Publications

2018

A Genomic Outlook on Bioremediation: The Case of Arsenic Removal
Plewniak F, Crognale S, Rossetti S and Bertin PN
Front. Microbiol. (2018), 9:820, doi: 10.3389/fmicb.2018.00820

2017

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
Prigent, S., Frioux, C., Dittami, S. M., Thiele, S., Larhlimi, A., Collet, G., Gutknecht, F., Got, J., Eveillard, D., Bourdon, J., Plewniak, F., Tonon, T., Siegel, A.
PLoS Comput Biol 13: e1005276, Kaleta, C (ed), (2017).

2016

The microbial genomics of arsenic
Andres J., Bertin P.N. 
FEMS Microbiol. Rev. (2016), 40: 299-322.

Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient
in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France
Volant A., Héry M., Desoeuvre A., Casiot C., Morin G., Bertin P. N. & Bruneel O.
Microb. Ecol. (2016) 72: 608–620.

Spatio-Temporal Detection of the Thiomonas Population and the Thiomonas Arsenite Oxidase Involved in Natural Arsenite Attenuation Processes in the Carnoulès Acid Mine Drainage.
Hovasse A, Bruneel O, Casiot C, Desoeuvre A, Farasin J, Hery M, Van Dorsselaer A, Carapito C and Arsène-Ploetze F
Front. Cell Dev. Biol. (2016), 4:3. doi: 10.3389/fcell.2016.00003

Arsenite response in Coccomyxa sp. Carn explored by transcriptomic and non-targeted metabolomic approaches.
Koechler S, Bertin PN, Plewniak F, Baltenweck R, Casiot C, Heipieper HJ, Bouchez O, Arsène-Ploetze F, Hugueney P, Halter D.
Environ Microbiol. (2016), Jan 15. doi: 10.1111/1462-2920.13227.

Comparative proteomics of Acidithiobacillus ferrooxidans grown in the presence and absence of uranium.
Dekker L., Arsène-Ploetze F., Santini J.
Res Microbiol. (2016), 167: 234-239.

2015

Recent advances in microbiology : towards new horizons ?
Bertin P.N.
Res. Microbiol. (2015), 166: 727-728

Thiomonas sp. CB2 is able to degrade urea and promote toxic metal precipitation in acid mine drainage waters supplemented with urea.
Julien Farasin, Jérémy Andres, Corinne Casiot, Valérie Barbe, Jacques Faerber, David Halter, Dimitri Heintz, Sandrine Koechler, Didier Lièvremont, Raphael Lugan, Marie Marchal, Frédéric Plewniak, Fabienne Séby, Philippe N Bertin, Florence Arsene-Ploetze
Frontiers in Microbiology (2015), 6: 993

Adaptation in toxic environments: arsenic genomic islands in the bacterial genus Thiomonas.
Freel K, Krueger M, Farasin J, Brochier-Armanet C, Barbe V, Andres J, Cholley P-étienne, Dillies M-A, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppée J-Y, Bertin PN, Heipieper HJ, Arsene-Ploetze F.
PLoS ONE, (2015), Sep 30;10(9):e0139011. doi: 10.1371/journal.pone.0139011.

Environmental microbiology as a mosaic of explored ecosystems and issues.
Faure D, Bonin P, Duran R; Microbial Ecology EC2CO consortium.
Environ Sci Pollut Res Int. (2015), Sep;22(18):13577-98. doi: 10.1007/s11356-015-5164-5.

Toxic metal resistance in biofilms: diversity of microbial responses and their evolution.
Koechler S, Farasin J, Cleiss-Arnold J, Arsène-Ploetze F.
Res Microbiol. (2015), Apr 11. pii: S0923-2508(15)00060-1. doi: 10.1016/j.resmic.2015.03.008.

Contributions of descriptive and functional genomics to microbial ecology.
Bertin P, Michotey V. & Normand P.
In J.C. Bertrand et al. (eds), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology, Springer, pp. 831-846.

Métagénomique environnementale.
Bertin P, Plewniak F.
In M.-C. Champomier-Vergés, M. Zagorec (eds) La métagénomique – Développements et futures applications, Editions QUAE, pp. 89-96.

Constitutive arsenite oxidase expression detected in the arsenic hypertolerant Pseudomonas xanthomarina S11.
Koechler S, Arsène-Ploetze F, Brochier C, Cholet F, Jost B, Lièvremont D, Plewniak F, Philipps M, Salmeron A, Bertin PN, Lett MC.
Res. Microbiol. (2015), Apr;166(3):205-14. doi: 10.1016/j.resmic.2015.02.010. Epub 2015 Mar 6.

