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1. Metatranscriptomic outlook on green and brown food webs in acid mine drainage

Author: Odile Bruneel, Simona Crognale, Odile Sismeiro, Jean-Yves Coppée, Simona Rossetti, Frédéric Plewniak, Philippe N. Bertin, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), 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), Pôle Biomics (C2RT), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), Biologie des Bactéries pathogènes à Gram-positif - Biology of Gram-Positive Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris] (IP), This study was supported by the Agence Nationale de la Recherche (ANR) within the scope of the ANR-12-ADAP-0013 project and benefited from the financial support of the DMO/DMA project subsidized by the CNRS national pro-gramme EC2CO-MicrobiEn., ANR-12-ADAP-0013,THIOFILM,Rôle des biofilms dans l'adaptation et la variabilité génomique des bactéries du genre Thiomonas, impliqués dans les processus de remédiation naturelle dans les drainages miniers :(2012), Consiglio Nazionale delle Ricerche [Roma] (CNR), 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 Pasteur [Paris]-Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]
Subjects: Food Chain, [SDV]Life Sciences [q-bio], Decomposer, 03 medical and health sciences, Nutrient, Rivers, Phytoplankton, Animals, Organic matter, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Riparian zone, Trophic level, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, geography, geography.geographical_feature_category, Primary producers, 030306 microbiology, Ecology, Eukaryota, 15. Life on land, Acid mine drainage, Agricultural and Biological Sciences (miscellaneous), chemistry, Prokaryotic Cells, 13. Climate action, Environmental science
Abstract: International audience; Acid mine drainages (AMDs), metal‐rich acidic effluents generated by mining activities, are colonized by prokaryotic and eukaryotic microorganisms widely distributed among different phyla. We compared metatranscriptomic data from two sampling stations in the Carnoulès AMD and from a third station in the nearby Amous River, focussing on processes involved in primary production and litter decomposition. A synergistic relationship between the green and brown food webs was favoured in the AMD sediments by the low carbon content and the availability of mineral nutrients: primary production of organic matter would benefit C‐limited decomposers whose activity of organic matter mineralization would in turn profit primary producers. This balance could be locally disturbed by heterogeneous factors such as an input of plant debris from the riparian vegetation, strongly boosting the growth of Tremellales which would then outcompete primary producers. In the unpolluted Amous River on the contrary, the competition for limited mineral nutrients was dominated by the green food web, fish and bacterivorous protists having a positive effect on phytoplankton. These results suggest that in addition to direct effects of low pH and metal contamination, trophic conditions like carbon or mineral nutrient limitations also have a strong impact on assembly and activities of AMDs' microbial communities.
Published: 2021
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2. 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
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3. Homogenous nuclear magnetic resonance probe using the space harmonics suppression method

Author: P. de Pellegars, L. Pan, R. Sidi-Boulenouar, E. Nativel, M. Zanca, E. Alibert, S. Rousset, M. Cardoso, J.-L. Verdeil, N. Bertin, C. Goze-Bac, J. Muller, R. Schimpf, C. Coillot, Société d’accélération du Transfert de Technologies [Languedoc Roussillon] (AxLR – SaTT), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut d’Electronique et des Systèmes (IES), Térahertz, hyperfréquence et optique (TéHO), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Gui de Chauliac, Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Groupe d'étude des semiconducteurs (GES), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Reinvent Systems for Science & Discovery (RS2D), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: Materials science, Physics::Medical Physics, Spectroscopie RMN, 010402 general chemistry, 01 natural sciences, Signal, lcsh:Technology, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Nuclear magnetic resonance, Imagerie par résonance magnétique, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Electrical and Electronic Engineering, Génie électronique, Instrumentation, Electrical conductor, lcsh:T, Champ magnétique, Pulse sequence, Magnetostatics, 0104 chemical sciences, Magnetic field, [SPI.TRON]Engineering Sciences [physics]/Electronics, Electromagnetic coil, Harmonics, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.PHYS.PHYS-MED-PH]Physics [physics]/Physics [physics]/Medical Physics [physics.med-ph], U30 - Méthodes de recherche, Excitation
Abstract: Nuclear magnetic resonance imaging (MRI) has became an unavoidable medical tool in spite of its poor sensitivity. This fact motivates the efforts to enhance the nuclear magnetic resonance (NMR) probe performance. Thus, the nuclear spin excitation and detection, classically performed using radio-frequency coils, are required to be highly sensitive and homogeneous. The space harmonics suppression (SHS) method, already demonstrated to construct coil producing homogenous static magnetic field, is used in this work to design radio-frequency coils. The SHS method is used to determine the distribution of the electrical conductive wires which are organized in a saddle-coil-like configuration. The theoretical study of these SHS coils allows one to expect an enhancement of the signal-to-noise ratio with respect to saddle coil. Coils prototypes were constructed and tested to measure 1H NMR signal at a low magnetic field (8 mT) and perform MRI acquired at a high magnetic field (3 T). The signal-to-noise ratios of these SHS coils are compared to the one of saddle coil and birdcage (in the 3 T case) of the same size under the same pulse sequence conditions demonstrating the performance enhancement allowed by the SHS coils.
Published: 2020
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4. Simulation of tomato production under photovoltaic greenhouses

