The Vogel Lab

Prof. Timothy M. Vogel
Université Claude Bernard Lyon 1

Laboratoire Ampère
Ecole Centrale de Lyon
Université de Lyon
36 avenue Guy de Collongue
69134 Ecully cedex
France








vogel@univ-lyon.fr
+33 (0) 472 18 65 14

Research Interests

Our environmental microbiology research concerns the ability of bacteria to adapt to different environments. An excellent model for this adaptation is the fate and effects of xenobiotic compounds. While our work on xenobiotic compounds has included work from soil bioremediation and groundwater treatment to degradation pathways, much of our current microbial ecology research is on the perturbations of microbial communities and the adaptation of microorganisms to xenobiotic compounds (either by mutation, gene transfer or gene shuffling). In addition, within gene transfer, our current research also includes the fate of DNA from transgenic plants – its movement, degradation and potential transfer to bacteria.

Our environmental genomics (mostly metagenomics) involves exploring the functional and structural relationships between the environmental genetic resources within a given ecosystem (currently: polluted soil (chlorinated compounds and petroleum hydrocarbons, microbial fuel cells) and bacterial adaptation and evolution. High throughput techniques, such as microarrays and “next generation sequencing”, are used to produce data that supports relevant hypotheses.

Our environmental bioengineering work centers around the biodegradation of contaminants in the subsurface and the applications of microbial fuel cells (MFCs). Modeling is an important aspect of this work along with the application of modern molecular biology methods.

Current Research Projects

  • EiCLaR: Enhanced in situ bioremediation for contaminated land remediation
  • SARA: Surveillance of emerging pathogens and antibiotic resistances in aquatic ecosystems
  • CONTACT: Consequences of antimicrobials and antiparasitics administration in fish farming for aquatic ecosystems

Curriculum Vitae

Professor, 2000 -The University of Lyon (Université Claude Bernard Lyon1, Ecole Centrale de Lyon)
R&D Project Manager, 1998- 2000, Rhodia Eco Services
Animateur Scientifique et Technique, 1994-1997, Rhône-Poulenc Industrialisation
Expert d’Environnement, 1992-1994, Rhône-Poulenc Industrialisation
Assistant Professor, 1988-1993 The University of Michigan.
Assistant Professor, 1987-1988, Michigan State University.
Acting Instructor, Fall 1985, Stanford University.
Research Assistant, 1981-1987, Stanford University.
Organic Geochemist, 1979-1982, U.S. Geological Survey.

Education

Ph.D. Environmental Engineering (Microbiology), 1988, Stanford University
M.S. Environmental Engineering, 1983, Stanford University
B.S. Geology, 1979, University of Washington, Seattle.
B.S. Biological Oceanography, 1979, University of Washington, Seattle.

Publications (2015 - 2021)

Finn D.R., Bergk-Pinto B., Hazard C., Nicol G.W., Tebbe C., Vogel T.M. 2021. Functional trait relationships demonstrate life strategies in terrestrial prokaryotes. FEMS Microbiology Ecology, 97, fiab068. doi.org/10.1093/femsec/fiab068

Ramos, D.T., Corseuil, H.X., Vogel T.M. 2021. Back to the wild: polluted sites remediation and biosphere resilience. bioRxiv doi.org/10.1101/2021.04.22.441002

Sanchez-Cid, C.; Guironnet, A.;Wiest, L.; Vulliet, E.; Vogel, T.M. 2021. Gentamicin Adsorption onto Soil Particles Prevents Overall Short-Term Effects on the Soil Microbiome and Resistome. Antibiotics 2021, 10, 191. doi.org/10.3390/antibiotics10020191

Larose, C., Maccario, L., Vogel,T.M. 2021. Microbiology of the Cryosphere: Diversity, Habitat Constraints and Ecology. Chapter in Advances in Atmospheric Chemistry – Volume 3, World Scientific Publishing Company.

Tignat-Perrier, R., Dommergue, A., Thollot, A., Magand, O., Amato, P., Joly, M., Sellegri, K., Vogel ,T.M., Larose, C. 2020. Seasonal shift in airborne microbial communities. Science of the Total Environment 716 doi.org/10.1016/j.scitotenv

Zhu, C., Miller, M., Lusskin, N., Bergk Pinto, B., Lorrie Maccario, L., Haggblom, M., Vogel, T.M., Larose, C., Bromberg, Y. 2020.   Snow Microbiome Functional Analyses Reveal Novel Microbial Metabolism of Complex Organic Compounds. MicrobiologyOpen. 2020;9:e1100. doi.org/10.1002/mbo3.1100

Tignat-Perrier, R., Dommergue, A., Vogel, T.M., Larose, C. 2020. Microbial Ecology of the Planetary Boundary Layer. Atmosphere 2020, 11, 1296; doi:10.3390/atmos11121296

Finn, D. R., Yu, J., Ilhan, Z. E., Fernandes, V. M. C., Penton, C. R., Krajmalnik-Brown, R., Garcia-Pichel, F., Vogel, T. M. 2020. MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data. FEMS Microbiology Ecology, 96, doi:10.1093/femsec/fiaa131

Holland AT, Bergk Pinto B, Layton R, Williamson CJ, Anesio AM, Vogel TM, Larose C and Tranter M. 2020. Over Winter Microbial Processes in a Svalbard Snow Pack: An Experimental Approach. Front. Microbiol. 11:1029. doi: 10.3389/fmicb.2020.01029

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, 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

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

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, doi.org/10.1093/femsle/fnz180

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.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

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

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

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, doi.org/10.1016/j.bios.2016.10.096

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

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.

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

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

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

Maccario L, Sanguino L, Vogel TM, Larose 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

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: