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1. High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water

Author

Jarrige, Domitille, Haridas, Sajeet, Bleykasten-Grosshans, Claudine, Joly, Muriel, Nadalig, Thierry, Sancelme, Martine, Vuilleumier, Stéphane, Grigoriev, Igor V, Amato, Pierre, and Bringel, Françoise

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Saccharomyces cerevisiae, Water, Basidiomycota, Sequence Analysis, DNA, Tremellaceae, mitochondrial genome, de novo sequencing, fungi, airborne microorganisms, transposable elements, Dioszegia hungarica strain PDD-24b-2, aeromicrobiology, fungal spore, cold environment, Dioszegia hungarica strain PDD-24b-2, Tremellaceae, Biochemistry and cell biology, Statistics
Abstract

The genome of the basidiomycete yeast Dioszegia hungarica strain PDD-24b-2 isolated from cloud water at the summit of puy de Dôme (France) was sequenced using a hybrid PacBio and Illumina sequencing strategy. The obtained assembled genome of 20.98 Mb and a GC content of 57% is structured in 16 large-scale contigs ranging from 90 kb to 5.56 Mb, and another 27.2 kb contig representing the complete circular mitochondrial genome. In total, 8,234 proteins were predicted from the genome sequence. The mitochondrial genome shows 16.2% cgu codon usage for arginine but has no canonical cognate tRNA to translate this codon. Detected transposable element (TE)-related sequences account for about 0.63% of the assembled genome. A dataset of 2,068 hand-picked public environmental metagenomes, representing over 20 Tbp of raw reads, was probed for D. hungarica related ITS sequences, and revealed worldwide distribution of this species, particularly in aerial habitats. Growth experiments suggested a psychrophilic phenotype and the ability to disperse by producing ballistospores. The high-quality assembled genome obtained for this D. hungarica strain will help investigate the behavior and ecological functions of this species in the environment.

Published
2022

3. Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems.

Author

Frindte, Katharina, Kalyuzhnaya, Marina G, Bringel, Françoise, Dunfield, Peter F, Jetten, Mike SM, Khmelenina, Valentina N, Klotz, Martin G, Murrell, J Colin, Op den Camp, Huub JM, Sakai, Yasuyoshi, Semrau, Jeremy D, Shapiro, Nicole, DiSpirito, Alan A, Stein, Lisa Y, Svenning, Mette M, Trotsenko, Yuri A, Vuilleumier, Stéphane, Woyke, Tanja, and Knief, Claudia

Subjects
Biochemistry and Cell Biology, Genetics, Microbiology
Abstract

The genomes of the aerobic methanotrophs "Methyloterricola oryzae" strain 73aT and Methylomagnum ishizawai strain 175 were sequenced. Both strains were isolated from rice plants. Methyloterricola oryzae strain 73aT represents the first isolate of rice paddy cluster I, and strain 175 is the second representative of the recently described genus Methylomagnum.

Published
2017

4. Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems

Author

Flynn, James D, Hirayama, Hisako, Sakai, Yasuyoshi, Dunfield, Peter F, Klotz, Martin G, Knief, Claudia, Camp, Huub JM Op den, Jetten, Mike SM, Khmelenina, Valentina N, Trotsenko, Yuri A, Murrell, J Colin, Semrau, Jeremy D, Svenning, Mette M, Stein, Lisa Y, Kyrpides, Nikos, Shapiro, Nicole, Woyke, Tanja, Bringel, Françoise, Vuilleumier, Stéphane, DiSpirito, Alan A, and Kalyuzhnaya, Marina G

Subjects
Microbiology, Biological Sciences, Genetics, Life Below Water
Abstract

The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems.

Published
2016

5. Draft Genomes of Gammaproteobacterial Methanotrophs Isolated from Terrestrial Ecosystems

Author

Hamilton, Richard, Kits, K Dimitri, Ramonovskaya, Victoria A, Rozova, Olga N, Yurimoto, Hiroya, Iguchi, Hiroyuki, Khmelenina, Valentina N, Sakai, Yasuyoshi, Dunfield, Peter F, Klotz, Martin G, Knief, Claudia, Camp, Huub JM Op den, Jetten, Mike SM, Bringel, Françoise, Vuilleumier, Stéphane, Svenning, Mette M, Shapiro, Nicole, Woyke, Tanja, Trotsenko, Yuri A, Stein, Lisa Y, and Kalyuzhnaya, Marina G

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Biochemistry and Cell Biology
Abstract

Genome sequences of Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata, Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems.

