, P. Vogel, T.M. 2011. Metagenomic mining for microbiologists. ISME Journal 5: 1837-1843.

Monier J-M, Demanèche S, Delmont TO, Mathieu A, Vogel, T.M. and Simonet P. 2011. Metagenomic exploration of antibiotic resistance in soil. Current Opinion in Microbiology. 14: 236-243.

Lombard N, Prestat E, Van Elsas JD and Simonet P. 2011.Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microb. Ecol 78: 31-49.

Simonet P., Plomion C and Martin F. Quand la génomique rencontre l’écologie. Biofutur, 319:26-29

Demanèche S, Monier J-M, Dugat-Bony E and Simonet P. 2011. Exploration of horizontal gene transfer between transplastomic tobacco and plant‐associated bacteria. FEMS Microb. Ecol. 78: 129-136.

Larose, C., Dommergue, A., De Angelis, M., Cossa, D., Averty, B., Marusczak, N., Soumis, N., Schneider, D., and Ferrari, C.: 2011. Springtime changes in snow chemistry lead to new insights into mercury methylation in the arctic, Geochim. Cosmochim.Acta, in Press.

Demanèche S, Brard C, Lima O, Binet F and Simonet P. 2011. Development of a new tool to improve gene transfer frequency calculations. J. Microbiol. Methods. 86: 255-257.

Delmont TO, Robe P, Clark I, Simonet P and Vogel TM. 2011. Metagenomic comparison of direct and indirect soil DNA extraction approaches. J. Microbiol. Methods. 86: 397-400.

Delmont, T. O., L. Franqueville, S. Jacquiod, P. Simonet and T. M. Vogel. 2011. Soil Metagenomic Exploration of the Rare Biosphere. In De Bruijn, F. J. (ed.), Handbook of Molecular Microbial Ecology, Volume I: Metagenomics and Complementary Approaches, First Edition. Wiley-Blackwell.

Simonet P. 2011. Approches métagénomiques pour l’étude de la microflore du sol et implications dans le domaine de la santé. Revue du Rhumatisme 78S

Petric I, Philippot L, Abbate C, Bispo A, Chesnot T, Hallin S, Laval K,  Lebeau T, Lemanceau P, Leyval C, Lindstrom K, Pandard P, Romero E, Sarr A, Schloter M, Simonet P, Smalla K, Wilke BM and Martin-Laurent F. 2011. Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples".J. Microbiol. Methods. 84:454-460.

Gilbert, J., O'Dor, R., Vogel, T. 2011. Survey data are still vital to science. Nature 469:162. doi:10.1038/469162a

Delmont T.O., Robe P, Cecillon S, Clark I.M., Constancias F, Simonet P, Hirsch P.R., Vogel TM. 2011. Accessing Microbial Diversity for Soil Metagenomic Studies. Appl Environ Microbiol. 77:1315–1324


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

Sapkota AR, Berger S, Vogel T.M. 2010. Human pathogens abundant in the bacterial metagenome of cigarettes. Environ Health Perspect. 118:351-6.

Héry M, Sanguin H, Perez Fabiel S, Lefebvre X, Vogel T.M., Paul E, Alfenore S. 2010. Monitoring of bacterial communities during low temperature thermal treatment of activated sludge combining DNA phylochip and respirometry techniques. Water Res. 2010 44:6133-43.

Pontiroli A, Ceccherini MT, Poté J, Wildi W, Kay E, Nannipieri P, Vogel T.M., Simonet P, Monier JM. 2010. Long-term persistence and bacterial transformation potential of transplastomic plant DNA in soil. Res Microbiol. 161:326-34.

Lyon, D., Buret, F., Vogel, T.M., Monier J-M. 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, 10:285-92..

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.14:205-12.

Malandain, C., Fayolle-Guichard, F., Vogel, T.M. 2010. Cytochromes P450-mediated degradation of  fuel oxygenates by environmental isolates; FEMS Microbial Ecology 72:289-96.

Dommergue A, Larose C, Faïn X, Clarisse O, Foucher D, Hintelmann H, Schneider D, Ferrari CP. 2010. Deposition of mercury species in the Ny-Alesund area (79 degrees N) and their transfer during snowmelt. Environ Sci Technol. 44:901-7.

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

Poté J, Ceccherini MT, Rosselli W, Wildi W, Simonet P and Vogel T.M. 2010. Leaching and transformability of transgenic DNA in unsaturated soil columns. Ecotoxicology and Environmental Safety. 73:67-72.


