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1. Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8

Author

Dean Thompson, Valérie Cognat, Michael Goodfellow, Sandrine Koechler, Dimitri Heintz, Christine Carapito, Alain Van Dorsselaer, Huda Mahmoud, Vartul Sangal, and Wael Ismail

Subjects
biodesulfurization, Rhodococcus, 4S pathway, phylogenomics, dibenzothiophene, average nucleotide identity, Microbiology, QR1-502
Abstract

Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non–destructive sulfur–specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be re-classified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.

Published
2020
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3. In situ metabolic activities of uncultivated Ferrovum sp. CARN8 evidenced by metatranscriptomic analysis

Author

Odile Bruneel, Frédéric Plewniak, Denis Le Paslier, Marina Héry, Philippe N. Bertin, Sandrine Koechler, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microorganism, Population, Respiratory chain, Microbiology, Genome, In situ metabolism, 03 medical and health sciences, Bacterial Proteins, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Ammonium Compounds, education, Molecular Biology, Gene, 030304 developmental biology, 0303 health sciences, education.field_of_study, Sewage, Metagenome assembled genome, biology, 030306 microbiology, Betaproteobacteria, Nitrogenase, Gene Expression Regulation, Bacterial, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 6. Clean water, Biochemistry, Nitrogen fixation, Metagenomics, Gene expression, Transcriptome, Bacteria
Abstract

International audience; Amongst iron-oxidizing bacteria playing a key role in the natural attenuation of arsenic in acid mine drainages (AMDs), members of the Ferrovum genus were identified in mine effluent or water treatment plants, and were shown to dominate biogenic precipitates in field pilot experiments. In order to address the question of the in situ activity of the uncultivated Ferrovum sp. CARN8 strain in the Carnoul es AMD, we assembled its genome using metagenomic and metatranscriptomic sequences and we determined standardized expression values for protein-encoding genes. Our results showed that this microorganism was indeed metabolically active and allowed us to sketch out its metabolic activity in its natural environment. Expression of genes related to the respiratory chain and carbon fixation suggests aerobic energy production coupled to ferrous iron oxidation and chemolithoautotrophic growth. Notwithstanding the presence of nitrogenase genes in its genome, expression data also indicated that Ferrovum sp. CARN8 relied on ammonium import rather than nitrogen fixation. The expression of flagellum and chemotaxis genes hints that at least a proportion of this strain population was motile. Finally, apart from some genes related to metal resistance showing surprisingly low expression values, genes involved in stress response were well expressed as expected in AMDs.

Published
2020
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4. Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8

Author

Christine Carapito, Wael Ismail, Sandrine Koechler, Alain Van Dorsselaer, Michael Goodfellow, Dimitri Heintz, Valérie Cognat, Vartul Sangal, Dean Thompson, Huda Mahmoud, Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), Operon, lcsh:QR1-502, digital DNA-DNA hybridization, Microbiology, Genome, lcsh:Microbiology, 03 medical and health sciences, Phylogenomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Rhodococcus, Sciences du Vivant [q-bio]/Biologie végétale, dibenzothiophene, biodesulfurization, Gene, 030304 developmental biology, Genetics, 0303 health sciences, biology, 030306 microbiology, Strain (biology), average nucleotide identity, phylogenomics, Rhodococcus rhodochrous, C500, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 4S pathway, Bacteria
Abstract

International audience; Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non-destructive sulfur-specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be reclassified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.

Published
2020
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5. Constitutive arsenite oxidase expression detected in arsenic-hypertolerant Pseudomonas xanthomarina S11

Author

Marie-Claire Lett, Muriel Philipps, Sandrine Koechler, Florence Goulhen-Chollet, Céline Brochier-Armanet, Frédéric Plewniak, Philippe N. Bertin, Audrey Heinrich-Salmeron, Bernard Jost, Florence Arsène-Ploetze, Didier Lièvremont, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, Arsenites, Operon, [SDV]Life Sciences [q-bio], Pseudomonas xanthomarina, Microbiology, Genome, Mining, Arsenic, chemistry.chemical_compound, Plasmid, Bacterial Proteins, Pseudomonas, Drug Resistance, Bacterial, Molecular Biology, Gene, Phylogeny, Arsenite, Base Sequence, biology, Arsenite Transporting ATPases, Arsenate, Gene Expression Regulation, Bacterial, General Medicine, biology.organism_classification, Molecular biology, chemistry, Arsenates, France, Oxidoreductases, Oxidation-Reduction, Bacteria, Plasmids
Abstract