Published
2015

6. Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki

Author

Sharp, Christine E, Smirnova, Angela V, Kalyuzhnaya, Marina G, Bringel, Françoise, Hirayama, Hisako, Jetten, Mike SM, Khmelenina, Valentina N, Klotz, Martin G, Knief, Claudia, Kyrpides, Nikos, Camp, Huub JM Op den, Reshetnikov, Alexander S, Sakai, Yasuyoshi, Shapiro, Nicole, Trotsenko, Yuri A, Vuilleumier, Stéphane, Woyke, Tanja, and Dunfield, Peter F

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Biotechnology, Biochemistry and Cell Biology
Abstract

Methylohalobius crimeensis strain 10Ki is a moderately halophilic aerobic methanotroph isolated from a hypersaline lake in the Crimean Peninsula, Ukraine. This organism has the highest salt tolerance of any cultured methanotroph. Here, we present a draft genome sequence of this bacterium.

Published
2015

10. Exploring metabolic acclimation of the cloud microflora to contrasting summer day and winter night conditions using metatranscriptomics and fluxomics approaches

Author

Joly, Muriel, primary, Jarrige, Domitille, additional, Vyscocil, Jonathan, additional, Rossi, Florent, additional, Judon, Céline, additional, Bringel, Françoise, additional, Muller, Emilie E.L., additional, Vuilleumier, Stéphane, additional, Nadalig, Thierry, additional, Portais, Jean-Charles, additional, Peyriga, Lindsay, additional, Bellvert, Floriant, additional, Kulyk, Hanna, additional, Bianco, Angelica, additional, Deguillaume, Laurent, additional, Delort, Anne-Marie, additional, and Amato, Pierre, additional

Published
2023
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13. Additional file 2 of A putatively new family of alphaproteobacterial chloromethane degraders from a deciduous forest soil revealed by stable isotope probing and metagenomics

Author

Kröber, Eileen, Kanukollu, Saranya, Wende, Sonja, Bringel, Françoise, and Kolb, Steffen

Abstract

Additional file 2. Figure S1: CH3Cl degradation in deciduous forest soil samples during SIP incubations. Figure S2: CH3Cl degradation in control deciduous forest soil samples during SIP incubations. Figure S3: Relative distribution of terminal restriction fragments detected by bacterial T-RFLP of fractionated DNA from [13C]-CH3Cl and [12C]-CH3Cl SIP incubations of mineral and organic soil samples and degraded leave samples from Steigerwald after incorporation of 100 μmol C g-1 sample, Figure S4: Relative distribution and phylogenetic affiliation of OTUs detected by bacterial 16S rRNA high-throughput amplicon sequencing of samples before SIP experiments (T0) and fractionated DNA from [13C]-CH3Cl and [12C]-CH3Cl SIP incubations of mineral and organic soil samples and degraded leave samples from Steigerwald after incorporation of 100 μmol C g−1 sample. Figure S5: Average nucleotide identity (ANI) analysis of “Degraded leaves bin 11” and the closely related Granulicella mallensis and AAI analysis between those two species. Figure S6: Metabolic reconstruction of [13C]-CH3Cl labelled metagenome assembled genome “Degraded leaves bin 11” (closely related to Granulicella mallensis). Table S1: Summary of metagenome-assembled genomes (MAGs) from the CH3Cl-stable isotope probing enrichment.

