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1. Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere

Author

Jordan Pinto, Raphaël Lami, Marc Krasovec, Régis Grimaud, Laurent Urios, Josselin Lupette, Marie-Line Escande, Frédéric Sanchez, Laurent Intertaglia, Nigel Grimsley, Gwenaël Piganeau, and Sophie Sanchez-Brosseau

Subjects
Marinobacter, bacteria, Ostreococcus, phycosphere, phytoplankton, cocultures, Biology (General), QH301-705.5
Abstract

Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phycospheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B12 while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the ‘opportunistic’ behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions.

Published
2021
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2. Quorum sensing in biofilms: a key mechanism to target in ecotoxicological studies

Author

Raphaël Lami, Laurent Urios, Maëlle Molmeret, and Régis Grimaud

Subjects
General Medicine, Applied Microbiology and Biotechnology, Microbiology
Abstract

Our environment is heavily contaminated by anthropogenic compounds, and this issue constitutes a significant threat to all life forms, including biofilm-forming microorganisms. Cell-cell interactions shape microbial community structures and functions, and pollutants that affect intercellular communications impact biofilm functions and ecological roles. There is a growing interest in environmental science fields for evaluating how anthropogenic pollutants impact cell-cell interactions. In this review, we synthesize existing literature that evaluates the impacts of quorum sensing (QS), which is a widespread density-dependent communication system occurring within many bacterial groups forming biofilms. First, we examine the perturbating effects of environmental contaminants on QS circuits; and our findings reveal that QS is an essential yet underexplored mechanism affected by pollutants. Second, our work highlights that QS is an unsuspected and key resistance mechanism that assists bacteria in dealing with environmental contamination (caused by metals or organic pollutants) and that favors bacterial growth in unfavourable environments. We emphasize the value of considering QS a critical mechanism for monitoring microbial responses in ecotoxicology. Ultimately, we determine that QS circuits constitute promising targets for innovative biotechnological approaches with major perspectives for applications in the field of environmental science.

Published
2022
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3. Marine Bacterial Models for Experimental Biology

Author

Sophie Sanchez-Brosseau, Raphaël Lami, Christophe Six, Laurent Urios, Nyree J. West, Fabien Joux, Régis Grimaud, François Thomas, LAMI, Raphaël, Agnes Boutet, and Bernd Schierwater

Subjects
[SDE] Environmental Sciences, Experimental biology, Computational biology, Biology
Published
2021
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5. Corrigendum to 'Description of Palleronia rufa sp. nov., a biofilm-forming and AHL-producing Rhodobacteraceae, reclassification of Hwanghaeicola aestuarii as Palleronia aestuarii comb. nov., Maribius pontilimi as Palleronia pontilimi comb. nov., Maribius salinus as Palleronia salina comb. nov., Maribius pelagius as Palleronia pelagia comb. nov. and emended description of the genus Palleronia' [Syst. Appl. Microbiol. 43 (1) (2020) 126018]

Author

Claudie Barnier, Camille Clerissi, Raphaël Lami, Laurent Intertaglia, Philippe Lebaron, Régis Grimaud, and Laurent Urios

Subjects
Applied Microbiology and Biotechnology, Microbiology, Ecology, Evolution, Behavior and Systematics
Published
2022
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6. Biocorrosion detection by sulphur isotopic fractionation measurements

Author

Laurent Urios, S. Mostefaoui, Florence Mercier-Bion, Delphine Neff, Yannick Linard, Didier Crusset, Philippe Dillmann, Sophie Grousset, Valérie Deydier, Alexandre Dauzères, Laboratoire Archéomatériaux et Prévision de l'Altération (LAPA - UMR 3685), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Institut de Recherches sur les Archéomatériaux (IRAMAT), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Technologie de Belfort-Montbeliard (UTBM), Agence Nationale pour la Gestion des Déchets Radioactifs (ANDRA), PSE-ENV/SEDRE/LETIS, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), 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, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), IRAMAT - Laboratoire Métallurgies et Cultures (IRAMAT - LMC), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Technologie de Belfort-Montbeliard (UTBM), PLATIN' (PLATeau d'Isotopie de Normandie, France) core facility and MNHN (Museum, National d’Histoire Naturelle, Paris, France) for the sulphur isotopic analysis., Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Université Bordeaux Montaigne (UBM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'étude et de recherche sur les transferts et les interactions dans les sous-sols (IRSN/PSE-ENV/SEDRE/LETIS), Service des déchets radioactifs et des transferts dans la géosphère (IRSN/PSE-ENV/SEDRE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN)-Institut de Radioprotection et de Sûreté Nucléaire (IRSN), and Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Université Bordeaux Montaigne (UBM)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Université Bordeaux Montaigne (UBM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Abiotic component, Materials science, Micron size, 020209 energy, General Chemical Engineering, Metallurgy, Radioactive waste, chemistry.chemical_element, 02 engineering and technology, General Chemistry, Fractionation, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Sulfur, Corrosion, chemistry, iron sulphide, microbiological corrosion, 0202 electrical engineering, electronic engineering, information engineering, NanoSIMS, General Materials Science, 0210 nano-technology, sulphur isotopic fractionation
Abstract

International audience; This innovative study presents a local diagnosis approach based on nanoSIMS technique to determine the biotic/abiotic origin of iron sulphides of (sub)micron size heterogeneously located in the corrosion product layers of iron. For iron coupons corroded in controlled conditions, negative δ34Ssulphides-sulphates were obtained in biotic conditions contrary to δ34Ssulphides-sulphates obtained in abiotic ones. These results underline that nanoSIMS is a reliable local technique to detect the formation origin of (sub)micron iron sulphides. This successful methodology was then applied to a complex system representative of an iron corroded in the conditions similar to those of radioactive wastes storage in geological medium.