Pseudomonas xanthomarina S11 is an arsenite-oxidizing bacterium isolated from an arsenic-contaminated former gold mine in Salsigne, France. This bacterium showed high resistance to arsenite and was able to oxidize arsenite to arsenate at concentrations up to 42.72 mM As[III]. The genome of this strain was sequenced and revealed the presence of three ars clusters. One of them is located on a plasmid and is organized as an “arsenic island” harbouring an aio operon and genes involved in phosphorous metabolism, in addition to the ars genes. Neither the aioXRS genes nor a specific sigma-54-dependent promoter located upstream of aioBA genes, both involved in regulation of arsenite oxidase expression in other arsenite-oxidizing bacteria, could be identified in the genome. This observation is in accordance with the fact that no difference was observed in expression of arsenite oxidase in P. xanthomarina S11, whether or not the strain was grown in the presence of As[III].

Published
2015
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6. Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite

Author

Sandrine Koechler, Caroline Proux, Bernd Jagla, Aline Huber, Mathieu Erhardt, Hugo Varet, Marie-Agnès Dillies, Julien Farasin, Jean-Yves Coppée, Florence Arsène-Ploetze, Romain Briandet, Julien Deschamps, Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris] (IP), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut de biologie moléculaire des plantes (IBMP), This work was supported by the Université de Strasbourg (UdS), the Centre National de la Recherche Scientifique (CNRS) and the Region Alsace to J.F. This study was financed by the THIOFILM (ANR-12-ADAP-0013) projects. Julien Farasin was supported by the Agence Nationale de la Recherche, ANR THIOFILM (ANR-12-ADAP-0013), ANR-12-ADAP-0013,THIOFILM,Rôle des biofilms dans l'adaptation et la variabilité génomique des bactéries du genre Thiomonas, impliqués dans les processus de remédiation naturelle dans les drainages miniers :(2012), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]

Subjects
0301 basic medicine, Arsenites, [SDV]Life Sciences [q-bio], 030106 microbiology, chemistry.chemical_element, Bioengineering, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Applied Microbiology and Biotechnology, Biochemistry, biofilm, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Bioremediation, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Drug Resistance, Bacterial, Extreme environment, Arsenic, ComputingMilieux_MISCELLANEOUS, Research Articles, Burkholderiales, Arsenite, biology, Gene Expression Profiling, Biofilm, Thiomonas, Special Issue Article, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, chemistry, Biofilms, Environmental Pollutants, Bacteria, Locomotion, Biotechnology
Abstract

Bacteria of the genus Thiomonas are found ubiquitously in arsenic contaminated waters such as acid mine drainage (AMD), where they contribute to the precipitation and the natural bioremediation of arsenic. In these environments, these bacteria have developed a large range of resistance strategies among which the capacity to form particular biofilm structures. The biofilm formation is one of the most ubiquitous adaptive response observed in prokaryotes to various stresses, such as those induced in the presence of toxic compounds. This study focused on the process of biofilm formation in three Thiomonas strains (CB1, CB2 and CB3) isolated from the same AMD. The results obtained here show that these bacteria are all capable of forming biofilms, but the architecture and the kinetics of formation of these biofilms differ depending on whether arsenite is present in the environment and from one strain to another. Indeed, two strains favoured biofilm formation, whereas one favoured motility in the presence of arsenite. To identify the underlying mechanisms, the patterns of expression of some genes possibly involved in the process of biofilm formation were investigated in Thiomonas sp. CB2 in the presence and absence of arsenite, using a transcriptomic approach (RNA-seq). The findings obtained here shed interesting light on how the formation of biofilms, and the motility processes contribute to the adaptation of Thiomonas strains to extreme environments.

Published
2017
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7. Erratum to: Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans

Author

Odile Sismeiro, Florence Goulhen-Chollet, Philippe N. Bertin, Caroline Proux, Florence Hommais, Sandrine Koechler, Florence Arsène-Ploetze, Jean-Yves Coppé, Didier Lièvremont, Marie-Agnès Dillies, Jessica Cleiss-Arnold, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Chromatine et Régulation de la Pathogénie bactérienne (CRP), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Dynamique, évolution et expression de génomes de microorganismes (DEEGM), and Rodrigue, Agnès

Subjects
0301 basic medicine, Microbiology (medical), Transcription, Genetic, Arsenites, [SDV]Life Sciences [q-bio], 030106 microbiology, Arsenite oxidase, Molecular Sequence Data, lcsh:QR1-502, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Bacterial Proteins, Oxalobacteraceae, Gene expression, Operon, Amino Acid Sequence, Herminiimonas arsenicoxydans, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, biology, Base Sequence, Gene Expression Profiling, Quorum Sensing, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Gene Expression Regulation, Bacterial, biology.organism_classification, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Parasitology, Genes, Bacterial, Mutation, Erratum, Oxidoreductases, Sequence Alignment, Metabolic Networks and Pathways, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism.In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (sigma54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 sigma54-dependent promoter motif was identified upstream of aoxAB coding sequences.These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.