Author: G. Vercambre, H. Fatnassi, C. Poncet, N. Bertin, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV]Life Sciences [q-bio], Photovoltaic system, Environmental engineering, Greenhouse, 04 agricultural and veterinary sciences, Horticulture, serre Venlo, 7. Clean energy, 01 natural sciences, la tomate, la production, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Production (economics), Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, modèle tomgro, serre asymétrique, 010606 plant biology & botany
Abstract: International audience; The aim of this study is to evaluate the effect of shading induced by the photovoltaic panels on crop yields inside the greenhouse. The yield performance has been evaluated by using the tomato plant growth TOMGRO model. This model predicts the number and dry mass of leaves, stem segments and fruits, as well as the increase in leaf area as new organs are initiated, age, and senesce or are picked. The model uses a source-sink approach for partitioning carbohydrate into growth of different organs. TOMGRO was applied to simulate tomato production under two different photovoltaic greenhouse types: Venlo and Asymmetric. In each greenhouse, the plant density varied from low density (1.5 plants m-2) to high density (5 plants m-2). On the basis of these simulations, it has been observed that the decreased crop yields caused by shading may reach 70% under the asymmetric greenhouse with a planting density of 5 plants m-2 and 58% under Venlo greenhouse with a planting density of 1.5 plants m-2.
Published: 2017
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5. 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

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

Author: Odile Bruneel, Marina Héry, Philippe N. Bertin, Corinne Casiot, Angélique Desoeuvre, Aurélie Volant, Guillaume Morin, Hydrosciences Montpellier (HSM), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de minéralogie, cristallographie de Paris (LMCP), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Geologic Sediments, Eukaryotic diversity, 030106 microbiology, Biodiversity, Soil Science, Environmental pollution, Viridiplantae, Ecological succession, Biology, Community spatial dynamics, Mining, Arsenic, 03 medical and health sciences, Acid mine drainage, Rivers, Microbial ecology, RNA, Ribosomal, 18S, Ecosystem, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Phylogeny, Ecology, Evolution, Behavior and Systematics, Base Sequence, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, Water Pollution, Fungi, Community structure, Eukaryota, Species diversity, DNA, Hydrogen-Ion Concentration, 15. Life on land, Classification, biology.organism_classification, High-Throughput Screening Assays, 030104 developmental biology, Alveolata, [SDE]Environmental Sciences, France, Environmental Pollution, Sequence Analysis, Stramenopiles, Water Pollutants, Chemical
Abstract: International audience; Microscopic eukaryotes play a key role in ecosystem functioning, but their diversity remains largely unexplored in most environments. To advance our knowledge of eukaryotic microorganisms and the factors that structure their communities, high-throughput sequencing was used to characterize their diversity and spatial distribution along the pollution gradient of the acid mine drainage at Carnoulès (France). A total of 16,510 reads were retrieved leading to the identification of 323 OTUs after normalization. Phylogenetic analysis revealed a quite diverse eukaryotic community characterized by a total of eight high-level lineages including 37 classes. The majority of sequences were clustered in four main groups: Fungi, Stramenopiles, Alveolata and Viridiplantae. The Reigous sediments formed a succession of distinct ecosystems hosting contrasted eukaryotic communities whose structure appeared to be at least partially correlated with sediment mineralogy. The concentration of arsenic in the sediment was shown to be a significant factor driving the eukaryotic community structure along this continuum.
Published: 2016
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7. 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
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8. 16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage

Author: Claudine Médigue, Denis Le Paslier, Anne Fahy, Béatrice Lauga, Robert Duran, Ludovic Giloteaux, Jean Weissenbach, Philippe N. Bertin, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and RARE project no. 07-BLAN-0108
Subjects: Molecular Sequence Data, Soil Science, Niche conservatism, Biology, Mining, Arsenic, Actinobacteria, 03 medical and health sciences, chemistry.chemical_compound, Acid mine drainage, RNA, Ribosomal, 16S, Soil Pollutants, Cloning, Molecular, Phylogeny, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, DNA Primers, 030304 developmental biology, Arsenite, Genetics, Arsenic metabolism genes, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, Base Sequence, Ecology, Reverse Transcriptase Polymerase Chain Reaction, 030306 microbiology, Arsenite Transporting ATPases, Bacterial distribution, Thiomonas, Biodiversity, Sequence Analysis, DNA, Acidithiobacillus, biology.organism_classification, 16S ribosomal RNA, Acidobacteria, chemistry, Bacterial diversity, Candidatus, France, Oxidoreductases, Functional gene diversity, Bacteria
Abstract: cited By 5; International audience; To gain an in-depth insight into the diversity and the distribution of genes under the particular evolutionary pressure of an arsenic-rich acid mine drainage (AMD), the genes involved in bacterial arsenic detoxification (arsB, ACR3) and arsenite oxidation (aioA) were investigated in sediment from Carnoulès (France), in parallel to the diversity and global distribution of the metabolically active bacteria. The metabolically active bacteria were affiliated mainly to AMD specialists, i.e., organisms detected in or isolated from AMDs throughout the world. They included mainly Acidobacteria and the non-affiliated “Candidatus Fodinabacter communificans,” as well as Thiomonas and Acidithiobacillus spp., Actinobacteria, and unclassified Gammaproteobacteria. The distribution range of these organisms suggested that they show niche conservatism. Sixteen types of deduced protein sequences of arsenite transporters (5 ArsB and 11 Acr3p) were detected, whereas a single type of arsenite oxidase (AioA) was found. Our data suggested that at Carnoulès, the aioA gene was more recent than those encoding arsenite transporters and subjected to a different molecular evolution. In contrast to the 16S ribosomal RNA (16S rRNA) genes associated with AMD environments worldwide, the functional genes aioA, ACR3, and to a lesser extent arsB, were either novel or specific to Carnoulès, raising the question as to whether these functional genes are specific to high concentrations of arsenic, AMD-specific, or site-specific
Published: 2015
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9. Diversity and spatiotemporal dynamics of bacterial communities: Physicochemical and other drivers along an acid mine drainage