Published
2022
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17. Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics

Author

Hayoun, Karim, Geersens, Emilie, Laczny, Cedric Christian, Halder, Rashi, Lázaro Sánchez, Carmen, Manna, Abhijit, Bringel, Françoise, Ryckelynck, Michaël, Wilmes, Paul, Muller, Emilie, Alpha-Bazin, Armengaud, and Vuilleumier, Stéphane

Subjects
genome sequencing, Nanopore, Microbiologie [F11] [Sciences du vivant], Hyphomicrobium, dcm genes, pan-proteomics, Microbiology [F11] [Life sciences], dehalogenation, differential proteomics, dichloromethane
Published
2020

20. Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics

Author

Hayoun, Karim, primary, Geersens, Emilie, additional, Laczny, Cédric C., additional, Halder, Rashi, additional, Lázaro Sánchez, Carmen, additional, Manna, Abhijit, additional, Bringel, Françoise, additional, Ryckelynck, Michaël, additional, Wilmes, Paul, additional, Muller, Emilie E. L., additional, Alpha-Bazin, Béatrice, additional, Armengaud, Jean, additional, and Vuilleumier, Stéphane, additional

Published
2020
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23. Special issue 'Microbial one-carbon metabolism of natural and engineered systems'

Author

Bringel, Françoise, EL Muller, Emilie, Vuilleumier, Stéphane, Génétique moléculaire, génomique, microbiologie (GMGM), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDE.IE]Environmental Sciences/Environmental Engineering, [SDE.MCG]Environmental Sciences/Global Changes, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, carbon cycling, synthetic biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, one-carbon metabolism, microbial ecology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract

International audience; The goal of this Special Issue will be to provide a broad overview of the recent breakthroughs and current questions in the dynamic field of microbial C1 metabolism, as a crucial component of the biogeochemical processes of the planet in the Anthropocene. Contributions will range from the molecular level of model systems, to the global scale of environmental ecosystems, biogeochemical cycles, and natural and engineered ecosystems. The Special Issue will present fundamental and applied research on microorganisms, both cultured and uncultured, that are able to use C1 compounds, and compounds lacking carbon–carbon bonds for growth, including, for example, autotrophs, methylotrophs, phototrophs, methanogens, and acetogens. Topics will cover the physiology, genetics, ecology, and evolution of the microbial C1 metabolism in emblematic environments and ecosystems, corresponding to processes of chemical and light energy conversion, key enzymes of microbial C1 metabolism, and biotechnological applications in the context of the ongoing massive global change.

Published
2019

26. 13C‐chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern.

Author

Kröber, Eileen, Wende, Sonja, Kanukollu, Saranya, Buchen‐Tschiskale, Caroline, Besaury, Ludovic, Keppler, Frank, Vuilleumier, Stéphane, Kolb, Steffen, and Bringel, Françoise

Subjects
OZONE layer depletion, METHYL chloride, METHYLOTROPHIC bacteria, ORGANOHALOGEN compounds, FERNS, OZONE layer
Abstract

Summary: Chloromethane (CH3Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH3Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH3Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH3Cl‐degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13C‐labelled CH3Cl combined with metagenomics. Metagenome‐assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH3Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH3Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH3Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA‐independent pathway may drive CH3Cl degradation in the investigated tree ferns. [ABSTRACT FROM AUTHOR]

Published
2021
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27. Microbial sink of an abundant halogenated hydrocarbon in soil and at the soil-plant-atmosphere interphase - Microorganisms as sinks of atmospheric chloromethane

Author

Kröber, Eileen, Morawe, Mareen, Chaignaud, Pauline, Besaury, Ludovic, Vuilleumier, Stéphane, Bringel, Françoise, Kolb, Steffen, Leibniz-Zentrum für Agrarlandschaftsforschung (ZALF), Leibniz Association, Universität Bayreuth, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), and ANR-14-CE35-0005,CHLOROFILTER,Impact of microorganisms as sinks of atmospheric chloromethane(2014)

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV]Life Sciences [q-bio], chloromethane, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, methylotrophy, one-carbon metabolism, ComputingMilieux_MISCELLANEOUS, plant microbiome, soil
Abstract

International audience

Published
2018

28. A Promiscuous CYP706A3 Reduces Terpene Volatile Emission from Arabidopsis Flowers, Affecting Florivores and the Floral Microbiome

