Stéphane Vuilleumier

• Comparative genomics of bacterial C1 metabolism
• Bacterial dehalogenative metabolism
• Analysis of microbial diversity in polluted environments
• Bioremediation of sites contaminated by halogenated pollutants
• Microbial glutathione S-transferases

149 peer-reviewed publications (see list below or full list of publications), including 125 journal articles, 1 edited book, 14 book chapters and 7 proceedings and reports.

• 2002-present : Professor, Environmental Biology and Microbiology, Université Louis Pasteur Strasbourg, since 2009 Université de Strasbourg, France
  Group leader, (currently 4 permanent academic staff, 2 technicians, 1 post-doc, 2 Ph.D. students, 1 final year undergraduate), UMR 7156 CNRS
• 1996-2001 : Group leader (Oberassistent), Institute of Microbiology, ETH Zurich, Switzerland

• 1993-1996 : Postdoctoral research associate with Prof. T. Leisinger, ETH Zurich
• 1990-1993 : Postdoctoral fellow, MRC Unit for Protein Function and Design, and Cambridge Centre for Protein Engineering, Cambridge, England, with Prof. A. R. Fersht
• 1986-1990 : Doctoral studies and Ph. D. Thesis (Dr. Phil. II), Institute of Organic Chemistry, University of Basel (Prof. M. Mutter, supervisor), Switzerland
• 1981-1985 : Studies in organic chemistry, biochemistry and molecular biology and Degree in Natural Sciences (Dipl. Natw. ETHZ), ETH Zurich (Diploma work in bioorganic chemistry under the supervision of Dr. B. Martinoni and Prof. D. Arigoni)
• 1981 : Baccalauréat es Sciences (Maturité fédérale type C), Neuchâtel, Switzerland

• 1994-present : Supervisor or co-supervisor of 12 Ph.D. theses:
  Emilie Geersens (2017-), Jing Luo (2017-), Louis Hermon (2014-2017), Omniea Elsayed Azzam (2011-2015), Farhan Muhammad Ul Haque (2009-2013), Emilie Muller (2007-2011; PhD Prize "Region", Société de Biologie de Strasbourg, 2011)), Sandro Roselli (2006-2009), Christian Penny (2005-2009), Tatina Todorova (2004-2007), Edith Hourcade (2003-2007), Martin Kayser (1998-2001), Alex Studer (1997-2001), Daniel Gisi (1994-1998).
  Hosting and supervision of 3 exchange PhD students:
  Maria-Angela Dean (1998, University of Ferrara), Gareth Evans (1999, University of Aberdeen), Maria Torgonskaya (2006, Pushchino), Ehssan Torabi (2016, Iran).
• 1998-2009 : Mentoring of 7 postdoctoral students:
  Todd Vannelli (1997-1999), Michael Messmer (1998-1999), Sudhakar Gandhi (2003), Niamh Gilmartin (2004-2006), Jeannette Achilles (2008), Charline Wiegert (2017-2018), Abhijit Manna (2019-).
• 1993-2012 : Supervision or cosupervision of 21 final year Diploma and Master undergraduate students (6 months - 1 year each):
  Alain Tissot (1993), Karin Wüthrich (1994), Kurt Zoller, Hubert Traber (1995), Helga Sorribas (1996), Laurent Willi (1997), Michael Stumpp (1998), Sandra Oelhafen (1999), Julien Maillard (1999), Rainer Büchele (2000), Fabien Tschudy (2004), Christian Penny (2005), Sandro Roselli (2006), Olivier Schätzle (2007), David Lalouana, Déborah Schnell (2008), Muhammad Farhan Ul Haque, Adeline Dropsy (2009), Santiago Guerrero, Louise Ott, Agustina Llanos (2010), Pauline Chaignaud (2012), Farah Hajjar, Clément Descarpentries, Bruno Maucourt (2013), Emmanuel Duval, Elova Loga (2016), Marceau Levasseur (2017), Carmen Lazaro Sanchez (2018-2019).

• 2002-present : Responsibility or co-responsibility of lectures and courses at Bachelor and Master levels in Life sciences and Environmental sciences curricula. Currently:
  
  • Introductory course in ecology and environmental biology (Bachelor 1^st year, L1S2)
  • Microbial chemistry (Bachelor 2^nd year, L2S3)
  • Introduction to practical research work in the lab (Bachelor 3^rd year, L3S6)
  • Study of scientific publications (Bachelor 3^rdyear, L3S6)
  • Microbial metabolic diversity (Master 1^st year, M1S1)
  • Microbial ecology (Master 2^nd year, M2S3)
  • Interdisciplinary Project in Environmental Sciences (Master 2^nd year, M2S3)
  • Introductory Course, Biological Chemistry (Master 1^st year)
• 1997-2001 : Lectures in molecular microbiology, ETH Zurich, and University of Lausanne, Switzerland
• 1994-2001 : Co-organization of laboratory practical courses in experimental biology and gene technology, ETH Zurich