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

Author: Maes, A., Gracia, C., Bréchemier-Baey, D., Hamman, P., Chatre, E., Lemelle, L., P. N., Bertin, Hajnsdorf, E., Régulation de l'expression génétique chez les microorganismes (REGCM), Centre National de la Recherche Scientifique (CNRS), and Gauthier, Laurence
Subjects: [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2013

11. CFD study of climate conditions under greenhouses equipped with photovoltaic panel

Author: M. M. Muller, H. Fatnassi, Richard Brun, Christine Poncet, N. Bertin, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, cfd, photovoltaic panels, climate, solar radiation, microclimat, 020209 energy, teneur en vapeur d'eau, 02 engineering and technology, panneau solaire photo-voltaïque, Horticulture, modèle, 01 natural sciences, 7. Clean energy, culture sous serre, 0202 electrical engineering, electronic engineering, information engineering, Photovoltaic system, 15. Life on land, Agricultural sciences, radiation solaire, température de l'air, 13. Climate action, Environmental science, Sciences agricoles, 010606 plant biology & botany, Marine engineering
Abstract: International audience; Predicting accurately the microclimate distributed inside greenhouse equipped with photovoltaic panels is a prerequisite for sustainable energy-saving greenhouse management. It can also help to improve designers in improving the design of these kinds of greenhouse while enhancing the radiation transmission inside. This study is an essential prerequisite for research on crop namely those adapted to specific conditions in greenhouses equipped with photovoltaic panels. With this mind, the solar radiation distribution, thermal air, water vapour and dynamics fields were simulated using the CFD model in two types of greenhouses (Asymmetric and Venlo) equipped with photovoltaic panels on their roof, as well as crop cover characteristics and the interactions between crops and airflow. A detailed description of the thermal, dynamic and radiation fields inside the greenhouse were obtained and the analysis of data collected during this study show that (i) the solar radiation is more evenly distributed in the Venlo greenhouse than in the Asymmetric greenhouse. On an average, the solar radiation transmission in the Asymmetric greenhouse is 41.6% whereas that of the Venlo greenhouse is 46%. These luminosity values are not well adapted to plant requirements. (ii) For the same boundary conditions, the Venlo greenhouse has a cooler climate than the Asymmetrical greenhouse (-3°C in summer and -3°C in winter). This effect is beneficial in summer, but not interesting in winter. The various different openings in the Venlo greenhouse help to maintain temperature control and a homogeneous climate (temperature variation of 5°C in summer and 3.3°C in winter)
Published: 2013
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12. 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
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13. Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments

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

Author: V. Baldazzi, M. Génard, N. Bertin, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Eranet Erasysbio+ FRIM, and International Society for Horticultural Science (ISHS). INT.
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0303 health sciences, model, Cell division, food and beverages, Horticulture, Biology, tomato, 01 natural sciences, 03 medical and health sciences, Botany, water and carbon fluxes, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, fruit development, fruit growth, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; The development of a new organ is the results of coordinated events of cell division and expansion. Fruit growth starts immediately after bloom with intensive cell division. As development proceeds, the proliferative activity of cells progressively slows down giving way to a phase of pure cell enlargement, during fruit growth and ripening. Modeling the way cell division and expansion progress together is crucial to understand the emergence of specific morphological traits ( fruit size, weight, shape and texture) and their dependence on environmental factors. Models already exist for cell division and late fruit growth ( cell expansion), but the coupling of the two processes have not been addressed yet in fruit. Here we propose a first integrated model of tomato fruit development, explicitly coupling cell proliferation and expansion. The model is used to predict the evolution of cell number, size and ages during fruit development, under different environmental conditions.
Published: 2012

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

Author: Françoise Elbaz-Poulichet, Odile Bruneel, Sophie Delpoux, Angélique Desoeuvre, Aurélie Volant, Corinne Casiot, Marina Héry, Philippe N. Bertin, J.-C. Personné, Béatrice Lauga, Guillaume Morin, Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de minéralogie et de physique des milieux condensés (IMPMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de Biologie du Développement de Marseille (IBDM), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Thaumarchaeota, Nitrosopumilus, RNA, Archaeal, Microbiology, Arsenic, 03 medical and health sciences, Acid mine drainage, Microbial ecology, RNA, Ribosomal, 16S, Groundwater, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, Diversity, biology, 030306 microbiology, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, Lead and zinc mine, Biodiversity, General Medicine, Hydrogen-Ion Concentration, biology.organism_classification, Archaea, Thermoplasmatales, [SDE]Environmental Sciences, Molecular Medicine, Nitrification, France, Euryarchaeota, Water Microbiology
Abstract: cited By 15; International audience; The Carnoulès mine is an extreme environment located in the South of France. It is an unusual ecosystem due to its acidic pH (2–3), high concentration of heavy metals, iron, and sulfate, but mainly due to its very high concentration of arsenic (up to 10 g L−1 in the tailing stock pore water, and 100–350 mg L−1 in Reigous Creek, which collects the acid mine drainage). Here, we present a survey of the archaeal community in the sediment and its temporal variation using a culture-independent approach by cloning of 16S rRNA encoding genes. The taxonomic affiliation of Archaea showed a low degree of biodiversity with two different phyla: Euryarchaeota and Thaumarchaeota. The archaeal community varied in composition and richness throughout the sampling campaigns. Many sequences were phylogenetically related to the order Thermoplasmatales represented by aerobic or facultatively anaerobic, thermoacidophilic autotrophic or heterotrophic organisms like the organotrophic genus Thermogymnomonas. Some members of Thermoplasmatales can also derive energy from sulfur/iron oxidation or reduction. We also found microorganisms affiliated with methanogenic Archaea (Methanomassiliicoccus luminyensis), which are involved in the carbon cycle. Some sequences affiliated with ammonia oxidizers, involved in the first and rate-limiting step in nitrification, a key process in the nitrogen cycle were also observed, including Candidatus Nitrososphaera viennensis and Candidatus nitrosopumilus sp. These results suggest that Archaea may be important players in the Reigous sediments through their participation in the biochemical cycles of elements, including those of carbon and nitrogen.
Published: 2012
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17. Taxonomic and functional prokaryote diversity in mildly arsenic-contaminated sediments