Author

Boachon, Benoît, primary, Burdloff, Yannick, additional, Ruan, Ju-Xin, additional, Rojo, Rakotoharisoa, additional, Junker, Robert R., additional, Vincent, Bruno, additional, Nicolè, Florence, additional, Bringel, Françoise, additional, Lesot, Agnès, additional, Henry, Laura, additional, Bassard, Jean-Etienne, additional, Mathieu, Sandrine, additional, Allouche, Lionel, additional, Kaplan, Ian, additional, Dudareva, Natalia, additional, Vuilleumier, Stéphane, additional, Miesch, Laurence, additional, André, François, additional, Navrot, Nicolas, additional, Chen, Xiao-Ya, additional, and Werck-Reichhart, Danièle, additional

Published
2019
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29. Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance

Author

Marchioni Eric, Bringel Françoise, Izquierdo Esther, Horvatovich Peter, Hamon Erwann, Aoudé-Werner Dalal, and Ennahar Saïd

Subjects
Microbiology, QR1-502
Abstract

Abstract Background Lactic acid bacteria are commonly marketed as probiotics based on their putative or proven health-promoting effects. These effects are known to be strain specific but the underlying molecular mechanisms remain poorly understood. Therefore, unravelling the determinants behind probiotic features is of particular interest since it would help select strains that stand the best chance of success in clinical trials. Bile tolerance is one of the most crucial properties as it determines the ability of bacteria to survive in the small intestine, and consequently their capacity to play their functional role as probiotics. In this context, the objective of this study was to investigate the natural protein diversity within the Lactobacillus plantarum species with relation to bile tolerance, using comparative proteomics. Results Bile tolerance properties of nine L. plantarum strains were studied in vitro. Three of them presenting different bile tolerance levels were selected for comparative proteomic analysis: L. plantarum 299 V (resistant), L. plantarum LC 804 (intermediate) and L. plantarum LC 56 (sensitive). Qualitative and quantitative differences in proteomes were analyzed using two-dimensional electrophoresis (2-DE), tryptic digestion, liquid chromatography-mass spectrometry analysis and database search for protein identification. Among the proteins correlated with differences in the 2-DE patterns of the bacterial strains, 15 have previously been reported to be involved in bile tolerance processes. The effect of a bile exposure on these patterns was investigated, which led to the identification of six proteins that may be key in the bile salt response and adaptation in L. plantarum: two glutathione reductases involved in protection against oxidative injury caused by bile salts, a cyclopropane-fatty-acyl-phospholipid synthase implicated in maintenance of cell envelope integrity, a bile salt hydrolase, an ABC transporter and a F0F1-ATP synthase which participate in the active removal of bile-related stress factors. Conclusions These results showed that comparative proteomic analysis can help understand the differential bacterial properties of lactobacilli. In the field of probiotic studies, characteristic proteomic profiles can be identified for individual properties that may serve as bacterial biomarkers for the preliminary selection of strains with the best probiotic potential.

Published
2011
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30. Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere

Author

Farhan Ul Haque, Muhammad, Besaury, Ludovic, Nadalig, Thierry, Bringel, Françoise, Mutterer, Jérome, Schaller, Hubert, Vuilleumier, Stéphane, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Clermont-Ferrand (ICCF), SIGMA Clermont (SIGMA Clermont)-Institut de Chimie du CNRS (INC)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Higher Education Commission Pakistan, REALISE, the Alsace network of laboratories in environmental sciences and engineering (realise.unistra.fr), INSU - CNRS EC2CO project PLANTACHLORE, and DFG-ANR project CHLOROFILTER [ANR-14-CE35-0005-01, DFG KE 884/10-1]

Subjects
Arabidopsis Proteins, [SDV]Life Sciences [q-bio], lcsh:R, fungi, Arabidopsis, lcsh:Medicine, food and beverages, Biodiversity, Methyltransferases, Article, Bacterial Proteins, Gene Expression Regulation, Plant, [SDE]Environmental Sciences, Methyl Chloride, lcsh:Q, lcsh:Science
Abstract

