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1. Characterisation of hydrocarbon degradation, biosurfactant production, and biofilm formation in Serratia sp. Tan611: a new strain isolated from industrially contaminated environment in Algeria

Author: Emmanuelle Leize-Wagner, Philippe N. Bertin, Lisa Gil, Frédéric Plewniak, Farid Bensalah, Annela Semai, Céline Lopez-Roques, Céline Vandecasteele, Armelle Charrié-Duhaut, Amalia Sayeh, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université d'Oran 1 Ahmed Ben Bella [Oran], Chimie de la matière complexe (CMC), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CNRS national program EC2CO-MicrobiEn: DMO/DMA project, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Aromatic hydrocarbon catabolism, Serratia, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Microbiology, Total petroleum hydrocarbons (TPH), 03 medical and health sciences, Bioremediation, Dioxygenase, RNA, Ribosomal, 16S, Food science, Molecular Biology, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Strain (chemistry), 030306 microbiology, Biofilm, Biosurfactant, General Medicine, biology.organism_classification, 16S ribosomal RNA, Hydrocarbons, 6. Clean water, Biodegradation, Environmental, Petroleum, Hydrocarbon, chemistry, 13. Climate action, Algeria, Biofilms, n-alkanes, Bacteria
Abstract: A novel bacterial strain was isolated from industrially contaminated waste water. In the presence of crude oil, this strain was shown to reduce the rate of total petroleum hydrocarbons (TPH) up to 97.10% in 24 h. This bacterium was subsequently identified by 16S rRNA gene sequence analysis and affiliated to the Serratia genus by the RDP classifier. Its genome was sequenced and annotated, and genes coding for catechol 1,2 dioxygenase and naphthalene 1,2-dioxygenase system involved in aromatic hydrocarbon catabolism, and LadA-type monooxygenases involved in alkane degradation, were identified. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of crude oil after biological treatment showed that Serratia sp. Tan611 strain was able to degrade n-alkanes (from C-13 to C-25). This bacterium was also shown to produce a biosurfactant, the emulsification index (E24) reaching 43.47% and 65.22%, against vegetable and crude oil, respectively. Finally, the formation of a biofilm was increased in the presence of crude oil. These observations make Serratia sp. Tan611 a good candidate for hydrocarbon bioremediation.
Published: 2021

2. In situ metabolic activities of uncultivated Ferrovum sp. CARN8 evidenced by metatranscriptomic analysis

Author: Odile Bruneel, Frédéric Plewniak, Denis Le Paslier, Marina Héry, Philippe N. Bertin, Sandrine Koechler, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microorganism, Population, Respiratory chain, Microbiology, Genome, In situ metabolism, 03 medical and health sciences, Bacterial Proteins, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Ammonium Compounds, education, Molecular Biology, Gene, 030304 developmental biology, 0303 health sciences, education.field_of_study, Sewage, Metagenome assembled genome, biology, 030306 microbiology, Betaproteobacteria, Nitrogenase, Gene Expression Regulation, Bacterial, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 6. Clean water, Biochemistry, Nitrogen fixation, Metagenomics, Gene expression, Transcriptome, Bacteria
Abstract: International audience; Amongst iron-oxidizing bacteria playing a key role in the natural attenuation of arsenic in acid mine drainages (AMDs), members of the Ferrovum genus were identified in mine effluent or water treatment plants, and were shown to dominate biogenic precipitates in field pilot experiments. In order to address the question of the in situ activity of the uncultivated Ferrovum sp. CARN8 strain in the Carnoul es AMD, we assembled its genome using metagenomic and metatranscriptomic sequences and we determined standardized expression values for protein-encoding genes. Our results showed that this microorganism was indeed metabolically active and allowed us to sketch out its metabolic activity in its natural environment. Expression of genes related to the respiratory chain and carbon fixation suggests aerobic energy production coupled to ferrous iron oxidation and chemolithoautotrophic growth. Notwithstanding the presence of nitrogenase genes in its genome, expression data also indicated that Ferrovum sp. CARN8 relied on ammonium import rather than nitrogen fixation. The expression of flagellum and chemotaxis genes hints that at least a proportion of this strain population was motile. Finally, apart from some genes related to metal resistance showing surprisingly low expression values, genes involved in stress response were well expressed as expected in AMDs.
Published: 2020

3. Complete Genome Sequence of Microbacterium sp. Strain Nx66, Isolated from Waters Contaminated with Petrochemicals in El Saf-Saf Valley, Algeria

Author: Philippe N. Bertin, Frédéric Plewniak, Benoît Jaulhac, Nardjess Chéraiti, Ludivine Malherbe, Mourad Bensouilah, Céline Vandecasteele, Salima Tighidet, Pierre H. Boyer, Amalia Sayeh, Lisa Gil, Yosr Memmi, Laurence Zilliox, Céline Lopez-Roques, Laboratoire d'Ecobiologie des Milieux Marins et Littoraux, Université Badji Mokhtar - Annaba [Annaba] (UBMA), Laboratoire de Génétique Moléculaire [CHRU Strasbourg], CHRU Strasbourg, Laboratoire de Microbiologie Appliquée, Université Abderrahmane Mira [Béjaïa], Université Mohamed Akli Ouelhadj de Bouira (UMAOB), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées et de Technologies, Centre National de Référence Borréliose, Laboratoire de Bactériologie, CHRU Strasbourg-CHRU Strasbourg, DMO/DMA project - CNRS national program EC2CO-MicrobiEn French National Research Agency (ANR)ANR-10-INBS-09, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Whole genome sequencing, 0303 health sciences, Strain (chemistry), Genome Sequences, 0206 medical engineering, Illumina miseq, 02 engineering and technology, Biology, Genome, 6. Clean water, Microbacterium sp, 03 medical and health sciences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Immunology and Microbiology (miscellaneous), Botany, Genetics, Nanopore sequencing, Molecular Biology, 020602 bioinformatics, 030304 developmental biology
Abstract: Microbacterium sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42 Mb and one plasmid of 34.22 kb.
Published: 2020

4. Microorganisms and metals: a love-hate relationship?

Author: Philippe N. Bertin
Subjects: Psychoanalysis, Bacteria, Bacterial Proteins, Metals, Love–hate relationship, Biological Transport, General Medicine, Biology, Carrier Proteins, Molecular Biology, Microbiology, Introductory Journal Article
Published: 2020

