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1. Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation

Author: Michel Mench, Fabienne Battaglia-Brunet, Philippe N. Bertin, Frédéric Plewniak, Simona Rossetti, Simona Crognale, and Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)
Subjects: Health, Toxicology and Mutagenesis, Microorganism, Microbial genomics, chemistry.chemical_element, Review Article, 010501 environmental sciences, 01 natural sciences, Arsenic, Soil, 03 medical and health sciences, Bioremediation, Biotransformation, Humans, Soil Pollutants, Environmental Chemistry, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, Bioprocess, Ecosystem, Phytomanagement, 030304 developmental biology, 0105 earth and related environmental sciences, 2. Zero hunger, 0303 health sciences, business.industry, Water, Correction, General Medicine, Contamination, Pollution, Environmentally friendly, Phytoremediation, Biotechnology, Biodegradation, Environmental, Metabolism, chemistry, 13. Climate action, Environmental science, business
Abstract: Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.
Published: 2021
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2. Arsenite response inCoccomyxasp. Carn explored by transcriptomic and non-targeted metabolomic approaches

Author: Philippe N. Bertin, Philippe Hugueney, Olivier Bouchez, Frédéric Plewniak, Corinne Casiot, Sandrine Koechler, Florence Arsène-Ploetze, Hermann J. Heipieper, Raymonde Baltenweck, and David Halter
Subjects: 0301 basic medicine, Genetics, Euglena gracilis, biology, ved/biology, 030106 microbiology, ved/biology.organism_classification_rank.species, Arsenate, chemistry.chemical_element, Glutathione, medicine.disease_cause, biology.organism_classification, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, Metabolomics, chemistry, Biochemistry, medicine, Coccomyxa, Ecology, Evolution, Behavior and Systematics, Arsenic, Oxidative stress, Arsenite
Abstract: Arsenic is a toxic metalloid known to generate an important oxidative stress in cells. In the present study, we focused our attention on an alga related to the genus Coccomyxa, exhibiting an extraordinary capacity to resist high concentrations of arsenite and arsenate. The integrated analysis of high-throughput transcriptomic data and non-targeted metabolomic approaches highlighted multiple levels of protection against arsenite. Indeed, Coccomyxa sp. Carn induced a set of transporters potentially preventing the accumulation of this metalloid in the cells and presented a distinct arsenic metabolism in comparison to another species more sensitive to that compound, i.e. Euglena gracilis, especially in regard to arsenic methylation. Interestingly, Coccomyxa sp. Carn was characterized by a remarkable accumulation of the strong antioxidant glutathione (GSH). Such observation could explain the apparent low oxidative stress in the intracellular compartment, as suggested by the transcriptomic analysis. In particular, the high amount of GSH in the cell could play an important role for the tolerance to arsenate, as suggested by its partial oxidation into oxidized glutathione in presence of this metalloid. Our results therefore reveal that this alga has acquired multiple and original defence mechanisms allowing the colonization of extreme ecosystems such as acid mine drainages.
Published: 2016
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3. A Genomic Outlook on Bioremediation: The Case of Arsenic Removal

Author: Simona Crognale, Philippe N. Bertin, Simona Rossetti, and Frédéric Plewniak
Subjects: 0301 basic medicine, Microbiology (medical), Pollution, microorganism, Biogeochemical cycle, Environmental remediation, Mini Review, media_common.quotation_subject, lcsh:QR1-502, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Bioremediation, Biotransformation, bioremediation, genomics, media_common, Pollutant, arsenic, ecosystem ecology, bioremediation/phytoremediation, Arsenic contamination of groundwater, Phytoremediation, 030104 developmental biology, Environmental science, Biochemical engineering
Abstract: Microorganisms play a major role in biogeochemical cycles. As such they are attractive candidates for developing new or improving existing biotechnological applications, in order to deal with the accumulation and pollution of organic and inorganic compounds. Their ability to participate in bioremediation processes mainly depends on their capacity to metabolize toxic elements and catalyze reactions resulting in, for example, precipitation, biotransformation, dissolution, or sequestration. The contribution of genomics may be of prime importance to a thorough understanding of these metabolisms and the interactions of microorganisms with pollutants at the level of both single species and microbial communities. Such approaches should pave the way for the utilization of microorganisms to design new, efficient and environmentally sound remediation strategies, as exemplified by the case of arsenic contamination, which has been declared as a major risk for human health in various parts of the world.
Published: 2018
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4. 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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5. Arsenic hypertolerance in the protistEuglena mutabilisis mediated by specific transporters and functional integrity maintenance mechanisms

Author: Philippe N. Bertin, David Halter, Julie Poulain, Frédéric Plewniak, Florence Arsène-Ploetze, Jérémy Andres, and Corinne Da Silva
Subjects: biology, Membrane transport protein, Mutagenesis, Protein turnover, chemistry.chemical_element, Protist, biology.organism_classification, medicine.disease_cause, Microbiology, Euglena, Cell biology, Transcriptome, chemistry.chemical_compound, chemistry, Botany, biology.protein, medicine, Ecology, Evolution, Behavior and Systematics, DNA, Arsenic
Abstract: Arsenic is a toxic metalloid known to cause multiple and severe cellular damages, including lipid peroxidation, protein misfolding, mutagenesis and double and single-stranded DNA breaks. Thus, exposure to this compound is lethal for most organisms but some species such as the photosynthetic protist Euglena mutabilis are able to cope with very high concentrations of this metalloid. Our comparative transcriptomic approaches performed on both an arsenic hypertolerant protist, i.e. E. mutabilis, and a more sensitive one, i.e. E. gracilis, revealed multiple mechanisms involved in arsenic tolerance. Indeed, E. mutabilis prevents efficiently the accumulation of arsenic in the cell through the expression of several transporters. More surprisingly, this protist induced the expression of active DNA reparation and protein turnover mechanisms, which allow E. mutabilis to maintain functional integrity of the cell under challenging conditions. Our observations suggest that this protist has acquired specific functions regarding arsenic and has developed an original metabolism to cope with acid mine drainages-related stresses.
Published: 2014
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6. Rapid Impact of Phenanthrene and Arsenic on Bacterial Community Structure and Activities in Sand Batches

