Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH‐2 strain
Identifieur interne : 001496 ( Istex/Corpus ); précédent : 001495; suivant : 001497Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH‐2 strain
Auteurs : Boyang Ji ; Sheng-Da Zhang ; Pascal Arnoux ; Zoe Rouy ; François Alberto ; Nadège Philippe ; Dorothée Murat ; Wei-Jia Zhang ; Jean-Baptiste Rioux ; Nicolas Ginet ; Monique Sabaty ; Sophie Mangenot ; Nathalie Pradel ; Jiesheng Tian ; Jing Yang ; Lichen Zhang ; Wenyan Zhang ; Hongmiao Pan ; Bernard Henrissat ; Pedro M. Coutinho ; Ying Li ; Tian Xiao ; Claudine Médigue ; Valérie Barbe ; David Pignol ; Emmanuel Talla ; Long-Fei WuSource :
- Environmental Microbiology [ 1462-2912 ] ; 2014-02.
Abstract
Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane‐bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH‐2. The high number of repeats and transposable elements account for the differences in QH‐2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH‐2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium‐quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH‐2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH‐2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH‐2 neither has TonB and TonB‐dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH‐2 to marine sediments in comparison with its closely related freshwater counterparts.
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DOI: 10.1111/1462-2920.12180
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QH‐2 strain</title><author><name sortKey="Ji, Boyang" sort="Ji, Boyang" uniqKey="Ji B" first="Boyang" last="Ji">Boyang Ji</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Zhang, Sheng A" sort="Zhang, Sheng A" uniqKey="Zhang S" first="Sheng-Da" last="Zhang">Sheng-Da Zhang</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Arnoux, Pascal" sort="Arnoux, Pascal" uniqKey="Arnoux P" first="Pascal" last="Arnoux">Pascal Arnoux</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation></author><author><name sortKey="Rouy, Zoe" sort="Rouy, Zoe" uniqKey="Rouy Z" first="Zoe" last="Rouy">Zoe Rouy</name><affiliation><mods:affiliation>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, F‐91057, Evry, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Centre National de la Recherche Scientifique, Unité Mixte de Recherche 80302 rue Gaston Crémieux, F‐91057, Evry, France</mods:affiliation></affiliation><affiliation><mods:affiliation>UEVE, Université d'Evry, boulevard François Mitterrand, F‐91025, Evry, France</mods:affiliation></affiliation></author><author><name sortKey="Alberto, Francois" sort="Alberto, Francois" uniqKey="Alberto F" first="François" last="Alberto">François Alberto</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Philippe, Nadege" sort="Philippe, Nadege" uniqKey="Philippe N" first="Nadège" last="Philippe">Nadège Philippe</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Current Address: Information Génomique et Structurale, UMR7256, CNRS, Aix‐Marseille Université, 13288 Marseille Cedex 09, IMM, FR3479, France</mods:affiliation></affiliation></author><author><name sortKey="Murat, Dorothee" sort="Murat, Dorothee" uniqKey="Murat D" first="Dorothée" last="Murat">Dorothée Murat</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Zhang, Wei Ia" sort="Zhang, Wei Ia" uniqKey="Zhang W" first="Wei-Jia" last="Zhang">Wei-Jia Zhang</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</mods:affiliation></affiliation><affiliation><mods:affiliation>Current Address: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</mods:affiliation></affiliation></author><author><name sortKey="Rioux, Jean Aptiste" sort="Rioux, Jean Aptiste" uniqKey="Rioux J" first="Jean-Baptiste" last="Rioux">Jean-Baptiste Rioux</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation></author><author><name sortKey="Ginet, Nicolas" sort="Ginet, Nicolas" uniqKey="Ginet N" first="Nicolas" last="Ginet">Nicolas Ginet</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation></author><author><name sortKey="Sabaty, Monique" sort="Sabaty, Monique" uniqKey="Sabaty M" first="Monique" last="Sabaty">Monique Sabaty</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation></author><author><name sortKey="Mangenot, Sophie" sort="Mangenot, Sophie" uniqKey="Mangenot S" first="Sophie" last="Mangenot">Sophie Mangenot</name><affiliation><mods:affiliation>Laboratoire de Finition, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, CP 5706 – 91057, Evry cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Pradel, Nathalie" sort="Pradel, Nathalie" uniqKey="Pradel N" first="Nathalie" last="Pradel">Nathalie Pradel</name><affiliation><mods:affiliation>Aix‐Marseille Université, Université du Sud Toulon‐Var, CNRS/INSU, IRD, MIO, UM110, F‐13288, Marseille, France</mods:affiliation></affiliation></author><author><name sortKey="Tian, Jiesheng" sort="Tian, Jiesheng" uniqKey="Tian J" first="Jiesheng" last="Tian">Jiesheng Tian</name><affiliation><mods:affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</mods:affiliation></affiliation></author><author><name sortKey="Yang, Jing" sort="Yang, Jing" uniqKey="Yang J" first="Jing" last="Yang">Jing Yang</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</mods:affiliation></affiliation></author><author><name sortKey="Zhang, Lichen" sort="Zhang, Lichen" uniqKey="Zhang L" first="Lichen" last="Zhang">Lichen Zhang</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Zhang, Wenyan" sort="Zhang, Wenyan" uniqKey="Zhang