• 2017-2020: DEHALOFLUIDX (ANR, coordinator)
• 2017-2018: 2D-DCM (EC2CO CNRS, coordinator LHyGeS)
• 2016-2018: URCforSR (Interreg, coordinator for Strasbourg)
• 2015: HICAR (Idex interdisciplinaire, coordinator ICPEES)
• 2014-2017: CHLOROFILTER (ANR, coordinator F. Bringel)
• 2013-2014: TOP-DCM (EC2CO, coordinator F. Bringel)
• 2012-2014 : BIOMASSE-OUI (Intereg Offensive Sciences)
• 2012-2014 : ELISE (Feder, Agence de l'eau, coordinator BRGM)
• 2010-2014 : FP7 People CSI-ENVIRONMENT (European Union): Isotope forensics meets biogeochemistry - linking sources and sinks of organic contaminants (coordinator: UFZ Leipzig)

• Regular reviewer activity for J. Bacteriol., Microbiology, Appl. Environ. Microbiol., FEMS Microbiol. Lett.; occasional reviews for FEMS Microbiol Ecol, Biodegradation, Bioremediation J, Environ. Microbiol., Environ. Sci. Technol., Environ. Sci. Poll. Rep., Arch. Microbiol., Res. Microbiol., Molec. Ecol., Nucl. Acids Res., Roy. Soc. Biol. Lett., J. Mol. Biol., Sci. Asia
• Evaluation expert for the French AERES (LSTM Montpellier, 2010), ANR (PIrIBIO, 2009), CNRS INSU programs (2006, 2007, 2009), Irish Scientific Foundation (2004), Lyon I University Research Development Program (2004, 2005), Bureau de Ressources Génétiques (2003), IFR 86, Marseille (research unit reconduction, 2003), ACI microbiologie (2003).
• 2010-present : Coordination of manual online annotation of methanotroph genomes, methanoscope project (Genoscope microscope platform)
• 2010-present : Coordinating Member for the French partner, EU TEMPUS project "Qualifications Framework for Ecology and Environmental Management (QualFEEM)" (Freiburg University, Landau-Koblenz University, Université de Strasbourg, Aston University (UK), the State Universities of Tyumen, Omsk, Novosibirsk, and Altai, (Russian Federation), and the Chamber of Commerce of Tyumen).
• 2009-present : Member of maître de conférences (assistant professor) and chaire
  d'excellence recruitment committees, Université de Strasbourg (2009), Université de Metz
  (2010, 2011), Université d'Évry-Val-d'Essonne (2011)
• 2009-present : Member of the advisory board, University of Strasbourg library
• 2006-present : Coordination of manual online annotation of Methylobacterium genomes, methyloscope project (Genoscope microscope platform)
• 2004-present : Examiner and reviewer of 5 PhD theses at Université Louis Pasteur, Strasbourg and of 8 PhD theses elsewhere in France
• 2008-present : Member of the advisory board (comité des sages) of Région Alsace for scientific research
• 2004-present : Vice-president, board of directors, RITTMO (Recherche Innovation Transfert de Technologie pour les Matières fertilisantes Organiques)
• 2003-present : Member of the steering committee, REALISE Regional Research Network in Environmental Sciences
• 2006 : Examiner and reviewer, Habilitation thesis, Caroline Grégoire (ENGEES / LHyGES, Strasbourg)
• 2005-2009 : Coordinating Member for the French partner, EU TEMPUS project SWREC "Securing Water Resources through Educational Change" (Freiburg University, Landau-Koblenz University, Université Louis Pasteur, Tyumen University (Russia)
• 2005-2008 : Chair, Master in Environmental Sciences "Physique, Chimie et Biologie de l'Environnement", Bachelor-Master-Doctorate reform
• 2005-2009 : External member of the recruitment committee, Université de Haute Alsace (Sections 64-68)
• 2005-2008 : Member of the steering committee for Ecoentreprises, Région Alsace
• 2003-2009 : Member of the recruitment committee, Faculty of Biology (Section 67), Université Louis Pasteur
• 2003-2005 : In charge of the project for a joint Master in Environmental Sciences of Université Louis Pasteur and Université de Haute-Alsace

• 2016 : Chair (2014 Vice-Chair), Gordon Conference on The Molecular Basis of Microbial One Carbon Metabolism
  
• 2002-2005 : CNRS ATIP career development award
• 2002 : Received first, CNRS section 21 CR1 recruitment campaign
• 2001 : Venia legendi (Habilitation), ETH Zurich (Privat Docent)
• 1999 : Habilitation à diriger les recherches (équivalence), France
• 1990-1992 : Postdoctoral fellowship, Swiss National Research Fund
• 1986-1989 : PhD grant, Fonds der Chemischen Industrie, Basel

• 2011
  
  • Radboud University Nijmegen, Holland (2 March 2011)
• 2010
  
  • University of Warwick, UK (14 November 2010)
  • Discussion leader, Genomics and Metagenomics session, Gordon Conference on The Molecular Basis of Microbial One Carbon Metabolism (August 1), Bates College, Lewiston, Maine
  • INRA, Champenoux (28 May)
  • Biovalley Biomarker Meeting, Mulhouse (26 May)
  • Intersol 2010, Paris (17 March)
• 2009
  
