Pascal Simonet

CNRS Director of Research, Emeritus

Laboratoire Ampère, UMR CNRS 5005
Ecole Centrale de Lyon
Université de Lyon
36 avenue Guy de Collongue
69134 Ecully cedex
+33 (0) 478 43 37 17

Research Interests

Dr. Pascal Simonet obtained his PhD in 1983. His research group investigated the evolution potential of bacteria in environments such as the soil and plants. For more than 15 years the research group entitled « Gene Transfer and Bacterial Adaptation » that he led at the University of Lyon has had the general objectives of determining the involvement of horizontal gene transfers (HGT) in the adaptation and evolution of bacteria to new environments. Studies of the group focused mainly on natural genetic transformation and also, but at a lesser extent, on conjugation. These objectives lead the group to develop soil DNA extraction methods and it was among the first to investigate environmental bacteria with metagenomic approaches. Several of the studies were devoted to investigate the fate of DNA released by genetically engineered organisms including the possibility that recombinant DNA, and particularly antibiotic resistance genes transforms indigenous bacteria. The group also demonstrated a transforming effect on soil bacteria of lightning-generated electrical conditions that motivated the move to the “Laboratoire Ampère” (UMR CNRS 5005) at Ecole Centrale de Lyon (ECL) for developing the “Environmental Microbial Genomics” group (département Bioingéniérie). Dr. Pascal Simonet has co-authored more than 100 scientific papers.

Curriculum Vitae

  • 2006- 2021: PI in the Working group “Environmental Microbial Genomics”, UMR CNRS 5005, Laboratoire Ampère, Ecole Centrale de Lyon.
  • 1990- 2006: PI in the Working group “Horizontal gene transfer and bacterial adaptation” at UMR CNRS 5557, Ecologie Microbienne du sol, Université de Lyon.
  • 1983-1990: Scientist in the Working group “Frankia symbiosis” at UMR CNRS 5557, Ecologie Microbienne du sol, Université de Lyon.       
  • 1982 -1983: Post-doctoral position at the department of forestry, University Laval, Québec, Canada

Promotions and Education

  • 2005: Promotion to the grade : « Directeur de Recherche de 1ère classe »
  • 1993: Promotion to the grade : « Directeur de Recherche de 2ème classe ».
  • 1990: Habilitation à diriger les recherches (HDR). University of Lyon.
  • 1988: Promotion to the grade: « Chargé de Recherche 1ère classe »
  • 1984: Integration at CNRS as a Scientist.
  • 1983: PhD in microbiology. University of Lyon.

Memberships and Committees

  • Editorial board of Research in Microbiology (full editor since 2007), Annals of Microbiology (full editor 2008-2012), ISME Journal (since 2007), Applied and Environmental Microbiology (until 2012)
  • Since 2011, Member of the Scientific Committee of Plant Health and Environment (SPE) department of INRA.
  • Since 2008, Member of the French council (Scientific committee) “Haut Conseil des Biotechnologies” (HCB)”
  • 1990-2008, Member of the French committee “Commission de Génie Génétique” (CGG)
  • 2000-2008, Member of the Biotechnology Committee at the French Food Security Commission (AFSSA)
  • 2005, President of the Organizing committee of the 8th Symposium on Bacterial Genetics and Ecology. BAGECO-08. June 26-29 2005, Lyon
  • 1995-2005, Member of the former National Ecotoxicology Commission (PNETOX)

Reviewing Appointments

  • Agence Nationale Recherche (ANR), France
  • Agence Evaluation Recherche (AERES), France
  • INRA : Recruitments, Promotions, Projects and Careers
  • F.R.S.-FNRS, Belgium
  • Israel Science Foundation (ISF), Israel
  • Chinese Academy of Sciences, Strategic Priority Research Program (Type-B), China
  • WO-Expertpanel Molecular and Cellular Biology (Bio1), Belgique
  • ECOS : Evaluation-orientation de la COopération Scientifique Programme de coopération et de partenariat universitaire technique et scientifique France-Amérique Latine
  • Progr. Hospitalier Recherche Clinique PHRC, France
  • INRA : Département SPE, France
  • CNRS : Programme GESSOL, France
  • CNRS-INEE: Génom.  Environnement. (APEGE).
  • Conseil Région d’Aquitaine, France
  • Conseil Région Bretagne, France
  • Conseil Région Pays de la Loire, France
  • Conseil Région Ile de France, France
  • Ville de Paris: Médecine et Santé, France
  • Convergence-UPMC, France
  • Convergence-Sorbonne Universités, France

Publications (2013 - 2019)