Author: Philippe N. Bertin, Florence Arsène-Ploetze, Florence Goulhen-Chollet, Christine Carapito, Corinne Leyval, Simon Devin, Jessica Poirel, Aurélie Cébron, Pascale Bauda, Patrick Billard, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-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), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Univesité de Strasbourg, CNRS UMR7178, Inst Pluridisciplinaire Hubert Curien, Lab Spectrometrie Masse Bioorgan, F-67087 Strasbourg, France
Subjects: Proteome, Plant Exudates, DIVERSITY, Soil Science, chemistry.chemical_element, Polycyclic aromatic hydrocarbon, SOIL MICROBIAL COMMUNITY, Biology, HORIZONTAL GENE-TRANSFER, Arsenic, Microbiology, chemistry.chemical_compound, HEAVY-METALS, Stress, Physiological, RNA, Ribosomal, 16S, Soil Pollutants, PTERIS-VITTATA, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, Arsenite, 2. Zero hunger, Pollutant, chemistry.chemical_classification, Rhizosphere, Bacteria, Ecology, CLEAVAGE PATHWAYS, Arsenate, RHIZOSPHERE, Phenanthrenes, CONTAMINATED SOILS, Phenanthrene, Silicon Dioxide, 6. Clean water, chemistry, Genes, Bacterial, 13. Climate action, Environmental chemistry, [SDE]Environmental Sciences, Metabolome, PSEUDOMONAS, OXIDIZING BACTERIA, Soil microbiology
Abstract: International audience; The impact of both organic and inorganic pollution on the structure of soil microbial communities is poorly documented. A short-time batch experiment (6 days) was conducted to study the impact of both types of pollutants on the taxonomic, metabolic and functional diversity of soil bacteria. For this purpose sand spiked with phenanthrene (500 mg kg(-1) sand) or arsenic (arsenite 0.66 mM and arsenate 12.5 mM) was supplemented with artificial root exudates and was inoculated with bacteria originated from an aged PAH and heavy-metal-polluted soil. The bacterial community was characterised using bacterial strain isolation, TTGE fingerprinting and proteomics. Without pollutant, or with phenanthrene or arsenic, there were no significant differences in the abundance of bacteria and the communities were dominated by Pseudomonas and Paenibacillus genera. However, at the concentrations used, both phenanthrene or arsenic were toxic as shown by the decrease in mineralisation activities. Using community-level physiological profiles (Biolog Ecoplates (TM)) or differential proteomics, we observed that the pollutants had an impact on the community physiology, in particular phenanthrene induced a general cellular stress response with changes in the central metabolism and membrane protein synthesis. Real-time PCR quantification of functional genes and transcripts revealed that arsenic induced the transcription of functional arsenic resistance and speciation genes (arsB, ACR3 and aioA), while no transcription of PAH-degradation genes (PAH-dioxygenase and catechol-dioxygenase) was detected with phenanthrene. Altogether, in our tested conditions, pollutants do not have a major effect on community abundance or taxonomic composition but rather have an impact on metabolic and functional bacterial properties.
Published: 2013
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7. Surface properties and intracellular speciation revealed an original adaptive mechanism to arsenic in the acid mine drainage bio-indicator Euglena mutabilis

Author: Frédéric Plewniak, Stéphane Simon, Philippe N. Bertin, Marie Marchal, Corinne Casiot, Hermann J. Heipieper, David Halter, Florence Arsène-Ploetze, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Hydrosciences Montpellier (HSM), 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), Department of Environmental Biotechnology [UFZ Leipzig], Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Groupement de Recherche Eau, Sol, Environnement (GRESE), and Université de Limoges (UNILIM)
Subjects: inorganic chemicals, Euglena gracilis, Membrane Fluidity, Surface Properties, Gliding motility, [SDE.MCG]Environmental Sciences/Global Changes, Hydrophobicity, ved/biology.organism_classification_rank.species, chemistry.chemical_element, AMD, 010501 environmental sciences, Biology, 01 natural sciences, Applied Microbiology and Biotechnology, Euglena, Arsenic, 03 medical and health sciences, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Membrane fluidity, Soil Pollutants, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], 030304 developmental biology, 0105 earth and related environmental sciences, chemistry.chemical_classification, 0303 health sciences, ved/biology, Cell Membrane, Fatty Acids, Euglena mutabilis, Fatty acid, Drug Tolerance, General Medicine, biology.organism_classification, Adaptation, Physiological, Unsaturation index, Biochemistry, chemistry, Arsenic speciation, [SDE]Environmental Sciences, Metalloid, Hydrophobic and Hydrophilic Interactions, Locomotion, Intracellular, Biotechnology
Abstract: International audience; Euglena mutabilis is a protist ubiquitously found in extreme environments such as acid mine drainages which are often rich in arsenic. The response of E. mutabilis to this metalloid was compared to that of Euglena gracilis, a protist not found in such environments. Membrane fatty acid composition, cell surface properties, arsenic accumulation kinetics, and intracellular arsenic speciation were determined. The results revealed a modification in fatty acid composition leading to an increased membrane fluidity in both Euglena species under sublethal arsenic concentrations exposure. This increased membrane fluidity correlated to an induced gliding motility observed in E. mutabilis in the presence of this metalloid but did not affect the flagellar dependent motility of E. gracilis. Moreover, when compared to E. gracilis, E. mutabilis showed highly hydrophobic cell surface properties and a higher tolerance to water-soluble arsenical compounds but not to hydrophobic ones. Finally, E. mutabilis showed a lower accumulation of total arsenic in the intracellular compartment and an absence of arsenic methylated species in contrast to E. gracilis. Taken together, our results revealed the existence of a specific arsenical response of E. mutabilis that may play a role in its hypertolerance to this toxic metalloid.
Published: 2011
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8. Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France