  • Genoscope, Evry (10 December)
  • University of Washington, Seattle (3 April)
  • Harvard University, Cambridge (20 March)
• 2008
  
  • Gordon Conference on The Molecular Basis of Microbial One Carbon Metabolism, Bates College,
  • Lewiston, Maine (20 July)
  • Universität Konstanz (19 May)
  • Universität Freiburg (4 February)
• 2007
  
  • Société Française de Microbiologie, Nantes, France (29 May)
  • IBMC, Porto (26 January)

• SFM, Société Française de Microbiologie (France)
• VAAM, Verein für Allgemeine und Angewandte Mikrobiologie (Germany)
• ASM, American Society for Microbiology (USA)
• ISME, International Society for Microbial Ecology (USA)

2024

Renaudie M., Dumas C., Vuilleumier S. & Ernst B. (2024). Spontaneous dark fermentation in a pre-seeded liquid-gas membrane bioreactor : Impact of wine and coffee biowaste microflora on continuous biohydrogen production. J Cleaner Prod 437, art. 140759. https://doi.org/10.1016/j.jclepro.2024.140759

2023

Hellal, J., Barthelmebs, L., Bérard, A., Cébron, A., Cheloni, G., Colas, S., Cravo-Laureau, C., De Clerck, C., Gallois, N., Hery, M., Martin-Laurent, F., Martins, J., Morin, S., Palacios, C., Pesce, S., Richaume-Jolion, A. & Vuilleumier, S. (2023) Combining multi-phase flow and pathway-specific reactive transport modeling to investigate the impact of water table fluctuations on dichloromethane biodegradation. FEMS Microbiol Ecol FEMSEC-23-04-0164.R1, accepted.

Prieto-Espinoza, M., Di Chiara Roupert, R., Muller, EEL., Vuilleumier, S., Imfeld, G. & Weill, S. (2023) Combining multi-phase flow and pathway-specific reactive transport modeling to investigate the impact of water table fluctuations on dichloromethane biodegradation. Adv Water Res, in press.

Wasmund, K., Trueba-Santiso , A., Vicent, T., Adrian, L., Vuilleumier, S. & Marco-Urrea S (2023) Proteogenomics of the novel Dehalobacterium formicoaceticum strain EZ94 highlights a key role of methyltransferases during anaerobic dichloromethane degradation. Environ Sci Pollut Res 30, 80602-80612.

Husser, C., Vuilleumier, S. & Ryckelynk, M. (2023) FluorMango, an RNA-based fluorogenic biosensor for the direct and specific detection of fluoride. Small, 19, 2205232.

2022

Chaignaud, P., Gruffaz, C., Borreca, A., Fouteau, S., Kuhn, L., Masbou, J., Rouy, Z., Hammann, P., Imfeld, G., Roche, D. & Vuilleumier, S. (2023) A methylotrophic bacterium growing with the antidiabetic drug Metformin as its sole carbon, nitrogen and energy source. Microorganisms. 10(11):2302.

Renaudie, M., Dumas, C., Vuilleumier, S., & Ernst, B (2022) New way of valorization of raw coffee silverskin: Biohydrogen and acetate production by dark fermentation without exogenous inoculum. Bioresource Technology Reports. 17, 100918.

Jarrige, D., Haridas, S., Bleykasten-Grosshans, C., Joly, M., Nadalig, T., Sancelme, M., Vuilleumier, S., Grigoriev, I., Amato, P. & Bringel, F. (2022) High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water. Genes Genomes Genetics.

Jarrige, D., Nadalig, T., Joly, M., Sancelme, M., Vuilleumier, S., Amato, P. &Bringel, F.(2022) Complete genome of Sphingomonas aerolata PDD-32b-11, isolated from cloud water at the summit of puy de Dôme, France. Microbiology Resource Announcements, 11 (10) e00684-22.

Maucourt, B., Roche, D., Chaignaud, P., Vuilleumier, S. & Bringel, F.(2022) Genome-wide transcription start sites mapping in Methylorubrum grown with dichloromethane and methanol. Microorganisms, 10, 1301.

Renaudie, M., Dumas, C., Vuilleumier, S. & Ernst, B. (2022) New way of valorization of raw coffee silverskin: biohydrogen and acetate production by dark fermentation without exogenous inoculum.Biores. Technol. Rep. 17, art. 100918.

2021

Prieto, M., Weill, S., Belfort, B., Muller, EEL., Masbou, J., Lehmann, F., Vuilleumier, S., Imfeld, G. (2021) Water table fluctuations affect dichloromethane biodegradation in lab-scale aquifers contaminated with organohalides. Water Res. 203, art. 117530.

Kröber, E., Wende, S., Kanukollu, S., Buchen-Tschiskale, C., Besaury, L., Keppler, F., Vuilleumier, S., Kolb, S. & Bringel, F. (2021) 13C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern. Environ. Microbiol. 23, 4450-4465.

Renaudie, M., Clion, V., Dumas, C., Vuilleumier, S. & Ernst, B. (2021) Intensification and optimization of continuous hydrogen production by dark fermentation in a new design liquid/gas hollow fiber membrane bioreactor. Chem. Eng. J. 416, art. 129068.