Published
2017

8. Toxic metal resistance in biofilms: diversity of microbial responses and their evolution

Author

Florence Arsène-Ploetze, Julien Farasin, Sandrine Koechler, and Jessica Cleiss-Arnold

Subjects
Resistance (ecology), Bacteria, Gene Transfer, Horizontal, Multispecies biofilms, Microorganism, Biofilm, Adaptation, Biological, High density, General Medicine, Biology, Microbiology, Biological Evolution, Bacterial Adhesion, 3. Good health, Cell biology, Single species, Biofilms, Metals, Heavy, Horizontal gene transfer, Drug Resistance, Bacterial, Adaptation, Molecular Biology
Abstract

Since biofilms are an important issue in the fields of medicine and health, several recent microbiological studies have focused on their formation and their contribution to toxic compound resistance mechanisms. In this review, we describe how metals impact biofilm formation and resistance, and how biofilms can help cells resist toxic metals. First, the organic matrix acts as a barrier isolating the cells from many environmental stresses. Secondly, the metabolism of the cells changes, and a slowly-growing or non-growing sub-population of cells known as persisters emerges. Thirdly, in the case of multispecies biofilms, metabolic interactions are developed, allowing cells to be more persistent or to have greater capacity to survive than a single species biofilm. Finally, we discuss how the high density of the cells may promote horizontal gene transfer processes, resulting in the acquisition of new features. All these crucial mechanisms enable microorganisms to survive and colonize toxic environments, and probably accelerate ongoing evolutionary processes.

Published
2015

9. Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium

Author

Philippe N. Bertin, Daniel Muller, Didier Lièvremont, Philippe Riegel, Diliana D. Simeonova, Sandrine Koechler, Marie-Claire Lett, Sophie Mangenot, Génétique moléculaire, génomique, microbiologie (GMGM), and Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Oxidation-Reduction, MESH: Genome, Bacterial, MESH: Nucleic Acid Hybridization, chemistry.chemical_compound, RNA, Ribosomal, 16S, Herminiimonas arsenicoxydans, MESH: Phylogeny, MESH: RNA, Ribosoma, Phylogeny, Betaproteobacteria, Arsenite, 0303 health sciences, Sewage, biology, Fatty Acids, Nucleic Acid Hybridization, Herminiimonas, General Medicine, Catalase, Aerobiosis, 6. Clean water, MESH: Fatty Acids, RNA, Bacterial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Nitrates, Herminiimonas aquatilis, MESH: Arsenites, MESH: RNA, Bacterial, Oxidoreductases, Oxidation-Reduction, DNA, Bacterial, Arsenites, MESH: Oxalobacteraceae, Molecular Sequence Data, Microbiology, 03 medical and health sciences, Species Specificity, MESH: Aerobiosis, MESH: Catalase, Oxalobacteraceae, MESH: Oxidoreductases, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Molecular Sequence Data, Nitrates, 030306 microbiology, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, MESH: DNA, Bacterial, Culture Media, chemistry, MESH: Culture Media, Genome, Bacterial, Bacteria
Abstract

An arsenite-oxidizing bacterium, designated strain ULPAs1T, was isolated from industrial sludge heavily contaminated with arsenic. Cells of this isolate were Gram-negative, curved rods, motile by means of a polar flagellum. The strain was positive for oxidase and catalase activities, was able to reduce nitrate to nitrite, used acetate, lactate and peptone as organic carbon sources under aerobic conditions and was able to oxidize arsenite (As[III]) to arsenate (As[V]). 16S rRNA gene sequence analysis and the absence of dodecanoic fatty acids suggested that this strain represents a member of the genusHerminiimonasof the familyOxalobacteraceae, orderBurkholderialesin theBetaproteobacteria. Genomic DNA–DNA hybridization between strain ULPAs1TandHerminiimonas fonticolaS-94Tand between strain ULPAs1TandHerminiimonas aquatilisCCUG 36956Trevealed levels of relatedness of T(=CCM 7303T=DSM 17148T=LMG 22961T) is the type strain of a novel species ofHerminiimonas, for which the nameHerminiimonas arsenicoxydanssp. nov. is proposed.