16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage.
Fahy A, Giloteaux L, Bertin P, Le Paslier D, Médigue C, Weissenbach J, Duran R, Lauga B.
Microbiol. Ecol. (2015), Jul;70(1):154-67. doi: 10.1007/s00248-014-0558-3. Epub 2015 Jan 16.

Proteomic tools to decipher microbial community structure and functioning.
Florence Arsène-Ploetze, Philippe N. Bertin, Christine Carapito.
Environ Sci Pollut Res Int. (2015),Sep;22(18):13599-612. doi: 10.1007/s11356-014-3898-0. Epub 2014 Dec 5.

Arsenic hypertolerance in the protist E. mutabilis is mediated by specific transporters and functional integrity maintenance mechanisms. 
David Halter, Jérémy Andres, Frédéric Plewniak, Julie Poulain, Corinne Da Silva, Florence Arsène-Ploetze, Philippe N. Bertin
Environ. Microbiology (2015) Jun;17(6):1941-9. doi: 10.1111/1462-2920.12474. Epub 2014 Apr 28.

 

2014

Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and others drivers along an acid mine drainage.
Aurélie Volant, Odile Bruneel, Angélique Desoeuvre, Marina Héry, Corinne Casiot, Noëlle Bru, Sophie Delpoux, Fabien Javerliat, Robert Duran, Philippe Bertin, Françoise Elbaz-Poulichet, Béatrice Lauga
FEMS Microbiol. Ecology (2014) Oct;90(1):247-63. doi: 10.1111/1574-6941.12394. Epub 2014 Sep 9.

Differential expression of Ixodes ricinus salivary gland proteins in the presence of the Borrelia burgdorferi sensu lato complex
Violaine Cotté, Laurence Sabatier, Gilles Schnell, Annick Carmi-Leroy, Jean-Claude Rousselle, Florence Arsène-Ploetze, Laurence Malandrin, Natacha Sertour, Abdelkader Namane, Elisabeth Ferquel and Valérie Choumet
J. Proteomics (2014) 96: 29-43

Rapid impact of phenanthrene and arsenic on bacterial community structure and activities in sand batches.
Aurélie Cébron, Florence Arsène-Ploetze, Pascale Bauda, Philippe N. Bertin, Patrick Billard, Cristine Carapito, Simon Devin, Florence Goulhen-Chollet, Jessica Poirel, Corinne Leyval
Microbial Ecology (2014) 67: 129-144.


2013

Genome sequence of Halomonas sp. Strain A3H3, isolated from arsenic-rich marine sediments.
Sandrine Koechler, Frédéric Plewniak, Valérie Barbe, Fabienne Battaglia-Brunet, Bernard Jost, Catherine Joulian, Muriel Philipps, Serge Vicaire, Stéphanie Vincent, Tao Ye, Philippe N. Bertin
Genome Announc. (2013), 1(5)doi:pii: e00819-13. 10.1128/genomeA.00819-13

Arsenic dispersion induced by microbial activity in Mediterranean marine sediments
Frédéric Plewniak, Sandrine Koechler, Benjamin Navet, Eric Dugat-Bony, Olivier Bouchez, Pierre Peyret, Fabienne Seby, Fabienne Battaglia-Brunet, Philippe N. Bertin
Molecular Ecology. (2013), 22(19):4870-83, doi: 10.1111/mec.12432

Yeast and bacterial diversity along a transect in an acidic, As–Fe rich environment revealed by cultural approaches
François Delavat, Marie-Claire Lett, Didier Lièvremont
Science of The Total Environment, (2013), Volumes 463–464, 1 October 2013, Pages 823–828

Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium Rhizobium sp. NT-26.
Andres J., Arsène-Ploetze F., Barbe V., Brochier-Armanet C., Cleiss-Arnold J., Coppée J.Y., Dillies M.A., Geist L., Joublin A., Koechler S., Lassalle F., Marchal M., Médigue C., Muller D., Nesme X., Plewniak F., Proux C., Ramirez-Bahena M.H., Schenowitz C., Sismeiro O., Vallenet D., Santini J.M., Bertin P.N.
Genome Biology and Evolution. (2013) 5(5):934-53. doi: 10.1093/gbe/evt061.