Hellal, J., , Joulian, C., Urien, C., Ferreira, S., Denonfoux, J., Hermon, L., Vuilleumier, S. & Imfeld, G. (2021) Chlorinated ethene biodegradation and associated bacterial taxa in multi-polluted groundwater: Insights from biomolecular markers and stable isotope analysis. Sci Total Environ. 319, art. 142950.

François, E., Dumas, C., Gougeon, R., Alexandre, H., Vuilleumier, S. & Ernst, B. (2021) Unexpected high production of biohydrogen from the endogenous fermentation of grape must deposits.Bioresource Technol, 320, art. 124334.

Renaudie, M., Dumas, C., Vuilleumier, S. & Ernst, B. (2021) Biohydrogen production in a continuous liquid/gas hollow fiber membrane bioreactor: Efficient retention of hydrogen producing bacteria via granule and biofilm formation. Bioresource Technol. 319, art. 124203.

2020

Hayoun, K., Geersens, E., Laczny, C.C., Halder, R., Lázaro Sánchez, C., Manna, A., Bringel, F., Ryckelynck, M., Wilmes, P., Muller, E.E.L., Alpha-Bazin, B., Armengaud, J. & Vuilleumier, S. (2020)Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms , 8, 1876.

Maucourt, B., Vuilleumier, S., & Bringel, F. (2020) Transcriptional regulation of organohalide pollutant utilisation in bacteria, FEMS Microbiology Reviews, in press.

Torabi, E., Wiegert, C., Guyot, B., Vuilleumier, S. & Imfeld, G. (2020) Dissipation of butachlor and Smetolachlor in agricultural soils and responses of bacterial communities: insights from compoundspecific isotope and biomolecular analyses.J. Environ. Sci. 92, 163-175.

Keppler, F., Barnes, J.D., Horst, A., Bahlmann, E., Luo, J., Nadalig, T., Greule, M., Hartmann, S.C.,  & Vuilleumier, S. (2020) Chlorine isotope fractionation of the major chloromethane degradation processes in the environment. Environ. Sci. Technol.54, 3, 1634-1645.

2019

Boachon, B., Burdloff, Y., Ruan, J.-X., Rojo, R.,  Bruno, V., Robert, J., Bringel, F., Lesot, A., Henry, L., Bassard,  J.E., Matthieu, S., Lionel, A., Kaplan, I., Dudareva, N., Vuilleumier, S., Laurence, M. André, F., Navrot, N., Chen, X.-Y. & Werck D. (2019) A promiscuous cyp706a3 reduces terpene volatile emission from Arabidopsis flowers, with impacts on florivores and floral microbiome. Plant Cell. 31, 2947-2972.

Chevallier, M.L., Della-Negra, O., Chaussonnerie, S., Barbance, A., Muselet, D., Lagarde, F., Darii, E., Ugarte, E.,  Lescop, E., Fonknechten, N., Weissenbach, J., Woignier, T., Gallard, J-F., Vuilleumier, S.,  Imfeld, G., Le Paslier, D. &  Saaidi, P-L. (2019) Natural chlordecone degradation revealed by numerous transformation products characterized in key French West Indies environmental compartments. Environ. Sci. Technol.53, 6133-6143.

Elahi, A., Ajaz, M., Rehman, A., Vuilleumier, S., Khan, Z. & Hussain, S.Z. (2019). Isolation, characterization, and multiple heavy metal-resistant and hexavalent chromium-reducing Microbacterium testaceum B-HS2 from tannery effluent. J King Saud University, 31, 1437-144.

Bringel, F., Besaury, L., Amato, P., Kröber, E., Kolb, S., Keppler, F., Vuilleumier, S. & Nadalig, T. (2019) Methylotrophs and Methylotroph Populations for Chloromethane Degradation. In Methylotrophs and Methylotroph Communities, Ed : L. Chistoserdova, Caister Academic Press, Chap. 8, 149-171.

Loyaux-Lawniczak, S., Vuilleumier, S. & Geoffroy, V. (2019). Efficient reduction of iron oxides by
Paenibacillus spp. strains isolated from tropical soils. Geomicrobiol. J.36, 423-432.

Hermon, L., Hellal, J., Denonfoux, J., Vuilleumier, S., Imfeld, G., Ferreira, S. & Joulian, C. (2019). Functional genes and bacterial communities during organohalide respiration of chloroethenes in microcosms of multi-contaminated groundwater. Front. Microbiol.10, art. 89.

Torgonskaya, M.T., Zyakun, A.M., Trotsenko, Y.A., Laurinavichius, K.S., Kümmel, S., Vuilleumier, S. & Richnow, H.H. (2019). Individual stages of bacterial dichloromethane degradation mapped by stable carbon and chlorine isotope abundance ratios. J. Environ. Sci.78, 147-160.

2018

Imfeld, G., Besaury, L., Maucourt, B., Donadello,S., Baran, N. & Vuilleumier, S. (2018) Toward Integrative Bacterial Monitoring of Metolachlor Toxicity in Groundwater. Front. Microbiol. 9:2053. 