5. 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

6. 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

7. Proteomic tools to decipher microbial community structure and functioning

Author: Philippe N. Bertin, Christine Carapito, and Florence Arsène-Ploetze
Subjects: Proteomics, Proteome, Health, Toxicology and Mutagenesis, Quantitative proteomics, Community proteomics, Computational biology, Biology, LC-SRM, Bioinformatics, Bacterial protein, 03 medical and health sciences, Metaproteomics, Bacterial Proteins, Microbial ecology, Environmental Microbiology, Animals, Humans, Environmental Chemistry, Microbial Ecology of the Continental and Coastal Environments, Targeted proteomics, 030304 developmental biology, 0303 health sciences, Mass spectrometry, 030306 microbiology, Microbiota, General Medicine, Pollution, Microbial population biology, Metagenomics, Microbial Interactions, DECIPHER
Abstract: Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.
Published: 2014

8. Erratum to: Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans

Author: Odile Sismeiro, Florence Goulhen-Chollet, Philippe N. Bertin, Caroline Proux, Florence Hommais, Sandrine Koechler, Florence Arsène-Ploetze, Jean-Yves Coppé, Didier Lièvremont, Marie-Agnès Dillies, Jessica Cleiss-Arnold, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Chromatine et Régulation de la Pathogénie bactérienne (CRP), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Dynamique, évolution et expression de génomes de microorganismes (DEEGM), and Rodrigue, Agnès
Subjects: 0301 basic medicine, Microbiology (medical), Transcription, Genetic, Arsenites, [SDV]Life Sciences [q-bio], 030106 microbiology, Arsenite oxidase, Molecular Sequence Data, lcsh:QR1-502, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Bacterial Proteins, Oxalobacteraceae, Gene expression, Operon, Amino Acid Sequence, Herminiimonas arsenicoxydans, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, biology, Base Sequence, Gene Expression Profiling, Quorum Sensing, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Gene Expression Regulation, Bacterial, biology.organism_classification, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Parasitology, Genes, Bacterial, Mutation, Erratum, Oxidoreductases, Sequence Alignment, Metabolic Networks and Pathways, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism.In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (sigma54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 sigma54-dependent promoter motif was identified upstream of aoxAB coding sequences.These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.
Published: 2017

9. 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

10. 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

11. 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

12. 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

13. 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

14. Contributions of Descriptive and Functional Genomics to Microbial Ecology

Author: Philippe Normand, Valérie Michotey, Philippe N. Bertin, Orange Labs [Cesson-Sévigné], Orange Labs, MEB, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-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-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), Jean-Claude Bertrand, Pierre Caumette, Philippe Lebaron, Robert Matheron, Philippe Normand, Télesphore Sime-Ngando, Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), 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), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), and 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)
Subjects: 0303 health sciences, 030306 microbiology, Ecology, Ecology (disciplines), [SDV]Life Sciences [q-bio], Genomics, Computational biology, Biology, Proteomics, Genome, 03 medical and health sciences, Metabolomics, Microbial ecology, Metagenomics, Functional genomics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: Originally, “genomics” was used only to describe a scientific discipline which consisted in mapping, sequencing, and analyzing genomes. Nowadays, this term is widely used by a growing number of people in a broader sense to describe global techniques for studying genomes including from a functional point of view. These include the analysis of messenger RNAs (transcriptomics), protein contents (proteomics), and metabolites (metabolomics). At a higher level of complexity, it also describes the so-called “meta” approaches that allow to investigate the ecology of microbial communities, including uncultured microorganisms. Based on the use of recent technological developments, the numerous examples provide an integrated view of how microorganisms adapt to particular ecological niches and participate in the dynamics of ecosystems.
Published: 2015

15. 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

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

Author: Philippe N. Bertin, Daniel Muller, Didier Lièvremont, Philippe Riegel, Diliana D. Simeonova, Sandrine Koechler, Marie-Claire Lett, Sophie Mangenot, Génétique moléculaire, génomique, microbiologie (GMGM), and Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Oxidation-Reduction, MESH: Genome, Bacterial, MESH: Nucleic Acid Hybridization, chemistry.chemical_compound, RNA, Ribosomal, 16S, Herminiimonas arsenicoxydans, MESH: Phylogeny, MESH: RNA, Ribosoma, Phylogeny, Betaproteobacteria, Arsenite, 0303 health sciences, Sewage, biology, Fatty Acids, Nucleic Acid Hybridization, Herminiimonas, General Medicine, Catalase, Aerobiosis, 6. Clean water, MESH: Fatty Acids, RNA, Bacterial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Nitrates, Herminiimonas aquatilis, MESH: Arsenites, MESH: RNA, Bacterial, Oxidoreductases, Oxidation-Reduction, DNA, Bacterial, Arsenites, MESH: Oxalobacteraceae, Molecular Sequence Data, Microbiology, 03 medical and health sciences, Species Specificity, MESH: Aerobiosis, MESH: Catalase, Oxalobacteraceae, MESH: Oxidoreductases, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Molecular Sequence Data, Nitrates, 030306 microbiology, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, MESH: DNA, Bacterial, Culture Media, chemistry, MESH: Culture Media, Genome, Bacterial, Bacteria
Abstract: An arsenite-oxidizing bacterium, designated strain ULPAs1T, was isolated from industrial sludge heavily contaminated with arsenic. Cells of this isolate were Gram-negative, curved rods, motile by means of a polar flagellum. The strain was positive for oxidase and catalase activities, was able to reduce nitrate to nitrite, used acetate, lactate and peptone as organic carbon sources under aerobic conditions and was able to oxidize arsenite (As[III]) to arsenate (As[V]). 16S rRNA gene sequence analysis and the absence of dodecanoic fatty acids suggested that this strain represents a member of the genusHerminiimonasof the familyOxalobacteraceae, orderBurkholderialesin theBetaproteobacteria. Genomic DNA–DNA hybridization between strain ULPAs1TandHerminiimonas fonticolaS-94Tand between strain ULPAs1TandHerminiimonas aquatilisCCUG 36956Trevealed levels of relatedness of T(=CCM 7303T=DSM 17148T=LMG 22961T) is the type strain of a novel species ofHerminiimonas, for which the nameHerminiimonas arsenicoxydanssp. nov. is proposed.
Published: 2006

