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Daniel Muller

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Publications

Two novel species isolated from wheat rhizospheres in Serbia: Pseudomonas serbica sp. nov. and Pseudomonas serboccidentalis sp. nov.

Irena Todorović , Danis Abrouk , Martina Kyselková , Céline Lavire , Marjolaine Rey
Systematic and Applied Microbiology, 2023, 46 (4), pp.126425. ⟨10.1016/j.syapm.2023.126425⟩
Journal articles hal-04244409v1
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A metagenomic lens into endosphere microbial communities, promises, and discoveries

Bartholomew Saanu Adeleke , Daniel Muller , Olubukola Oluranti Babalola
Letters in Applied Microbiology, 2023, 76 (2), ⟨10.1093/lambio/ovac030⟩
Journal articles hal-04244433v1
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Genomic content of wheat has a higher influence than plant domestication status on the ability to interact with Pseudomonas plant growth‐promoting rhizobacteria

Cécile Gruet , Maroua Alaoui , Florence Gerin , Claire Prigent-Combaret , Andreas Börner
Plant, Cell and Environment, 2023, 46 (12), pp.3933-3948. ⟨10.1111/pce.14698⟩
Journal articles hal-04245524v1
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Microbial diversity in soils suppressive to Fusarium diseases

Irena Todorović , Yvan Moënne-Loccoz , Vera Raic , Jelena Jovičić-Petrović , Daniel Muller
Frontiers in Plant Science, 2023, 14, ⟨10.3389/fpls.2023.1228749⟩
Journal articles hal-04320379v1
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Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere

Cécile Gruet , Danis Abrouk , Andreas Börner , Daniel Muller , Yvan Moënne-Loccoz
Plant, Cell and Environment, 2023, 46 (3), pp.1018-1032. ⟨10.1111/pce.14508⟩
Journal articles hal-04317066v1
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Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome

Cécile Gruet , Daniel Muller , Yvan Moënne-Loccoz
Frontiers in Microbiology, 2022, 12, pp.782135. ⟨10.3389/fmicb.2021.782135⟩
Journal articles hal-03514878v1
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Effect of Inoculation Level on the Impact of the PGPR Azospirillum lipoferum CRT1 on Selected Microbial Functional Groups in the Rhizosphere of Field Maize

Sébastien Renoud , Danis Abrouk , Claire Prigent Combaret , Florence Wisniewski-Dyé , Laurent Legendre
Microorganisms, 2022, 10 (2), pp.325. ⟨10.3390/microorganisms10020325⟩
Journal articles hal-03579580v1
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Rhizophere analysis of auxin producers harboring the phenylpyruvate decarboxylase pathway

Cécile Gruet , Andréa Oudot , Danis Abrouk , Yvan Moënne-Loccoz , Daniel Muller
Applied Soil Ecology, 2022, 173, pp.104363. ⟨10.1016/j.apsoil.2021.104363⟩
Journal articles hal-03533870v1
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Field Site-Specific Effects of an Azospirillum Seed Inoculant on Key Microbial Functional Groups in the Rhizosphere

Sébastien Renoud , Jordan Vacheron , Danis Abrouk , Claire Prigent Combaret , Laurent Legendre
Frontiers in Microbiology, 2022, 12, pp.760512. ⟨10.3389/fmicb.2021.760512⟩
Journal articles hal-03763575v1
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Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities

Beatriz Manriquez , Daniel Muller , Claire Prigent-Combaret , Claire Prigent Combaret
Frontiers in Microbiology, 2021, 12, ⟨10.3389/fmicb.2021.619122⟩
Journal articles hal-03300724v1

Author Correction: Complex ecological interactions of Staphylococcus aureus in tampons during menstruation

Isaline Jacquemond , Anaëlle Muggeo , Gery Lamblin , Anne Tristan , Yves Gillet
Scientific Reports, 2020, 10 (1), pp.1848. ⟨10.1038/s41598-020-57947-2⟩
Journal articles hal-04245533v1
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Secondary metabolites from plant‐associated Pseudomonas are overproduced in biofilm

Laura Rieusset , Marjolaine Rey , Daniel Muller , Jordan Vacheron , Florence Gerin
Microbial Biotechnology, 2020, 13 (5), pp.1562-1580. ⟨10.1111/1751-7915.13598⟩
Journal articles hal-03000801v1
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Vaginal Tampon Colonization by Staphylococcus aureus in Healthy Women