Vogel T.M., 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..

Mercier A, Bertolla F, Passelègue-Robe E and Simonet P. 2009. Influence of DNA conformation and role of comA and recA on natural transformation in Ralstonia solanacearum. Can. J. Microbiol. 55: 762-770.

Sørensen SJ, Haubjerg Nicolaisen M, Ron E and Simonet P. 2009. Molecular tools in rhizosphere microbiologyfrom single-cell to whole-community analysis. Plant Soil, 321: 483

Pontiroli A, Rizzi A, Simonet P, Daffonchio D, Vogel T.M. 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.

Vogel T.M., Hirsch PR, Simonet P, Jansson J, , Tiedje JM, Van Elsas JD, Nalin R Philippot L, and Bailey MJ. 2009. Advantages of the metagenomic approach for soil exploration. Nature Reviews Microbiology 7, 756–757


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

Lefevre F, Robe P, Jarrin C, Ginolhac A, Zago C, Auriol D, Vogel T. M.,  Simonet P and Nalin R. 2008 Drugs from hidden bugs: Discovery from untapped  resources. Res. Microbiol159:153-161.

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.

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

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. Methods73:73-77.


Mercier, A., Bertolla, F., Passelègue-Robe E. and P. Simonet. 2007.  Natural transformation-based foreign DNA acquisition in a Ralstonia  solanacearum mutS mutant. Res. Microbiol. 158: 537-544.

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 TM 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 TM 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 TM 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

Mercier, A., E. Kay and P. Simonet. 2006. Horizontal gene transfer by natural transformation in soil environment. In Nannipieri, P.and K. Smalla (ed.), Nucleic Acids and Proteins in Soils. Spinger-Verlag, Berlin, Heidelberg.

Lombard, N., J. Bailly, R. Marmeisse and P. Simonet. 2006. La métagénomique des communautés microbiennes. Biofutur 268:24-27


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.

Sanguin H., Herrera A., Oger-Desfeux C., Dechesne A., Simonet P., Navarro E., Vogel T.M., Moënne-Loccoz Y., Nesme X., Grundmann G.L. 2005. Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ. Microbiol. (in press)

Bertrand H., Poly F., Van T. V., Lombard N., Nalin R., Vogel T.M. and 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., Robe P., Perrière G., Vogel T. M. , Simonet P. and Nalin R. 2005. Type I PKS may have evolved through horizontal gene transfer. Journal of Molecular Evolution.  60:5.

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., Gillet, B., Robe, P., Pujic, P., Tuphile, K.,Bertrand, H., Vogel,T.M., Perrière, G., Simonet, P., and Nalin, R. 2004. Phylogenetic Analysis of Polyketide Synthase I Domains from Soil Metagenomic Libraries Allows Selection of Promising Clones. Appl. Environ. Microbiol. .70:5522-5527.

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

Kay, E., Chabrillat, G., Vogel, T.M., Simonet, P. 2003. Intergeneric transfer of chromosomal and conjugative plasmid genes between Ralstonia solanacearum and Acinetobacter sp. BD413.  Molecular Plant-Microbe Interactions, 16:74-82.


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

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

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

Dechesne, A., Pallud, C., Debouzie, D., Flandrois, J.P., Vogel, T.M., Gaudet, J.P. and 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., 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 Appl. Environ. Microbiol. 68: 3345-3351.


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. Appl. Environ. Microbiol. 67: 3440-3444.

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., Jocteur-Monrozier L., Quiquampoix H. and Simonet P. 2001. Evaluation of Biological and Physical Protection against Nuclease Degradation of Clay-Bound Plasmid DNA. Appl. Environ. Microbiol. 2001. 67:293-299.

Demaneche S., Kay E., Gourbiere F. and Simonet P. 2001. Natural Transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in Soil. Appl. Environ. Microbiol.;67 :2617-2621

Courtois S., Frostegard A, Goransson P, Depret G, Jeannin P and Simonet P. 2001. Quantification of bacterial subgroups in soil; comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ. Microbiol. 3 : 431-439.

Clerc-Bardin S., Karray F., Frostegard A., Pernodet J.-L. and Simonet P. 2001. Development of a conditional lethal system for a Streptomyces lividans strain and its use to investigate conjugative transfer in soil. FEMS Microbiol. Ecol. 38 : 115-121


Poly F., Chenu C., Simonet P., Rouiller J. and Jocteur Monrozier L. 2000. Differences between linear chromosomal and supercoiled plasmid DNA in their mechanisms and extent of adsorption on clay minerals. Langmuir. 16 : 1233-1238.