Published
2020
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7. Pleomorphochaeta naphthae sp. nov., a new anaerobic fermentative bacterium isolated from an oil field

Author

Michel Magot, Boussad Arroua, Agnès Hirschler-Réa, Patrick Bouriat, Laurent Urios, Régis Grimaud, Anthony Ranchou-Peyruse, 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 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), Laboratoire des Fluides Complexes et leurs Réservoirs (LFCR), and TOTAL FINA ELF-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, 0301 basic medicine, [SDV]Life Sciences [q-bio], Microbiology, Pleomorphochaeta, 03 medical and health sciences, chemistry.chemical_compound, Glycolipid, Genus, RNA, Ribosomal, 16S, Oil and Gas Fields, Phospholipids, Phylogeny, Ecology, Evolution, Behavior and Systematics, Base Composition, Phylogenetic tree, biology, Strain (chemistry), Fatty Acids, Sphaerochaeta, Sequence Analysis, DNA, General Medicine, biology.organism_classification, 16S ribosomal RNA, Spirochaetaceae, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Bacterial Typing Techniques, 030104 developmental biology, Congo, Biochemistry, chemistry, Pleomorphochaeta naphthae, lipids (amino acids, peptides, and proteins), Fermentation, Glycolipids, Bacteria, DNA
Abstract

International audience; A novel anaerobic fermentative bacterium, strain SEBR 4209T, was isolated from a water sample of a Congolese oil field. Strain SEBR 4209T is phylogenetically related to the genus Pleomorphochaeta , in the family Spirochaetaceae . Its closest relatives are Pleomorphochaeta caudata SEBR 4223T (94.5 % 16S rRNA gene sequence similarity) and Pleomorphochaeta multiformis MO-SPC2T (94.3 % similarity). Like the other members of this genus, cells have a pleomorphic morphology, in particular an annular shape and long stalks. Optimal growth was observed at 37 °C, at pH between 6.8 and 7.0, and with 40 g l−1 NaCl. This strain was only able to grow by fermentation of carbohydrates. The fermentation products from glucose utilization were acetate, ethanol, CO2 and H2. Predominant fatty acids were C14 : 0, C14 : 0 DMA, C16 : 0 and C16 : 1ω7c. The major polar lipids were phosphoglycolipids, phospholipids and glycolipids. The G+C content of the DNA was 29.6 mol%. Based on phenotypic characteristics and phylogenetic traits, strain SEBR 4209T is considered to represent a novel species of the genus Pleomorphochaeta , for which the name Pleomorphochaeta naphthae sp. nov. is proposed. The type strain is SEBR 4209T (=DSM 104684T=JCM 31871T).

Published
2018
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8. Biofilm formation as a microbial strategy to assimilate particulate substrates

Author

Régis Grimaud, Laurent Urios, Pierre Sivadon, Claudie Barnier, 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 Conseil Général des Pyrénées Atlantique

Subjects
Pollution, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, media_common.quotation_subject, Extracellular digestion, Microbial Consortia, Microbial metabolism, Bacterial Adhesion, 03 medical and health sciences, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Ecosystem, Organic Chemicals, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, media_common, Total organic carbon, 0303 health sciences, Bacteria, 030306 microbiology, Chemistry, Biofilm, Assimilation (biology), [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [CHIM.MATE]Chemical Sciences/Material chemistry, Particulates, Agricultural and Biological Sciences (miscellaneous), [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Carbon, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.POLY]Chemical Sciences/Polymers, 13. Climate action, Environmental chemistry, Biofilms, Particulate Matter, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; In most ecosystems, a large part of the organic carbon is not solubilized in the water phase. Rather, it occurs as particles made of aggregated hydrophobic and/or polymeric natural or man‐made organic compounds. These particulate substrates are degraded by extracellular digestion/solubilization implemented by heterotrophic bacteria that form biofilms on them. Organic particle‐degrading biofilms are widespread and have been observed in aquatic and terrestrial natural ecosystems, in polluted and man‐driven environments and in the digestive tracts of animals. They have central ecological functions as they are major players in carbon recycling and pollution removal. The aim of this review is to highlight bacterial adhesion and biofilm formation as central mechanisms to exploit the nutritive potential of organic particles. It focuses on the mechanisms that allow access and assimilation of non‐dissolved organic carbon, and considers the advantage provided by biofilms for gaining a net benefit from feeding on particulate substrates. Cooperative and competitive interactions taking place in biofilms feeding on particulate substrates are also discussed.

Published
2019
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9. Description of Palleronia rufa sp. nov., a biofilm-forming and AHL-producing Rhodobacteraceae, reclassification of Hwanghaeicola aestuarii as Palleronia aestuarii comb. nov., Maribius pontilimi as Palleronia pontilimi comb. nov., Maribius salinus as Palleronia salina comb. nov., Maribius pelagius as Palleronia pelagia comb. nov. and emended description of the genus Palleronia

Author

Philippe Lebaron, Laurent Intertaglia, Régis Grimaud, Raphaël Lami, Laurent Urios, Camille Clerissi, Claudie Barnier, 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), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Centre National de la Recherche Scientifique (CNRS)-EDF (EDF)-PIERRE FABRE-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), BIOPIC platform, Conseil Général des Pyrénées-Atlantiques, and Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA)

Subjects
DNA, Bacterial, Acyl-Butyrolactones, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Applied Microbiology and Biotechnology, Microbiology, Roseobacter group, 03 medical and health sciences, Mola, Bacterial Proteins, New Caledonia, Species Specificity, Genus, RNA, Ribosomal, 16S, Sequence Homology, Nucleic Acid, Botany, Seawater, Rhodobacteraceae, Maribius, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Genes, Essential, biology, Strain (chemistry), 030306 microbiology, Biofilm, Quorum Sensing, Sequence Analysis, DNA, Roseobacter, biology.organism_classification, 16S ribosomal RNA, Palleronia, Biofilms, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial
Abstract