Myriam Chiaruzzi , Alexia Barbry , Anaëlle Muggeo , Anne Tristan , Isaline Jacquemond
Applied and Environmental Microbiology, 2020, 86 (18), pp.e01249-20. ⟨10.1128/AEM.01249-20⟩
Journal articles hal-02989503v2
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Co-occurrence of rhizobacteria with nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities in the maize rhizosphere

Sébastien Renoud , Marie-Lara Bouffaud , Audrey Dubost , Claire Prigent-Combaret , Laurent Legendre
FEMS Microbiology Ecology, 2020, 96 (5), ⟨10.1093/femsec/fiaa062⟩
Journal articles hal-02547931v1
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Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov

Vahid Keshavarz-Tohid , Jordan Vacheron , Audrey Dubost , Claire Prigent-Combaret , Parissa Taheri
Systematic and Applied Microbiology, 2019, 42 (4), pp.468-480. ⟨10.1016/j.syapm.2019.04.004⟩
Journal articles hal-02392254v1
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Complex ecological interactions of Staphylococcus aureus in tampons during menstruation

Isaline Jacquemond , Anaëlle Muggeo , Gery Lamblin , Anne Tristan , Yves Gillet
Scientific Reports, 2018, 8 (1), pp.9942. ⟨10.1038/s41598-018-28116-3⟩
Journal articles hal-01910908v1
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Draft genome sequence of plant growth-promoting bacillus altitudinis strain pae4

Nahed Abdel Ghaffar Abdel Aziz Ibrahim , Mohamed Nabil Abdel Mageed Omar , Ghada A. Abu El Heba , Yvan Moenne-Loccoz , Claire Prigent Combaret
Microbiology Resource Announcements, 2018, 7 (13), pp.1-2. ⟨10.1128/MRA.00962-18⟩
Journal articles hal-02159605v1
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1-Aminocyclopropane-1-carboxylate deaminase producers associated to maize and other Poaceae species

Marie-Lara Bouffaud , Sébastien Renoud , Audrey Dubost , Yvan Moënne-Loccoz , Daniel Muller
Microbiome, 2018, 6 (1), ⟨10.1186/s40168-018-0503-7⟩
Journal articles hal-02148378v1

Impact of currently marketed tampons and menstrual cups on Staphylococcus aureus growth and TSST-1 production in vitro

Louis Nonfoux , Myriam Chiaruzzi , Cédric Badiou , Jessica Baude , Anne Tristan
Applied and Environmental Microbiology, 2018, 84 (12), ⟨10.1128/AEM.00351-18⟩
Journal articles hal-01911407v1

Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere

Jordan Vacheron , Audrey Dubost , David Chapulliot , Claire Prigent-Combaret , Daniel Muller
Genome Announcements, 2017, 5 (15), pp.e00122-17. ⟨10.1128/genomeA.00122-17⟩
Journal articles hal-02487196v1
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Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Florent Lassalle , Rémi Planel , Simon Penel , David Chapulliot , Valérie Barbe
Genome Biology and Evolution, 2017, 9 (12), pp.3413 - 3431. ⟨10.1093/gbe/evx255⟩
Journal articles hal-01913841v1
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Differential contribution of plant-beneficial functions from Pseudomonas kilonensis F113 to root system architecture alterations in Arabidopsis thaliana and Zea mays

Jordan Vacheron , Guilhem Desbrosses , Sébastien Renoud , Rosa-Maria Padilla-Aguilar , Vincent Walker
Molecular Plant-Microbe Interactions, 2017, 31 (2), ⟨10.1094/MPMI-07-17-0185-R⟩
Journal articles hal-01613633v1
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Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the pseudomonas spp. reveals unexpected polyphyletism

Juliana Almario , Maxime Bruto , Jordan Vacheron , Claire Prigent-Combaret , Yvan Moenne-Loccoz
Frontiers in Microbiology, 2017, 8, ⟨10.3389/fmicb.2017.01218⟩
Journal articles hal-01608669v1

Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of bean from Iran for controlling Rhizoctonia solani

Vahid Keshavarz-Tohid , Parissa Taheri , Daniel Muller , Claire Prigent-Combaret , Jordan Vacheron
Research in Microbiology, 2017, 168 (8), pp.760-772. ⟨10.1016/j.resmic.2017.08.002⟩
Journal articles hal-02487202v1