Bertolla F., Pepin R., Passelegue-Robe E., Paget E., Simkin A., Nesme X. and Simonet P. 2000. Plant Genome Complexity May Be a Factor Limiting In Situ the Transfer of Transgenic Plant Genes to the Phytopathogen Ralstonia solanacearum. Appl. Environ. Microbiol. 66 : 4161-4167

Bertolla F., Kay E. and Simonet P. 2000. Potential dissemination of antibiotic resistance genes from transgenic plants to microorganisms. Infect Control Hosp Epidemiol J. 21 : 390-393

Simonet P. 2000. Evaluation des potentialités de transfert de l'ADN des plantes transgéniques vers les bactéries du sol. OCL 7 : 320-323

Souteyrand E. Chen C., Cloarec J.P., Nesme X., Simonet P., Navarro I. and Martin J. R. 2000. Comparison between electrochemical and optoelectrochemical impedance measurements for detection of DNA hybridization. Appl. Biochem. Biotech.; 89 (2-3) : 195-207.


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

Bertolla F., Frostegard A., Brito B., Nesme X. and Simonet P. 1999. During infection of its host, the plant pathogen Ralstonia solanacearum naturally develops a state of competence and exchanges genetic material. Mol. Plant-Microbe Interact., 12, 467-472.

Bertolla F. and Simonet P. 1999. Horizontal gene transfers in the environment : Natural transformation as a putative process for gene transfers between transgenic plants and micro-organisms. Research in Microbiol 150, 5409-5420.

Navarro E., Jaffre T., Gauthier D., Gourbière F., Rinaudo G., Simonet P. and Normand P. 1999. Distribution of Gymnostoma spp. microsymbiotic Frankia strains in New Caledonia is related to soil type and to host-plant species. Molecular Ecology: 8 : 1781-1788.

Bertolla F. et Simonet P. 1999. Plants and microbes - A relationship under surveillance. Biofutur : 185 : 20-22.

Frostegard A., Courtois S., Ramisse V., Clerc S ., Bernillon D., Le Gall F., Jeannin P., Nesme X. and Simonet P. 1999. Quantification of Bias Related to the Extraction of DNA Directly from Soils. Appl. Environ. Microbiol., 65 : 5409-5420.

Simonet P., Navarro E., Rouvier C., Reddell P., Zimpfer J., Dommergues Y., Bardin R., Combarro P., Hamelin J., Domenach A.-M., Gourbière F., Prin Y., Dawson J. O. and Normand P. 1999. Co-evolution between Frankia populations and host plants in the family Casuarinaceae and consequent patterns of global dispersal. Environ. Microbiol. 1 : 525-533.

Fernandez M.P., Rouvier C, Orso S., Navarro E., Rinaudo G., Misra A.K., Simonet P., Reddell P., Prin Y., et Normand P. 1999. Phylogeny of Frankia  and related genera (Geodermatophilus, Acidothermus, Sporichthya, Blastococcus and Actinoplanes) and population biology. p63-75. In Biotechnology-and-biodiversity in agriculture/forestry, B.N. Prasad ed., Science Publishers INC, Enfield, N. H.

Nalin R., Normand P., Simonet P. and Domenach A.M. 1999. Polymerase chain reaction and hybridization on DNA extracted from soil as a tool for Frankia spp. population distribution studies in soil. Can. J. Microbiol. 77 : 1239-1247.


Paget E., Lebrun M., Freyssinet G. and Simonet P. 1998. The fate of recombinant plant DNA in soil. Eur. J. Soil Biol., 34, 81-88.

Clerc S and Simonet P. 1998. A review of available systems to investigate transfer of DNA to indigenous soil bacteria. Anto. van Leew. 73:15-23.

Navarro E, Rouvier C, Normand P Domenach A-M, Simonet P and Prin Y. 1998. Evolution of Frankia-Casuarinaceae interactions. Genet . Sel. Evol. 30 (Suppl. 1) S357-S372.

Nalin R, Ranjard L, Nazaret S and Simonet P. 1998. La biologie moléculaire en écologie microbienne du sol: Application à l'analyse de la structure des communautés bactériennes. Bull. Soc. Fr. Microbiol. 13 : 21-26.


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

Paget E and Simonet P. 1997. Development of engineered genomic DNA to monitor the natural transformation of Pseudomonas stutzeri in soil-like microcosms. Can. J. Microbiol. 43, 78-84.