International audience; Chloromethane (CH(3)Cl) is a toxic gas mainly produced naturally, in particular by plants, and its emissions contribute to ozone destruction in the stratosphere. Conversely, CH(3)Cl can be degraded and used as the sole carbon and energy source by specialised methylotrophic bacteria, isolated from a variety of environments including the phyllosphere, i.e. the aerial parts of vegetation. The potential role of phyllospheric CH(3)Cl-degrading bacteria as a filter for plant emissions of CH(3)Cl was investigated using variants of Arabidopsis thaliana with low, wild-type and high expression of HOL1 methyltransferase previously shown to be responsible for most of CH(3)Cl emissions by A. thaliana. Presence and expression of the bacterial chloromethane dehalogenase cmuA gene in the A. thaliana phyllosphere correlated with HOL1 genotype, as shown by qPCR and RT-qPCR. Production of CH(3)Cl by A. thaliana paralleled HOL1 expression, as assessed by a fluorescence-based bioreporter. The relation between plant production of CH(3)Cl and relative abundance of CH(3)Cl-degrading bacteria in the phyllosphere suggests that CH(3)Cl-degrading bacteria co-determine the extent of plant emissions of CH(3)Cl to the atmosphere.

Published
2017

31. Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium

Author

Chaignaud, Pauline, Maucourt, Bruno, Weiman, Marion, Alberti, Adriana, Kolb, Steffen, Cruveiller, Stéphane, Vuilleumier, Stéphane, Bringel, Françoise, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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 Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Universität Bayreuth, 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), and 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)

Subjects
Microbiology (medical), genomic island, genome adaptation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], chloromethane, GEI, dehalogenation, methylotrophy, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, dichloromethane, Original Research
Abstract

International audience; Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains. In terms of gene content, adaptation toward dehalogenation appears limited, strains CM4 and DM4 sharing between 75 and 85% of their genome with other strains of M. extorquens. Transcript abundance in cultures of strain CM4 grown with chloromethane and of strain DM4 grown with dichloromethane was compared to growth with methanol as a reference C1 growth substrate. Previously identified strain-specific dehalogenase-encoding genes were the most transcribed with chlorinated methanes, alongside other genes encoded by genomic islands (GEIs) and plasmids involved in growth with chlorinated compounds as carbon and energy source. None of the 163 genes shared by strains CM4 and DM4 but not by other strains of M. extorquens showed higher transcript abundance in cells grown with chlorinated methanes. Among the several thousand genes of the M. extorquens core genome, 12 genes were only differentially abundant in either strain CM4 or strain DM4. Of these, 2 genes of known function were detected, for the membrane-bound proton translocating pyrophosphatase HppA and the housekeeping molecular chaperone protein DegP. This indicates that the adaptive response common to chloromethane and dichloromethane is limited at the transcriptional level, and involves aspects of the general stress response as well as of a dehalogenation-specific response to intracellular hydrochloric acid production. Core genes only differentially abundant in either strain CM4 or strain DM4 total 13 and 58 CDS, respectively. Taken together, the obtained results suggest different transcriptional responses of chloromethane- and dichloromethane-degrading M. extorquens strains to dehalogenative metabolism, and substrate- and pathway-specific modes of growth optimization with chlorinated methanes.

Published
2017

32. The Phyllosphere as a habitat for microbial trace gas consumers

Author

Bringel, Françoise, Couée, Ivan, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Steffen Kolb, Marcus A. Horn, J. Colin Murrell, Claudia Knief, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Briand, Valerie

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

33. Promiscuous CYP706A3 Reduces Terpene Volatile Emission from Arabidopsis Flowers, Affecting Florivores and the Floral Microbiome.

Author

1, Benoît Boachon, Burdloff, Yannick, Ruan, Ju-Xin, Rojo, Rakotoharisoa, Junker, Robert R., Vincent, Bruno, Nicolè, Florence, Bringel, Françoise, Lesot, Agnès, Henry, Laura, Bassard, Jean-Etienne, Mathieu, Sandrine, Allouche, Lionel, Kaplan, Ian, Dudareva, Natalia, Vuilleumier, Stéphane, Miesch, Laurence, André, François, Navrot, Nicolas, and Chen, Xiao-Ya

Published
2019
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34. Chloromethane formation and degradation in the fern phyllosphere

Author

Jaeger, Nicole, primary, Besaury, Ludovic, additional, Röhling, Amelie Ninja, additional, Koch, Fabien, additional, Delort, Anne-Marie, additional, Gasc, Cyrielle, additional, Greule, Markus, additional, Kolb, Steffen, additional, Nadalig, Thierry, additional, Peyret, Pierre, additional, Vuilleumier, Stéphane, additional, Amato, Pierre, additional, Bringel, Françoise, additional, and Keppler, Frank, additional