An improved stable isotope N-terminal labeling approach with light/heavy TMPP to automate proteogenomics data validation : dN-TOP.
Bertaccini D, Vaca S, Carapito C, Arsène-Ploetze F, Van Dorsselaer A, Schaeffer-Reiss C.
J Proteome Res. (2013) Jun 7;12(6):3063-70. doi: 10.1021/pr4002993

Bacterial metabolism of environmental arsenic - mechanisms and
biotechnological applications
Martin C. Kruger, Philippe N. Bertin, Hermann J. Heipieper, Florence Arsène-Ploetze
Applied Microbiology and Biotechnology. (2013) May;97(9):3827-41. doi:10.1007/s00253-013-4838-5.

The first genomic and proteomic characterization of a deep-sea sulfate reducer : insights into the piezophilic lifestyle of Desulfovibrio piezophilus
Pradel N., Ji B., Gimenez G., Talla E., Lenoble P., Garel M., Tamburini C., Fourquet P., Lebrun R., Bertin P., Denis Y., Pophillat M., Barbe V., Ollivier B., Dolla A.
PLoS One. (2013) 8(1):e55130. doi: 10.1371/journal.pone.0055130.

Genome sequence of the sulfate-reducing bacterium Desulfotomaculum hydrothermale Lam5T.
Amin O., Fardeau M.L., Valette O., Hirschler-Réa A., Barbe V., Médigue C., Vacherie B., Ollivier B., Bertin P., Dolla A.
Genome Announcements. (2013) Jan;1(1). doi:pii: e00114-12. 10.1128/genomeA.00114-12.

Complete genome sequence of the piezophilic mesophilic sulfate-reducing bacterium Desulfovibrio hydrothermalis AM13T.
Ji B., Gimenez G., Barbe V., Vacherie B., Rouy Z., Amrani A., Fardeau M.L., Bertin P., Alazard D., Leroy S., Talla E., Ollivier B., Dolla A., Pradel N.
Genome Announcements. (2013) Jan;1(1). pii: e00226-12. doi: 10.1128/genomeA.00226-12.

Role of polyadenylation in regulation of the flagella cascade and motility in Escherichia coli
Maes A., Gracia C., Bréchemier D., Hamman P., Chatre E., Lemelle L., Bertin P.N., Hajnsdorf E.
Biochimie. (2013) Feb;95(2):410-8. doi: 10.1016/j.biochi.2012.10.017.

2012

Archaeal Diversity: Temporal Variation in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France
A. Volant, A. Desoeuvre, C. Casiot, S. Delpoux, G. Morin, J.C.Personné, F. Elbaz-Poulichet, B. Lauga, P. Bertin and O. Bruneel
Extremophiles. (2012). 16 (4): 645-657, DOI: 10.1007/s00792-012-0466-8

Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches.
François Delavat, Marie-Claire Lett, Didier Lièvremont
Biol Direct. (2012). Sep 10;7:28. doi: 10.1186/1745-6150-7-28.

Amylases without known homologues discovered in an acid mine drainage: significance and impact.
François Delavat, Vincent Phalip, Anne Forster, Frédéric Plewniak, Marie-Claire Lett and Didier Lièvremont
Scientific reports. (2012). 2 : 354, DOI: 10.1038/ srep00354

Microbial arsenic response and metabolism in the genomics era.
Philippe N. Bertin, Lucie Geist, David Halter, Sandrine Koechler, Marie Marchal, Florence Arsène-Ploetze.
in J.M. Santini, S.A. Ward (eds) Arsenic in the environment (2012). pp. 99-114.

Remediation using arsenite-oxidizing bacteria
François Delavat, Marie-Clairre Lett, Didier Lièvremont
in J.M. Santini, S.A. Ward (eds) Arsenic in the environment (2012). pp. 145-159

Deciphering the role of Paenibacillus strain Q8 in the organic matter recycling in the acid mine drainage of Carnoules.
François Delavat, Vincent Phalip, Anne Forster, Marie-Claire Lett, Didier Lièvremont .
microbial cell factories. (2012). 11(1):16.

In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bioindicator, Euglena mutabilis.
David Halter, Florence Goulhen-Chollet, Sébastien Gallien, Corinne Casiot, Jérôme Hamelin, Françoise Gilard, Dimitri Heintz, Christine Schaeffer, Christine Carapito, Alain Van Dorsselaer, Guillaume Tcherkez, Florence Arsène-Ploetze, Philippe N. Bertin.
ISME J. (2011).  Jan 12. doi : 10.1038/ismej.2011.198.

Proteomics as a tool for the characterization of microbial isolates and complex communities.
Florence Arsène-Ploetze, Christine Carapito, Frédéric Plewniak, and Philippe N. Bertin.
Proteomics as a Tool for the Characterization of Microbial Isolates and Complex Communities, Proteomic Applications in Biology, Joshua L. Heazlewood and Christopher J. Petzold, Subject editors : Tsz-Kwong Man, Ricardo J. Flores (Ed.), ISBN : 978-953-307-613-3, InTech. (2012). Available from : http://www.intechopen.com/articles/...