Lebaron P, Bauda P, Lett M C, Duval -Iflah Y, Simonet P, Jacq E, Franck N, Roux B, Baleux B, Faurie G, Hubert JC, Normand P, Prieur D, Schmitt S, and Block JC (1997) Recombinant plasmid mobilization between E. coli strains in seven sterile microcosms. Can. J. Microbiol. 43, 534-540.

Bertolla F, Van Gijsegem F, Nesme X and Simonet P. 1997. Conditions for natural transformation of R solanacearum. Appl. Environ. Microbiol 63: 4965-4968.

Nesme X et Simonet P. 1997. Devenir de l'ADN dans le sol. OCL 4 (2):107-110.

Simonet P and Nesme X. 1997. Plantes transgénique, les risques. Potentialités de dissémination aux microorganismes du sol. La lettre des Sciences de la Vie, Bio 70, Les plantes transgéniques, Enjeux  et Risques. pp. 38-39.


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

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

Clerc S and Simonet P. 1996. Efficiency of the transfer of a pSAM2-derivative plasmid between two strains of Streptomyces lividans in conditions ranging from agar slants to non sterile soil microcosms. FEMS Microbiol Ecol. 21, 157-165

Rouvier C., Prin Y., Reddell P., Normand P and Simonet P. 1996, Genetic diversity among Frankia strains nodulating members of the family Casuarinaceae in Australia revealed by PCR and restriction fragment lenght polymorphism. Appl. Environ. Microbiol. 62, 979-985.

Clerc S and Simonet P. 1996 Transfert conjugatif de gènes au sein de populations indigènes du sol: Nécessité d'un système de contre-sélection. Bull. Soc. Fr. Microbiol. (11) (H.S.) 33-38.

Normand P., Ponsonnet C., Nesme X., Neyra M., Simonet P. 1996. ITS analysis of prokaryotes. In : Molecular Microbial Ecology Manual, A.D.L. Akkermans, J.D. van Elsas, F.J. de Bruijn ed., Kluwer Academic Publishers, Dordrecht, The Netherlands 3.4.5:1-12.

Picard C, Nesme X, Simonet P. 1996. Detection and enumeration of soil bacteria using the MPN-PCR technique. In : Molecular Microbial Ecology Manual, A.D.L. Akkermans, J.D. van Elsas, F.J. de Bruijn ed., Kluwer Academic Publishers, Dordrecht, Pays-Bas 2.7.3:1-9.

Rouvier C, Schwencke J, Prin Y., Navarro E, Benoist P, Müller A, Girgis M, Selim S, Reddell P, Gauthier D, Rinaudo G, Normand P and Simonet P. 1996. Biologie et diversité génétique des souches de Frankia associées aux Casuarinacées. Acta Bot. Gallica 143, 1-14.


Simonet P, Bally R et Normand P. L'Ecologie Microbienne du Sol révolutionnée par les techniques d'étude de l'ADN. R. Barbeault et J.-M. Legay (eds.), Editions Lavoisier (1995).

Nesme X., Picard C., Simonet P. 1995. Specific DNA sequences for detection of soil bacteria. In : Nucleic acids in the environment, J.T. Trevor, J.D. van Elsas ed., Springer-Verlag, Berlin, p. 111-139.

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

Simonet P, Nazaret S and Normand P. (1994). Molecular characterization and detection of the actinomycete Frankia in the environment. In : Molecular Ecology of rhizosphere microorganisms. O'Gara F, Dowling DN, Boesten B (eds). VCH, Weinheim, New-York, Basel, Cambridge, Tokyo, pp 121-132.

Simonet P, Bosco M, Moiroud A and Normand P. (1994). Molecular characterization of Frankia microsymbionts from spore-positive and spore-negative nodules in a natural alder stand. Appl. Environ. Microbiol. 60:1335-1341.

Paget E. and Simonet P. 1994. On the track of natural transformation in soil. FEMS Microbiol Ecol. 15, 109-118.


Poupard P, Simonet P, Cavelier N and Bardin R. (1993). Molecular characterization of Pseudocercosporella herpotrichoides isolates by amplification of ribosomal DNA internal transcribed spacers. Plant Pathol. 42: 873-881.        

Prin Y, Mallein-Gerin F, and Simonet P. (1993). Identification and localization of Frankia strains in Alnus nodules by in situ hybridization of nifH mRNA with strain-specific oligonucleotide probes. J. Exp. Bot. 44: 815-820.