Let the core microbiota be functional

Philippe P. Lemanceau , Manuel Blouin , Daniel Muller , Yvan Moenne-Loccoz
Trends in Plant Science, 2017, 22 (7), pp.583-595. ⟨10.1016/j.tplants.2017.04.008⟩
Journal articles hal-01608595v1

Expression on roots and contribution to maize phytostimulation of 1-aminocyclopropane-1-decarboxylate deaminase gene acdS in Pseudomonas fluorescens F113

Jordan Vacheron , Emeline Combes-Meynet , Vincent Walker , B. Gouesnard , Daniel Muller
Plant and Soil, 2016, 407 (1-2), pp.187-202. ⟨10.1007/s11104-016-2907-0⟩
Journal articles hal-02466011v1

Is plant evolutionary history impacting recruitment of diazotrophs and nifH expression in the rhizosphere?

Marie-Lara Bouffaud , Sebastien Renoud , Yvan Moënne-Loccoz , Daniel Muller
Scientific Reports, 2016, 6, pp.21690. ⟨10.1038/srep21690⟩
Journal articles hal-02466010v1
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Fluorescent Pseudomonas Strains with only Few Plant-Beneficial Properties Are Favored in the Maize Rhizosphere

Jordan Vacheron , Yvan Moënne-Loccoz , Audrey Dubost , Maximilien Gonçalves-Martins , Daniel Muller
Plant Biotic Interactions, 2016, 7, pp.1212. ⟨10.3389/fpls.2016.01212⟩
Journal articles hal-02466008v1

Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis

Florent Lassalle , Daniel Muller , Xavier Nesme
Research in Microbiology, 2015, 166 (10), pp.729-741. ⟨10.1016/j.resmic.2015.06.008⟩
Journal articles hal-02547960v1
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Comparative genomics of environmental and clinical stenotrophomonas maltophiliaStrains with different antibiotic resistance profiles

Benjamin Youenou , Sabine Favre-Bonte , Josselin Bodilis , Elisabeth Brothier , Audrey Dubost
Genome Biology and Evolution, 2015, 7 (9), pp.2484-2505. ⟨10.1093/gbe/evv161⟩
Journal articles hal-01605055v1

Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers' fields

Martina Kyselková , Juliana Almario , Jan Kopecký , Markéta Ságová-Marečková , Jacqueline Haurat
Environmental Microbiology Reports, 2014, ⟨10.1111/1758-2229.12131⟩
Journal articles hal-01010640v1

Rhizosphere microbial communities associated with Rhizoctonia damage at the field and disease patch scale

Suzanne Donn , Juliana Almario , Daniel Muller , Yvan Moënne-Loccoz , Vadakattu V.S.R. Gupta
Applied Soil Ecology, 2014, 78, pp.37-47. ⟨10.1016/j.apsoil.2014.02.001⟩
Journal articles hal-01010607v1

Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria

Maxime Bruto , Claire Prigent-Combaret , Daniel Muller , Yvan Moënne-Loccoz
Scientific Reports, 2014, 4, pp.6261. ⟨10.1038/srep06261⟩
Journal articles hal-02487456v1

Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes

Maxime Bruto , Claire Prigent-Combaret , P. Luis , Yvan Moënne-Loccoz , Daniel Muller
Proceedings of the Royal Society B: Biological Sciences, 2014, 281 (1789), pp.20140848. ⟨10.1098/rspb.2014.0848⟩
Journal articles hal-02487460v1

Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid

Martha H. Ramírez-Bahena , Ludovic Vial , Florent Lassalle , Benjamin Diel , David Chapulliot
Molecular Phylogenetics and Evolution, 2014, 73, pp.202-207. ⟨10.1016/j.ympev.2014.01.005⟩
Journal articles hal-01010660v1

Rhizosphere ecology and phytoprotection in soils naturally suppressive to Thielaviopsis black root rot of tobacco

Juliana Almario , Daniel Muller , Geneviève Défago , Yvan Moënne-Loccoz
Environmental Microbiology, 2014, pp.1-12. ⟨10.1111/1462-2920.12459⟩
Journal articles hal-01010573v1

Root microbiome relates to plant host evolution in maize and other Poaceae

Marie-Lara Bouffaud , Marie-Andrée Poirier , Daniel Muller , Yvan Moënne-Loccoz
Environmental Microbiology, 2014, ⟨10.1111/1462-2920.12442⟩
Journal articles hal-01010591v1

Investigating the species and strain diversity of agrobacteria by MLSA: toward a phylogenetically relevant redefinition of the genus Agrobacterium.