17. DNA bridging: a property shared among H-NS-like proteins

Author: Philippe N. Bertin, Rolf Wagner, Gijs J.L. Wuite, Martijn S. Luijsterburg, Evelyne Krin, Remus T. Dame, and Physics of Living Systems
Subjects: DNA, Bacterial, Plasma protein binding, Biology, medicine.disease_cause, Microscopy, Atomic Force, Microbiology, DNA-binding protein, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Consensus Sequence, Consensus sequence, medicine, Molecular Biology, Escherichia coli, Escherichia coli Proteins, biology.organism_classification, Chromatin, DNA-Binding Proteins, chemistry, Biochemistry, Trans-Activators, DNA, Bacteria, Molecular Chaperones, Protein Binding
Abstract: The nucleoid-associated protein H-NS is thought to play an essential role in the organization of bacterial chromatin in Escherichia coli . Homologues, often with very low sequence identity, are found in most gram-negative bacteria. Microscopic analysis reveals that, despite limited sequence identity, their structural organization results in similar DNA binding properties.
Published: 2005

18. H-NS in Gram-negative bacteria: a family of multifaceted proteins

Author: Philippe N. Bertin and Christian Tendeng
Subjects: Microbiology (medical), Mutation, Gram-negative bacteria, biology, Structural gene, biology.organism_classification, medicine.disease_cause, Microbiology, DNA-binding protein, Phenotype, DNA-Binding Proteins, Evolution, Molecular, Infectious Diseases, Bacterial Proteins, Virology, Gram-Negative Bacteria, Gene expression, medicine, Escherichia coli, Bacteria, Forecasting
Abstract: DNA-packaging and the control of gene expression constitute a major challenge for bacteria to survive and adapt to environmental changes. The use of multiple strategies to solve these problems could explain the presence of various nucleoid-associated proteins in bacteria. H-NS, one of these proteins, has been extensively studied in Escherichia coli, and a variety of phenotypes have been associated with a mutation in its structural gene. However, the role of H-NS in bacterial physiology and its mechanism of action are still a matter of debate. The expanding number of H-NS-related proteins identified in Gram-negative bacteria reveals interesting clues about their structure-function-evolution relationship.
Published: 2003

19. Transcription Regulation Coupling of the Divergent argG and metY Promoters in Escherichia coli K-12

Author: Philippe N. Bertin, Evelyne Krin, Annie Kolb, Christine Laurent-Winter, and Antoine Danchin
Subjects: Cyclic AMP Receptor Protein, Saccharomyces cerevisiae Proteins, Transcription, Genetic, Arginine, Carbon-Oxygen Lyases, Molecular Sequence Data, Regulator, Repressor, Genetics and Molecular Biology, Argininosuccinate Synthase, Biology, Microbiology, Eukaryotic translation, Bacterial Proteins, Multienzyme Complexes, Transcription (biology), Escherichia coli, Transcriptional regulation, Amino Acid Sequence, Promoter Regions, Genetic, Molecular Biology, Regulation of gene expression, Cysteine Synthase, Binding Sites, Base Sequence, Escherichia coli Proteins, Promoter, Gene Expression Regulation, Bacterial, Repressor Proteins, Biochemistry, Mutation
Abstract: The cAMP-catabolite activator protein (CAP) complex is a pleiotropic regulator that regulates a vast number of Escherichia coli genes, including those involved in carbon metabolism. We identified two new targets of this complex: argG , which encodes the arginosuccinate synthase involved in the arginine biosynthetic pathway, and metY , which encodes one of the two methionine tRNA initiators, tRNAf2Met. The cAMP-CAP complex activates argG transcription and inhibits metY transcription from the same DNA position. We also show that ArgR, the specific repressor of the arginine biosynthetic pathway, together with its arginine cofactor, acts on the regulation of metY mediated by CAP. The regulation of the two divergent promoters is thus simultaneously controlled not only by the cAMP-CAP complex, a global regulator, but also by a specific regulator of arginine metabolism, suggesting a previously unsuspected link between carbon metabolism and translation initiation.
Published: 2003

20. A Novel H-NS-like Protein from an Antarctic Psychrophilic Bacterium Reveals a Crucial Role for the N-terminal Domain in Thermal Stability

Author: Antoine Danchin, Antoine Marin, Philippe N. Bertin, Christian Tendeng, Evelyne Krin, and Olga Soutourina
Subjects: Circular dichroism, Hot Temperature, Protein family, Molecular Sequence Data, Antarctic Regions, Rhodobacter sphaeroides, medicine.disease_cause, Biochemistry, Protein Structure, Secondary, Rhodobacter capsulatus, Structure-Activity Relationship, Bacterial Proteins, Drug Stability, Escherichia coli, medicine, Amino Acid Sequence, Psychrobacter, Psychrophile, Molecular Biology, Peptide sequence, Protein secondary structure, Rhodobacter, Acinetobacter, biology, Circular Dichroism, DNA, Cell Biology, biology.organism_classification, Cold Temperature, DNA-Binding Proteins, Siberia, Dimerization, Sequence Alignment, Gammaproteobacteria
Abstract: We describe here new members of the H-NS protein family identified in a psychrotrophic Acinetobacter spp. bacterium collected in Siberia and in a psychrophilic Psychrobacter spp. bacterium collected in Antarctica. Both are phylogenetically closely related to the HvrA and SPB Rhodobacter transcriptional regulators. Their amino acid sequence shares 40% identity, and their predicted secondary structure displays a structural and functional organization in two modules similar to that of H-NS in Escherichia coli. Remarkably, the Acinetobacter protein fully restores to the wild-type H-NS-dependent phenotypes, whereas the Psychrobacter protein is no longer able to reverse the effects of H-NS deficiency in an E. coli mutant strain above 30 degrees C. Moreover, in vitro experiments demonstrate that the ability of the Psychrobacter H-NS protein to bind curved DNA and to form dimers is altered at 37 degrees C. The construction of hybrid proteins containing the N- or the C-terminal part of E. coli H-NS fused to the C- or N-terminal part of the Psychrobacter protein demonstrates the role of the N-terminal domain in this process. Finally, circular dichroism analysis of purified H-NS proteins suggests that, as compared with the E. coli and Acinetobacter proteins, the alpha-helical domain displays weaker intermolecular interactions in the Psychrobacter protein, which may account for the low thermal stability observed at 37 degrees C.
Published: 2003

21. Recent advances in microbiology: towards new horizons?

Author: Philippe N. Bertin
Subjects: New horizons, Research, Environmental Microbiology, Genomics, General Medicine, Biology, Molecular Biology, Microbiology
Published: 2015