Chaignaud P., Morawe M., Besaury L., Kröber E., Vuilleumier S., Bringel F. & Kolb S. (2018). Methanol consumption drives the bacterial chloromethane sink in a forest soil. ISME J.12, 2681-2693.

Hermon L., Denonfoux J., Hellal J., Joulian C., Ferreira S., Vuilleumier S. & Imfeld G (2018). Dichloromethane biodegradation in multi-contaminated groundwater: insights from biomolecular and compound-specific isotope analyses. Water Res. 142, 217-226.

Bibi-Triki, S., Husson, G., Maucourt, B., Vuilleumier, S., Carapito, C. & Bringel, F.  (2018) N-terminome and proteogenomic analysis of the Methylobacteriumextorquens DM4 reference strain for dichloromethane utilization.J. Proteomics. 179, 131-139.

Jaeger, N., Besaury, L., Röhling, A.N., Koch, F., Delort, A.-M., Gasc, C., Greule, M.,  Kolb, S., Nadalig, T., Peyret, P., Vuilleumier, S., Amato, P., Bringel, F. &  Keppler, F. (2018) Chloromethane formation and degradation in the fern phyllosphere. Sci. Total Environ. 634, 1278-1287.

Jaeger, N., , Besaury, L., Kröber, E., Delort, A-M, Greule, M., Lenhart, K., Nadalig, T., Vuilleumier, S., Amato, P., Kolb, S., Bringel, F. & Keppler, F. (2018) Chloromethane degradation in soils - a combined microbial and two-dimensional stable isotope approach. J. Environ.Qual.47, 254-262.

2017

Farhan Ul Haque, M., Besaury, L., Nadalig, T., Bringel, F., Mutterer, J., Schaller, H. & Vuilleumier, S. (2017) Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere.  Scientific Reports7, 17589.

Bringel, F. & Vuilleumier, S. (2017). Metabolic regulation: A master role for ribulose-1,5-bisphosphate in one-carbon assimilation. Curr. Biol. 27, R1127-R1129.

Chaignaud, P., Maucourt, B., Weiman, M., Alberti, A., Kolb, S., Cruveiller, S., Vuilleumier, S. & Bringel, F. (2017). Genomic and transcriptomic analysis of growth-supporting dehalogenation of chlorinated methanes in Methylobacterium. Front. Microbiol. 8:1600.

Bringel, F., Postema, C.P., Mangenot, S., Bibi-Triki, S., Chaignaud, P., Farhan Ul Haque, M., Gruffaz, C., Hermon, L., Louhichi, Y., Maucourt, B., Muller, E.E.L., Nadalig, T., Lajus, A., Rouy, Z., Médigue, C., Barbe, V., Janssen, D.B. & Vuilleumier, S. (2017) Genome sequence of the dichloromethane-degrading bacterium Hyphomicrobium sp. strain GJ21. Genome Announc. 5, art. 00622-17.

Frindte, K., Kalyuzhnaya, M., Bringel, F., Dunfield, P., Jetten, M., Khmelenina, V., Klotz, M., Murrell, C., Op Den Camp, H., Sakai, Y., Semrau, J., Shapiro, N., Dispirito, A., Stein, L., Svenning, M., Trotsenko, Y., Vuilleumier, S., Woyke, T. & Knief, C. (2017) Draft genome sequences of two gammaproteobacterial methanotrophs isolated from rice ecosystems. Genome Announc.5, art. 00526-17.

2016

Michener, J.K., Vuilleumier, S., Bringel, F., Marx, C.J (2016). Transfer of a catabolic pathway for chloromethane in Methylobacterium strains highlights different limitations for growth with chloromethane or with dichloromethane. Front. Microbiol. 7:1116.

Dispirito, A.A., Semrau, J.D., Murrell, J.C., Gallagher, W.H., Dennison, C., Vuilleumier, S. (2016). Methanobactin and the link between copper and bacterial methane oxidation.Microbiol Mol Biol Rev. 80, 387-409.

Flynn, J., Hirayama, H., Sakai, Y., Dunfield, PF., Klotz, MG., Knief, C., Op den Camp, HJ., Jetten, MJM., Khmelenina, VN., Trotsenko, YA., Murrell, JC., Semrau, JD., Svenning, MM., Stein, LY., Kyrpides, N., Shapiro, N., Woyke, T., Bringel, F., Vuilleumier, S., DiSpirito, AA., Kalyuzhnaya, MG. (2016). Draft genomes of gammproteobacterial methanotrophs isolated from marine ecosystems. Genome Announc. 4(1):e01629-15.

2015

Flynn, J., Hirayama, H., Sakai, Y., Dunfield, PF., Klotz, MG., Knief, C., Op den Camp, HJ., Jetten, MJM., Khmelenina, VN., Trotsenko, YA., Murrell, JC., Semrau, JD., Svenning, MM., Stein, LY., Kyrpides, N., Shapiro, N., Woyke, T., Bringel, F., Vuilleumier, S., DiSpirito, AA., Kalyuzhnaya, MG. (2015). Draft genomes of gammproteobacterial methanotrophs isolated from marine ecosystems. Genome Announc. 4(1):e01629-15.