Published
2006
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10. Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments

Author

Frédéric Plewniak, Muriel Philipps, Sandrine Koechler, Philippe N. Bertin, Fabienne Battaglia-Brunet, Tao Ye, Valérie Barbe, Stéphanie Vincent, Bernard Jost, Serge Vicaire, and Catherine Joulian

Subjects
Whole genome sequencing, biology, Strain (chemistry), Chromosome, chemistry.chemical_element, biology.organism_classification, Genome, Microbiology, chemistry.chemical_compound, Plasmid, chemistry, Genetics, Prokaryotes, Molecular Biology, Bacteria, Arsenic, Arsenite
Abstract

We report the genome sequence of Halomonas sp. strain A3H3, a bacterium with a high tolerance to arsenite, isolated from multicontaminated sediments of the l'Estaque harbor in Marseille, France. The genome is composed of a 5,489,893-bp chromosome and a 157,085-bp plasmid.

Published
2013
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11. Subinhibitory Arsenite Concentrations Lead to Population Dispersal in Thiomonas sp

Author

Romain Briandet, Philippe N. Bertin, Marie Marchal, David Halter, Michael Dubow, Marie-Claire Lett, Sandrine Koechler, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microorganism, Applied Microbiology, Microbial metabolism, Colony Count, Microbial, lcsh:Medicine, biofilm, chemistry.chemical_compound, stress, viabilité, Nucleic Acids, Molecular Cell Biology, souche, Extreme environment, lcsh:Science, Arsenite, Cellular Stress Responses, 0303 health sciences, education.field_of_study, Multidisciplinary, tolerance, biology, Polysaccharides, Bacterial, Microbial Growth and Development, Thiomonas, Betaproteobacteria, Extracellular Matrix, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, bioremediation, metabolism, viability, strains, oxidation, cell, Research Article, Arsenites, Movement, Population, Microbiology, Microbial Ecology, 03 medical and health sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, métabolisme, Biology, 030304 developmental biology, 030306 microbiology, tolérance, lcsh:R, Biofilm, oxydation, biology.organism_classification, bioremédiation, chemistry, 13. Climate action, Biofilms, Biological dispersal, lcsh:Q, cellule
Abstract

International audience; Biofilms represent the most common microbial lifestyle, allowing the survival of microbial populations exposed to harsh environmental conditions. Here, we show that the biofilm development of a bacterial species belonging to the Thiomonas genus, frequently found in arsenic polluted sites and playing a key role in arsenic natural remediation, is markedly modified when exposed to subinhibitory doses of this toxic element. Indeed, arsenite [As(III)] exposure led to a considerable impact on biofilm maturation by strongly increasing the extracellular matrix synthesis and by promoting significant cell death and lysis within microcolonies. These events were followed by the development of complex 3D-biofilm structures and subsequently by the dispersal of remobilized cells observed inside the previously formed hollow voids. Our results demonstrate that this biofilm community responds to arsenite stress in a multimodal way, enhancing both survival and dispersal. Addressing this complex bacterial response to As(III) stress, which might be used by other microorganisms under various adverse conditions, may be essential to understand how Thiomonas strains persist in extreme environments.

Published
2011
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12. Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics

Author

Odile Bruneel, Denis Le Paslier, Damien Mornico, Eric Pelletier, Adam Alexander T. Smith, Béatrice Chane-Woon-Ming, Philippe N. Bertin, Sandrine Koechler, Robert Duran, Florence Goulhen-Chollet, Sebastien Gallien, Marie Marchal, Florence Arsène-Ploetze, David Vallenet, Corinne Casiot, Alexandra Calteau, Jean Weissenbach, Nuria Fonknechten, Jessica Cleiss-Arnold, Christine Schaeffer, Béatrice Lauga, Violaine Bonnefoy, Ludovic Giloteaux, Claudine Médigue, Alain Van Dorsselaer, David Halter, Audrey Heinrich-Salmeron, Françoise Elbaz-Poulichet, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale et microbiologie (IBSM), Université de la Méditerranée - Aix-Marseille 2-Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UMR 7156 Génétique Moléculaire, Génomique et Microbiologie, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Laboratoire de spectrométrie de masse bioorganique, Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique, Département des Sciences Analytiques, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France (LSMBO-DSA-IPHC), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Proteomics, Iron, Microorganism, Microbial metabolism, Genomics, functional ecology, Microbiology, Mining, Arsenic, 03 medical and health sciences, uncultured microorganism, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, bacterial phylum, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], extreme environment, Herminiimonas arsenicoxydans, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Ecosystem, Phylogeny, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, synecology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, Bacteria, biology, Reverse Transcriptase Polymerase Chain Reaction, 030306 microbiology, Phylum, Ecology, microbial genomics, 15. Life on land, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 13. Climate action, Metagenomics, Candidatus, Original Article, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Sulfur
Abstract