Author: David Halter, Florence Goulhen-Chollet, Audrey Cordi, Fabienne Séby, Christophe Pagnout, Christine Schaeffer, Philippe N. Bertin, Sebastien Gallien, Simonetta Gribaldo, Didier Montaut, Florence Arsène-Ploetze, Pascale Bauda, Alain Van Dorsselaer, Christine Carapito, Audrey Heinrich-Salmeron, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Interactions Ecotoxicologie, Biodiversité, Ecosystèmes (LIEBE), Université Paul Verlaine - Metz (UPVM)-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Ultra Traces Analyses Aquitaine (UT2A), Ultra Traces Analyses Aquitaine, Audrey Cordi was supported by grants from the French Ministry of Research and the 'Zone Atelier Moselle' (ZAM) project. Audrey Heinrich-Salmeron, David Halter and Sebastien Gallien were supported by grants from the French Ministry of Research and the Université de Strasbourg. Florence Goulhen-Chollet was supported by the Agence Nationale de la Recherche (ANR), RARE project (Reactivity of an Arsenic-Rich Ecosystem). This study was financed by the EC2CO program (Institut National des Sciences de l’Univers, CNRS) and BRG., This work was performed in the framework of the Groupement de Recherche 'Métabolisme de l’Arsenic chez les micro-organismes: de la résistance à la détoxication' (GDR2909-CNRS)., ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007), Institut Pasteur [Paris], Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, Geologic Sediments, Thaumarchaeota, MESH: Archaea/metabolism, MESH: Environmental Pollutants/metabolism, [SDV]Life Sciences [q-bio], MESH: Bacteria/genetics, MESH: Archaea/classification, Polymerase Chain Reaction, MESH: DNA, Archaeal/analysis, RNA, Ribosomal, 16S, MESH: Archaea/isolation & purification, MESH: Ecosystem, MESH: Geologic Sediments/microbiology, MESH: Phylogeny, Phylogeny, 0303 health sciences, biology, Ecology, Planctomycetes, MESH: Microbial Consortia/physiology, General Medicine, Biodiversity, Adaptation, Physiological, DNA, Archaeal, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Arsenic/metabolism, Environmental Pollutants, France, Proteobacteria, MESH: Archaea/genetics, MESH: Bacteria/metabolism, DNA, Bacterial, MESH: Rivers/microbiology, MESH: RNA, Ribosomal, 16S/analysis, Gene Transfer, Horizontal, Microbial Consortia, Environmental genomics, Microbiology, Mining, MESH: Biodiversity, Arsenic, 03 medical and health sciences, Rivers, Metaproteomics, MESH: DNA, Bacterial/analysis, Molecular Biology, Ecosystem, 030304 developmental biology, MESH: Proteomics, Bacteria, 030306 microbiology, Phylum, Bacteroidetes, Prokaryote, MESH: Polymerase Chain Reaction, biology.organism_classification, Archaea, MESH: Adaptation, Physiological, MESH: RNA, Ribosomal, 16S/genetics, MESH: Gene Transfer, Horizontal, MESH: DNA, Bacterial/genetics, MESH: France, Metagenomics, MESH: DNA, Archaeal/genetics, MESH: Bacteria/classification, human activities, Acidobacteria, MESH: Bacteria/isolation & purification
Abstract: International audience; Arsenic-resistant prokaryote diversity is far from being exhaustively explored. In this study, the arsenic-adapted prokaryotic community present in a moderately arsenic-contaminated site near Sainte-Marie-aux-Mines (France) was characterized, using metaproteomic and 16S rRNA-encoding gene amplification. High prokaryotic diversity was observed, with a majority of Proteobacteria, Acidobacteria and Bacter-oidetes, and a large archaeal community comprising Euryarchaeaota and Thaumarchaeota. Metaproteomic analysis revealed that Proteobacteria, Planctomycetes and Cyanobacteria are among the active bacteria in this ecosystem. Taken together, these results highlight the unsuspected high diversity of the arsenic-adapted prokaryotic community, with some phyla never having been described in highly arsenic-exposed sites.
Published: 2011
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18. Subinhibitory Arsenite Concentrations Lead to Population Dispersal in Thiomonas sp