X. Nesme , D. Costechareyre , M. H. R. Bahena , Daniel Muller , J. Nesme
Frontiers in Plant-Microbe Interaction, 2013
Journal articles hal-02522212v1

Effect of Clay Mineralogy on Iron Bioavailability and Rhizosphere Transcription of 2,4-Diacetylphloroglucinol Biosynthetic Genes in Biocontrol Pseudomonas protegens

Juliana Almario , Claire Prigent-Combaret , Daniel Muller , Yvan Moënne-Loccoz
Molecular Plant-Microbe Interactions, 2013, 26 (5), pp.566-574. ⟨10.1094/MPMI-11-12-0274-R⟩
Journal articles hal-02522202v1
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Plant growth-promoting rhizobacteria and root system functioning

Jordan Vacheron , G. Desbrosses , Marie.-Lara Bouffaud , B. Touraine , Yvan Moënne-Loccoz
Frontiers in Plant Science, 2013, 4, pp.356. ⟨10.3389/fpls.2013.00356⟩
Journal articles hal-02522224v1

Assessment of the relationship between geologic origin of soil, rhizobacterial community composition and soil receptivity to tobacco black root rot in Savoie region (France)

Juliana Almario , Martina Kyselková , J. Kopecký , M. Ságová-Marečková , Daniel Muller
Plant and Soil, 2013, pp.1-12. ⟨10.1007/s11104-013-1677-1⟩
Journal articles hal-02522203v1

Unexpected phytostimulatory behavior for Escherichia coli and Agrobacterium tumefaciens model strains.

Vincent Walker , Maxime Bruto , Floriant Bellvert , René Bally , Daniel Muller
Molecular Plant-Microbe Interactions, 2013, 26 (5), pp.495-502. ⟨10.1094/MPMI-12-12-0298-R⟩
Journal articles hal-00965830v1
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Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

Jérémy Andres , Florence Arsène-Ploetze , Valérie Barbe , Céline Brochier-Armanet , Jessica Cleiss-Arnold
Genome Biology and Evolution, 2013, 5 (5), pp.934-53. ⟨10.1093/gbe/evt061⟩
Journal articles hal-00972245v1

Monitoring of the relation between 2,4-diacetylphloroglucinol-producing Pseudomonas and Thielaviopsis basicola populations by real-time PCR in tobacco black root-rot suppressive and conducive soils

Juliana Almario , Yvan Moënne-Loccoz , Daniel Muller
Soil Biology and Biochemistry, 2012, ⟨10.1016/j.soilbio.2012.09.003⟩
Journal articles hal-02532808v1

Unified Nomenclature for Genes Involved in Prokaryotic Aerobic Arsenite Oxidation

Marie-Claire Lett , Daniel Muller , Didier Lièvremont , Simon Silver , Joanne Santinid
Journal of Bacteriology, 2012, pp.207-208. ⟨10.1128/JB.06391-11⟩
Journal articles halsde-00722718v1

Rapid and simultaneous detection of linear chromosome and large plasmids in Proteobacteria

Martha Helena Ramírez-Bahena , Xavier Nesme , Daniel Muller
Journal of Basic Microbiology, 2012, 52 (52), pp.1-4. ⟨10.1002/jobm.201100278⟩
Journal articles halsde-00723073v1

Is diversification history of maize influencing selection of soil bacteria by roots?

Marie-Lara Bouffaud , Martina Kyselková , Brigitte Gouesnard , Genevieve Grundmann , Daniel Muller
Molecular Ecology, 2012, 21 (1), pp.195-206. ⟨10.1111/j.1365-294X.2011.05359.x⟩
Journal articles halsde-00722561v1
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Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Florent Lassalle , Tony Campillo , Ludovic Vial , Jessica Baude , Denis Costechareyre
Genome Biology and Evolution, 2011, 3 (3), pp.762-781. ⟨10.1093/gbe/evr070⟩
Journal articles halsde-00723400v1

Development of a real-time PCR method to quantify the PGPR strain Azospirillum lipoferum CRT1 on maize seedlings

Olivier Couillerot , Marie-Lara Bouffaud , Baudoin Ezékiel , Daniel Muller , Jesus Caballero-Mellado
Soil Biology and Biochemistry, 2010, 42 (12), pp.2298-2305. ⟨10.1016/j.soilbio.2010.09.003⟩
Journal articles hal-00874738v1
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Structure, function, and evolution of the Thiomonas spp. genome.