Al Dine, EJ., Mokbel, H., Elmoll, A., Massemin, S., Vuilleumier, S., Toufaily, J., Hanieh, T. & Millet, M. (2015) Concomitant evaluation of atmospheric levels of polychlorinated biphenyls, organochlorine pesticides, and polycyclic aromatic hydrocarbons in Strasbourg (France) using pine needle passive samplers. Environ. Sci. Pollut. Res.22, 17850-17859.

Penny, C., Gruffaz, C., Nadalig, T., Cauchie, H.-M., Vuilleumier, S. & Bringel, F. (2015) Tetrachloromethane-degrading bacterial enrichment cultures and isolates from a contaminated aquifer. Microorganisms 3, 327-343.

Sharp, C., Smirnova, A., Kalyuzhnaya, M., Bringel, F., Hirayama, H., Jetten, M., Khmelenina, V., Klotz, M., Knief, C., Kyrpides, N., Op den Camp, H., Reshetnikov, A., Sakai, Y., Shapiro, N., Trotsenko, Y., Vuilleumier, S., Woyke, T. & Dunfield, P. (2015) Draft genome sequence of the moderately halophilic methanotroph, Methylohalobius crimeensis strain 10Ki.Genome Announc.3(3):e00644-15

Hamilton, R., Kits, J., Ramonovskay, V., Rozova, ON., Yurimoto, H., Iguchi, H., Khmelenina, VN., Sakai, Y., Dunfield, PF., Klotz, MG., Knief, C., Op den Camp, HJM., Jetten, MSM., Bringel, F., Vuilleumier, S., Svenning, MM., Shapiro, N., Woyke, T., Trotsenko, YA., Stein, LY. & Kalyuzhnaya, MG. (2015) Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc.3(3):e00515-15

Elsayed, O.F., Maillard, E., Vuilleumier, S., Millet, M. & Imfeld, G. (2015) Degradation of chloroacetanilide herbicides and bacterial community composition in lab-scale wetlands. Sci. Tot. Environ.520, 222-231.

2014

Michener, J.K., Camargo Neves, A.A., Vuilleumier, S., Bringel, F. & Marx, C.J. (2014). Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement. eLife 2014; 3:04279.

Nadalig, T.,Greule, M., Bringel, F., Keppler, F. & Vuilleumier, S. (2014) Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation. Front. Microbiol.5: 523

Elsayed, O., Maillard, E., Vuilleumier, S. & Imfeld, G. (2014) Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor. Sci. Tot. Environ. 499, 327-335.

Ghiglione, J.F., Martin-Laurent, F., Stachowski-Haberkorn, S., Pesce, S. & Vuilleumier, S. (2014) The coming of age of Microbial Ecotoxicology: report on the first two meetings in France. Environ. Sci. Pollut. Rep. ESPR-D-14-02278.

Michener, J., Vuilleumier, S., Bringel, F. & Marx, C. (2014) Phylogeny poorly predicts the utility of a challenging horizontally-transferred gene in Methylobacterium strains. J. Bacteriol.196, 2101-2107.

Vorobev, A., Jagadevan, S., Jain, S., Anantharaman, K., Dick, G., Vuilleumier, S. & Semrau, J.D. (2014) Genomic and transcriptomic analysis of Methylocystis strain SB2 grown on methane and on ethanol. Appl. Environ. Microbiol.80, 3044-3052.

Elsayed, O., Maillard, E., Vuilleumier, S., Nijenhuis, I., Richnow, H.H. & Imfeld, G. (2014) Using compound specific isotope analysis to assess the degradation of chloroacetanilide herbicides in lab-scale wetlands. Chemosphere99, 89-95.

2013

Kalyuzhnaya, M.G., Yang, S., Rozova, O.N., Smalley, N.E., Clubb, J., Lamb, A., Nagana Gowda, G.A., Raftery, D., Fu, Y., Bringel, F., Vuilleumier, S., Trotsenko, Y.A., Beck, D., Khmelenina, V.N. & Lidstrom, M.E. (2013) Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nature Communications4, 2785.

Nadalig, T., Greule, M., Bringel, F., Vuilleumier, S. & Keppler, F. (2013) Hydrogen and carbon isotope fractionation during degradation of chloromethane by methylotrophic bacteria. MicrobiologyOpen2 (6), 893-900.

Farhan Ul Haque, MF., Nadalig, T., Bringel, F., Schaller, H. & Vuilleumier, S. (2013) A fluorescence-based bacterial bioreporter for the specific detection of methyl halide emissions in the environment. Appl. Environ. Microbiol.79, 6561-6567.