Published
2018
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36. Chloromethane Degradation in Soils: A Combined Microbial and Two-Dimensional Stable Isotope Approach

Author

Jaeger, Nicole, primary, Besaury, Ludovic, additional, Kröber, Eileen, additional, Delort, Anne-Marie, additional, Greule, Markus, additional, Lenhart, Katharina, additional, Nadalig, Thierry, additional, Vuilleumier, Stéphane, additional, Amato, Pierre, additional, Kolb, Steffen, additional, Bringel, Françoise, additional, and Keppler, Frank, additional

Published
2018
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38. Transfer of a Catabolic Pathway for Chloromethane in Methylobacterium Strains Highlights Different Limitations for Growth with Chloromethane or with Dichloromethane

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Michener, Joshua K, Vuilleumier, Stéphane, Bringel, Françoise, Marx, Christopher J., Massachusetts Institute of Technology. Department of Biological Engineering, Michener, Joshua K, Vuilleumier, Stéphane, Bringel, Françoise, and Marx, Christopher J.

Abstract

Chloromethane (CM) is an ozone-depleting gas, produced predominantly from natural sources, that provides an important carbon source for microbes capable of consuming it. CM catabolism has been difficult to study owing to the challenging genetics of its native microbial hosts. Since the pathways for CM catabolism show evidence of horizontal gene transfer, we reproduced this transfer process in the laboratory to generate new CM-catabolizing strains in tractable hosts. We demonstrate that six putative accessory genes improve CM catabolism, though heterologous expression of only one of the six is strictly necessary for growth on CM. In contrast to growth of Methylobacterium strains with the closely related compound dichloromethane (DCM), we find that chloride export does not limit growth on CM and, in general that the ability of a strain to grow on DCM is uncorrelated with its ability to grow on CM. This heterologous expression system allows us to investigate the components required for effective CM catabolism and the factors that limit effective catabolism after horizontal transfer., National Institutes of Health (U.S.) (Grant F32 GM106629)

Published
2017

40. Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21

Author

Bringel, Françoise, primary, Postema, Christiaan P., additional, Mangenot, Sophie, additional, Bibi-Triki, Sabrina, additional, Chaignaud, Pauline, additional, Farhan Ul Haque, Muhammad, additional, Gruffaz, Christelle, additional, Hermon, Louis, additional, Louhichi, Yousra, additional, Maucourt, Bruno, additional, Muller, Emilie E. L., additional, Nadalig, Thierry, additional, Lajus, Aurélie, additional, Rouy, Zoé, additional, Médigue, Claudine, additional, Barbe, Valérie, additional, Janssen, Dick B., additional, and Vuilleumier, Stéphane, additional

Published
2017
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42. Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics

Author

Bringel, Françoise, Couée, Ivan, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
plant–microorganism interactions, aerial plant organs, environmental genomics, volatile organic compounds, plant-microorganism interactions, lcsh:QR1-502, phyllosphere–atmosphere interface, Review, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microbiology, phyllosphere-atmosphere interface, lcsh:Microbiology, global change
Abstract

International audience; The phyllosphere, which lato sensu consists of the aerial parts of plants, and therefore primarily, of the set of photosynthetic leaves, is one of the most prevalent microbial habitats on earth. Phyllosphere microbiota are related to original and specific processes at the interface between plants, microorganisms and the atmosphere. Recent –omics studies have opened fascinating opportunities for characterizing the spatio-temporal structure of phyllosphere microbial communities in relation with structural, functional, and ecological properties of host plants, and with physico-chemical properties of the environment, such as climate dynamics and trace gas composition of the surrounding atmosphere. This review will analyze recent advances, especially those resulting from environmental genomics, and how this novel knowledge has revealed the extent of the ecosystemic impact of the phyllosphere at the interface between plants and atmosphere. Highlights• The phyllosphere is one of the most prevalent microbial habitats on earth. • Phyllosphere microbiota colonize extreme, stressful, and changing environments.• Plants, phyllosphere microbiota and the atmosphere present a dynamic continuum. • Phyllosphere microbiota interact with the dynamics of volatile organic compounds and atmospheric trace gasses.