22. Identification, Characterization, and Regulation of a Cluster of Genes Involved in Carbapenem Biosynthesis in Photorhabdus luminescens

Author: Philippe N. Bertin, Antoine Danchin, Frank Kunst, Sylviane Derzelle, and Eric Duchaud
Subjects: Operon, Molecular Sequence Data, Mutagenesis (molecular biology technique), Genetics and Molecular Biology, Applied Microbiology and Biotechnology, Genome, Microbiology, Bacterial Proteins, Photorhabdus luminescens, Antibiosis, Gram-Negative Bacteria, Gene, Base Sequence, Ecology, biology, Gene Expression Regulation, Bacterial, biology.organism_classification, Culture Media, Carbon-Sulfur Lyases, Quorum sensing, Carbapenems, Multigene Family, bacteria, Autoinducer, Photorhabdus, human activities, Transcription Factors, Food Science, Biotechnology
Abstract: The luminescent entomopathogenic bacterium Photorhabdus luminescens produces several yet-uncharacterized broad-spectrum antibiotics. We report the identification and characterization of a cluster of eight genes (named cpmA to cpmH ) responsible for the production of a carbapenem-like antibiotic in strain TT01 of P. luminescens . The cpm cluster differs in several crucial aspects from other car operons. The level of cpm mRNA peaks during exponential phase and is regulated by a Rap/Hor homolog identified in the P. luminescens genome. Marker-exchange mutagenesis of this gene in the entomopathogen decreased antibiotic production. The luxS -like signaling mechanism of quorum sensing also plays a role in the regulation of the cpm operon. Indeed, luxS , which is involved in the production of a newly identified autoinducer, is responsible for repression of cpm gene expression at the end of the exponential growth phase. The importance of this carbapenem production in the ecology of P. luminescens is discussed.
Published: 2002

23. Analyse globale des transcrits

Author: Florence Hommais and Philippe N. Bertin
Subjects: General Medicine, Biology, Microbiology, Molecular biology, Analysis method
Abstract: Resume Au cours des quinze dernieres annees, le developpement considerable du sequencage de l'ADN genomique a permis la publication, des 1995, des premiers genomes complets de microorganismes procaryotes [8] et de celui de la levure Saccharomyces cerevisiae [13]. Pour la premiere fois, les scientifiques ont eu acces a l'ensemble des elements permettant l'elaboration et le fonctionnement d'une cellule. En consequence, l'utilisation de methodes d'analyse globale encore appelees « analyse a grande echelle a s'est largement accrue [15]. Ainsi, au lieu d'etudier les genes ou les proteines individuellement, les profils des organismes peuvent maintenant etre dresses dans leur integralite. En particulier, l'analyse de l'ensemble des transcrits d'une cellule ou « transcriptome a [34] permet de quantifier simultanement l'expression des genes dans une cellule entiere [23]. Grâce a ces nouvelles donnees, la comprehension des reseaux de regulation dans la cellule et/ou l'etude de la variabilite genetique trouvent un nouvel essor. Au stade actuel, il nous parait important de faire le point sur les applications potentielles et les avancees technologiques de cette approche novatrice.
Published: 2002

24. 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

25. Isolation and Characterization of vicH , Encoding a New Pleiotropic Regulator in Vibrio cholerae

Author: Christian Tendeng, Sylvie Rimsky, Cyril Badaut, Pierre Gounon, Evelyne Krin, Saravuth Ngo, Antoine Danchin, and Philippe N. Bertin
Subjects: Molecular Sequence Data, Virulence, Genetics and Molecular Biology, Cross Reactions, Flagellum, Biology, medicine.disease_cause, Microbiology, Bacterial Proteins, Glucosides, Genes, Regulator, Escherichia coli, medicine, Genomic library, Amino Acid Sequence, RNA, Messenger, Cloning, Molecular, Promoter Regions, Genetic, Vibrio cholerae, Molecular Biology, Gene, Benzyl Alcohols, Genetics, Base Sequence, Genetic Complementation Test, Polysaccharides, Bacterial, Gene Expression Regulation, Bacterial, biology.organism_classification, Cold Temperature, DNA-Binding Proteins, Complementation, RNA, Bacterial, Phenotype, Genes, Bacterial, Salmonella enterica, Mutation, Sequence Alignment
Abstract: During the last decade, the hns gene and its product, the H-NS protein, have been extensively studied in Escherichia coli . H-NS-like proteins seem to be widespread in gram-negative bacteria. However, unlike in E. coli and in Salmonella enterica serovar Typhimurium, little is known about their role in the physiology of those organisms. In this report, we describe the isolation of vicH , an hns -like gene in Vibrio cholerae , the etiological agent of cholera. This gene was isolated from a V. cholerae genomic library by complementation of different phenotypes associated with an hns mutation in E. coli . It encodes a 135-amino-acid protein showing approximately 50% identity with both H-NS and StpA in E. coli . Despite a low amino acid conservation in the N-terminal part, VicH is able to cross-react with anti-H-NS antibodies and to form oligomers in vitro. The vicH gene is expressed as a single gene from two promoters in tandem and is induced by cold shock. A V. cholerae wild-type strain expressing a vicHΔ92 gene lacking its 3′ end shows pleiotropic alterations with regard to mucoidy and salicin metabolism. Moreover, this strain is unable to swarm on semisolid medium. Similarly, overexpression of the vicH wild-type gene results in an alteration of swarming behavior. This suggests that VicH could be involved in the virulence process in V. cholerae , in particular by affecting flagellum biosynthesis.
Published: 2000

26. Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125

Author: Zoé Rouy, David Vallenet, Andreas Bernsel, Christine Ho, Evelyne Krin, Claudine Médigue, Angela Duilio, Gennaro Marino, Agnieszka Sekowska, Valérie Barbe, Géraldine Pascal, Antoine Danchin, Maria Luisa Tutino, Philippe N. Bertin, Eduardo P. C. Rocha, Georges Feller, Gunnar von Heijne, Johan Nilsson, Frankie Cheung, Sophie Mangenot, Stéphane Cruveiller, Salvino D'Amico, Ermenegilda Parrilli, Gang Fang, Claudine, Mdigue, Evelyne, Krin, Graldine, Pascal, Valrie, Barbe, Andreas, Bernse, PHILIPPE N., Bertin, Frankie, Cheung, Stphane, Cruveiller, Salvino, D'Amico, Duilio, Angela, Gang, Fang, Georges, Feller, Christine, Ho, Sophie, Mangenot, Marino, Gennaro, Johan, Nilsson, Parrilli, Ermenegilda, EDUARDO P. C., Rocha, Zo, Rouy, Agnieszka, Sekowska, Tutino, MARIA LUISA, David, Vallenet, GUNNAR VON, Heijne, and Antoine, Danchin
Subjects: Proteome, Molecular Sequence Data, Origin of replication, Genome, Pseudoalteromonas haloplanktis, Genetics, Antarctic bacterium, Asparagine, Psychrophile, Genetics (clinical), chemistry.chemical_classification, biology, Articles, Free Radical Scavengers, biology.organism_classification, Adaptation, Physiological, Amino acid, Cold Temperature, Pseudoalteromonas, RNA, Bacterial, Biochemistry, chemistry, Pseusoalteromonas haloplankti, Reactive Oxygen Species, Bacteria, Genome, Bacterial
Abstract: A considerable fraction of life develops in the sea at temperatures lower than 15°C. Little is known about the adaptive features selected under those conditions. We present the analysis of the genome sequence of the fast growing Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. We find that it copes with the increased solubility of oxygen at low temperature by multiplying dioxygen scavenging while deleting whole pathways producing reactive oxygen species. Dioxygen-consuming lipid desaturases achieve both protection against oxygen and synthesis of lipids making the membrane fluid. A remarkable strategy for avoidance of reactive oxygen species generation is developed by P. haloplanktis, with elimination of the ubiquitous molybdopterin-dependent metabolism. The P. haloplanktis proteome reveals a concerted amino acid usage bias specific to psychrophiles, consistently appearing apt to accommodate asparagine, a residue prone to make proteins age. Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome.
Published: 2005

27. 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

28. 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

29. Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5T

Author: Benoit Vacherie, Alain Dolla, Philippe N. Bertin, Claudine Médigue, Agnès Hirschler-Réa, Bernard Ollivier, Odile Valette, Marie-Laure Fardeau, Valérie Barbe, Oulfat Amin, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie et Biotechnologie des Environements Chauds (MICROBIOTECH), Université de Provence - Aix-Marseille 1, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, 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), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Interactions et Modulateurs de Réponses (IMR), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genetics, Whole genome sequencing, 0303 health sciences, Hot spring, Desulfotomaculum hydrothermale, biology, 030306 microbiology, biology.organism_classification, C content, Genome, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, chemistry, Prokaryotes, Sulfate, Molecular Biology, Bacteria, 030304 developmental biology
Abstract: Here, we report the draft genome sequence of Desulfotomaculum hydrothermale , a sulfate-reducing, spore-forming bacterium isolated from a Tunisian hot spring. The genome is composed of 2.7 Mb, with a G+C content of 49.48%, and it contains 2,643 protein-coding sequences.
Published: 2013

30. 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

31. Complete Genome Sequence of the Piezophilic, Mesophilic, Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13(T.)

Author: Valérie Barbe, Benoit Vacherie, Bernard Ollivier, Boyang Ji, Didier Alazard, Marie-Laure Fardeau, Zoé Rouy, Sabine Leroy, Philippe N. Bertin, Gregory Gimenez, Alain Dolla, Nathalie Pradel, Amira Amrani, Emmanuel Talla, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-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), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie et Biotechnologie des Environements Chauds (MICROBIOTECH), Université de Provence - Aix-Marseille 1, Orange Labs [Cesson-Sévigné], Orange Labs, Institut TELECOM/TELECOM Lille1, Institut Mines-Télécom [Paris] (IMT), Department of Chemistry, University of Ngaoundéré, Interactions et Modulateurs de Réponses (IMR), Centre National de la Recherche Scientifique (CNRS), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Département de Chimie [Univ Ngaoundéré] (UN-FS), Faculté de Sciences [Univ Ngaoundéré] (UN-FS), Université de Ngaoundéré/University of Ngaoundéré [Cameroun] (UN)-Université de Ngaoundéré/University of Ngaoundéré [Cameroun] (UN), Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes ( URMITE ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR48, INSB-INSB-Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), CEA/DSV/FAR/IG/Genoscope Laboratoire de Génomique Comparative, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Microbiologie et Biotechnologie des Environements Chauds ( MICROBIOTECH ), Institut Mines-Télécom [Paris], University of Ngaoundere, Interactions et Modulateurs de Réponses ( IMR ), Centre National de la Recherche Scientifique ( CNRS ), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: Chimie analytique, méthode d'analyse, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Plasmid, séquençage, Genetics, PHYLOGENIE, échantillon, 14. Life underwater, Prokaryotes, BACTERIE MESOPHILE, Sulfate, Molecular Biology, 030304 developmental biology, bactérie, Whole genome sequencing, 0303 health sciences, SULFATOREDUCTION, acide gras, biology, 030306 microbiology, génome, Desulfovibrio hydrothermalis, biology.organism_classification, GENE, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, STRUCTURE GENETIQUE, chemistry, SEQUENCAGE, Analytical chemistry, Bacteria, Mesophile
Abstract: Desulfovibrio hydrothermalis AM13 T is a piezophilic, mesophilic, hydrogenotrophic sulfate-reducing bacterium collected from a deep-sea hydrothermal chimney on the East Pacific Rise (2,600 m depth, 13°N). We report the genome sequence of this bacterium, which includes a 3,702,934-bp chromosome and a circular plasmid of 5,328 bp.
Published: 2013

32. The First Genomic and Proteomic Characterization of a Deep-Sea Sulfate Reducer: Insights into the Piezophilic Lifestyle of Desulfovibrio piezophilus