Khmelenina, V.N., Beck, D., Munk, C., Davenport, K., Daligault, H., Erkkila, T., Goodwin, L., Gu, W., Lo, C-C., Scholz, M., Teshima, H., Xu, Y., Chain, P., Bringel, F., Vuilleumier, S., DiSpirito, A., Dunfield, P., Jetten, M.S.M., Klotz, M.G., Knief, C., Murrell, J.C., Op den Camp, H.J.M., Sakai, Y., Semrau, S., Svenning, M., Stein, L.Y., Trotsenko, Y.A. & Kalyuzhnaya, M.G. (2013) Draft genome sequence of Methylomicrobium buryatense 5G, a haloalkaline-tolerant methanotrophic bacterium. Genome Announc.1(4):e00053-13

Semrau, J.D., Jagadevan, S., DiSpirito, A.A., Khalifa, A., Scanlan, J., Bergman, B.H., Freemeier, B.C., Baral, B.S., Bandow, N.L., Vorobev, A., Haft, D.H., Vuilleumier, S. & Murrell, J.C. (2013) Methanobactin and MmoD work in concert to act as the “copper-switch” in methanotrophs. Environ. Microbiol.15 (11) 3077-3086.

Kits, K., Kalyuzhnaya, M., Klotz, M., Jetten, M., Op den Camp, H., Vuilleumier, S., Bringel, F., DiSpirito, A., Murrell, C., Bruce, D., Cheng, J-F., Copeland, A., Goodwin, L., Hauser, L., Lajus, A., Land, M., Lapidus, A., Lucas, S., Médigue, C., Pitluck, S., Woyke, T., Zeytun, A. & Stein, L. (2013) Genome sequence of the obligate Gammaproteobacterial methanotroph Methylomicrobium album strain BG8. Genome Announc.1(2):e00170-13.

Roselli, S., Nadalig, T., Vuilleumier, S. & Bringel, F. (2013) The 380 kb pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: A proteomic and bioinformatics study. PLoS ONE, 8(4), e56598.

2012

Marx, C.J., Bringel, F., Chistoserdova, L., Moulin, L., Farhan Ul Haque, M., Fleischman, D.E., Gruffaz, C., Jourand, P., Knief, C., Lee, M-C., Muller, E.E.L., Nadalig, T., Peyraud, R., Roselli, S., Russ, L., Goodwin, L.A., Ivanova, N., Kyrpides, N., Lajus, A., Land, M.L., Médigue, C., Mikhailova, N., Nolan, M., Woyke, T., Stolyar, S., Vorholt, J.A. & Vuilleumier, S. (2012). Complete genome sequences of six strains of the genus Methylobacterium. J. Bacteriol. 194, 4746-4748.

Khadem, F.A., Wieczorek, A.S., Pol, A., Vuilleumier, S., Harhangi, H.R., Dunfield, P.F., Kalyuzhnaya, M.G., Murrell, J.C., Francoijs, K-J., Stunnenberg, H.G., Stein, L.Y., DiSpirito, A.A., Semrau, J.D., Lajus, A., Médigue, C., Klotz, M.G., Jetten, M.S.M. & Op den Camp, H.J.M. (2012). Draft genome sequence of the volcano-inhabiting thermoacidophilic methanotroph Methylacidiphilum fumariolicum strain SolV. J. Bacteriol.194, 3729-3730.

Imfeld, G. & Vuilleumier, S. (2012). Measuring the effects of pesticides on bacterial communities in soil: a critical review. Eur. J. Soil Biol.49, 22-30.

Vuilleumier, S., Khmelenina, V.N., Bringel, F., Reshetnikov, A.S., Lajus, A., Mangenot, S., Rouy, Z., Op den Camp, H.J.M., Jetten, M.S.M., DiSpirito, A.A., Dunfield, P., Klotz, M.G., Semrau, J.D., Stein, L.Y., Barbe, V., Médigue, C., Trotsenko Y.A. & Kalyuzhnaya, M.G. (2012). Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z. J. Bacteriol. 194, 551-552.

2011

Boden, R., Cunliffe, M., Scanlan, J., Moussard, H., Kitz, K., Klotz, M.G., Jetten, M.S.M., Vuilleumier, S., Han, J., Peters, L., Mikhailova, N., Teshima, N., Tapia, R., Kyrpides, N., Ivanova, N., Pagani, I., Cheng, J-F., Goodwin, L., Han, C., Hauser, L., Land, M., Lapidus, A., Lucas, S., Pitluck, S., Woyke, T., Stein, L.Y. & Murrell, J.C. (2011). Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J. Bacteriol.193, 7001-7002.

Svenning, M.M., Hestnes, A.G., Wartiainen, I., Stein, L.Y., Klotz, M.G., Kalyuzhnaya, M.G., Spang, A., Bringel, F., Vuilleumier, S., Lajus, A., Médigue, C., Bruce, D.C., Cheng, J.F., Goodwin, L., Ivanova, N., Han, J., Han, C.S., Hauser, L., Held, B., Land, M.L., Lapidus, A., Lucas, S., Nolan, M., Pitluck, S. & Woyke, T. (2011). Genome sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96. J. Bacteriol.193, 6418-6419.

Vuilleumier, S., Nadalig, T., Farhan Ul Haque, M., Magdelenat, G., Lajus, A., Roselli, S., Muller, E.E.L., Gruffaz, C., Barbe, V., Médigue, C. & Bringel, F. (2011) Complete genome sequence of the chloromethane-degrading strain Hyphomicrobium sp. strain MC1. J. Bacteriol.193, 5035-5036.