Published
2015

43. Les microbiomes de la phyllosphère

Author

Bringel, Françoise, Couée, Ivan, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Marie-Christine Champomier-Vergès, Monique Zagorec, Briand, Valerie, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2015

44. Les Microbiomes de la phyllosphère : structure, fonctions, interactions

Author

Bringel, Françoise, Couée, Ivan, Briand, Valerie, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2015

46. Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems

Author

Flynn, James D., primary, Hirayama, Hisako, additional, Sakai, Yasuyoshi, additional, Dunfield, Peter F., additional, Klotz, Martin G., additional, Knief, Claudia, additional, Op den Camp, Huub J. M., additional, Jetten, Mike S. M., additional, Khmelenina, Valentina N., additional, Trotsenko, Yuri A., additional, Murrell, J. Colin, additional, Semrau, Jeremy D., additional, Svenning, Mette M., additional, Stein, Lisa Y., additional, Kyrpides, Nikos, additional, Shapiro, Nicole, additional, Woyke, Tanja, additional, Bringel, Françoise, additional, Vuilleumier, Stéphane, additional, DiSpirito, Alan A., additional, and Kalyuzhnaya, Marina G., additional

Published
2016
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48. Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki

Author

Sharp, Christine E., primary, Smirnova, Angela V., additional, Kalyuzhnaya, Marina G., additional, Bringel, Françoise, additional, Hirayama, Hisako, additional, Jetten, Mike S. M., additional, Khmelenina, Valentina N., additional, Klotz, Martin G., additional, Knief, Claudia, additional, Kyrpides, Nikos, additional, Op den Camp, Huub J. M., additional, Reshetnikov, Alexander S., additional, Sakai, Yasuyoshi, additional, Shapiro, Nicole, additional, Trotsenko, Yuri A., additional, Vuilleumier, Stéphane, additional, Woyke, Tanja, additional, and Dunfield, Peter F., additional

Published
2015
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49. Draft Genomes of Gammaproteobacterial Methanotrophs Isolated from Terrestrial Ecosystems

Author

Hamilton, Richard, primary, Kits, K. Dimitri, additional, Ramonovskaya, Victoria A., additional, Rozova, Olga N., additional, Yurimoto, Hiroya, additional, Iguchi, Hiroyuki, additional, Khmelenina, Valentina N., additional, Sakai, Yasuyoshi, additional, Dunfield, Peter F., additional, Klotz, Martin G., additional, Knief, Claudia, additional, Op den Camp, Huub J. M., additional, Jetten, Mike S. M., additional, Bringel, Françoise, additional, Vuilleumier, Stéphane, additional, Svenning, Mette M., additional, Shapiro, Nicole, additional, Woyke, Tanja, additional, Trotsenko, Yuri A., additional, Stein, Lisa Y., additional, and Kalyuzhnaya, Marina G., additional

Published
2015
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50. Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