Author: Matthieu Pophillat, Patricia Lenoble, Emmanuel Talla, Boyang Ji, Gregory Gimenez, Marc Garel, Alain Dolla, Nathalie Pradel, Régine Lebrun, Yann Denis, Valérie Barbe, Patrick Fourquet, Philippe N. Bertin, Bernard Ollivier, Christian Tamburini, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), MEB, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche en Biologie et Epidémiologie Parasitaires, Institut de Médecine Tropicale du Service de Santé des Armées-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)-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 d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Microbiologie de la Méditerranée (IMM), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -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 Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, Proteome, Hydrostatic pressure, lcsh:Medicine, Outer membrane proteins, Biochemistry, Microbial Physiology, Aspartic acid, Asparagine, Amino Acids, lcsh:Science, Alanine, chemistry.chemical_classification, Genetics, 0303 health sciences, Multidisciplinary, Sulfates, Genomics, Adaptation, Physiological, Lipids, Functional Genomics, Amino acid, Atmospheric Pressure, Multigene Family, Desulfovibrio, Biological transport, Oxidation-Reduction, Research Article, Oceans and Seas, Marine Biology, Biology, Biosynthesis, Microbiology, Microbial Ecology, 03 medical and health sciences, Extremophiles, Protein metabolism, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Pressure, 14. Life underwater, 030304 developmental biology, Comparative genomics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 030306 microbiology, lcsh:R, Proteins, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, chemistry, lcsh:Q, Energy Metabolism, Protein Abundance
Abstract: Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle.
Published: 2013

33. Role of polyadenylation in regulation of the flagella cascade and motility in Escherichia coli

Author: Laurence Lemelle, Céline Gracia, Philippe Hamman, Alexandre Maes, Dominique Bréchemier, Philippe N. Bertin, Elodie Chatre, and Eliane Hajnsdorf
Subjects: Membrane permeability, Polyadenylation, Transcription, Genetic, Mutant, Sigma Factor, Flagellum, medicine.disease_cause, Biochemistry, Microbiology, Bacterial Proteins, Transcription (biology), Vancomycin, Gene expression, medicine, Escherichia coli, Promoter Regions, Genetic, biology, Escherichia coli Proteins, Polynucleotide Adenylyltransferase, General Medicine, Gene Expression Regulation, Bacterial, Cell biology, Anti-Bacterial Agents, Flagella, Mutation, biology.protein, Trans-Activators, Flagellin
Abstract: Polyadenylation is recognized as part of a surveillance machinery for eliminating defective RNA molecules in eukaryotes and prokaryotes. Escherichia coli strains, deficient in poly(A)polymerase I (PAP I), expressed less flagellin compared to wild-type strains. Because flagellin synthesis is a late step in the flagellar biosynthesis pathway, we assessed the role of PAP I in this cascade and in flagella function. Transcription of flhDC, fliA, and fliC was decreased in the PAP I mutant. These results provide evidence that polyadenylation positively controls the expression of genes belonging to the flagellar biosynthesis pathway and that this effect is mediated through the FlhDC master regulator. However, the downshift in flagella gene expression in the mutant strain did not provoke any noticeable defects in the synthesis of flagella, in biofilm formation and in swimming speed although there was a reduction in motility on soft agar. Our data support an alternative hypothesis that the reduced motility of the mutant resulted from an alteration of the cell membrane composition caused in part by the higher level of GlmS (Glucosamine-6P synthase) which accumulates in the mutant. In agreement with this hypothesis the mutant is more sensitive to hydrophobic agents and antibiotics and in particular to vancomycin. We propose that PAP I participates in the ability of the bacteria to adapt to and survive detrimental conditions by constantly monitoring and adjusting to its environment.
Published: 2012

34. In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis

Author: Philippe N. Bertin, Jérôme Hamelin, Dimitri Heintz, Christine Carapito, Corinne Casiot, Guillaume Tcherkez, Sebastien Gallien, Christine Schaeffer, Florence Goulhen-Chollet, Alain Van Dorsselaer, Françoise Gilard, Florence Arsène-Ploetze, David Halter, Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Université Montpellier 2 - Sciences et Techniques (UM2), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Biologie des Plantes (IBP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche [ANR 07-BLANC-0118], French Ministry of Education and Research, and ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007)
Subjects: Metabolite, [SDV]Life Sciences [q-bio], Biology, Photosynthesis, medicine.disease_cause, Microbiology, Euglena, Mining, 03 medical and health sciences, chemistry.chemical_compound, Metabolomics, proteomics, Botany, parasitic diseases, medicine, Organic matter, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Ecosystem, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, 030306 microbiology, Aquatic ecosystem, fungi, Euglena mutabilis, Protist, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Metabolism, 15. Life on land, biology.organism_classification, chemistry, [SDE]Environmental Sciences, Original Article, France, Acids, primary production
Abstract: International audience; Euglena mutabilis is a photosynthetic protist found in acidic aquatic environments such as peat bogs, volcanic lakes and acid mine drainages (AMDs). Through its photosynthetic metabolism, this protist is supposed to have an important role in primary production in such oligotrophic ecosystems. Nevertheless, the exact contribution of E. mutabilis in organic matter synthesis remains unclear and no evidence of metabolite secretion by this protist has been established so far. Here we combined in situ proteo-metabolomic approaches to determine the nature of the metabolites accumulated by this protist or potentially secreted into an AMD. Our results revealed that the secreted metabolites are represented by a large number of amino acids, polyamine compounds, urea and some sugars but no fatty acids, suggesting a selective organic matter contribution in this ecosystem. Such a production may have a crucial impact on the bacterial community present on the study site, as it has been suggested previously that prokaryotes transport and recycle in situ most of the metabolites secreted by E. mutabilis. Consequently, this protist may have an indirect but important role in AMD ecosystems but also in other ecological niches often described as nitrogen-limited.
Published: 2012

35. Proteomics as a Tool for the Characterization of Microbial Isolates and Complex Communities

Author: Philippe N. Bertin, Florence Arsène-Ploetze, Christine Carapito, and Frédéric Plewniak
Subjects: Three-domain system, Proteome, Aucun, Genomics, Computational biology, Biology, Adaptation, Proteomics, Bioinformatics, Gene, Genome, Organism
Abstract: Proteins may be considered as the main effectors of biological responses of organisms to specific environmental conditions, instead of messenger RNAs. Indeed, a modulation in their activity does not always depend on a modified expression of the corresponding genes but rather on post-translational modifications. Proteome analysis may therefore constitute an appropriate approach to address the question of organism adaptation to environmental stresses or growth under extreme conditions. Recently, the knowledge of the organisms’ physiology has led to deep changes in the investigation methods, favouring the use of global analysis methods in complement with conventional strategies. Instead of studying individual proteins or metabolic products, the integral profile of organisms can now be established. This may be of importance when studying adaptive and stress responses in microorganisms because of their multifactorial character. In particular, the differential analysis in various growth conditions of the whole protein content (« proteome »), which allows the simultaneous quantification of gene products in an organism, represents part of the so-called integrative biology (Bertin et al., 2008). Genomics is a conceptual approach that aims to study the biology of microorganisms by analysing the complete genetic information they contain. This scientific discipline really emerged more than fifteen years ago with the characterization of the first complete genome of autonomous organisms (Bertin et al., 2008). An important reduction of sequencing costs associated with new high-throughput technologies has led to an explosion of genomic programs that now concern organisms in all domains of life (http://www.genomeonline.org). Most of the descriptive and functional genomic efforts initially focused on human pathogens, such as bacteria and parasites, and next, on higher eukaryotes. More recently, there has been a growing interest in microorganisms isolated from various habitats, including extreme ecological niches, to characterize specific properties that allow these organisms to grow in such environments. The field of application of proteomics thus expended in line with genomics. These works should lead not only to a
Published: 2012