Kittichotirat, W., Good, N., Hall, R., Bringel, F., Lajus, A., Médigue, C., Smalley, N., Beck, D., Bumgarner, R., Vuilleumier, S. & Kalyuzhnaya, M.G. (2011). Genome sequence of Methyloversatilis universalis FAM5^T, a methylotrophic representative of the order Rhodocyclales. J. Bacteriol.193, 4541-4542.

Muller, E., Hourcade, E., Louhichi-Jelail, Y., Hammann, P., Vuilleumier, S. & Bringel, F. (2011) Functional genomics of dichloromethane utilisation in Methylobacterium extorquens DM4. Environ. Microbiol.13, 2518-2535.

Semrau, J.D., DiSpirito, A.A. & Vuilleumier, S. (2011) Facultative methanotrophy: False leads, true results, and suggestions for future research. FEMS Microbiol. Lett.323, 1-12.

Muller, E., Bringel, F. & Vuilleumier, S. (2011) Dichloromethane-degrading bacteria in the genomic age. Res Microbiol.162, 869-876.

Nadalig, T., Farhan Ul Haque, M., Roselli, S., Schaller, H., Bringel, F. & Vuilleumier, S. (2011) Detection and isolation of chloromethane-degrading bacteria from the Arabidopsis thaliana phyllosphere, and characterization of chloromethane utilisation genes. FEMS Microbiol. Ecol. 77, 438-448.

Bois, P., Huguenot, D., Norini, M.P., Farhan Ul Haque, M., Vuilleumier, S. & Lebeau, T. (2011). Herbicide degradation and copper complexation by bacterial mixed cultures from a vineyard stormwater basin. J. Soils Sedim.11, 860-873.

Torgonskaya, M.L., Doronina, N.V., Hourcade, E., Trotsenko, Y. & Vuilleumier, S. (2011) Chloride-specific adaptive response in aerobic methylotrophic dichloromethane-utilising bacteria. J. Basic Microbiol. 51, 296-303.

Stein, L.Y., Bringel, F., DiSpirito, A.A., Han, S., Jetten, M.S.M., Kalyuzhnaya, M.G., Kits, K.D., Klotz, M.G., Op den Camp, H.J.M., Semrau, J.D., Vuilleumier, S., Bruce, F., Cheng, J.F., Copeland, A., Davenport, K.W., Goodwin, L., Han, S., Hauser, L., Lajus, A., Land, M.L., Lapidus, A., Lucas, S., Médigue, C., Pitluck, S. & Woyke, T. (2011). Genome sequence of the methanotrophic Alphaproteobacterium, Methylocystis sp. Rockwell (ATCC 49242). J. Bacteriol.193, 2668-2669.

Imfeld, G., Bringel, F. & Vuilleumier, S. (2011) Bacterial tolerance in contaminated soils: potential of the PICT approach in microbial ecology. In: Tolerance to Environmental Contaminants (Amiard-Triquet C, Rainbow PS, Roméo M), CRC Press, Boca Raton, Chapter 14, 335-364.

2010

Rozova, O.N., Khmelenina, V.N., Vuilleumier, S. & Trotsenko, Y.A. (2010) Characterization of recombinant pyrophosphate-dependent 6-phosphofructokinase from halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Res. Microbiol. 160, 861-868

Stein, L.Y., Semrau, J.D., DiSpirito, A.A., Crombie, A., Murrell, J.C., Vuilleumier, S., Kalyuzhnaya, M.G., Op den Camp, H.J.M., Bringel, F., Bruce, F., Cheng, J.F., Copeland, A.,  Goodwin, L., Han, S., Hauser, L., Jetten, M.S.M., Lajus, A., Land, M.L., Lapidus, A., Lucas, S., Médigue, C., Pitluck, S., Woyke, T., Yoon, S., Zeytun, A. & Klotz, M.G. (2010) Genome sequence of the obligate methanotroph, Methylosinus trichosporium strain OB3b. J. Bacteriol. 192, 6497-6498

Krentz, B.D., Mulheron, H.J., Semrau, J.D., DiSpirito, A.A., Bandow, N.L., Haft, D.H., Vuilleumier, S., Murrell, J.C., McEllistrem, M.T., Hartsel, S.C. & Gallagher, W.H. (2010) A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain SB2 predicts methanobactins are synthesized from diverse ribosomally produced peptide precursors modified to create a common core for binding and reducing copper ions. Biochemistry 49, 10117-10130

Todorova, T.T., Kujumdzieva, A.V. & Vuilleumier, S. (2010). Non-enzymatic roles for the URE2 glutathione S-transferase in the response of Saccharomyces cerevisiae to arsenic. Arch. Microbiol. 192, 909-918

Penny, C., Vuilleumier, S. & Bringel, F. (2010) Microbial degradation of tetrachloromethane: mechanisms and perspectives for bioremediation. FEMS Microbiol. Ecol.74, 257-275

Penny, C., Nadalig, T., Alioua, M., Gruffaz, C., Vuilleumier, S. & Bringel, F. (2010). Coupling of denaturing high-performance liquid chromatography and terminal restriction fragment length polymorphism with precise fragment size calling for microbial community profiling and characterization. Appl. Environ. Microbiol.76, 648-651.