Author

Vuilleumier, Stéphane, Chistoserdova, Ludmila, Lee, Ming-Chun, Bringel, Françoise, Lajus, Aurélie, Zhou, Yang, Gourion, Benjamin, Barbe, Valérie, Chang, Jean, Cruveiller, Stéphane, Dossat, Carole, Gillett, Will, Gruffaz, Christelle, Haugen, Eric, Hourcade, Edith, Levy, Ruth, Mangenot, Sophie, Muller, Emilie, Nadalig, Thierry, Pagni, Marco, Penny, Christian, Peyraud, Rémi, Robinson, David G., Roche, David, Rouy, Zoé, Saenampechek, Channakhone, Salvignol, Grégory, Vallenet, David, Wu, Zaining, Marx, Christopher J., Vorholt, Julia A., Olson, Maynard V., Kaul, Rajinder, Weissenbach, Jean, Médigue, Claudine, Lidstrom, Mary E., Ahmed, Niyaz, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), University of Washington [Seattle], Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology, University of Kansas [Lawrence] (KU), ETH Zurich, Institute of Microbiology, Zurich, Switzerland, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Vital-IT, Swiss Institute of Bioinformatics [Genève] (SIB), Department of Genome Sciences [Seattle] (GS), Department of Medicine, Department of Microbiology, University of Washington, University of Washington [Seattle]-Departement of Microbiology, SV was supported by a CNRS ATIP career development award, a CNRS USA mobility grant and a Ge ́noscope sequencing grant, and also by the Integrated Computational Genomics Resources of the Swiss Institute of Bioinformatics (RITA-CT-2006-026204) together with MP. Annotation was supported by a grant from MRT/ANR PFTV 2007, MicroScope project. CP, EH and EM were supported by PhD grants from the Government of Luxembourg, the French Ministry of Research and Région Alsace, respectively. RP was supported by ETH (ETH-25 08-2). ML, DGR, and CJM were supported by NSF (IOB-0612591), the Clarke-Cooke Fund, and the Harvard University Microbial Sciences Initiative. LC and MEL were supported by NIH (GM 58933)., De Hoest, Nathalie, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Swiss Federal Institute for Environmental Science and Technology [Dübendorf] (EAWAG), EPFL Institut de Génie de l'environnement EPFL (EPFL), Université de Lausanne (UNIL), Cold and Arid Regions Environmental and Engineering Research Institute, Ningbo Institute of Technology (NIT), Institute of Hydrobiology - Chinese Academy of Sciences, Marine and Estuarine Fisheries (Ministry of Agriculture), State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences [Beijing] (CAS), Institute of Applied Mechanics, National Taiwan University [Taiwan] (NTU), ONERA - The French Aerospace Lab [Châtillon], ONERA, Bureau d'Économie Théorique et Appliquée (BETA), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Neuro-anatomie fonctionnelle du comportement et de ses troubles, Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR70-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de Séquençage, Université d'Évry-Val-d'Essonne (UEVE), Laboratoire Hétéroéléments et Coordination (DCPH), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Kirchhoff Institut für Physik, Universität Heidelberg [Heidelberg], IFREMER (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), University of Ulster, The Institute of Hydrology, Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Institut Pierre-Simon-Laplace (IPSL), École normale supérieure - Paris (ENS Paris)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National d'Études Spatiales [Toulouse] (CNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Department of Paleoclimatology and Geomorphology [Amsterdam], Vrije Universiteit Amsterdam [Amsterdam] (VU), 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), Laboratoire d'Electronique et des Technologies de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Institut fur Theorie der Kondensierten Materie, Universität Karlsruhe (TH), Department of Physics, Duke University [Durham], Duke Physics, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), 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 d'Évry-Val-d'Essonne (UEVE)-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 Paris-Saclay, ONERA-Université Paris Saclay (COmUE), Université de Lorraine (UL)-Université de Strasbourg (UNISTRA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR70-Institut National de la Santé et de la Recherche Médicale (INSERM), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National d'Études Spatiales [Toulouse] (CNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Microbiologie Fondamentale et Pathogénicité (MFP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Harvard University

Subjects
Genome evolution, lcsh:Medicine, Biotechnology/Environmental Microbiology, Genome, Models, Biological, Microbiology, 03 medical and health sciences, Methylamines, Formaldehyde, Gene cluster, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Microbiology/Environmental Microbiology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Genetics and Genomics/Genomics, lcsh:Science, 030304 developmental biology, bactérie, Genetics, Comparative genomics, 0303 health sciences, Multidisciplinary, Microbiology/Microbial Evolution and Genomics, biology, Models, Genetic, 030306 microbiology, génome, Methanol, Microbiology and Parasitology, lcsh:R, Genome project, biology.organism_classification, Genetics and Genomics/Microbial Evolution and Genomics, Microbiologie et Parasitologie, Genetics and Genomics/Genome Projects, Methylobacterium, Chromosomal region, Microbiology/Microbial Physiology and Metabolism, lcsh:Q, Methylobacterium extorquens, Acyl Coenzyme A, Biotechnology/Bioengineering, Genetics and Genomics/Comparative Genomics, Genome, Bacterial, Research Article
Abstract

Background Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. Methodology/Principal Findings The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name “island integration determinant” (iid). Conclusion/Significance These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles., PLoS ONE, 4 (5), ISSN:1932-6203

Published
2009

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