36. 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

37. 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

38. Subinhibitory Arsenite Concentrations Lead to Population Dispersal in Thiomonas sp

Author: Romain Briandet, Philippe N. Bertin, Marie Marchal, David Halter, Michael Dubow, Marie-Claire Lett, Sandrine Koechler, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microorganism, Applied Microbiology, Microbial metabolism, Colony Count, Microbial, lcsh:Medicine, biofilm, chemistry.chemical_compound, stress, viabilité, Nucleic Acids, Molecular Cell Biology, souche, Extreme environment, lcsh:Science, Arsenite, Cellular Stress Responses, 0303 health sciences, education.field_of_study, Multidisciplinary, tolerance, biology, Polysaccharides, Bacterial, Microbial Growth and Development, Thiomonas, Betaproteobacteria, Extracellular Matrix, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, bioremediation, metabolism, viability, strains, oxidation, cell, Research Article, Arsenites, Movement, Population, Microbiology, Microbial Ecology, 03 medical and health sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, métabolisme, Biology, 030304 developmental biology, 030306 microbiology, tolérance, lcsh:R, Biofilm, oxydation, biology.organism_classification, bioremédiation, chemistry, 13. Climate action, Biofilms, Biological dispersal, lcsh:Q, cellule
Abstract: International audience; Biofilms represent the most common microbial lifestyle, allowing the survival of microbial populations exposed to harsh environmental conditions. Here, we show that the biofilm development of a bacterial species belonging to the Thiomonas genus, frequently found in arsenic polluted sites and playing a key role in arsenic natural remediation, is markedly modified when exposed to subinhibitory doses of this toxic element. Indeed, arsenite [As(III)] exposure led to a considerable impact on biofilm maturation by strongly increasing the extracellular matrix synthesis and by promoting significant cell death and lysis within microcolonies. These events were followed by the development of complex 3D-biofilm structures and subsequently by the dispersal of remobilized cells observed inside the previously formed hollow voids. Our results demonstrate that this biofilm community responds to arsenite stress in a multimodal way, enhancing both survival and dispersal. Addressing this complex bacterial response to As(III) stress, which might be used by other microorganisms under various adverse conditions, may be essential to understand how Thiomonas strains persist in extreme environments.
Published: 2011

39. Unsuspected Diversity of Arsenite-Oxidizing Bacteria Revealed by a Widespread Distribution of the aoxB Gene in Prokaryotes

Author: Christophe Pagnout, Céline Brochier-Armanet, David Halter, Audrey Cordi, Elham Abbaszadeh-fard, Didier Montaut, Florence Arsène-Ploetze, Pascale Bauda, Philippe N. Bertin, Fabienne Séby, Audrey Heinrich-Salmeron, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-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), 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), 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), Ultra Traces Analyses Aquitaine (UT2A), and Ultra Traces Analyses Aquitaine
Subjects: DNA, Bacterial, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Arsenites, Sequence analysis, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Sequence Homology, 010501 environmental sciences, 01 natural sciences, Applied Microbiology and Biotechnology, Microbial Ecology, Bacterial genetics, 03 medical and health sciences, Phylogenetics, Environmental Microbiology, Cluster Analysis, Gene, Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0105 earth and related environmental sciences, Genetics, 0303 health sciences, Bacteria, Ecology, biology, Prokaryote, Sequence Analysis, DNA, biology.organism_classification, Archaea, DNA, Archaeal, Horizontal gene transfer, France, Oxidoreductases, Oxidation-Reduction, Food Science, Biotechnology
Abstract: In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity of aoxB genes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterial aoxB genes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading of aoxB in prokaryotic communities.
Published: 2011

40. 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

41. 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

42. 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

43. Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans

Author: Didier Lièvremont, Jessica Cleiss-Arnold, Philippe N. Bertin, Florence Arsène-Ploetze, Odile Sismeiro, Sandrine Koechler, Jean-Yves Coppée, Florence Hommais, Caroline Proux, Marie-Agnès Dillies, Florence Goulhen-Chollet, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris], Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Financial support came from the Centre National de la Recherche Scientifique, the Agence Nationale de la Recherche (ANR 07-BLAN-0118 project) and the Université de Strasbourg., ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007), and Institut Pasteur [Paris] (IP)
Subjects: Microbiology (medical), MESH: Operon, MESH: Mutation, Operon, MESH: Oxalobacteraceae, lcsh:QR1-502, MESH: Sequence Alignment, MESH: Amino Acid Sequence, MESH: Base Sequence, Microbiology, MESH: Quorum Sensing, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, MESH: Gene Expression Profiling, Sigma factor, Gene expression, Research article, MESH: Oxidoreductases, Herminiimonas arsenicoxydans, Gene, MESH: Bacterial Proteins, 030304 developmental biology, Arsenite, Genetics, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, MESH: Conserved Sequence, MESH: Molecular Sequence Data, biology, 030306 microbiology, MESH: Transcription, Genetic, biology.organism_classification, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, MESH: Metabolic Networks and Pathways, rpoN, Transposon mutagenesis, MESH: Arsenites, MESH: Genes, Bacterial
Abstract: Background Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism. Results In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (σ54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 σ54-dependent promoter motif was identified upstream of aoxAB coding sequences. Conclusion These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.
Published: 2010

44. Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data

Author: Christine Carapito, Michaël Heymann, Sandrine Koechler, Philippe N. Bertin, Evelyne Turlin, Claudine Médigue, Alain Van Dorsselaer, Valérie Kugler, Florence Arsène-Ploetze, Stéphanie Weiss, Stéphane Cruveiller, Magalie Stauffert, Jessica Cleiss, Jean-Yves Coppée, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-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), 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), Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris] (IP), 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 Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique, 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), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), 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 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), Compartimentation et dynamique cellulaires (CDC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-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), 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), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris], 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), and Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Proteomics, Proteome, Arsenites, Biology, Tandem mass spectrometry, Models, Biological, Biochemistry, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, Oxalobacteraceae, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Herminiimonas arsenicoxydans, 030304 developmental biology, Arsenite, Genetics, Gel electrophoresis, 0303 health sciences, 030306 microbiology, General Medicine, Genome project, biology.organism_classification, chemistry, Oxidation-Reduction, Genome, Bacterial
Abstract: International audience; The arsenite-oxidizing strain Herminiimonas arsenicoxydans proteome was investigated with gel electrophoresis and tandem mass spectrometry analyses. The comparison of experimental and theoretical M(r) and pI, as well as that of peptide sequences identified by MS and predicted protein sequences, allowed the correction of five protein annotations. More importantly, the functional analysis of SDS- and 2D-PAGE proteome maps obtained in the presence of arsenic, combined with partial transcriptomic results indicate that H. arsenicoxydans expressed genes and proteins required not only for arsenic detoxification or stress response but also involved in motility, exopolysaccharide synthesis, phosphate import or energetic metabolism. This study provides therefore new insights into the adaptation processes of H. arsenicoxydans in response to arsenic.
Published: 2009

45. 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

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

Author: Marianne Quéméneur, Michel Jauzein, Audrey Heinrich-Salmeron, Didier Lièvremont, Catherine Joulian, Daniel Muller, Philippe N. Bertin, Francis Garrido, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-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), Laboratoire de Biologie Tumorale, CRLCC Paul Strauss, XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), 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), Génétique moléculaire, génomique, microbiologie ( GMGM ), 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 ), and Bureau de Recherches Géologiques et Minières (BRGM) ( BRGM )
Subjects: Chemoautotrophic Growth, MESH: Sequence Analysis, Protein, MESH: Amino Acid Sequence, MESH: Base Sequence, Polymerase Chain Reaction, MESH : Arsenites, Conserved sequence, Sequence Analysis, Protein, RNA, Ribosomal, 16S, MESH : Genetic Markers, MESH : DNA, Bacterial, Soil Pollutants, MESH: Genetic Variation, MESH: Phylogeny, MESH : Proteobacteria, Phylogeny, 0303 health sciences, MESH: Conserved Sequence, MESH : Amino Acid Sequence, MESH : Genes, Bacterial, Bacterial, MESH : Oxidoreductases, MESH: RNA, Ribosomal, 16S, MESH : DNA Primers, MESH: Arsenites, Proteobacteria, Genetic Markers, MESH: DNA Primers, 16S, Sequence analysis, Arsenites, MESH : Soil Microbiology, Molecular Sequence Data, MESH: Biodiversity, 03 medical and health sciences, Phylogenetics, MESH : Conserved Sequence, MESH : Bacteria, Amino Acid Sequence, MESH: Oxidoreductases, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Oxidation-Reduction, Ribosomal, MESH: Soil Pollutants, MESH: Molecular Sequence Data, Bacteria, 030306 microbiology, Alphaproteobacteria, Genetic Variation, MESH: Polymerase Chain Reaction, DNA, Ribosomal RNA, MESH: DNA, Bacterial, Genes, MESH : Sequence Analysis, Protein, MESH : Sequence Analysis, DNA, MESH: Oxidation-Reduction, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, MESH: Genetic Markers, Applied Microbiology and Biotechnology, MESH : Soil Pollutants, MESH : Biodiversity, MESH : Polymerase Chain Reaction, Betaproteobacteria, Conserved Sequence, Soil Microbiology, Genetics, Ecology, biology, Biodiversity, MESH: Genes, Bacterial, Oxidoreductases, Oxidation-Reduction, Sequence Analysis, Biotechnology, DNA, Bacterial, MESH : Chemoautotrophic Growth, Microbial Ecology, MESH : Genetic Variation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, DNA Primers, Base Sequence, Protein, MESH : Phylogeny, Sequence Analysis, DNA, MESH: Proteobacteria, biology.organism_classification, 16S ribosomal RNA, MESH: Chemoautotrophic Growth, MESH : RNA, Ribosomal, 16S, MESH: Bacteria, MESH: Soil Microbiology, Genes, Bacterial, RNA, MESH : Base Sequence, Food Science
Abstract: A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria -, Betaproteobacteria -, and Gammaproteobacteria -related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.
Published: 2008

47. Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems

Author: Philippe Normand, Philippe N. Bertin, Claudine Médigue, 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), Structure et évolution des génomes (SEG), CNS-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), 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), 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), 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 ), Structure et évolution des génomes ( SEG ), CNS-Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -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 ), Génomique métabolique (UMR 8030), 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), 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, 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 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Proteomics, MESH: Sequence Analysis, DNA, MESH : Proteomics, Microbial, MESH : Ecosystem, Environmental Microbiology, MESH: Ecosystem, 0303 health sciences, Ecology, MESH: Protein Array Analysis, MESH: Genomics, MESH: Proteomics, MESH: Environmental Microbiology, MESH : Protein Array Analysis, Genomics, MESH: Genetics, Microbial, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Sequence Analysis, Genetics, Microbial, Protein Array Analysis, Computational biology, Biology, MESH : Genetics, Microbial, Microbiology, 03 medical and health sciences, MESH: Gene Expression Profiling, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Ecosystem, MESH : Bacteria, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, Ecological niche, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Bacteria, 030306 microbiology, MESH : Gene Expression Profiling, Gene Expression Profiling, MESH : Genomics, Sequence Analysis, DNA, DNA, MESH : Environmental Microbiology, MESH: Bacteria, Metagenomics, Mrna profiling, Microbial genome, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, MESH : Sequence Analysis, DNA
Abstract: International audience; Microbial genome sequencing has, for the first time, made accessible all the components needed for both the elaboration and the functioning of a cell. Associated with other global methods such as protein and mRNA profiling, genomics has considerably extended our knowledge of physiological processes and their diversity not only in human, animal and plant pathogens but also in environmental isolates. At a higher level of complexity, the so-called meta approaches have recently shown great promise in investigating microbial communities, including uncultured micro-organisms. Combined with classical methods of physico-chemistry and microbiology, these endeavours should provide us with an integrated view of how micro-organisms adapt to particular ecological niches and participate in the dynamics of ecosystems.
Published: 2008

48. 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

49. 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

50. 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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