International audience; Strain MOLA 401T was isolated from marine waters in the southwest lagoon of New Caledonia and was shown previously to produce an unusual diversity of quorum sensing signaling molecules. This strain was Gram-negative, formed non-motile cocci and colonies were caramel. Optimum growth conditions were 30 °C, pH 8 and 3% NaCl (w/v). Based on 16S rRNA gene sequence analysis, this strain was found to be closely related to Pseudomaribius aestuariivivens NBRC 113039T (96.9% of similarity), Maribius pontilimi DSM 104950T (96.4% of similarity) and Palleronia marisminoris LMG 22959T (96.3% of similarity), belonging to the Roseobacter group within the family Rhodobacteraceae. As its closest relatives, strain MOLA 401T is able to form a biofilm on polystyrene, supporting the view of Roseobacter group strains as prolific surface colonizers. An in-depth genomic study allowed us to affiliate strain MOLA 401T as a new species of genus Palleronia and to reaffiliate some of its closest relatives in this genus. Consequently, we describe strain MOLA 401T (DSM 106827T = CIP 111607T = BBCC 401T) for which we propose the name Palleronia rufa sp. nov. We also propose to emend the description of the genus Palleronia and to reclassify Maribius and Hwanghaeicola species as Palleronia species

Published
2020
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10. Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater

Author

Laurent Intertaglia, Philippe Lebaron, Sonja K. Fagervold, Nicole Batailler, Laurent Urios, and Marcelino T. Suzuki

Subjects
DNA, Bacterial, Ubiquinone, Molecular Sequence Data, Biology, Microbiology, Mediterranean sea, Genus, RNA, Ribosomal, 16S, Botany, Gammaproteobacteria, Mediterranean Sea, Seawater, Gene, Phylogeny, Ecology, Evolution, Behavior and Systematics, chemistry.chemical_classification, Base Composition, Strain (chemistry), Phylogenetic tree, Fatty Acids, Fatty acid, Sequence Analysis, DNA, General Medicine, biology.organism_classification, 16S ribosomal RNA, Bacterial Typing Techniques, chemistry
Abstract

A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115T, was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115T was shown to belong to the Gammaproteobacteria , adjacent to members of the genera Marinicella , Arenicella and Kangiella , sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the Gammaproteobacteria . The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115T included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115T should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115T ( = CIP 110343T = DSM 25350T).

Published
2013
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11. Pleomorphochaeta caudata gen. nov., sp. nov., an anaerobic bacterium isolated from an offshore oil well, reclassification of Sphaerochaeta multiformis MO-SPC2T as Pleomorphochaeta multiformis MO-SPC2T comb. nov. as the type strain of this novel genus and emended description of the genus Sphaerochaeta

Author

Anthony Ranchou-Peyruse, Laurent Urios, Magali Ranchou-Peyruse, Michel Magot, Régis Grimaud, Boussad Arroua, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement (LCPME), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), and Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA)

Subjects
0301 basic medicine, DNA, Bacterial, 030106 microbiology, Pleomorphochaeta caudata, Microbiology, Pleomorphochaeta, 03 medical and health sciences, Type (biology), Genus, RNA, Ribosomal, 16S, [CHIM]Chemical Sciences, Oil and Gas Fields, Seawater, Ecology, Evolution, Behavior and Systematics, Phospholipids, Phylogeny, Base Composition, biology, Phylogenetic tree, Strain (chemistry), Fatty Acids, Sphaerochaeta, General Medicine, Sequence Analysis, DNA, biology.organism_classification, 16S ribosomal RNA, Spirochaetaceae, Bacterial Typing Techniques, Congo, lipids (amino acids, peptides, and proteins), Glycolipids, Bacteria
Abstract

International audience; A strictly anaerobic Gram-stain-negative bacterium, designated strain SEBR 4223T, was isolated from the production water of an offshore Congolese oil field. Cells were non-motile, pleomorphic and had spherical, annular or budding shapes, often exhibiting long stalks. Strain SEBR 4223T grew on a range of carbohydrates, optimally at 37 °C and pH 7, in a medium containing 40 g l−1 NaCl. Predominant fatty acids were C14 : 0, C14 : 0 DMA, C16 : 0 and C16 : 1ω7c and the major polar lipids were phosphoglycolipids, phospholipids, glycolipids and diphosphatidylglycerol. The G+C content of the DNA was 28.7 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain SEBR 4223T and Sphaerochaeta multiformis MO-SPC2T formed a cluster with similarity to other species of the genus Sphaerochaeta of of less than 86 %. On the basis of the phenotypic characteristics and taxonomic analyses, we propose a novel genus, Pleomorphochaeta gen. nov., to accommodate the novel species Pleomorphochaeta caudata sp. nov., with SEBR 4223T (=DSM 103077T=JCM 31 475T) as the type strain. We also propose the reclassification of Sphaerochaeta multiformis MO SPC2T as Pleomorphochaeta multiformis MO-SPC2T comb. nov., the type strain of this novel genus and emend description of the genus Sphaerochaeta

Published
2016
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12. Microbial diversity of the 180 million-year-old Toarcian argillite from Tournemire, France

Author

François Marsal, Laurent Urios, Delphine Pellegrini, Michel Magot, 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), PRP-DGE/SEDRAN/BERIS, and Institut de Radioprotection et de Sûreté Nucléaire (IRSN)