Author: Odile Bruneel, Marina Héry, Philippe N. Bertin, Corinne Casiot, Angélique Desoeuvre, Aurélie Volant, Guillaume Morin, Hydrosciences Montpellier (HSM), 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), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire de minéralogie, cristallographie de Paris (LMCP), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Geologic Sediments, Eukaryotic diversity, 030106 microbiology, Biodiversity, Soil Science, Environmental pollution, Viridiplantae, Ecological succession, Biology, Community spatial dynamics, Mining, Arsenic, 03 medical and health sciences, Acid mine drainage, Rivers, Microbial ecology, RNA, Ribosomal, 18S, Ecosystem, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Phylogeny, Ecology, Evolution, Behavior and Systematics, Base Sequence, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, Water Pollution, Fungi, Community structure, Eukaryota, Species diversity, DNA, Hydrogen-Ion Concentration, 15. Life on land, Classification, biology.organism_classification, High-Throughput Screening Assays, 030104 developmental biology, Alveolata, [SDE]Environmental Sciences, France, Environmental Pollution, Sequence Analysis, Stramenopiles, Water Pollutants, Chemical
Abstract: International audience; Microscopic eukaryotes play a key role in ecosystem functioning, but their diversity remains largely unexplored in most environments. To advance our knowledge of eukaryotic microorganisms and the factors that structure their communities, high-throughput sequencing was used to characterize their diversity and spatial distribution along the pollution gradient of the acid mine drainage at Carnoulès (France). A total of 16,510 reads were retrieved leading to the identification of 323 OTUs after normalization. Phylogenetic analysis revealed a quite diverse eukaryotic community characterized by a total of eight high-level lineages including 37 classes. The majority of sequences were clustered in four main groups: Fungi, Stramenopiles, Alveolata and Viridiplantae. The Reigous sediments formed a succession of distinct ecosystems hosting contrasted eukaryotic communities whose structure appeared to be at least partially correlated with sediment mineralogy. The concentration of arsenic in the sediment was shown to be a significant factor driving the eukaryotic community structure along this continuum.
Published: 2016
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9. The microbial genomics of arsenic

Author: Philippe N. Bertin and Jérémy Andres
Subjects: 0301 basic medicine, 030106 microbiology, Drug Resistance, Genomics, Computational biology, Biology, Microbiology, Genome, DNA sequencing, Arsenic, Transcriptome, 03 medical and health sciences, Phylogenetics, Metabolome, Phylogeny, Genetics, Bacteria, Archaea, Interspersed Repetitive Sequences, 030104 developmental biology, Infectious Diseases, Gene Expression Regulation, Metagenomics, Proteome, Oxidation-Reduction
Abstract: Arsenic, which is a major contaminant of many aquatic ecosystems worldwide, is responsible for serious public health issues. However, life has evolved various strategies for coping with this toxic element. In particular, prokaryotic organisms have developed processes enabling them to resist and metabolize this chemical. Studies based on genome sequencing and transcriptome, proteome and metabolome profiling have greatly improved our knowledge of prokaryotes' metabolic potential and functioning in contaminated environments. The increasing number of genomes available and the development of descriptive and comparative approaches have made it possible not only to identify several genetic determinants of the arsenic metabolism, but also to elucidate their phylogenetic distribution and their modes of regulation. In addition, studies using functional genomic tools have established the pleiotropic character of prokaryotes' responses to arsenic, which can be either common to several species or species-specific. These approaches also provide promising means of deciphering the functioning of microbial communities including uncultured organisms, the genetic transfers involved and the possible occurrence of metabolic interactions as well as the evolution of arsenic resistance and metabolism.
Published: 2015

10. 16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage

Author: Claudine Médigue, Denis Le Paslier, Anne Fahy, Béatrice Lauga, Robert Duran, Ludovic Giloteaux, Jean Weissenbach, Philippe N. Bertin, 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), 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), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-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)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and RARE project no. 07-BLAN-0108
Subjects: Molecular Sequence Data, Soil Science, Niche conservatism, Biology, Mining, Arsenic, Actinobacteria, 03 medical and health sciences, chemistry.chemical_compound, Acid mine drainage, RNA, Ribosomal, 16S, Soil Pollutants, Cloning, Molecular, Phylogeny, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, DNA Primers, 030304 developmental biology, Arsenite, Genetics, Arsenic metabolism genes, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, Base Sequence, Ecology, Reverse Transcriptase Polymerase Chain Reaction, 030306 microbiology, Arsenite Transporting ATPases, Bacterial distribution, Thiomonas, Biodiversity, Sequence Analysis, DNA, Acidithiobacillus, biology.organism_classification, 16S ribosomal RNA, Acidobacteria, chemistry, Bacterial diversity, Candidatus, France, Oxidoreductases, Functional gene diversity, Bacteria
Abstract: cited By 5; International audience; To gain an in-depth insight into the diversity and the distribution of genes under the particular evolutionary pressure of an arsenic-rich acid mine drainage (AMD), the genes involved in bacterial arsenic detoxification (arsB, ACR3) and arsenite oxidation (aioA) were investigated in sediment from Carnoulès (France), in parallel to the diversity and global distribution of the metabolically active bacteria. The metabolically active bacteria were affiliated mainly to AMD specialists, i.e., organisms detected in or isolated from AMDs throughout the world. They included mainly Acidobacteria and the non-affiliated “Candidatus Fodinabacter communificans,” as well as Thiomonas and Acidithiobacillus spp., Actinobacteria, and unclassified Gammaproteobacteria. The distribution range of these organisms suggested that they show niche conservatism. Sixteen types of deduced protein sequences of arsenite transporters (5 ArsB and 11 Acr3p) were detected, whereas a single type of arsenite oxidase (AioA) was found. Our data suggested that at Carnoulès, the aioA gene was more recent than those encoding arsenite transporters and subjected to a different molecular evolution. In contrast to the 16S ribosomal RNA (16S rRNA) genes associated with AMD environments worldwide, the functional genes aioA, ACR3, and to a lesser extent arsB, were either novel or specific to Carnoulès, raising the question as to whether these functional genes are specific to high concentrations of arsenic, AMD-specific, or site-specific
Published: 2015
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11. Diversity and spatiotemporal dynamics of bacterial communities: Physicochemical and other drivers along an acid mine drainage