Recorbet G, Picard C, Normand P and Simonet P. (1993). Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil. Appl. Environ. Microbiol. 59: 4289-4294.

Nesme X., Simonet P., Jocteur-Monrozier L., and Normand P. 1993. La PCR -appliquée à l'étude des bactéries du sol. In: La PCR: un procédé de réplication in vitro, D. Larzul (ed), Tec & Doc, Lavoisier, Paris, France, pp. 262-272.

Fernandez M., Navarro E., Nesme X., Simonet P., and Normand P. 1993. Problèmes et ubiquité de la systématique des microorganismes. Biosystema 8:69-78.

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

Assaf-Anid, N., Hayes, K.F., and 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., and Vogel, T.M. 1993. Effect of hydrogen peroxide on the biodegradation of PCBs in anaerobically dechlorinated river sediments. Biodegradation, 4:241-248.


Montgomery, L. and 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., and Vogel, T.M.  1992.  Biodegradation and transport of benzene and toluene in sandy aquifer materialWater Resources Research.28:1833-1847.

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

Navarro E, Simonet P, Normand P and Bardin R (1992) Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch Microbiol, 157, 107-115.

Normand P, Gouy M, Cournoyer B and Simonet P (1992) Nucleotide sequence of nifD from Frankia alni strain ArI3: phylogenetic inferences. Molecular Biology and Evolution, 9, 495-506.        

Normand P, Cournoyer B, Nazaret S and Simonet P (1992) Analysis of a ribosomal RNA operon in the actinomycete Frankia, 111, 119-124.

Bosco M, Fernandez MP, Simonet P, Materassi R and Normand P (1992) Evidence that some Frankia sp. strains are able to cross boundaries between Alnus and Elaeagnus host specificity groups. Appl Environ Microbiol, 58, 1569-1576.

Maggia L, Nazaret S and Simonet P (1992) Molecular characterization of a population of Frankia isolates from Casuarina equisetifolia root nodules harvested in west Africa. Acta Oecologica, 13, 453-461.

Rouvier C, Nazaret S, Fernandez MP, Picard B, Simonet P and Normand P (1992) rrn or nif intergenic spacers and isoenzyme patterns as tool to characterize Casuarina-infective Frankia strains. Acta Oecologica, 13, 487-495.

Picard C, Ponsonnet C, Paget E, Nesme X and Simonet P (1992) Detection and enumeration of bacteria in soil by direct DNA extraction and PCR. Appl Environ Microbiol, 58, 2717-2722.

Paget E, Jocteur Monrozier L and Simonet P (1992) Adsorption of DNA on clay minerals: Protection against DNase I and influence on gene transfer. FEMS Microbiol Letters, 97: 31-40.

Nick G, Paget E, Simonet P, Moiroud A and Normand P (1992) The nodular endophytes of Coriaria spp. form a distinc lineage within genus Frankia. Molecular Ecology, 1, 175-181.

Bally R., Simonet P, Haurat J and Normand P (1992) Characterization of Azospirillum irakense and Azospirillum lipoferum by direct sequencing of a PCR amplified 16S rDNA gene. Symbiosis, 13, 47-53.

Nazaret S, Simonet P and Normand P (1992) Contribution of molecular biology techniques to Frankia strain chracterisation and molecular ecology. In : Symbioses in Nitrogen-fixing trees. Subba Rao N. S. and Rodriguez-Barrueco C (Eds). Oxford & IBH publishing Co. PVT. LTD, New-Delhi, Bombay, Calcutta. pp. 211-231.


Simonet P, Grosjean M-C, Misra AK, Nazaret S, Cournoyer B and Normand P (1991) Frankia genus-specific characterization by polymerase chain reaction. Appl Environ Microbiol, 57, 3278-3286.

Nazaret S, Cournoyer B, Normand P and Simonet P (1991) Phylogenetic relationships among Frankia genomic species determined by use of amplified 16S rDNA sequences. J Bacteriol, 173, 4072-4078.

Misra AK, Paget E, Simonet P and Normand P (1991) Isolation and amplification of Frankia DNA from nodules of Alnus nepalensis and studies on overcoming foreign DNA contamination. Indian J Exp Biol, 29, 946-948.

Grosjean MC, Picard C, Nesme X, Nazaret S, Cournoyer B, Paget E, Simonet P, Normand P and Bardin R (1991) L'amplification enzymatique de l'ADN: un outil d'étude en Ecologie Microbienne. Phytoma, 430, 34.