Subjects
0303 health sciences, 030306 microbiology, Aerobic bacteria, Ecology, Microbial diversity, Microorganism, Geochemistry, Biodiversity, Heterotroph, Context (language use), Small ribosomal subunit, Pollution, 03 medical and health sciences, [SDU]Sciences of the Universe [physics], 13. Climate action, Geochemistry and Petrology, Environmental Chemistry, 14. Life underwater, human activities, Water content, Geology, 030304 developmental biology
Abstract

International audience; Even though the microbiology of various subsurface environments has been investigated for more than 30 a, the microbial diversity of deep argillaceous media is still poorly known. In the context of radioactive waste disposal in clayey formations, the consequence of microbial activity is of concern regarding e.g. the corrosion of metallic components. The purpose of the present work was to characterise the cultivable microbial diversity of different zones of the Toarcian argillite of Tournemire (France) as a preliminary indication regarding the potential of development of microbes in such subterrestrial environments. Cores were drilled in the Excavation Damaged Zone (EDZ) and in the deeper undisturbed zone of the argillite layer, as well as in a zone intersected by a geological fault. Samples from the wall of the drift were also collected. Microorganisms were cultivated from all samples, but the biodiversity differed depending mainly on the O 2 and moisture content. Aerobic bacteria were identified on the wall, in the EDZ and in the wet faulted area, whereas SO 4-reducing bacteria were isolated from the wet faulted area only. Anaerobic heterotrophs were cultivated from all zones. One hundred and twelve isolates were identified. Small ribosomal subunit gene sequences showed that bacteria of the undisturbed zone were affiliated to three genera only, whereas the three other sampled zones harbour more diverse microflora, including isolates closely related to taxons characterized from subsurface, deep marine and polar environments. © 2011 .

Published
2012
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13. Thermosipho atlanticus sp. nov., a novel member of the Thermotogales isolated from a Mid-Atlantic Ridge hydrothermal vent

Author

Anne Postec, Georges Barbier, Laurent Urios, Bernard Ollivier, Patricia Pignet, Valérie Cueff-Gauchard, Marie-Laure Fardeau, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, and Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)

Subjects
Arabinose, MESH: Hydrogen-Ion Concentration, MESH: Sequence Analysis, DNA, Hot Temperature, MESH: Saline Solution, Hypertonic, MESH: Movement, Cellobiose, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, chemistry.chemical_compound, RNA, Ribosomal, 16S, Thermophile, Deep sea vent, Anaerobiosis, Mid-Atlantic Region, Organic Chemicals, MESH: Phylogeny, Phylogeny, Acetic Acid, Base Composition, 0303 health sciences, Isovalerate, MESH: RNA, Bacterial: genetics, Ecology, MESH: Organic Chemicals: metabolism, Thermosipho atlanticus, General Medicine, Hydrogen-Ion Concentration, RNA, Bacterial, Water Microbiology, Marine microorganisms, MESH: RNA, Ribosomal, 16S: genetics, DNA, Bacterial, MESH: Acetic Acid: metabolism, Stereochemistry, Movement, MESH: Mid-Atlantic Region, Molecular Sequence Data, MESH: Hot Temperature, Thermotogales, Biology, DNA, Ribosomal, Microbiology, MESH: Fermentation, 03 medical and health sciences, Hemiterpenes, MESH: Base Composition, MESH: Anaerobiosis, MESH: Genes, rRNA, Yeast extract, MESH: DNA, Ribosomal: chemistry,isolation & purification, MESH: Hydrogen: metabolism, Pentanoic Acids, MESH: DNA, Bacterial: chemistry,isolation & purification, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Saline Solution, Hypertonic, MESH: Molecular Sequence Data, Bacteria, 030306 microbiology, Genes, rRNA, MESH: Pentanoic Acids: metabolism, Sequence Analysis, DNA, Ribosomal RNA, 16S ribosomal RNA, MESH: Bacteria: classification,cytology,isolation & purification,metabolism, MESH: Water Microbiology, chemistry, Fermentation, Hydrogen
Abstract

A novel anaerobic, thermophilic and heterotrophic bacterium, designated strain DV1140T, was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were non-motile straight rods, 1·8 μm long and 0·4 μm wide, surrounded by an outer sheath-like structure (toga). They grew at 45–80 °C (optimum 65 °C), pH 5·0–9·0 (optimum pH 6·0) and at sea salt concentrations of 20–60 g l−1(optimum 30 g l−1). Strain DV1140Twas able to ferment yeast extract, peptone, brain heart infusion, gelatin, starch, galactose, arabinose, glucose, trehalose and cellobiose. The fermentation products identified on glucose in the presence of yeast extract and peptone were acetate, isovalerate and hydrogen. The G+C content of the genomic DNA was 33 mol%. Phylogenetic analysis of the 16S rRNA gene sequence (GenBank accession number AJ577471) located the strain within the genusThermosiphoin the bacterial domain. On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species, for which the nameThermosipho atlanticussp. nov. is proposed. The type strain is DV1140T(=CIP 108053T=DSM 15807T).