International audience; By their metabolic activities, microorganisms have a crucial role in the biogeochemical cycles of elements. The complete understanding of these processes requires, however, the deciphering of both the structure and the function, including synecologic interactions, of microbial communities. Using a metagenomic approach, we demonstrated here that an acid mine drainage highly contaminated with arsenic is dominated by seven bacterial strains whose genomes were reconstructed. Five of them represent yet uncultivated bacteria and include two strains belonging to a novel bacterial phylum present in some similar ecosystems, and which was named 'Candidatus Fodinabacter communificans.' Metaproteomic data unravelled several microbial capabilities expressed in situ, such as iron, sulfur and arsenic oxidation that are key mechanisms in biomineralization, or organic nutrient, amino acid and vitamin metabolism involved in synthrophic associations. A statistical analysis of genomic and proteomic data and reverse transcriptase-PCR experiments allowed us to build an integrated model of the metabolic interactions that may be of prime importance in the natural attenuation of such anthropized ecosystems.

Published
2011
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13. Effect of arsenite on swimming motility delays surface colonization in Herminiimonas arsenicoxydans

Author

Sandrine Koechler, Marie Marchal, B. Kammerer, Philippe N. Bertin, Romain Briandet, UMR 7156 Génétique Moléculaire, Génomique et Microbiologie, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ANR COBIAS project, Groupement de Recherche - Metabolisme de l'Arsenic chez les Microorganismes GDR2909-CNRS, Génétique moléculaire, génomique, microbiologie (GMGM), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Arsenites, [SDV]Life Sciences [q-bio], Mutant, chemistry.chemical_element, Motility, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Oxalobacteraceae, Herminiimonas arsenicoxydans, Arsenic, 030304 developmental biology, Arsenite, 0303 health sciences, Microscopy, Confocal, biology, 030306 microbiology, Biofilm, Arsenate, biology.organism_classification, Cell biology, chemistry, Biofilms, Oxidoreductases, Oxidation-Reduction, Bacteria
Abstract

Herminiimonas arsenicoxydans is a Gram-negative bacterium able to detoxify arsenic-contaminated environments by oxidizing arsenite [As(III)] to arsenate [As(V)] and by scavenging arsenic ions in an extracellular matrix. Its motility and colonization behaviour have been previously suggested to be influenced by arsenite. Using time-course confocal laser scanning microscopy, we investigated its biofilm development in the absence and presence of arsenite. Arsenite was shown to delay biofilm initiation in the wild-type strain; this was partly explained by its toxicity, which caused an increased growth lag time. However, this delayed adhesion step in the presence of arsenite was not observed in either a swimming motility defective fliL mutant or an arsenite oxidase defective aoxB mutant; both strains displayed the wild-type surface properties and growth capacities. We propose that during the biofilm formation process arsenite acts on swimming motility as a result of the arsenite oxidase activity, preventing the switch between planktonic and sessile lifestyles. Our study therefore highlights the existence, under arsenite exposure, of a competition between swimming motility, resulting from arsenite oxidation, and biofilm initiation.

Published
2010
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14. Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans

Author

Didier Lièvremont, Jessica Cleiss-Arnold, Philippe N. Bertin, Florence Arsène-Ploetze, Odile Sismeiro, Sandrine Koechler, Jean-Yves Coppée, Florence Hommais, Caroline Proux, Marie-Agnès Dillies, Florence Goulhen-Chollet, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris], Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Financial support came from the Centre National de la Recherche Scientifique, the Agence Nationale de la Recherche (ANR 07-BLAN-0118 project) and the Université de Strasbourg., ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007), and Institut Pasteur [Paris] (IP)

Subjects
Microbiology (medical), MESH: Operon, MESH: Mutation, Operon, MESH: Oxalobacteraceae, lcsh:QR1-502, MESH: Sequence Alignment, MESH: Amino Acid Sequence, MESH: Base Sequence, Microbiology, MESH: Quorum Sensing, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, MESH: Gene Expression Profiling, Sigma factor, Gene expression, Research article, MESH: Oxidoreductases, Herminiimonas arsenicoxydans, Gene, MESH: Bacterial Proteins, 030304 developmental biology, Arsenite, Genetics, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, MESH: Conserved Sequence, MESH: Molecular Sequence Data, biology, 030306 microbiology, MESH: Transcription, Genetic, biology.organism_classification, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, MESH: Metabolic Networks and Pathways, rpoN, Transposon mutagenesis, MESH: Arsenites, MESH: Genes, Bacterial
Abstract

Background Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism. Results In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (σ54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 σ54-dependent promoter motif was identified upstream of aoxAB coding sequences. Conclusion These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.