Unified nomenclature for genes involved in prokaryotic aerobic arsenite oxidation.
Marie-Claire Lett, Daniel Muller, Didier Lièvremont, Simon Silver, Joanne Santini.
J. Bacteriol (2011).  Jan ;194(2):207-8.

2011

Surface properties and intracellular speciation revealed an original adaptive mechanism to arsenic in the acid mine drainage bio-indicator Euglena mutabilis.
David Halter, Corinne Casiot, Hermann Heipieper, Frédéric Plewniak, Marie Marchal, Stéphane Simon, Florence Arsène-Ploetze, Philippe Bertin
Applied Microbiology and Biotechnology. (2011). 93(4):1735-44.

Subinhibitory Arsenite Concentration Leads to Population Dispersal in Thiomonas sp.
Marie Marchal, Romain Briandet, David Halter, Sandrine Koechler, Michael S. DuBow, Marie-Claire Lett, Philippe N. Bertin
PLoS one. (2011). 6(8):e23181

Taxonomic and functional prokaryote diversity in mildly arsenic contaminated sediments.
David Halter, Audrey Cordi, Simonetta Gribaldo, Sébastien Gallien, Florence Goulhen-Chollet, Audrey Heinrich-Salmeron, Christine Carapito, Christophe Pagnout, Didier Montaut, Fabienne Seby, Alain Van Dorsselaer, Christine Schaeffer, Philippe N. Bertin, Pascale Bauda, Florence Arsène-Ploetze.
Res. Microbiol. (2011).162(9), 877-887.

Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics.
Bertin, P. N., A. Heinrich-Salmeron, E. Pelletier, F. Goulhen-Chollet, F. Arsène-Ploetze, S. Gallien, B. Lauga, C. Casiot, A. Calteau, D. Vallenet, V. Bonnefoy, O. Bruneel, B. Chane-Woon-Ming, J. Cleiss-Arnold, R. Duran, F. Elbaz-Poulichet, N. Fonknechten, L. Giloteaux, D. Halter, S. Koechler, M. Marchal, D. Mornico, C. Schaeffer, A. A. T. Smith, A. Van Dorsselaer, J. Weissenbach, C. Médigue, et D. Le Paslier.
ISME J. (2011). 5(11),1735-47.

Unsuspected diversity of arsenite-oxidizing bacteria revealed by a widespread distribution of the aoxB gene in prokaryotes.
Heinrich-Salmeron, A., A. Cordi, C. Brochier-Armanet, D. Halter, C. Pagnout, E. Abbaszadeh-Fard, D. Montaut, F. Seby, P. N. Bertin, P. Bauda, et F. Arsène-Ploetze.
Appl Environ Microbiol.  (2011). 77(13):4685-92.

Characterization of the active bacterial community involved in natural attenuation processes in arsenic-rich creek sediments.
O. Bruneel, A. Volant, S. Gallien, B. Chaumande, C. Casiot, C. Carapito, A. Bardil, G. Morin, G.E. Brown Jr., J.C Personné, D. Le Paslier, C. Schaeffer, A. Van Dorsselaer, P. N. Bertin, F. Elbaz-Pouliche, F. Arsène-Ploetze.
Microbial Ecology. (2011). 61, 793-810

2010

Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans.
Cleiss-Arnold J, Koechler S, Proux C, Fardeau ML, Dillies MA, Coppee JY, Arsene-Ploetze F, Bertin PN.
BMC Genomics. (2010).

Arsenite oxidase from Ralstonia sp. 22: characterization of the enzyme and its interaction with soluble cytochromes.
Lieutaud A, van Lis R, Duval S, Capowiez L, Muller D, Lebrun R, Lignon S, Fardeau ML, Lett MC, Nitschke W, Schoepp-Cothenet B.
J Biol Chem. (2010).

Effect of arsenite on swimming motility delays the surface colonization in Herminiimonas arsenicoxydans.
Marchal M., Briandet R., Koechler, S., Kammerer B., Bertin P.N.
Microbiology, (2010).

Structure, function, and evolution of the Thiomonas spp. genome.
Arsène-Ploetze F, Koechler S, Marchal M, Coppée JY, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan CG, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lièvremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Médigue C, Bertin PN.
PLoS Genet. (2010).

Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans.