Published
2004
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14. Methods for Studying Microorganisms in the Environment

Author

Vincent Grossi, Fabien Joux, Patrick Raimbault, Laurent Urios, Pierre Peyret, Laurent Intertaglia, Philippe Lebaron, Rutger De Wit, Valérie Michotey, Philippe Normand, Christian Tamburini, Jean-Claude Bertrand, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Ecologie des systèmes marins côtiers (Ecosym), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-PIERRE FABRE-EDF (EDF)-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), Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), 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), 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 de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-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 pluridisciplinaire de recherche sur l'environnement et les matériaux (IPREM), 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 Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-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), Laboratoire d'Océanographie Microbienne ( LOMIC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -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 ), Ecologie des systèmes marins côtiers ( Ecosym ), Université Montpellier 1 ( UM1 ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] ( LGL-TPE ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Observatoire océanologique de Banyuls ( OOB ), Laboratoire de Biodiversité et Biotechnologies Microbiennes ( LBBM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -PIERRE FABRE-EDF ( EDF ) -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 ), Conception, Ingénierie et Développement de l'Aliment et du Médicament ( CIDAM ), Université d'Auvergne - Clermont-Ferrand I ( UdA ), 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 ), Centre National de la Recherche Scientifique (CNRS)-EDF (EDF)-PIERRE FABRE-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microorganism, analyses, Biology, Cultural techniques, complex mixtures, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, 03 medical and health sciences, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, 030306 microbiology, Ecology, DNA microarray, 15. Life on land, Isolation (microbiology), Pigment analyses, Sampling techniques, Bacterial isolation, PCR, 13. Climate action, Molecular fingerprints, Phospholipid fatty acid, Microbial activities, Biochemical engineering, Microelectrodes, Biomarkers, Cytometry
Abstract

International audience; The main methods for the study of microorganisms in the environment (water, soil, sediment, biofilms), the different techniques of sampling for measuring biomass, the activities, and the diversity of the microorganisms are presented. To respond to these various issues, techniques as varied as those of flow cytometry, molecular biology, biochemistry, molecular isotopic tools, or electrochemistry are implemented. These different techniques are described with their advantages and disadvantages for different types of biotopes. The question of the isolation, culture, and conservation of microorganisms from the environment are also addressed. Without being exhaustive, this chapter emphasizes the importance of using appropriate and efficient methodological tools to properly explore the still mysterious compartment of microorganisms in the environment.

Published
2014
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15. Microbial Diversity at Iron-Clay Interfaces after 10 Years of Interaction Inside a Deep Argillite Geological Formation (Tournemire, France)

Author

François Marsal, Laurent Urios, Michel Magot, Delphine Pellegrini, 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), PRP-DGE/SEDRAN/BERIS, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), and Institut de Radioprotection et de SÛreté Nucléaire, IRSNCentre National de la Recherche Scientifique, CNRS

Subjects
0303 health sciences, geography, geography.geographical_feature_category, 030306 microbiology, Microbial diversity, Borehole, Radioactive waste, Context (language use), Fault (geology), Microbiology, 6. Clean water, Corrosion, 03 medical and health sciences, Geological formation, Mining engineering, [SDU]Sciences of the Universe [physics], Earth and Planetary Sciences (miscellaneous), Environmental Chemistry, Geology, 030304 developmental biology, General Environmental Science, Railway tunnel
Abstract

International audience; In the context of a geological disposal of radioactive waste in clayey formations, the consequences of microbial activity are of concern regarding the corrosion of metallic components. The purpose of the present work was to characterize the microbial diversity that may have impacted corrosion processes at the interface between re-compacted argillite and steel coupons after 10 years of interaction inside the Toarcian argillite layer in Tournemire (France) under in situ conditions. Several types of steel coupons were introduced in 1999 in two boreholes (so-called CR6 and CR8) drilled in the geological formation and filled with re-compacted argillite. CR6 borehole was drilled horizontally from a century-old railway tunnel and coupons were placed in the undisturbed argillite. CR8 borehole was drilled vertically under the tunnel, in conditions influenced by the draining of the Cernon fault water. CR6 and CR8 boreholes were overcored 10 years later and steel coupons as well as re-compacted argillite samples were analyzed separately. The characterization of their microbial diversity was carried out using culture media and molecular methods using 16S rRNA genes cloning. Data resulting from both approaches were complementary. Isolates and clone sequences were affiliated to only 3 bacterial phyla Firmicutes, Actinobacteria and Proteobacteria. The biodiversities differed depending on the steel type and the borehole considered, indicating the influence of both iron-clay interactions and in situ environmental conditions. This analysis has highlighted the presence of sulphate-reducing bacteria, iron-reducing bacteria and isolates capable to develop at high temperatures. These microorganisms can grow at the interfaces between materials in a very short period of time compared with planned durations of disposal. Thus, these results should be considered to assess the consequences of microbial activities on the evolution of the metallic components like overpacks. © 2013 Copyright Taylor and Francis Group, LLC.

Published
2013
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16. Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer

Author

Laurent Urios, Michel Magot, and Laurent Intertaglia

Subjects
DNA, Bacterial, food.ingredient, Molecular Sequence Data, Microbiology, food, Phylogenetics, RNA, Ribosomal, 16S, Agar, Ecology, Evolution, Behavior and Systematics, Pedobacter, Phylogeny, Base Composition, biology, Strain (chemistry), Phylogenetic tree, Ecology, Fatty Acids, Vitamin K 2, General Medicine, Sequence Analysis, DNA, 16S ribosomal RNA, biology.organism_classification, Molecular biology, Bacterial Typing Techniques, genomic DNA, France, Water Microbiology, Bacteria
Abstract

A Gram-negative bacterium, designated TF5-37.2-LB10T, was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10T contained menaquinone 7 and its major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The G+C content of the genomic DNA was 46 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain TF5-37.2-LB10T within the genus Pedobacter , family Sphingobacteriaceae . Pedobacter composti TR6-06T and Pedobacter oryzae DSM 19973T were the closest phylogenetic relatives (93.5 and 93.3 % 16S rRNA gene sequence similarity, respectively). On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain TF5-37.2-LB10T represents a novel species of the genus Pedobacter , for which the name Pedobacter tournemirensis sp. nov. is proposed. The type strain is TF5-37.2-LB10T ( = DSM 23085T = CIP 110085T = MOLA 820T).