Author: Marina Héry, Philippe N. Bertin, Robert Duran, Odile Bruneel, Fabien Javerliat, Béatrice Lauga, Françoise Elbaz-Poulichet, Olivier Bouchez, Aurélie Volant, Noëlle Bru, Angélique Desoeuvre, Corinne Casiot, Anne Fahy, Sophie Delpoux, Hydrosciences Montpellier (HSM), 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), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques et de leurs Applications [Pau] (LMAP), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA), FRB (Fondation pour la recherche sur la Biodiversite) program [AAP-IN-2009039], 'Observatoire de Recherche Mediterraneen de l'Environnement' (OSU-OREME), French Ministry of Education and Research, Direction Generale de l'Armement (DGA), Groupement de recherche: Metabolisme de l'Arsenic chez les Microorganismes [GDR2909CNRS], 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), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Domaine expérimental d'Auzeville (UE AUZEVILLE), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (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), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Virologie et Immunologie Moléculaires (VIM), and Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: Iron, Biodiversity, Biology, Applied Microbiology and Biotechnology, Microbiology, Mining, Microbial ecology, spatial and temporal dynamics, Phylogeny, Environmental gradient, Abiotic component, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Bacteria, Ecology, Sulfates, Water Pollution, arsenic, bacterial diversity, Acidithiobacillus, 15. Life on land, biology.organism_classification, Acid mine drainage, [SDE.ES]Environmental Sciences/Environmental and Society, Microbial population biology, 13. Climate action, [SDE]Environmental Sciences, Biological dispersal, Water Microbiology, Polymorphism, Restriction Fragment Length, Water Pollutants, Chemical, acid mine drainage
Abstract: cited By 15; International audience; Deciphering the biotic and abiotic factors that control microbial community structure over time and along an environmental gradient is a pivotal question in microbial ecology. Carnoulès mine (France), which is characterized by acid waters and very high concentrations of arsenic, iron, and sulfate, provides an excellent opportunity to study these factors along the pollution gradient of Reigous Creek. To this end, biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and high-throughput sequencing. Patterns of spatial and temporal variations in bacterial community composition linked to changes in the physicochemical conditions suggested that species-sorting processes were at work in the acid mine drainage. Arsenic, temperature, and sulfate appeared to be the most important factors that drove the composition of bacterial communities along this continuum. Time series investigation along the pollution gradient also highlighted habitat specialization for some major members of the community (Acidithiobacillus and Thiomonas), dispersal for Acidithiobacillus, and evidence of extinction/re-thriving processes for Gallionella. Finally, pyrosequencing revealed a broader phylogenetic range of taxa than previous clone library-based diversity. Overall, our findings suggest that in addition to environmental filtering processes, additional forces (dispersal, birth/death events) could operate in AMD community
Published: 2014
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12. 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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13. Arsenic hypertolerance in the protist Euglena mutabilis is mediated by specific transporters and functional integrity maintenance mechanisms

Author: David, Halter, Jérémy, Andres, Frédéric, Plewniak, Julie, Poulain, Corinne, Da Silva, Florence, Arsène-Ploetze, and Philippe N, Bertin
Subjects: Drug Resistance, Membrane Transport Proteins, Biological Transport, Photosynthesis, Arsenic, Euglena
Abstract: Arsenic is a toxic metalloid known to cause multiple and severe cellular damages, including lipid peroxidation, protein misfolding, mutagenesis and double and single-stranded DNA breaks. Thus, exposure to this compound is lethal for most organisms but some species such as the photosynthetic protist Euglena mutabilis are able to cope with very high concentrations of this metalloid. Our comparative transcriptomic approaches performed on both an arsenic hypertolerant protist, i.e. E. mutabilis, and a more sensitive one, i.e. E. gracilis, revealed multiple mechanisms involved in arsenic tolerance. Indeed, E. mutabilis prevents efficiently the accumulation of arsenic in the cell through the expression of several transporters. More surprisingly, this protist induced the expression of active DNA reparation and protein turnover mechanisms, which allow E. mutabilis to maintain functional integrity of the cell under challenging conditions. Our observations suggest that this protist has acquired specific functions regarding arsenic and has developed an original metabolism to cope with acid mine drainages-related stresses.
Published: 2013

14. Bacterial metabolism of environmental arsenic--mechanisms and biotechnological applications

Author: Hermann J. Heipieper, Florence Arsène-Ploetze, Martin C. Kruger, and Philippe N. Bertin
Subjects: inorganic chemicals, Anaerobic respiration, Microorganism, Microbial metabolism, chemistry.chemical_element, Biology, Applied Microbiology and Biotechnology, Arsenic, 03 medical and health sciences, Bioremediation, Bioreactors, Detoxification, 030304 developmental biology, 0303 health sciences, integumentary system, Bacteria, 030306 microbiology, General Medicine, Biodegradation, 6. Clean water, 3. Good health, Arsenic contamination of groundwater, Biodegradation, Environmental, chemistry, 13. Climate action, Environmental chemistry, Biotechnology
Abstract: Arsenic causes threats for environmental and human health in numerous places around the world mainly due to its carcinogenic potential at low doses. Removing arsenic from contaminated sites is hampered by the occurrence of several oxidation states with different physicochemical properties. The actual state of arsenic strongly depends on its environment whereby microorganisms play important roles in its geochemical cycle. Due to its toxicity, nearly all organisms possess metabolic mechanisms to resist its hazardous effects, mainly by active extrusion, but also by extracellular precipitation, chelation, and intracellular sequestration. Some microbes are even able to actively use various arsenic compounds in their metabolism, either as an electron donor or as a terminal electron acceptor for anaerobic respiration. Some microorganisms can also methylate inorganic arsenic, probably as a resistance mechanism, or demethylate organic arsenicals. Bioavailability of arsenic in water and sediments is strongly influenced by such microbial activities. Therefore, understanding microbial reactions to arsenic is of importance for the development of technologies for improved bioremediation of arsenic-contaminated waters and environments. This review gives an overview of the current knowledge on bacterial interactions with arsenic and on biotechnologies for its detoxification and removal.
Published: 2013

15. Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments

Author: Fabienne Battaglia-Brunet, Frédéric Plewniak, Benjamin Navet, Olivier Bouchez, Sandrine Koechler, Pierre Peyret, Philippe N. Bertin, Fabienne Séby, Eric Dugat-Bony, Génétique moléculaire, génomique, microbiologie (GMGM), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Ultra Traces Analyses Aquitaine (UT2A), Ultra Traces Analyses Aquitaine, Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), This work was supported by the Agence Nationale de la Recherche (ANR-2008-CESA-003), the Centre National de la Recherche Scientifique (CNRS) in the frame of the ‘Groupement de Recherche—Métabolisme de l'Arsenic chez les Microorganismes (GDR2909-CNRS)’ (http://gdr2909.alsace.cnrs.fr/) and the Université de Strasbourg (UdS)., and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: Geologic Sediments, Biogeochemical cycle, Microorganism, Microbial metabolism, arsenic pollution, chemistry.chemical_element, Biology, Arsenic, 03 medical and health sciences, chemistry.chemical_compound, Proteobacteria, Mediterranean Sea, Genetics, Water Pollutants, 14. Life underwater, metagenomic, Water pollution, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Sulfur-Reducing Bacteria, Sulfates, 030306 microbiology, Ecology, Arsenate, marine sediment, Sequence Analysis, DNA, 6. Clean water, microbial metabolism, Gene Ontology, chemistry, Microbial population biology, Genes, Bacterial, 13. Climate action, Metagenomics, Metagenome, France
Abstract: Chantier qualité GA; International audience; Microorganisms dwelling in sediments have a crucial role in biogeochemical cycles and are expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting major health risks for human populations. We present here a metagenomic study of the sediment from two harbours on the Mediterranean French coast, l'Estaque and St Mandrier. The first site is highly polluted with arsenic and heavy metals, while the arsenic concentration in the second site is below toxicity levels. The goal of this study was to elucidate the potential impact of the microbial community on the chemical parameters observed in complementary geochemical studies performed on the same sites. The metagenomic sequences, along with those from four publicly available metagenomes used as control data sets, were analysed with the RAMMCAP workflow. The resulting functional profiles were compared to determine the over-represented Gene Ontology categories in the metagenomes of interest. Categories related to arsenic resistance and dissimilatory sulphate reduction were over-represented in l'Estaque. More importantly, despite very similar profiles, the identification of specific sequence markers for sulphate-reducing bacteria and sulphur-oxidizing bacteria showed that sulphate reduction was significantly more associated with l'Estaque than with St Mandrier. We propose that biotic sulphate reduction, arsenate reduction and fermentation may together explain the higher mobility of arsenic observed in l'Estaque in previous physico-chemical studies of this site. This study also demonstrates that it is possible to draw sound conclusions from comparing complex and similar unassembled metagenomes at the functional level, even with very low sequence coverage
Published: 2013
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16. Archaeal diversity: Temporal variation in the arsenic-rich creek sediments of Carnoulès Mine, France

Author: Françoise Elbaz-Poulichet, Odile Bruneel, Sophie Delpoux, Angélique Desoeuvre, Aurélie Volant, Corinne Casiot, Marina Héry, Philippe N. Bertin, J.-C. Personné, Béatrice Lauga, Guillaume Morin, Hydrosciences Montpellier (HSM), 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), 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)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de minéralogie et de physique des milieux condensés (IMPMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-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), Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de Biologie du Développement de Marseille (IBDM), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Thaumarchaeota, Nitrosopumilus, RNA, Archaeal, Microbiology, Arsenic, 03 medical and health sciences, Acid mine drainage, Microbial ecology, RNA, Ribosomal, 16S, Groundwater, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, Diversity, biology, 030306 microbiology, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, Lead and zinc mine, Biodiversity, General Medicine, Hydrogen-Ion Concentration, biology.organism_classification, Archaea, Thermoplasmatales, [SDE]Environmental Sciences, Molecular Medicine, Nitrification, France, Euryarchaeota, Water Microbiology
Abstract: cited By 15; International audience; The Carnoulès mine is an extreme environment located in the South of France. It is an unusual ecosystem due to its acidic pH (2–3), high concentration of heavy metals, iron, and sulfate, but mainly due to its very high concentration of arsenic (up to 10 g L−1 in the tailing stock pore water, and 100–350 mg L−1 in Reigous Creek, which collects the acid mine drainage). Here, we present a survey of the archaeal community in the sediment and its temporal variation using a culture-independent approach by cloning of 16S rRNA encoding genes. The taxonomic affiliation of Archaea showed a low degree of biodiversity with two different phyla: Euryarchaeota and Thaumarchaeota. The archaeal community varied in composition and richness throughout the sampling campaigns. Many sequences were phylogenetically related to the order Thermoplasmatales represented by aerobic or facultatively anaerobic, thermoacidophilic autotrophic or heterotrophic organisms like the organotrophic genus Thermogymnomonas. Some members of Thermoplasmatales can also derive energy from sulfur/iron oxidation or reduction. We also found microorganisms affiliated with methanogenic Archaea (Methanomassiliicoccus luminyensis), which are involved in the carbon cycle. Some sequences affiliated with ammonia oxidizers, involved in the first and rate-limiting step in nitrification, a key process in the nitrogen cycle were also observed, including Candidatus Nitrososphaera viennensis and Candidatus nitrosopumilus sp. These results suggest that Archaea may be important players in the Reigous sediments through their participation in the biochemical cycles of elements, including those of carbon and nitrogen.
Published: 2012
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17. Taxonomic and functional prokaryote diversity in mildly arsenic-contaminated sediments