Florence Arsène-Ploetze , Sandrine Koechler , Marie Marchal , Jean-Yves Coppée , Michael Chandler
PLoS Genetics, 2010, 6 (2), pp.e1000859. ⟨10.1371/journal.pgen.1000859⟩
Journal articles hal-00463879v1
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Arsenite Oxidase from Ralstonia sp. 22: characterization of the enzyme and its interaction with soluble cytochromes.

Aurélie Lieutaud , Robert van Lis , Simon Duval , Line Capowiez , Daniel Muller
Journal of Biological Chemistry, 2010, 285 (27), pp.20433-20441. ⟨10.1074/jbc.M110.113761⟩
Journal articles hal-01602032v1

Arsenite oxidation by a chemoautotrophic moderately acidophilic Thiomonas sp.: from the strain isolation to the gene study.

M.-C. Lett , Aurélie Lieutaud , Daniel Muller , J. Ratouchniak , V. Bonnefoy
Environmental Microbiology, 2008, 10 (1), pp.228-37. ⟨10.1111/j.1462-2920.2007.01447.x⟩
Journal articles hal-00281294v1

Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria.

Marianne Quéméneur , Audrey Heinrich-Salmeron , Daniel Muller , Didier Lièvremont , Michel Jauzein
Applied and Environmental Microbiology, 2008, 74 (14), pp.4567-73. ⟨10.1128/AEM.02851-07⟩
Journal articles hal-00370780v1
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A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

Daniel Muller , Claudine Médigue , Sandrine Koechler , Valérie Barbe , ​mohamed Barakat
PLoS Genetics, 2007, 3 (4), pp.e53. ⟨10.1371/journal.pgen.0030053⟩
Journal articles hal-00340034v1

A Bacterial Effector Targets Mad2L2, an APC Inhibitor, to Modulate Host Cell Cycling

Hiroki Iwai , Minsoo Kim , Yuko Yoshikawa , Hiroshi Ashida , Michinaga Ogawa
Cell, 2007, 130 (4), pp.611-623. ⟨10.1016/j.cell.2007.06.043⟩
Journal articles hal-04245669v1

Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome.

Christine Carapito , Daniel Muller , Evelyne Turlin , Sandrine Koechler , Antoine Danchin
Biochimie, 2006, 88 (6), pp.595-606. ⟨10.1016/j.biochi.2005.11.004⟩
Journal articles hal-00370783v1

Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium.

Daniel Muller , Diliana D Simeonova , Philippe Riegel , Sophie Mangenot , Sandrine Koechler
International Journal of Systematic and Evolutionary Microbiology, 2006, 56 (Pt 8), pp.1765-9. ⟨10.1099/ijs.0.64308-0⟩
Journal articles hal-00113703v1

Arsenite oxidation in batch reactors with alginate‐immobilized ULPAs1 strain

Diliana Simeonova , Kalina Micheva , Daniel A.E. Muller , Florence Lagarde , Marie‐claire Lett
Biotechnology and Bioengineering, 2005, 91 (4), pp.441-446. ⟨10.1002/bit.20530⟩
Journal articles hal-04250284v1

Chemiluminescence of enterococci isolates from freshwater.

Philippe Andre , Catherine Metzger , Sophie Petey , Dominique J-M Vidon , Daniel Muller
Microbiology Letters, 2005, 245 (1), pp.123-9. ⟨10.1016/j.femsle.2005.02.036⟩
Journal articles hal-00106769v1

Microplate screening assay for the detection of arsenite-oxidizing and arsenate-reducing bacteria

Diliana Simeonova , Florence Lagarde , Daniel A.E. Muller , Veneta Groudeva , Marie-Claire Lett
FEMS Microbiology Letters, 2004, 237 (2), pp.249-253. ⟨10.1111/j.1574-6968.2004.tb09703.x⟩
Journal articles hal-04247135v1

Arsenite oxidase aox genes from a metal-resistant beta-proteobacterium.

Daniel Muller , Didier Lièvremont , Diliana Dancheva Simeonova , Jean-Claude Hubert , Marie-Claire Lett
Journal of Bacteriology, 2003, 185 (1), pp.135-41
Journal articles hal-00113723v1

Arsenite oxidase, an ancient bioenergetic enzyme.

Evelyne Lebrun , Myriam Brugna , Frauke Baymann , Daniel Muller , Didier Lièvremont
Mol Biol Evol, 2003, 20 (5), pp.686-93. ⟨10.1093/molbev/msg071⟩
Journal articles hal-00113712v1