Published
2012

17. Méthodes d'études des micro-organismes dans l'environnement. Chapitre 17

Author

Fabien Joux, Jean-Claude Bertrand, Rutger de Wit, Vincent Grossi, Laurent Intertaglia, Philippe Lebaron, Valerie Michotey, Philippe Normand, Pierre Peyret, Patrick Raimbault, Christian Tamburini, Laurent Urios, Laboratoire d'Océanographie Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Ecologie des systèmes marins côtiers (Ecosym), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-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), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-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), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), 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 Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - 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), and Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM)

Subjects
électrochimie, [SDV]Life Sciences [q-bio], micro-organisme, [SDE]Environmental Sciences, biochimie, biologie moléculaire, environnement, isotopie moléculaire
Abstract

Partie 5: Les outils de l'écologie microbienne; National audience

Published
2011

19. Thalassobaculum salexigens sp. nov., a new member of the family Rhodospirillaceae from the NW Mediterranean Sea, and emended description of the genus Thalassobaculum

Author

Laurent Intertaglia, Laurent Urios, Valérie Michotey, Françoise Lesongeur, Philippe Lebaron, Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)

Subjects
DNA, Bacterial, 010504 meteorology & atmospheric sciences, Molecular Sequence Data, DNA, Ribosomal, 01 natural sciences, Microbiology, Agar plate, 03 medical and health sciences, Mediterranean sea, MESH: Base Composition, MESH: Mediterranean Region, RNA, Ribosomal, 16S, Botany, Seawater, 14. Life underwater, MESH: Phylogeny, Rhodospirillaceae, Phylogeny, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, 030304 developmental biology, Base Composition, 0303 health sciences, MESH: DNA, Ribosomal, MESH: Molecular Sequence Data, biology, Phylogenetic tree, Mediterranean Region, 030306 microbiology, Ecology, Fatty Acids, MESH: Seawater, General Medicine, biology.organism_classification, 16S ribosomal RNA, MESH: DNA, Bacterial, MESH: Fatty Acids, MESH: RNA, Ribosomal, 16S, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Taxonomy (biology), Rhodospirillales, MESH: Rhodospirillaceae, Bacteria
Abstract

A novel Gram-negative bacteria, named CZ41_10aT, was isolated from coastal surface waters of the north-western Mediterranean Sea. Cells were motile, pleomorphic rods, 1.6 μm long and 0.7 μm wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the new isolate in the genus Thalassobaculum, a member of the family Rhodospirillaceae, class Alphaproteobacteria. Unlike Thalassobaculum litoreum CL-GR58T, its closest relative, strain CZ41_10aT was unable to grow anaerobically and did not exhibit nitrate reductase activity. On the basis of DNA–DNA hybridization, fatty acid content and physiological and biochemical characteristics, this isolate represents a novel species for which the name Thalassobaculum salexigens sp. nov. is proposed. The type strain is CZ41_10aT (=DSM 19539T=CIP 109064T=MOLA 84T). An emended description of the genus Thalassobaculum is also given.

Published
2010
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20. Nisaea denitrificans gen. nov., sp. nov. and Nisaea nitritireducens sp. nov., two novel members of the class Alphaproteobacteria from the Mediterranean Sea

Author

Laurent Urios, Laurent Intertaglia, Valérie Michotey, Philippe Lebaron, Françoise Lesongeur, Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie biologique de Banyuls (LOBB), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Genotype, RNA, Ribosomal, 16S, Nitrogen Compounds, MESH: Phylogeny, Phylogeny, ComputingMilieux_MISCELLANEOUS, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Base Composition, Phylogenetic tree, General Medicine, Bacterial Typing Techniques, MESH: RNA, Ribosomal, 16S, Phenotype, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Taxonomy (biology), MESH: Genes, Bacterial, Water Microbiology, MESH: Rhodospirillaceae, DNA, Bacterial, Genotype, MESH: Mediterranean Sea, Molecular Sequence Data, Biology, MESH: Phenotype, Microbiology, MESH: Bacterial Typing Techniques, Agar plate, MESH: Nitrogen Compounds, 03 medical and health sciences, MESH: Base Composition, Phylogenetics, MESH: Genes, rRNA, Mediterranean Sea, Seawater, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Molecular Sequence Data, 030306 microbiology, MESH: Seawater, Genes, rRNA, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, MESH: DNA, Bacterial, Rhodospirillaceae, MESH: Water Microbiology, genomic DNA, Genes, Bacterial, Bacteria
Abstract

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2008/publication-5294.pdf; International audience; Two novel Gram-negative bacteria, designated strains DR41_21(T) and DR41_18(T), were isolated from coastal, surface waters of the north-western Mediterranean Sea. The cells were motile, pleomorphic rods, 2.9 microm long and 0.9 microm wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 60 mol%. Phylogenetic analysis of 16S rRNA gene sequences positioned the isolates in the class Alphaproteobacteria within the family Rhodospirillaceae. The 16S rRNA gene sequence similarity of the two strains was 98.8 % but DNA-DNA hybridization indicated only 55 % relatedness. Strain DR41_21(T) was able to denitrify and possessed nirK and nosZ genes, unlike strain DR41_18(T), which possessed only nirK. These isolates represent two novel species of a new genus, Nisaea gen. nov., for which the names Nisaea denitrificans sp. nov. and Nisaea nitritireducens sp. nov. are proposed. The type strain of Nisaea denitrificans is DR41_21(T) (=DSM 18348(T)=CIP 109265(T)=OOB 129(T)) and the type strain of Nisaea nitritireducens is DR41_18(T) (=DSM 19540(T)=CIP 109601(T)=OOB 128(T)).