Koechler S, Cleiss-Arnold J, Proux C, Sismeiro O, Dillies MA, Goulhen-Chollet F, Hommais F, Lièvremont D, Arsène-Ploetze F, Coppée JY, Bertin PN.
BMC Microbiol. (2010).

2009

Arsenic in contaminated waters: biogeochemical cycle, microbial metabolism and biotreatment processes.
Lièvremont D, Bertin PN, Lett MC.
Biochimie. (2009).

Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes.

Bryan CG, Marchal M, Battaglia-Brunet F, Kugler V, Lemaitre-Guillier C, Lièvremont D, Bertin PN, Arsène-Ploetze F.
BMC Microbiol. (2009).

Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data.
Weiss S, Carapito C, Cleiss J, Koechler S, Turlin E, Coppee JY, Heymann M, Kugler V, Stauffert M, Cruveiller S, Médigue C, Van Dorsselaer A, Bertin PN, Arsène-Ploetze F.
Biochimie. (2009).

2008

Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria.
Quéméneur M, Heinrich-Salmeron A, Muller D, Lièvremont D, Jauzein M, Bertin PN, Garrido F, Joulian C.
Appl Environ Microbiol. (2008).

Arsenite oxidation by a chemoautotrophic moderately acidophilic Thiomonas sp.: from the strain isolation to the gene study.
Duquesne K, Lieutaud A, Ratouchniak J, Muller D, Lett MC, Bonnefoy V.
Environ Microbiol. (2008).

Heat-treated Saccharomyces cerevisiae for antimony speciation and antimony(III) preconcentration in water samples
.
Marcellino S, Attar H, Lièvremont D, Lett MC, Barbier F, Lagarde F.
Anal Chim Acta. (2008).

Analyse fonctionnelle de microorganismes et de communautés complexes par des approches (méta)protéomiques.
F. Arsène-Ploetze, F. Gouhlen-Chollet, B. Chaumande, S. Weiss, C. Carapito, J. Cleiss, S. Gallien, C. Schaeffer, Alain Van Dorsselaer and P. N. Bertin.
Les Actes du BRG. (2008).

Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems.
Bertin PN, Médigue C, Normand P.
Microbiology. (2008).

2007 et avant

A tale of two oxidation states: bacterial colonization of arsenic-rich environments.
Muller D, Médigue C, Koechler S, Barbe V, Barakat M, Talla E, Bonnefoy V, Krin E, Arsène-Ploetze F, Carapito C, Chandler M, Cournoyer B, Cruveiller S, Dossat C, Duval S, Heymann M, Leize E, Lieutaud A, Lièvremont D, Makita Y, Mangenot S, Nitschke W, Ortet P, Perdrial N, Schoepp B, Siguier P, Simeonova DD, Rouy Z, Segurens B, Turlin E, Vallenet D, Van Dorsselaer A, Weiss S, Weissenbach J, Lett MC, Danchin A, Bertin PN.
PLoS Genet. (2007).

Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium.
Muller D, Simeonova DD, Riegel P, Mangenot S, Koechler S, Lièvremont D, Bertin PN, Lett MC.
Int J Syst Evol Microbiol. (2006).

Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome.
Carapito C, Muller D, Turlin E, Koechler S, Danchin A, Van Dorsselaer A, Leize-Wagner E, Bertin PN, Lett MC.
Biochimie. (2006).

Arsenite oxidation in batch reactors with alginate-immobilized ULPAs1 strain.
Simeonova DD, Micheva K, Muller DA, Lagarde F, Lett MC, Groudeva VI, Lièvremont D.
Biotechnol Bioeng. (2005).

Microplate screening assay for the detection of arsenite-oxidizing and arsenate-reducing bacteria.
Simeonova DD, Lièvremont D, Lagarde F, Muller DA, Groudeva VI, Lett MC.
FEMS Microbiol Lett. (2004).

Arsenite oxidase, an ancient bioenergetic enzyme.
Lebrun E, Brugna M, Baymann F, Muller D, Lièvremont D, Lett MC, Nitschke W.
Mol Biol Evol. (2003).

Biological oxidation of arsenite: batch reactor experiments in presence of kutnahorite and chabazite.
Lièvremont D, N'negue MA, Behra P, Lett MC.
Chemosphere. (2003).

Arsenite oxidase aox genes from a metal-resistant beta-proteobacterium.
Muller D, Lièvremont D, Simeonova DD, Hubert JC, Lett MC.
J Bacteriol. (2003).

Oxidation of arsenite to arsenate by a bacterium isolated from an aquatic environment
.
Weeger W, Lièvremont D, Perret M, Lagarde F, Hubert JC, Leroy M, Lett MC.
Biometals. (1999).