Author: David Halter, Florence Goulhen-Chollet, Audrey Cordi, Fabienne Séby, Christophe Pagnout, Christine Schaeffer, Philippe N. Bertin, Sebastien Gallien, Simonetta Gribaldo, Didier Montaut, Florence Arsène-Ploetze, Pascale Bauda, Alain Van Dorsselaer, Christine Carapito, Audrey Heinrich-Salmeron, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Interactions Ecotoxicologie, Biodiversité, Ecosystèmes (LIEBE), Université Paul Verlaine - Metz (UPVM)-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), 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 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), Ultra Traces Analyses Aquitaine (UT2A), Ultra Traces Analyses Aquitaine, Audrey Cordi was supported by grants from the French Ministry of Research and the 'Zone Atelier Moselle' (ZAM) project. Audrey Heinrich-Salmeron, David Halter and Sebastien Gallien were supported by grants from the French Ministry of Research and the Université de Strasbourg. Florence Goulhen-Chollet was supported by the Agence Nationale de la Recherche (ANR), RARE project (Reactivity of an Arsenic-Rich Ecosystem). This study was financed by the EC2CO program (Institut National des Sciences de l’Univers, CNRS) and BRG., This work was performed in the framework of the Groupement de Recherche 'Métabolisme de l’Arsenic chez les micro-organismes: de la résistance à la détoxication' (GDR2909-CNRS)., ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007), Institut Pasteur [Paris], 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)-Institut Pluridisciplinaire Hubert Curien (IPHC), 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: Proteomics, Geologic Sediments, Thaumarchaeota, MESH: Archaea/metabolism, MESH: Environmental Pollutants/metabolism, [SDV]Life Sciences [q-bio], MESH: Bacteria/genetics, MESH: Archaea/classification, Polymerase Chain Reaction, MESH: DNA, Archaeal/analysis, RNA, Ribosomal, 16S, MESH: Archaea/isolation & purification, MESH: Ecosystem, MESH: Geologic Sediments/microbiology, MESH: Phylogeny, Phylogeny, 0303 health sciences, biology, Ecology, Planctomycetes, MESH: Microbial Consortia/physiology, General Medicine, Biodiversity, Adaptation, Physiological, DNA, Archaeal, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Arsenic/metabolism, Environmental Pollutants, France, Proteobacteria, MESH: Archaea/genetics, MESH: Bacteria/metabolism, DNA, Bacterial, MESH: Rivers/microbiology, MESH: RNA, Ribosomal, 16S/analysis, Gene Transfer, Horizontal, Microbial Consortia, Environmental genomics, Microbiology, Mining, MESH: Biodiversity, Arsenic, 03 medical and health sciences, Rivers, Metaproteomics, MESH: DNA, Bacterial/analysis, Molecular Biology, Ecosystem, 030304 developmental biology, MESH: Proteomics, Bacteria, 030306 microbiology, Phylum, Bacteroidetes, Prokaryote, MESH: Polymerase Chain Reaction, biology.organism_classification, Archaea, MESH: Adaptation, Physiological, MESH: RNA, Ribosomal, 16S/genetics, MESH: Gene Transfer, Horizontal, MESH: DNA, Bacterial/genetics, MESH: France, Metagenomics, MESH: DNA, Archaeal/genetics, MESH: Bacteria/classification, human activities, Acidobacteria, MESH: Bacteria/isolation & purification
Abstract: International audience; Arsenic-resistant prokaryote diversity is far from being exhaustively explored. In this study, the arsenic-adapted prokaryotic community present in a moderately arsenic-contaminated site near Sainte-Marie-aux-Mines (France) was characterized, using metaproteomic and 16S rRNA-encoding gene amplification. High prokaryotic diversity was observed, with a majority of Proteobacteria, Acidobacteria and Bacter-oidetes, and a large archaeal community comprising Euryarchaeaota and Thaumarchaeota. Metaproteomic analysis revealed that Proteobacteria, Planctomycetes and Cyanobacteria are among the active bacteria in this ecosystem. Taken together, these results highlight the unsuspected high diversity of the arsenic-adapted prokaryotic community, with some phyla never having been described in highly arsenic-exposed sites.
Published: 2011
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18. 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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19. 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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20. Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans

Author: Jean-Yves Coppée, Marie-Laure Fardeau, Marie-Agnès Dillies, Jessica Cleiss-Arnold, Philippe N. Bertin, Caroline Proux, Florence Arsène-Ploetze, Sandrine Koechler, 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] (IP), Laboratoire de Microbiologie IRD, JCA was supported by a grant from the French Ministry of Education and Research. 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. This work was done in the frame of the Groupement de Recherche (GDR2909-CNRS): ' Métabolisme de l'Arsenic chez les Micro-organismes'., ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007), and Institut Pasteur [Paris]
Subjects: inorganic chemicals, Time Factors, Transcription, Genetic, lcsh:QH426-470, Movement, lcsh:Biotechnology, Sulfur metabolism, chemistry.chemical_element, medicine.disease_cause, Arsenic, Transcriptome, 03 medical and health sciences, Bacterial Proteins, Stress, Physiological, Oxalobacteraceae, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, medicine, Genetics, Cluster Analysis, Herminiimonas arsenicoxydans, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Metabolism, biology.organism_classification, Molecular biology, Kinetics, lcsh:Genetics, chemistry, Biochemistry, Oxidation-Reduction, Oxidative stress, Bacteria, Research Article, Biotechnology
Abstract: Background Arsenic is present in numerous ecosystems and microorganisms have developed various mechanisms to live in such hostile environments. Herminiimonas arsenicoxydans, a bacterium isolated from arsenic contaminated sludge, has acquired remarkable capabilities to cope with arsenic. In particular our previous studies have suggested the existence of a temporal induction of arsenite oxidase, a key enzyme in arsenic metabolism, in the presence of As(III). Results Microarrays were designed to compare gene transcription profiles under a temporal As(III) exposure. Transcriptome kinetic analysis demonstrated the existence of two phases in arsenic response. The expression of approximatively 14% of the whole genome was significantly affected by an As(III) early stress and 4% by an As(III) late exposure. The early response was characterized by arsenic resistance, oxidative stress, chaperone synthesis and sulfur metabolism. The late response was characterized by arsenic metabolism and associated mechanisms such as phosphate transport and motility. The major metabolic changes were confirmed by chemical, transcriptional, physiological and biochemical experiments. These early and late responses were defined as general stress response and specific response to As(III), respectively. Conclusion Gene expression patterns suggest that the exposure to As(III) induces an acute response to rapidly minimize the immediate effects of As(III). Upon a longer arsenic exposure, a broad metabolic response was induced. These data allowed to propose for the first time a kinetic model of the As(III) response in bacteria.
Published: 2010
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21. Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes

Author: Christelle Lemaître-Guillier, Florence Arsène-Ploetze, Christopher G. Bryan, Fabienne Battaglia-Brunet, Marie Marchal, Didier Lièvremont, Philippe N. Bertin, Valérie Kugler, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Plateforme Protéomique, Centre National de la Recherche Scientifique (CNRS), Centre for Bioprocess Engineering Research, and Faculty of Engineering and the Built Environment
Subjects: Microbiology (medical), inorganic chemicals, Chemoautotrophic Growth, Arsenites, Operon, oxidation, lcsh:QR1-502, chemistry.chemical_element, Microbiology, lcsh:Microbiology, Beta-proteobacterium, Arsenic, 03 medical and health sciences, Species Specificity, Phylogenetics, Research article, Autotroph, genes, bacteria, Phylogeny, Betaproteobacteria, 030304 developmental biology, Genetics, 0303 health sciences, biology, integumentary system, 030306 microbiology, oxidase, Thiomonas, Thiobacilius, phylogenies, Mine Drainage Carnoules, biology.organism_classification, 16S ribosomal RNA, Adaptation, Physiological, Carbon, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, France, Bacteria
Abstract: Background Thiomonas strains are ubiquitous in arsenic-contaminated environments. Differences between Thiomonas strains in the way they have adapted and respond to arsenic have never been studied in detail. For this purpose, five Thiomonas strains, that are interesting in terms of arsenic metabolism were selected: T. arsenivorans, Thiomonas spp. WJ68 and 3As are able to oxidise As(III), while Thiomonas sp. Ynys1 and T. perometabolis are not. Moreover, T. arsenivorans and 3As present interesting physiological traits, in particular that these strains are able to use As(III) as an electron donor. Results The metabolism of carbon and arsenic was compared in the five Thiomonas strains belonging to two distinct phylogenetic groups. Greater physiological differences were found between these strains than might have been suggested by 16S rRNA/rpoA gene phylogeny, especially regarding arsenic metabolism. Physiologically, T. perometabolis and Ynys1 were unable to oxidise As(III) and were less arsenic-resistant than the other strains. Genetically, they appeared to lack the aox arsenic-oxidising genes and carried only a single ars arsenic resistance operon. Thiomonas arsenivorans belonged to a distinct phylogenetic group and increased its autotrophic metabolism when arsenic concentration increased. Differential proteomic analysis revealed that in T. arsenivorans, the rbc/cbb genes involved in the assimilation of inorganic carbon were induced in the presence of arsenic, whereas these genes were repressed in Thiomonas sp. 3As. Conclusion Taken together, these results show that these closely related bacteria differ substantially in their response to arsenic, amongst other factors, and suggest different relationships between carbon assimilation and arsenic metabolism.
Published: 2009
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22. 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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23. Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome

Author: Emmanuelle Leize-Wagner, Sandrine Koechler, Evelyne Turlin, Christine Carapito, Philippe N. Bertin, Alain Van Dorsselaer, Antoine Danchin, Marie-Claire Lett, Daniel Muller, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), 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)-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), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), 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), Laboratoire de Biologie Tumorale, CRLCC Paul Strauss, XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Génétique moléculaire, génomique, microbiologie (GMGM), Régulation de l'Expression Génétique (REG), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Substances naturelles/chimie moléculaire, Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, 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), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Université Louis Pasteur - Strasbourg I-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 ), XLIM ( XLIM ), Université de Limoges ( UNILIM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Génétique moléculaire, génomique, microbiologie ( GMGM ), Régulation de l'Expression Génétique ( REG ), Sciences Analytiques et Interactions Ioniques et Biomoléculaires ( DSA-IPHC ), Compartimentation et dynamique cellulaires ( CDC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -INSTITUT CURIE-Centre National de la Recherche Scientifique ( CNRS ), Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-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 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), 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 Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH : Molecular Sequence Data, MESH : RNA, Messenger, Messenger, Drug Resistance, MESH: Amino Acid Sequence, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Biochemistry, Genome, chemistry.chemical_compound, MESH : Bacterial Proteins, MESH: Betaproteobacteria, Peptide sequence, MESH: Bacterial Proteins, MESH : Betaproteobacteria, Arsenite, Genetics, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Genes, Bacterial, Bacterial, Betaproteobacteria, General Medicine, MESH : Arsenic, Metals, MESH: Genes, Bacterial, MESH : Genome, Bacterial, Molecular Sequence Data, chemistry.chemical_element, Biology, Arsenic, 03 medical and health sciences, Bacterial Proteins, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Amino Acid Sequence, Gene, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: RNA, Messenger, Two-dimensional gel electrophoresis, MESH: Metals, MESH: Molecular Sequence Data, 030306 microbiology, MESH : Metals, Arsenate, RNA, chemistry, Genes, Genes, Bacterial, Genome, Bacterial
Abstract: International audience; The effect of high concentrations of arsenic has been investigated in Caenibacter arsenoxydans, a beta-proteobacterium isolated from an arsenic contaminated environment and able to oxidize arsenite to arsenate. As the genome of this bacterium has not yet been sequenced, the use of a specific proteomic approach based on nano-high performance liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) studies and de novo sequencing to perform cross-species protein identifications was necessary. In addition, a random mutational analysis was performed. Twenty-two proteins and 16 genes were shown to be differentially accumulated and expressed, respectively, in cells grown in the presence of arsenite. Two genes involved in arsenite oxidation and one in arsenite efflux as well as two proteins responsible for arsenate reduction were identified. Moreover, numerous genes and proteins belonging to various functional classes including information and regulation pathways, intermediary metabolism, cell envelope and cellular processes were also up- or down-regulated, which demonstrates that bacterial response to arsenic is pleiotropic.
Published: 2006
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24. Structure, Function, and Evolution of the Thiomonas spp. Genome

Author: Florence Hommais, Jean Weissenbach, Odile Bruneel, Emmanuel Talla, Philippe N. Bertin, Patricia Siguier, Daniel Muller, Jean-Yves Coppée, Caroline Proux, Stéphanie Weiss, Valérie Barbe, Florence Arsène-Ploetze, Marie Marchal, Gregory Salvignol, Audrey Heinrich-Salmeron, Zoé Rouy, Fabienne Battaglia-Brunet, Didier Lièvremont, Christopher G. Bryan, Caroline Michel, Philippe Ortet, Sandrine Koechler, Céline Brochier-Armanet, Jessica Cleiss-Arnold, Mohamed Barakat, Michael Chandler, Stéphane Cruveiller, Djamila Slyemi, Aurélie Lieutaud, Catherine Joulian, Evelyne Krin, Violaine Bonnefoy, David Roche, Claudine Médigue, Mathieu Erhardt, 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], Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), 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), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-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, Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Hydrosciences Montpellier (HSM), 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), Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), 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), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Dynamique, évolution et expression de génomes de microorganismes (DEEGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), 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), 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), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-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), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris] (IP), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), 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), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), 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), and 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: Cancer Research, Prophages, MESH: Genome, Bacterial, Genome, MESH: Prophages, MESH: Genomic Islands, MESH: Genetic Variation, MESH: Betaproteobacteria, MESH: Evolution, Molecular, Genetics (clinical), Genetics, Comparative Genomic Hybridization, 0303 health sciences, biology, MESH: Energy Metabolism, Betaproteobacteria, Thiomonas, Genetics and Genomics/Microbial Evolution and Genomics, Adaptation, Physiological, Horizontal gene transfer, MESH: Genes, Bacterial, Metabolic Networks and Pathways, Research Article, Plasmids, Genome evolution, lcsh:QH426-470, Gene Transfer, Horizontal, Genomic Islands, MESH: Carbon, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Environment, Arsenic, Evolution, Molecular, 03 medical and health sciences, Genes, Duplicate, MESH: Plasmids, MESH: Arsenic, Microbiology/Environmental Microbiology, MESH: Environment, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Prophage, 030304 developmental biology, Comparative genomics, MESH: Genes, Duplicate, 030306 microbiology, Human evolutionary genetics, Genetic Variation, biology.organism_classification, MESH: Adaptation, Physiological, Carbon, MESH: Gene Transfer, Horizontal, MESH: Comparative Genomic Hybridization, lcsh:Genetics, Genes, Bacterial, MESH: Metabolic Networks and Pathways, Energy Metabolism, Genome, Bacterial
Abstract: Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live., Author Summary Recent advances in the field of arsenic microbial metabolism have revealed that bacteria colonize a large panel of highly contaminated environments. Belonging to the order of Burkholderiales, Thiomonas strains are ubiquitous in arsenic-contaminated environments. The genome of one of them, i.e. Thiomonas sp. 3As, was deciphered and compared to the genome of several other Thiomonas strains. We found that their flexible gene pool evolved to allow both the surviving and growth in their peculiar environment. In particular, the acquisition by strains of the same species of different genomic islands conferred heavy metal resistance and metabolic idiosyncrasies. Our comparative genomic analyses suggest that the natural environment influences the genomic evolution of these bacteria. Importantly, these results highlight the genomic variability that may exist inside a taxonomic group, enlarging the concept of bacterial species.
Published: 2010
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25. A Genomic Outlook on Bioremediation: The Case of Arsenic Removal