Published
2010
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15. A tale of two oxidation states: bacterial colonization of arsenic-rich environments

Author

Caroline Dossat, Barbara Schoepp, Jean Weissenbach, Yuko Makita, Valérie Barbe, Patricia Siguier, Béatrice Segurens, Michael Chandler, Wolfgang Nitschke, Sophie Mangenot, Zoé Rouy, Stéphanie Weiss, David Vallenet, Benoit Cournoyer, Diliana D. Simeonova, Philippe Ortet, Antoine Danchin, Florence Arsène-Ploetze, Sandrine Koechler, Christine Carapito, Mohamed Barakat, Evelyne Krin, Didier Lièvremont, Daniel Muller, Emmanuelle Leize, Simon Duval, Philippe N. Bertin, Marie-Claire Lett, Nicolas Perdrial, Michaël Heymann, Stéphane Cruveiller, Aurélie Lieutaud, Violaine Bonnefoy, Evelyne Turlin, Claudine Médigue, Emmanuel Talla, Alain Van Dorsselaer, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de géochimie de la surface (CGS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut national des sciences de l'Univers (INSU - CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Génétique moléculaire, génomique, microbiologie ( GMGM ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes ( LEMIRE ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Laboratoire de microbiologie et génétique moléculaires ( LMGM ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre de géochimie de la surface ( CGS ), Institut national des sciences de l'Univers ( INSU - CNRS ) -Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Structure et évolution des génomes ( SEG ), and CNS-Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
MESH: Oxidation-Reduction, Cancer Research, Drug Resistance, MESH : Models, Biological, QH426-470, MESH : Carbon, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Arsenic, Bacteria, Biodegradation, Environmental, Carbon, Bacterial, Energy Metabolism, Genome, Metals, Models, Biological, Oxidation-Reduction, Phylogeny, MESH: Biodegradation, Environmental, 0302 clinical medicine, Herminiimonas arsenicoxydans, MESH: Phylogeny, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), 0303 health sciences, Ecology, MESH: Energy Metabolism, MESH : Arsenic, 6. Clean water, Biodegradation, Environmental, Research Article, inorganic chemicals, MESH : Biodegradation, Environmental, MESH : Genome, Bacterial, Energy metabolism, chemistry.chemical_element, MESH: Carbon, Biology, Genomic databases, Microbiology, Models, Biological, 03 medical and health sciences, Bacterial colonization, Bioremediation, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, SDV:BBM, Genetics, MESH : Bacteria, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH : Oxidation-Reduction, MESH: Metals, 030306 microbiology, MESH : Metals, MESH: Models, Biological, MESH : Phylogeny, Computational Biology, Oxidation reduction, Genetics and Genomics, biology.organism_classification, Archaea, MESH : Energy Metabolism, Eubacteria, MESH: Bacteria, Positive chemotaxis, chemistry, 13. Climate action, Genome, Bacterial, 030217 neurology & neurosurgery
Abstract

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth., Author Summary Microorganisms play a crucial role in nutrient biogeochemical cycles. Arsenic is found throughout the environment from both natural and anthropogenic sources. Its inorganic forms are highly toxic and impair the physiology of most higher organisms. Arsenic contamination of groundwater supplies is giving rise to increasingly severe human health problems in both developing and industrial countries. In the present work, we investigated the metabolism of this metalloid in Herminiimonas arsenicoxydans, a representative organism of a novel bacterial genus widespread in aquatic environments. Examination of the genome sequence and experimental evidence revealed that it is remarkably capable of coping with arsenic. Our observations support the existence of multiple strategies allowing arsenic-metabolizing microbes to efficiently colonize toxic environments. In particular, arsenic oxidation and scavenging may have played a crucial role in the development of early stages of life on Earth. Such mechanisms may one day be exploited as part of a potential bioremediation strategy in toxic environments.

Published
2007
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