Published
2008
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21. Balneola alkaliphila sp. nov., a marine bacterium isolated from the Mediterranean Sea

Author

Laurent Intertaglia, Philippe Lebaron, Laurent Urios, Françoise Lesongeur, Laboratoire d'océanographie biologique de Banyuls (LOBB), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)

Subjects
DNA, Bacterial, MESH: Sequence Analysis, DNA, MESH: Mediterranean Sea, Sequence analysis, Molecular Sequence Data, Biology, Microbiology, DNA, Ribosomal, MESH: Bacterial Typing Techniques, Agar plate, 03 medical and health sciences, Mediterranean sea, MESH: Base Composition, Species Specificity, Phylogenetics, RNA, Ribosomal, 16S, Botany, MESH: Genes, rRNA, Mediterranean Sea, MESH: Species Specificity, Seawater, 14. Life underwater, MESH: Phylogeny, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, Base Composition, MESH: DNA, Ribosomal, MESH: Molecular Sequence Data, Phylogenetic tree, 030306 microbiology, Ecology, Bacteroidetes, MESH: Seawater, Genes, rRNA, General Medicine, Sequence Analysis, DNA, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, MESH: DNA, Bacterial, MESH: Bacteroidetes, Bacterial Typing Techniques, MESH: RNA, Ribosomal, 16S, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Bacteria
Abstract

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2008/publication-5292.pdf; International audience; A novel aerobic, Gram-negative bacterium, designated strain CM41_14b(T), was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were non-motile, straight rods, 2.6 microm long and 0.7 microm wide and formed pale-orange colonies on marine agar medium. The G+C content of the genomic DNA was 39 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain within the genus Balneola (phylum Bacteroidetes). On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species for which the name Balneola alkaliphila sp. nov. is proposed. The type strain is CM41_14b(T) (=DSM 19538(T)=CIP 109603(T)=OOB 103(T)).

Published
2008
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22. Haliea salexigens gen. nov., sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea

Author

Laurent Intertaglia, Philippe Lebaron, Laurent Urios, Françoise Lesongeur, Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie biologique de Banyuls (LOBB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)

Subjects
MESH: Sequence Analysis, DNA, MESH: Genotype, Mediterranean sea, RNA, Ribosomal, 16S, MESH: Phylogeny, Phylogeny, 0303 health sciences, Base Composition, MESH: DNA, Ribosomal, biology, Phylogenetic tree, Ecology, Alteromonadaceae, General Medicine, Bacterial Typing Techniques, MESH: RNA, Ribosomal, 16S, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Phenotype, Taxonomy (biology), DNA, Bacterial, MESH: Mediterranean Sea, Genotype, Sequence analysis, Molecular Sequence Data, MESH: Phenotype, Microbiology, DNA, Ribosomal, MESH: Bacterial Typing Techniques, 03 medical and health sciences, MESH: Base Composition, Species Specificity, Phylogenetics, Gammaproteobacteria, Botany, MESH: Genes, rRNA, Mediterranean Sea, MESH: Species Specificity, Seawater, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Molecular Sequence Data, 030306 microbiology, MESH: Seawater, Genes, rRNA, Sequence Analysis, DNA, Ribosomal RNA, biology.organism_classification, 16S ribosomal RNA, MESH: DNA, Bacterial, MESH: Alteromonadaceae
Abstract

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2008/publication-4193.pdf; International audience; A novel aerobic, Gram-negative bacterium, designated 3X/A02/235T, was isolated from the surface of coastal waters in the north-western Mediterranean Sea. Cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 61 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria and within the family Alteromonadaceae. On the basis of 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, this isolate represents a novel species of a novel genus, for which the name Haliea salexigens gen. nov., sp. nov. is proposed. The type strain of Haliea salexigens is 3X/A02/235T (=DSM 19537T =CIP 109602T =MOLA 286T).

Published
2008
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23. Melitea salexigens gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea

Author

Laurent Intertaglia, Laurent Urios, Philippe Lebaron, Françoise Lesongeur, Hélène Agogué, Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Royal Netherlands Institute for Sea Research (NIOZ), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, DNA, Bacterial, food.ingredient, Molecular Sequence Data, 010603 evolutionary biology, 01 natural sciences, Microbiology, DNA, Ribosomal, Melitea salexigens, 03 medical and health sciences, Mediterranean sea, food, Species Specificity, RNA, Ribosomal, 16S, Botany, Mediterranean Sea, Agar, Seawater, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, Base Composition, biology, Phylogenetic tree, Ecology, Alteromonadaceae, Fatty Acids, Genes, rRNA, General Medicine, Sequence Analysis, DNA, 16S ribosomal RNA, biology.organism_classification, Bacterial Typing Techniques, genomic DNA, Phenotype, Taxonomy (biology), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bacteria, Gammaproteobacteria
Abstract

International audience; A novel aerobic, Gram-negative bacterial strain, designated 5IX/A01/131 T , was isolated from waters in the coastal north-western Mediterranean Sea. The cells were motile, straight rods, 1.6 mm long and 0.5 mm wide, and formed cream colonies on marine 2216 agar. The G+C content of the genomic DNA was 57 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, strain 5IX/A01/ 131 T represents a novel genus and species, for which the name Melitea salexigens gen. nov., sp. nov. is proposed. The type strain of Melitea salexigens is 5IX/A01/131 T (=DSM 19753 T = CIP 109757 T = MOLA 225 T).