Author: Frédéric Plewniak, Simona Crognale, Simona Rossetti, and Philippe N. Bertin
Subjects: genomics, arsenic, bioremediation/phytoremediation, microorganism, ecosystem ecology, Microbiology, QR1-502
Abstract: Microorganisms play a major role in biogeochemical cycles. As such they are attractive candidates for developing new or improving existing biotechnological applications, in order to deal with the accumulation and pollution of organic and inorganic compounds. Their ability to participate in bioremediation processes mainly depends on their capacity to metabolize toxic elements and catalyze reactions resulting in, for example, precipitation, biotransformation, dissolution, or sequestration. The contribution of genomics may be of prime importance to a thorough understanding of these metabolisms and the interactions of microorganisms with pollutants at the level of both single species and microbial communities. Such approaches should pave the way for the utilization of microorganisms to design new, efficient and environmentally sound remediation strategies, as exemplified by the case of arsenic contamination, which has been declared as a major risk for human health in various parts of the world.
Published: 2018
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26. Thiomonas sp. CB2 is able to degrade urea and promote toxic metal precipitation in acid mine drainage waters supplemented with urea

Author: Julien eFarasin, Jérémy eAndres, Corinne eCasiot, Valérie eBarbe, Jacques eFaerber, David eHalter, Dimitri eHeintz, Sandrine eKoechler, Didier eLièvremont, Raphael eLugan, Marie eMarchal, Frédéric ePlewniak, Fabienne eSéby, Philippe N Bertin, and Florence eArsene-Ploetze
Subjects: Adaptation, Biological, Arsenic, metabolomics., aluminium, acid stress, Microbiology, QR1-502
Abstract: The acid mine drainage (AMD) in Carnoulès (France) is characterized by the presence of toxic metals such as arsenic. Several bacterial strains belonging to the Thiomonas genus, which were isolated from this AMD, are able to withstand these conditions. Their genomes carry several genomic islands (GEIs), which are known to be potentially advantageous in some particular ecological niches. This study focused on the role of the urea island present in the Thiomonas CB2 strain, which carry the genes involved in urea degradation processes. First, genomic comparisons showed that the genome of Thiomonas sp. CB2, which is able to degrade urea, contains a urea genomic island which is incomplete in the genome of other strains showing no urease activity. The urease activity of Thiomonas sp. CB2 enabled this bacterium to maintain a neutral pH in cell cultures in vitro and prevented the occurrence of cell death during the growth of the bacterium in a chemically defined medium. In AMD water supplemented with urea, the degradation of urea promotes iron, aluminium and arsenic precipitation. Our data show that ureC was expressed in situ, which suggests that the ability to degrade urea may be expressed in some Thiomonas strains in AMD, and that this urease activity may contribute to their survival in contaminated environments.
Published: 2015
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26 results on '"N. Bertin"'

1. Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation

2. Arsenite response inCoccomyxasp. Carn explored by transcriptomic and non-targeted metabolomic approaches

3. A Genomic Outlook on Bioremediation: The Case of Arsenic Removal

4. Constitutive arsenite oxidase expression detected in arsenic-hypertolerant Pseudomonas xanthomarina S11

5. Arsenic hypertolerance in the protistEuglena mutabilisis mediated by specific transporters and functional integrity maintenance mechanisms

6. Rapid Impact of Phenanthrene and Arsenic on Bacterial Community Structure and Activities in Sand Batches

7. Surface properties and intracellular speciation revealed an original adaptive mechanism to arsenic in the acid mine drainage bio-indicator Euglena mutabilis

8. Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France

9. The microbial genomics of arsenic

10. 16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage

11. Diversity and spatiotemporal dynamics of bacterial communities: Physicochemical and other drivers along an acid mine drainage

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

13. Arsenic hypertolerance in the protist Euglena mutabilis is mediated by specific transporters and functional integrity maintenance mechanisms

14. Bacterial metabolism of environmental arsenic--mechanisms and biotechnological applications

15. Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments

16. Archaeal diversity: Temporal variation in the arsenic-rich creek sediments of Carnoulès Mine, France

17. Taxonomic and functional prokaryote diversity in mildly arsenic-contaminated sediments

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

19. Effect of arsenite on swimming motility delays surface colonization in Herminiimonas arsenicoxydans

20. Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans

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

22. A tale of two oxidation states: bacterial colonization of arsenic-rich environments

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

24. Structure, Function, and Evolution of the Thiomonas spp. Genome

25. A Genomic Outlook on Bioremediation: The Case of Arsenic Removal

26. Thiomonas sp. CB2 is able to degrade urea and promote toxic metal precipitation in acid mine drainage waters supplemented with urea

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