Picard C, Ponsonnet C, Nazaret S, Normand P, Simonet P and Nesme X (1991) Application de l'amplification enzymatique de l'ADN à la détection de microorganismes dans le sol. Phytoma, 430, 37.

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

Nies, L. and 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)Appl. Environ. Microbiol.m 57:2771-2774.

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

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

Fathepure, B.Z. and Vogel, T.M. 1991. Complete  degradation of polychlorinated hydrocarbons by a two-stage biofilm reactor. Appl. Environ. Microbiol. , 57:3418-3422.

Assaf-Anid, N., Nies, L., and Vogel, T.M.  1991.  Reductive dechlorination of a PCB congener and hexachlorobenzene by vitamin B12. Appl. Environ. Microbiol.. 58:1057-1060.


Nies, L. and Vogel, T.M. 1990. Effects of organic substrates on dechlorination of Aroclor 1242 in anaerobic sediments. Appl. Environ. Microbiol., 56:2612-2617.

Simonet P, Normand P, Moiroud A and Bardin R (1990) Identification of Frankia strains by hybridization of Polymerase Chain Reaction products with strain-specific oligonucleotide probe. Arch Microbiol, 153, 235-240.

Simonet P, Normand P, Hirsh AM and Akkermans ADL (1990) The genetics of the Frankia-actinorhizal symbiosis. In Molecular Biology of Symbiotic Nitrogen Fixation. CRC press. Ed Gresshoff PM pp. 77-109.


Simonet P, NGuyen TL, Moiroud A and Bardin R (1989) Diversity of Frankia strains isolated from a single alder stand. Plant and Soil, 118, 13-22.

Nazaret S, Simonet P, Normand P and Bardin R (1989) Genetic diversity among Frankia strains isolated from Casuarina nodules. Plant and Soil, 118, 241-247.


Simonet P, Normand P and Bardin R (1988) Heterologous hybridization of Frankia DNA to Rhizobium meliloti and Klebsiella pneumoniae nif genes. FEMS Microbiol Letters, 55, 141-146.

Simonet P, NGuyen TL, Teissier Du Cros E and Bardin R (1988) Identification of Frankia strains by direct hybridization of crushed nodules. Appl. Environ. Microbiol.,, 54, 2500-2503.

Normand P, Simonet P and Bardin R (1988) Conservation of nif sequences in Frankia. Mol Gen Genet, 213, 238-246.


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

Grbi-Gali, D. and Vogel, T.M. 1987.  Transformation of toluene and benzene by mixed methanogenic culturesAppl. Environ. Microbiol., 53:254-260.

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

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

Normand P, Simonet P, Giasson L, Ravel-Chapuis P, Fortin JA and Lalonde M (1987) Presence of a linear plasmid-like DNA molecule in the fungal pathogen Ceratocystis fimbriata Ell. & Halst. Curr Genet, 11, 335-338.

Normand P, Simonet P, Prin Y and Moiroud A (1987) Formation and regeneration of Frankia protoplasts. Physiol Plantarum, 70, 259-266.


Vogel, T.M. and Grbi-Gali, D. 1986.  Incorporation of oxygen from water into toluene and benzene during methanogenic transformationAppl. Environ. Microbiol., 52:200-202.

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

Simonet P, Haurat J, Normand P, Bardin R and Moiroud A (1986) Localization of nif genes on a large plasmid in Frankia sp. strain ULQ0132105009. Mol Gen Genet, 204, 492-495.

1985 - 1981

Vogel, T.M. and McCarty, P.L. 1985.  Biotransformation of tetrachloroethylene to trichloroethylene, dichloroethylene, vinyl chloride, and carbon dioxide under methanogenic conditionsAppl. Environ. Microbiol. , 49:1080-1083.

Simonet P, Normand P, Moiroud A and Lalonde M (1985) Restriction enzyme digestion patterns of Frankia plasmids. Plant and soil, 87, 49-60.

Simonet P, Capellano A, Navarro E, Bardin R and Moiroud A (1984) An improved method for lysis of Frankia with achromopeptidase allows detection of new plasmids. Can J Microbiol 30, 1292-1295.

Faure-Raynaud M, Bonnefoy M-A, Perradin Y, Simonet P and Moiroud A (1984) Protoplast formation from Frankia strains. Microbios, 41, 159-166.

Normand P, Simonet P, Butour JL, Rosenberg C, Moiroud A and Lalonde M (1983) Plasmids in Frankia sp. J. Bacteriol,  155, 32-35.

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

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