Published
2008
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24. Balneola vulgaris gen. nov., sp. nov., a member of the phylum Bacteroidetes from the north-western Mediterranean Sea

Author

Erko Stackebrandt, Hélène Agogué, Philippe Lebaron, Laurent Urios, Françoise Lesongeur, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, Physiology, Molecular Sequence Data, Gene sequence, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Biochemistry, Microbiology, Agar plate, 03 medical and health sciences, Mediterranean sea, Species Specificity, Phylogenetics, RNA, Ribosomal, 16S, Sequence Homology, Nucleic Acid, Balneola vulgaris, Botany, Mediterranean Sea, 14. Life underwater, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, Bacteroidetes, 030306 microbiology, Ecology, Nucleic Acid Hybridization, General Medicine, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Culture Media, Agar, RNA, Bacterial, Coastal waters, Taxonomy (biology), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Water Microbiology, Genome, Bacterial, Locomotion, Bacteria
Abstract

A novel aerobic, Gram-negative bacterium, named 13IX/A01/164T, was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were motile, straight rods, 2.5 μm long and 0.2 μm wide, and formed orange colonies on marine agar medium. The G+C content of the genomic DNA of strain 13IX/A01/164T was 42 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the phylum Bacteroidetes within the family Crenotrichaceae. On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name Balneola vulgaris gen. nov., sp. nov. is proposed. The type strain of Balneola vulgaris is 13IX/A01/164T (=DSM 17893T=CIP 109092T=OOB 256T).

Published
2006
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25. Continuous enrichment culture and molecular monitoring to investigate the microbial diversity of thermophiles inhabiting deep-sea hydrothermal ecosystems

Author

Françoise Lesongeur, Anne Godfroy, Anne Postec, Joël Querellou, Bernard Ollivier, Laurent Urios, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, Hot Temperature, Pyrococcus, Microorganism, Molecular Sequence Data, Bacillus, Thermotogales, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, Microbiology, Enrichment culture, 03 medical and health sciences, Bioreactors, Sequence alignment, RNA, Ribosomal, 16S, Thermophile, Botany, Anaerobic digester, Bioreactor, Deep sea vent, Seawater, Atlantic Ocean, Ecosystem, Phylogeny, 030304 developmental biology, 0303 health sciences, Epsilonproteobacteria, Base Sequence, biology, 030306 microbiology, General Medicine, biology.organism_classification, Culture Media, Thermococcus, DNA, Archaeal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Hydrothermal vent
Abstract

The microflora developing during a continuous enrichment culture from a hydrothermal chimney sample was investigated by molecular methods. The culture was performed in a gas-lift bioreactor under anaerobic conditions, at 90 degrees C and pH 6.5, on a complex medium containing sulfur as the terminal electron acceptor. Archaeal and bacterial diversity was studied. Microorganisms affiliated with the genera Pyrococcus, Marinitoga, and Bacillus were detected through DGGE analysis of 16S rDNA. Additional sequences phylogenetically related to Thermococcus and epsilon-Proteobacteria were detected by cloning and sequencing of 16S rDNA from two samples of the enrichment culture. In comparison, the sequences retrieved from cloning analysis from an enrichment culture performed in a flask (batch condition) using the same culture medium showed that only members of the genus Thermococcus were cultivated. Therefore, continuous enrichment culture using the gas-lift bioreactor can be considered as an efficient and improved method for investigating microbial communities originating from deep-sea hydrothermal vents.

Published
2005
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26. Molecular structure of bacterial biofilms involved in iron biocorrosion

Author

Florence Mercier-Bion, Catherine Berthomieu, virginie chapon, Jean-Paul Gallien, Laurent Urios, Delphine Neff, Philippe Dillmann, Laboratoire Archéomatériaux et Prévision de l'Altération (LAPA - UMR 3685), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), IRAMAT - Laboratoire Métallurgies et Cultures (IRAMAT - LMC), Institut de Recherches sur les Archéomatériaux (IRAMAT), Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Université Bordeaux Montaigne (UBM)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Université Bordeaux Montaigne (UBM)-Centre National de la Recherche Scientifique (CNRS), 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), 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Technologie de Belfort-Montbeliard (UTBM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and 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)

Subjects
[CHIM.MATE]Chemical Sciences/Material chemistry
Abstract

International audience; To a better knowledge of iron biocorrosion mechanisms occurring in different applications (nuclear context, petroleum industry, cultural heritage,…), it is crucial to define which bacteria are active and their role. Despite a wide literature on the influence of bacteria on iron corrosion rates, most often considering a single metabolic group (Iron-Reducing Bacteria IRB, Sulfate-Reducing Bacteria SRB), the role of each species in a population involving various metabolisms possibly affecting corrosion remains unknown. At the same time, it is also essential to identify the corrosion products and to be able to link them to a possible bacterial activity. Our study is then devoted to the local diagnostic of the action of bacterial strains in iron corrosion. An innovative methodology for diagnosing the active bacterial strains in iron corrosion at the micrometric scale was developed by using vibrational techniques such as Attenuated Total Reflection Infra-Red ATR-IR and μRaman spectroscopies. The first step was the setup of a preparation protocol and its optimization for the characterization of bacteria by ATR-IR to obtain the vibrational fingerprint of bacterial strains performing metabolisms already identified in the nuclear context (IRB, SRB and sulfate-oxidizing bacteria SOB). The spectral fingerprint was also determined for iron coupons corroded in the presence of each strain. The question of the ability to discriminate the strains, whether planktonic or in biofilm, by their vibrational fingerprint was resolved. Indeed, the discrimination of the three bacterial strains was possible in the spectral region around 1000 cm-1. Furthermore, the strains evidenced spectra differences according to their growth mode: for strains in planktonic form, the most intense bands of the IR spectrum were those of amide I and II while for the ones in biofilm form, these were the bands of exopolysaccharides (compounds excreted by bacteria when they form biofilms) in the region around 1000 cm-1. These results allow discrimination by the ATR-IR spectrum of different bacterial strains in planktonic or in biofilm form. Since both the three strains but also their form (planktonic or biofilm) were distinguishable by their IR spectrum, experiments were conducted on iron coupons corroded with the bacterial consortium. The objective was to determine the active strains and to couple this information with the nature of the corrosion products. This diagnostic tool for bacterial signature determination can be transposed to a variety of corrosion problems providing significant benefits.

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