Author: Romain Briandet, Philippe N. Bertin, Marie Marchal, David Halter, Michael Dubow, Marie-Claire Lett, Sandrine Koechler, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microorganism, Applied Microbiology, Microbial metabolism, Colony Count, Microbial, lcsh:Medicine, biofilm, chemistry.chemical_compound, stress, viabilité, Nucleic Acids, Molecular Cell Biology, souche, Extreme environment, lcsh:Science, Arsenite, Cellular Stress Responses, 0303 health sciences, education.field_of_study, Multidisciplinary, tolerance, biology, Polysaccharides, Bacterial, Microbial Growth and Development, Thiomonas, Betaproteobacteria, Extracellular Matrix, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, bioremediation, metabolism, viability, strains, oxidation, cell, Research Article, Arsenites, Movement, Population, Microbiology, Microbial Ecology, 03 medical and health sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, métabolisme, Biology, 030304 developmental biology, 030306 microbiology, tolérance, lcsh:R, Biofilm, oxydation, biology.organism_classification, bioremédiation, chemistry, 13. Climate action, Biofilms, Biological dispersal, lcsh:Q, cellule
Abstract: International audience; Biofilms represent the most common microbial lifestyle, allowing the survival of microbial populations exposed to harsh environmental conditions. Here, we show that the biofilm development of a bacterial species belonging to the Thiomonas genus, frequently found in arsenic polluted sites and playing a key role in arsenic natural remediation, is markedly modified when exposed to subinhibitory doses of this toxic element. Indeed, arsenite [As(III)] exposure led to a considerable impact on biofilm maturation by strongly increasing the extracellular matrix synthesis and by promoting significant cell death and lysis within microcolonies. These events were followed by the development of complex 3D-biofilm structures and subsequently by the dispersal of remobilized cells observed inside the previously formed hollow voids. Our results demonstrate that this biofilm community responds to arsenite stress in a multimodal way, enhancing both survival and dispersal. Addressing this complex bacterial response to As(III) stress, which might be used by other microorganisms under various adverse conditions, may be essential to understand how Thiomonas strains persist in extreme environments.
Published: 2011
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19. 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
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20. Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics

Author: Odile Bruneel, Denis Le Paslier, Damien Mornico, Eric Pelletier, Adam Alexander T. Smith, Béatrice Chane-Woon-Ming, Philippe N. Bertin, Sandrine Koechler, Robert Duran, Florence Goulhen-Chollet, Sebastien Gallien, Marie Marchal, Florence Arsène-Ploetze, David Vallenet, Corinne Casiot, Alexandra Calteau, Jean Weissenbach, Nuria Fonknechten, Jessica Cleiss-Arnold, Christine Schaeffer, Béatrice Lauga, Violaine Bonnefoy, Ludovic Giloteaux, Claudine Médigue, Alain Van Dorsselaer, David Halter, Audrey Heinrich-Salmeron, Françoise Elbaz-Poulichet, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale et microbiologie (IBSM), Université de la Méditerranée - Aix-Marseille 2-Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UMR 7156 Génétique Moléculaire, Génomique et Microbiologie, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Laboratoire de spectrométrie de masse bioorganique, Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique, Département des Sciences Analytiques, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France (LSMBO-DSA-IPHC), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, Iron, Microorganism, Microbial metabolism, Genomics, functional ecology, Microbiology, Mining, Arsenic, 03 medical and health sciences, uncultured microorganism, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, bacterial phylum, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], extreme environment, Herminiimonas arsenicoxydans, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Ecosystem, Phylogeny, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, synecology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, Bacteria, biology, Reverse Transcriptase Polymerase Chain Reaction, 030306 microbiology, Phylum, Ecology, microbial genomics, 15. Life on land, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 13. Climate action, Metagenomics, Candidatus, Original Article, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Sulfur
Abstract: International audience; By their metabolic activities, microorganisms have a crucial role in the biogeochemical cycles of elements. The complete understanding of these processes requires, however, the deciphering of both the structure and the function, including synecologic interactions, of microbial communities. Using a metagenomic approach, we demonstrated here that an acid mine drainage highly contaminated with arsenic is dominated by seven bacterial strains whose genomes were reconstructed. Five of them represent yet uncultivated bacteria and include two strains belonging to a novel bacterial phylum present in some similar ecosystems, and which was named 'Candidatus Fodinabacter communificans.' Metaproteomic data unravelled several microbial capabilities expressed in situ, such as iron, sulfur and arsenic oxidation that are key mechanisms in biomineralization, or organic nutrient, amino acid and vitamin metabolism involved in synthrophic associations. A statistical analysis of genomic and proteomic data and reverse transcriptase-PCR experiments allowed us to build an integrated model of the metabolic interactions that may be of prime importance in the natural attenuation of such anthropized ecosystems.
Published: 2011
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21. Effect of arsenite on swimming motility delays surface colonization in Herminiimonas arsenicoxydans

Author: Sandrine Koechler, Marie Marchal, B. Kammerer, Philippe N. Bertin, Romain Briandet, UMR 7156 Génétique Moléculaire, Génomique et Microbiologie, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ANR COBIAS project, Groupement de Recherche - Metabolisme de l'Arsenic chez les Microorganismes GDR2909-CNRS, Génétique moléculaire, génomique, microbiologie (GMGM), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Arsenites, [SDV]Life Sciences [q-bio], Mutant, chemistry.chemical_element, Motility, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Oxalobacteraceae, Herminiimonas arsenicoxydans, Arsenic, 030304 developmental biology, Arsenite, 0303 health sciences, Microscopy, Confocal, biology, 030306 microbiology, Biofilm, Arsenate, biology.organism_classification, Cell biology, chemistry, Biofilms, Oxidoreductases, Oxidation-Reduction, Bacteria
Abstract: Herminiimonas arsenicoxydans is a Gram-negative bacterium able to detoxify arsenic-contaminated environments by oxidizing arsenite [As(III)] to arsenate [As(V)] and by scavenging arsenic ions in an extracellular matrix. Its motility and colonization behaviour have been previously suggested to be influenced by arsenite. Using time-course confocal laser scanning microscopy, we investigated its biofilm development in the absence and presence of arsenite. Arsenite was shown to delay biofilm initiation in the wild-type strain; this was partly explained by its toxicity, which caused an increased growth lag time. However, this delayed adhesion step in the presence of arsenite was not observed in either a swimming motility defective fliL mutant or an arsenite oxidase defective aoxB mutant; both strains displayed the wild-type surface properties and growth capacities. We propose that during the biofilm formation process arsenite acts on swimming motility as a result of the arsenite oxidase activity, preventing the switch between planktonic and sessile lifestyles. Our study therefore highlights the existence, under arsenite exposure, of a competition between swimming motility, resulting from arsenite oxidation, and biofilm initiation.
Published: 2010
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22. Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans

Author: Jean-Yves Coppée, Marie-Laure Fardeau, Marie-Agnès Dillies, Jessica Cleiss-Arnold, Philippe N. Bertin, Caroline Proux, Florence Arsène-Ploetze, Sandrine Koechler, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris] (IP), Laboratoire de Microbiologie IRD, JCA was supported by a grant from the French Ministry of Education and Research. Financial support came from the Centre National de la Recherche Scientifique, the Agence Nationale de la Recherche (ANR 07-BLAN-0118 project) and the Université de Strasbourg. This work was done in the frame of the Groupement de Recherche (GDR2909-CNRS): ' Métabolisme de l'Arsenic chez les Micro-organismes'., ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007), and Institut Pasteur [Paris]
Subjects: inorganic chemicals, Time Factors, Transcription, Genetic, lcsh:QH426-470, Movement, lcsh:Biotechnology, Sulfur metabolism, chemistry.chemical_element, medicine.disease_cause, Arsenic, Transcriptome, 03 medical and health sciences, Bacterial Proteins, Stress, Physiological, Oxalobacteraceae, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, medicine, Genetics, Cluster Analysis, Herminiimonas arsenicoxydans, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Metabolism, biology.organism_classification, Molecular biology, Kinetics, lcsh:Genetics, chemistry, Biochemistry, Oxidation-Reduction, Oxidative stress, Bacteria, Research Article, Biotechnology
Abstract: Background Arsenic is present in numerous ecosystems and microorganisms have developed various mechanisms to live in such hostile environments. Herminiimonas arsenicoxydans, a bacterium isolated from arsenic contaminated sludge, has acquired remarkable capabilities to cope with arsenic. In particular our previous studies have suggested the existence of a temporal induction of arsenite oxidase, a key enzyme in arsenic metabolism, in the presence of As(III). Results Microarrays were designed to compare gene transcription profiles under a temporal As(III) exposure. Transcriptome kinetic analysis demonstrated the existence of two phases in arsenic response. The expression of approximatively 14% of the whole genome was significantly affected by an As(III) early stress and 4% by an As(III) late exposure. The early response was characterized by arsenic resistance, oxidative stress, chaperone synthesis and sulfur metabolism. The late response was characterized by arsenic metabolism and associated mechanisms such as phosphate transport and motility. The major metabolic changes were confirmed by chemical, transcriptional, physiological and biochemical experiments. These early and late responses were defined as general stress response and specific response to As(III), respectively. Conclusion Gene expression patterns suggest that the exposure to As(III) induces an acute response to rapidly minimize the immediate effects of As(III). Upon a longer arsenic exposure, a broad metabolic response was induced. These data allowed to propose for the first time a kinetic model of the As(III) response in bacteria.
Published: 2010
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23. Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans

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

Author: Christelle Lemaître-Guillier, Florence Arsène-Ploetze, Christopher G. Bryan, Fabienne Battaglia-Brunet, Marie Marchal, Didier Lièvremont, Philippe N. Bertin, Valérie Kugler, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Plateforme Protéomique, Centre National de la Recherche Scientifique (CNRS), Centre for Bioprocess Engineering Research, and Faculty of Engineering and the Built Environment
Subjects: Microbiology (medical), inorganic chemicals, Chemoautotrophic Growth, Arsenites, Operon, oxidation, lcsh:QR1-502, chemistry.chemical_element, Microbiology, lcsh:Microbiology, Beta-proteobacterium, Arsenic, 03 medical and health sciences, Species Specificity, Phylogenetics, Research article, Autotroph, genes, bacteria, Phylogeny, Betaproteobacteria, 030304 developmental biology, Genetics, 0303 health sciences, biology, integumentary system, 030306 microbiology, oxidase, Thiomonas, Thiobacilius, phylogenies, Mine Drainage Carnoules, biology.organism_classification, 16S ribosomal RNA, Adaptation, Physiological, Carbon, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, France, Bacteria
Abstract: Background Thiomonas strains are ubiquitous in arsenic-contaminated environments. Differences between Thiomonas strains in the way they have adapted and respond to arsenic have never been studied in detail. For this purpose, five Thiomonas strains, that are interesting in terms of arsenic metabolism were selected: T. arsenivorans, Thiomonas spp. WJ68 and 3As are able to oxidise As(III), while Thiomonas sp. Ynys1 and T. perometabolis are not. Moreover, T. arsenivorans and 3As present interesting physiological traits, in particular that these strains are able to use As(III) as an electron donor. Results The metabolism of carbon and arsenic was compared in the five Thiomonas strains belonging to two distinct phylogenetic groups. Greater physiological differences were found between these strains than might have been suggested by 16S rRNA/rpoA gene phylogeny, especially regarding arsenic metabolism. Physiologically, T. perometabolis and Ynys1 were unable to oxidise As(III) and were less arsenic-resistant than the other strains. Genetically, they appeared to lack the aox arsenic-oxidising genes and carried only a single ars arsenic resistance operon. Thiomonas arsenivorans belonged to a distinct phylogenetic group and increased its autotrophic metabolism when arsenic concentration increased. Differential proteomic analysis revealed that in T. arsenivorans, the rbc/cbb genes involved in the assimilation of inorganic carbon were induced in the presence of arsenic, whereas these genes were repressed in Thiomonas sp. 3As. Conclusion Taken together, these results show that these closely related bacteria differ substantially in their response to arsenic, amongst other factors, and suggest different relationships between carbon assimilation and arsenic metabolism.
Published: 2009
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26. 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
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27. 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
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28. A tale of two oxidation states: bacterial colonization of arsenic-rich environments