  • 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 facotrs depends on the immigrated bacteria, as revealed by a soil microcosms experiment. mSystems. doi:10.1128/msystems.00496-19.
  • Larsson, D.G.J., Andremont, A., Bengtsson-Palme, J., Brandt, K.K., de Roda Husan, A.M., Fagerstedt, P., Fick, J., C-F., Gaze, W.H., Kuoda, M., Kvint, M., Laxminarayan, R., Manaia, C.M., Nielsen, K.M., Plant, L., Ploy, M-C., Segovia, C., Simonet, P., Smalla, K., Snape, J. Topp, E., van Hwngel, A.j., Verner-Jeffreys, D.W., Virta, M.P.J., Wellington, E.M., Wernersson, A.-S. 2018. Criticial knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environ Int. 117:132-138.
  • Zhu, Y.-G., Gillings, M., Simonet, P., Stekel, D., Banwart, S., Penuelas, J. 2018. Human dissemination of genes and microorganisms in Earth’s Critical Zone. Global Change Biology. 24:1488-1499.
  • Zhu, Y.-G., Gillings, M., Simonet, P., Stekel, D., Banwart, S., Penuelas, J. 2017. Microbial mass movements. Science. 357:1099-1100.
  • 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.
  • 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 exposed to simulated lightning. FEMS Microbiol Ecol. 93: doi: 10.1093/femsec/fix057.  
  • 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. 16:208-220.
  • Nesme J,  Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, LePaslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O’Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LFW, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu Y-G, Vogel TM and P Simonet. 2016. Back to the Future of Soil Metagenomics. Front. Microbiol. 7:73. doi: 10.3389/fmicb.2016.00073
  • 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, member 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.
  • 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. 2016. L’être vivant dans son environnement.  Livre blanc pour les sciences de la vie du XXIème siècle (eds T Gaude, C Jessus, Y Levy). CNRS Editions.
  • Simonet P and A Maître. 2016. De la santé de l’environnement à la santé humaine. Les Big Data à découvert (eds S Abiteboul, G Baldacci, P Besse, O Cappé, A Cappy, C Jeandel, D Joly, B Jouve, S Laugier, Y Maday, C Nédellec, J-N Patillon, M-C Rousset et H Touzet). CNRS Editions.
  • 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. 427: 306-313.
  • Nesme J and P. Simonet. 2015. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ. Microbiol. 17: 913-930.  (doi: 10.1111/1462-2920.12631).
  • Delmont, T. O., A. M. Eren, L. MacCario, E. Prestat, O. C. Esen, E. Pelletier, D. Le Paslier, P. Simonet and T. M. Vogel. 2015. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Front. Microbiol. 6:358.
  • Pivetal J, D. Royet, G. Ciuta, M. Frenéa-Robin, N. Haddour, N.M. Dempsey, F. Dumas-Bouchiat and P. Simonet. 2015. Micro-magnet arrays for specific single bacterial cell positioning. J. Magn. Magn. Mater. 380: 72-77.
  • Navarro E, O Fabrègue, R Scorretti, J Reboulet, P Simonet, L Dawson and S Demanèche. 2015. RisaAligner: a software to align fluorescent data between Agilent 2100 Bioanalyzer arrayschips; Application to soil microbial community analysis. BioTechniques 59: 347-358.
  • Pivetal J, M Frenea-Robin, N Haddour, C Vezy, LF Zanini, G Ciuta, NM Dempsey, F Dumas-Bouchiat, G Reyne, S Begin-Colin, D Felder-Flesh, C Ghobril, G. Pourroy  and P Simonet. 2015. Development and application of a DNA labeling method with magnetic nanoparticles to study the role of horizontal gene transfer between bacteria in soil pollutant bioremediation processes. Environ Sci Pollut Res. 22: 20322-20327. DOI 10.1007/s11356-015-5614-0
  • Delmont TO, Francioli D, Jacquesson S, Laoudi S, Mathieu A, Nesme J, Ceccherini M-T, Nannipieri P, Simonet P and Vogel TM. 2014. Microbial community development and unseen recovery in inoculated sterile soil. Biol. Fertil. Soils. 50: 1069-1076.
  • 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. 107: 84-91. doi: 10.1016/j.mimet.2014.09.006.
  • Pivetal J, Royet D, Ciuta G, Frenéa-Robin M, Haddour N, Dempsey NM, Dumas-Bouchiat F and Simonet P. 2014. Selective micro-patterning of microbial cells upon micro-magnet arrays for single cell analysis. J. Magn. Magn. Mater.
  • 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. 17: 913-930. doi: 10.1111/1462-2920.12631
  • 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.
  • 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.
  • Nesme J, Cécillon S, Delmont TO, Monier J-M, Vogel T.M and Simonet P. 2014. Large scale metagenomic-based study of antibiotic resistance in the environment. Current Biol. 24: 1096-1100.
  • 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 metagenoic library. J. Biotechnol. 190: 18-29. doi: 10.1016/j.jbiotec.2014.03.036.
  • Mathieu A, Delmont TO, Vogel TM, Robe P, Nalin R and Simonet P. 2013. Life on human surfaces: skin metagenomics. PLoS ONE 8(6): e65288. doi:10.1371/journal.pone.0065288.
  • Delmont TO, Simonet P, Vogel TM. 2013. Mastering methodological pitfalls for surviving the metagenomic jungle. BioEssays 35: 744–754.
  • 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.
  • Jacquiod S, Franqueville L, Cécillon S, Vogel TM and Simonet P. 2013. Soil bacterial community shift after chitin enrichment: An integrative metagenomic approach. PLoS ONE 8(11): e79699.
  • Simonet, P. 2013. Évolution de l’antibiorésistance dans le sol. ANSES: Les cahiers de la Recherche: Santé, Environnement, Travail. Octobre 2013 :42-44