Author: Caroline Dossat, Barbara Schoepp, Jean Weissenbach, Yuko Makita, Valérie Barbe, Patricia Siguier, Béatrice Segurens, Michael Chandler, Wolfgang Nitschke, Sophie Mangenot, Zoé Rouy, Stéphanie Weiss, David Vallenet, Benoit Cournoyer, Diliana D. Simeonova, Philippe Ortet, Antoine Danchin, Florence Arsène-Ploetze, Sandrine Koechler, Christine Carapito, Mohamed Barakat, Evelyne Krin, Didier Lièvremont, Daniel Muller, Emmanuelle Leize, Simon Duval, Philippe N. Bertin, Marie-Claire Lett, Nicolas Perdrial, Michaël Heymann, Stéphane Cruveiller, Aurélie Lieutaud, Violaine Bonnefoy, Evelyne Turlin, Claudine Médigue, Emmanuel Talla, Alain Van Dorsselaer, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de géochimie de la surface (CGS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut national des sciences de l'Univers (INSU - CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Génétique moléculaire, génomique, microbiologie ( GMGM ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes ( LEMIRE ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Laboratoire de microbiologie et génétique moléculaires ( LMGM ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre de géochimie de la surface ( CGS ), Institut national des sciences de l'Univers ( INSU - CNRS ) -Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Structure et évolution des génomes ( SEG ), and CNS-Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH: Oxidation-Reduction, Cancer Research, Drug Resistance, MESH : Models, Biological, QH426-470, MESH : Carbon, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Arsenic, Bacteria, Biodegradation, Environmental, Carbon, Bacterial, Energy Metabolism, Genome, Metals, Models, Biological, Oxidation-Reduction, Phylogeny, MESH: Biodegradation, Environmental, 0302 clinical medicine, Herminiimonas arsenicoxydans, MESH: Phylogeny, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), 0303 health sciences, Ecology, MESH: Energy Metabolism, MESH : Arsenic, 6. Clean water, Biodegradation, Environmental, Research Article, inorganic chemicals, MESH : Biodegradation, Environmental, MESH : Genome, Bacterial, Energy metabolism, chemistry.chemical_element, MESH: Carbon, Biology, Genomic databases, Microbiology, Models, Biological, 03 medical and health sciences, Bacterial colonization, Bioremediation, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, SDV:BBM, Genetics, MESH : Bacteria, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH : Oxidation-Reduction, MESH: Metals, 030306 microbiology, MESH : Metals, MESH: Models, Biological, MESH : Phylogeny, Computational Biology, Oxidation reduction, Genetics and Genomics, biology.organism_classification, Archaea, MESH : Energy Metabolism, Eubacteria, MESH: Bacteria, Positive chemotaxis, chemistry, 13. Climate action, Genome, Bacterial, 030217 neurology & neurosurgery
Abstract: Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth., Author Summary Microorganisms play a crucial role in nutrient biogeochemical cycles. Arsenic is found throughout the environment from both natural and anthropogenic sources. Its inorganic forms are highly toxic and impair the physiology of most higher organisms. Arsenic contamination of groundwater supplies is giving rise to increasingly severe human health problems in both developing and industrial countries. In the present work, we investigated the metabolism of this metalloid in Herminiimonas arsenicoxydans, a representative organism of a novel bacterial genus widespread in aquatic environments. Examination of the genome sequence and experimental evidence revealed that it is remarkably capable of coping with arsenic. Our observations support the existence of multiple strategies allowing arsenic-metabolizing microbes to efficiently colonize toxic environments. In particular, arsenic oxidation and scavenging may have played a crucial role in the development of early stages of life on Earth. Such mechanisms may one day be exploited as part of a potential bioremediation strategy in toxic environments.
Published: 2007
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29. Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome

Author: Emmanuelle Leize-Wagner, Sandrine Koechler, Evelyne Turlin, Christine Carapito, Philippe N. Bertin, Alain Van Dorsselaer, Antoine Danchin, Marie-Claire Lett, Daniel Muller, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire de Biologie Tumorale, CRLCC Paul Strauss, XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Génétique moléculaire, génomique, microbiologie (GMGM), Régulation de l'Expression Génétique (REG), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Substances naturelles/chimie moléculaire, Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), XLIM ( XLIM ), Université de Limoges ( UNILIM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Génétique moléculaire, génomique, microbiologie ( GMGM ), Régulation de l'Expression Génétique ( REG ), Sciences Analytiques et Interactions Ioniques et Biomoléculaires ( DSA-IPHC ), Compartimentation et dynamique cellulaires ( CDC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -INSTITUT CURIE-Centre National de la Recherche Scientifique ( CNRS ), Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-Centre National de la Recherche Scientifique ( CNRS ), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH : Molecular Sequence Data, MESH : RNA, Messenger, Messenger, Drug Resistance, MESH: Amino Acid Sequence, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Biochemistry, Genome, chemistry.chemical_compound, MESH : Bacterial Proteins, MESH: Betaproteobacteria, Peptide sequence, MESH: Bacterial Proteins, MESH : Betaproteobacteria, Arsenite, Genetics, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Genes, Bacterial, Bacterial, Betaproteobacteria, General Medicine, MESH : Arsenic, Metals, MESH: Genes, Bacterial, MESH : Genome, Bacterial, Molecular Sequence Data, chemistry.chemical_element, Biology, Arsenic, 03 medical and health sciences, Bacterial Proteins, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Amino Acid Sequence, Gene, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: RNA, Messenger, Two-dimensional gel electrophoresis, MESH: Metals, MESH: Molecular Sequence Data, 030306 microbiology, MESH : Metals, Arsenate, RNA, chemistry, Genes, Genes, Bacterial, Genome, Bacterial
Abstract: International audience; The effect of high concentrations of arsenic has been investigated in Caenibacter arsenoxydans, a beta-proteobacterium isolated from an arsenic contaminated environment and able to oxidize arsenite to arsenate. As the genome of this bacterium has not yet been sequenced, the use of a specific proteomic approach based on nano-high performance liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) studies and de novo sequencing to perform cross-species protein identifications was necessary. In addition, a random mutational analysis was performed. Twenty-two proteins and 16 genes were shown to be differentially accumulated and expressed, respectively, in cells grown in the presence of arsenite. Two genes involved in arsenite oxidation and one in arsenite efflux as well as two proteins responsible for arsenate reduction were identified. Moreover, numerous genes and proteins belonging to various functional classes including information and regulation pathways, intermediary metabolism, cell envelope and cellular processes were also up- or down-regulated, which demonstrates that bacterial response to arsenic is pleiotropic.
Published: 2006
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30. Cell division and cessation of cell proliferation in growing fruit

Author: M. Génard, S. Fishman, N. Bertin, ProdInra, Migration, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), and Institut National de la Recherche Agronomique (INRA)
Subjects: [SDE] Environmental Sciences, 0303 health sciences, Cell division, Cell growth, [SDV]Life Sciences [q-bio], 04 agricultural and veterinary sciences, Horticulture, Biology, Cell biology, [SDV] Life Sciences [q-bio], 03 medical and health sciences, Botany, [SDE]Environmental Sciences, PECHER, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience
Published: 2002

31. Insights into the formation of tomato quality during fruit development

Author: N Bertin, C Gary, M Buret, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ProdInra, Migration
Subjects: [SDE] Environmental Sciences, 0106 biological sciences, Vitamin, [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, [SDV]Life Sciences [q-bio], Fruit development, Titratable acid, Horticulture, Biology, 01 natural sciences, 040501 horticulture, chemistry.chemical_compound, Botany, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Genetics, Dry matter, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Sugar, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Fresh weight, food and beverages, 04 agricultural and veterinary sciences, [SDV.IDA] Life Sciences [q-bio]/Food engineering, Lycopene, [SDV] Life Sciences [q-bio], chemistry, [SDE]Environmental Sciences, Composition (visual arts), 0405 other agricultural sciences, 010606 plant biology & botany
Abstract: SummaryInfluence of the source-sink balance on the final quality of tomato was investigated in spring greenhouse production. Four treatments were compared differing by the fruit/leaf number ratio manipulated during either the cell division or the cell elongation periods of the sixth truss. At maturity, quality was assessed through fruit colour, firmness, fresh weight, titratable acidity, refractive index, and contents of dry matter, reducing sugars, (3-carotene, lycopene and C vitamin. (3-carotene and lycopene contents were correlated positively to each other, and negatively to fruit firmness. The refractive index, dry-matter and sugar contents were also positively correlated, but less under low competition during cell division. Fruit fresh weight was correlated with none of the qualitative parameters, and significantly differed among fruits within the sixth truss; however this relied only on the difference between the first fruit and the following ones. Fruit composition did not vary among basal and tip ...
Published: 2001

32. Tomato fruit-set : a case study for validation of the model TOMGRO

Author: C. Gary, N. Bertin, ProdInra, Migration, Unité de bioclimatologie, and Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0303 health sciences, [SDV]Life Sciences [q-bio], Horticulture, 01 natural sciences, Fruit set, [SDV] Life Sciences [q-bio], 03 medical and health sciences, RELATION PUITS SOURCE, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany, Mathematics
Abstract: National audience
Published: 1993

33. Tomato fruit set and competition for assimilates, during the early production period

Author: N. Bertin, C. Gary, Unité de bioclimatologie, Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: 0106 biological sciences, media_common.quotation_subject, [SDV]Life Sciences [q-bio], 04 agricultural and veterinary sciences, Horticulture, Biology, 01 natural sciences, Competition (biology), Fruit set, [SDV] Life Sciences [q-bio], Agronomy, RELATION PUITS SOURCE, 040103 agronomy & agriculture, Period (geology), 0401 agriculture, forestry, and fisheries, Production (economics), ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany, media_common
Abstract: International audience
Published: 1990

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33 results on '"N. Bertin"'

1. Metatranscriptomic outlook on green and brown food webs in acid mine drainage

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

3. Homogenous nuclear magnetic resonance probe using the space harmonics suppression method

4. Simulation of tomato production under photovoltaic greenhouses

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

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

7. Contributions of Descriptive and Functional Genomics to Microbial Ecology

8. 16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage

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

10. Role of polyadenylation in regulation of the flagella cascade and motility in E.coli

11. CFD study of climate conditions under greenhouses equipped with photovoltaic panel

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

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

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

15. A model of fruit growth integrating cell division and expansion processes

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

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

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

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

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

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

22. Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans

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

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

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

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

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

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

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

30. Cell division and cessation of cell proliferation in growing fruit

31. Insights into the formation of tomato quality during fruit development

32. Tomato fruit-set : a case study for validation of the model TOMGRO

33. Tomato fruit set and competition for assimilates, during the early production period

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