W" first="Wenyan" last="Zhang">Wenyan Zhang</name><affiliation><mods:affiliation>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</mods:affiliation></affiliation></author><author><name sortKey="Pan, Hongmiao" sort="Pan, Hongmiao" uniqKey="Pan H" first="Hongmiao" last="Pan">Hongmiao Pan</name><affiliation><mods:affiliation>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</mods:affiliation></affiliation></author><author><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name><affiliation><mods:affiliation>Architecture et Fonction des Macromolécules Biologiques, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, F‐13288, Marseille Cedex 9, France</mods:affiliation></affiliation></author><author><name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M." last="Coutinho">Pedro M. Coutinho</name><affiliation><mods:affiliation>Architecture et Fonction des Macromolécules Biologiques, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, F‐13288, Marseille Cedex 9, France</mods:affiliation></affiliation></author><author><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name><affiliation><mods:affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</mods:affiliation></affiliation><affiliation><mods:affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Xiao, Tian" sort="Xiao, Tian" uniqKey="Xiao T" first="Tian" last="Xiao">Tian Xiao</name><affiliation><mods:affiliation>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</mods:affiliation></affiliation><affiliation><mods:affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Medigue, Claudine" sort="Medigue, Claudine" uniqKey="Medigue C" first="Claudine" last="Médigue">Claudine Médigue</name><affiliation><mods:affiliation>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, F‐91057, Evry, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Centre National de la Recherche Scientifique, Unité Mixte de Recherche 80302 rue Gaston Crémieux, F‐91057, Evry, France</mods:affiliation></affiliation><affiliation><mods:affiliation>UEVE, Université d'Evry, boulevard François Mitterrand, F‐91025, Evry, France</mods:affiliation></affiliation></author><author><name sortKey="Barbe, Valerie" sort="Barbe, Valerie" uniqKey="Barbe V" first="Valérie" last="Barbe">Valérie Barbe</name><affiliation><mods:affiliation>Laboratoire de Finition, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, CP 5706 – 91057, Evry cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Pignol, David" sort="Pignol, David" uniqKey="Pignol D" first="David" last="Pignol">David Pignol</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Talla, Emmanuel" sort="Talla, Emmanuel" uniqKey="Talla E" first="Emmanuel" last="Talla">Emmanuel Talla</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: wu@imm.cnrs.fr</mods:affiliation></affiliation></author><author><name sortKey="Wu, Long Ei" sort="Wu, Long Ei" uniqKey="Wu L" first="Long-Fei" last="Wu">Long-Fei Wu</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:C0D72C039B1913DF00DDF28B0AD54DB8B082BE3F</idno><date when="2014" year="2014">2014</date><idno type="doi">10.1111/1462-2920.12180</idno><idno type="url">https://api.istex.fr/ark:/67375/WNG-T71MC176-8/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">001496</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001496</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH‐2 strain</title><author><name sortKey="Ji, Boyang" sort="Ji, Boyang" uniqKey="Ji B" first="Boyang" last="Ji">Boyang Ji</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Zhang, Sheng A" sort="Zhang, Sheng A" uniqKey="Zhang S" first="Sheng-Da" last="Zhang">Sheng-Da Zhang</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Arnoux, Pascal" sort="Arnoux, Pascal" uniqKey="Arnoux P" first="Pascal" last="Arnoux">Pascal Arnoux</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation></author><author><name sortKey="Rouy, Zoe" sort="Rouy, Zoe" uniqKey="Rouy Z" first="Zoe" last="Rouy">Zoe Rouy</name><affiliation><mods:affiliation>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, F‐91057, Evry, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Centre National de la Recherche Scientifique, Unité Mixte de Recherche 80302 rue Gaston Crémieux, F‐91057, Evry, France</mods:affiliation></affiliation><affiliation><mods:affiliation>UEVE, Université d'Evry, boulevard François Mitterrand, F‐91025, Evry, France</mods:affiliation></affiliation></author><author><name sortKey="Alberto, Francois" sort="Alberto, Francois" uniqKey="Alberto F" first="François" last="Alberto">François Alberto</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Philippe, Nadege" sort="Philippe, Nadege" uniqKey="Philippe N" first="Nadège" last="Philippe">Nadège Philippe</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Current Address: Information Génomique et Structurale, UMR7256, CNRS, Aix‐Marseille Université, 13288 Marseille Cedex 09, IMM, FR3479, France</mods:affiliation></affiliation></author><author><name sortKey="Murat, Dorothee" sort="Murat, Dorothee" uniqKey="Murat D" first="Dorothée" last="Murat">Dorothée Murat</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Zhang, Wei Ia" sort="Zhang, Wei Ia" uniqKey="Zhang W" first="Wei-Jia" last="Zhang">Wei-Jia Zhang</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</mods:affiliation></affiliation><affiliation><mods:affiliation>Current Address: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</mods:affiliation></affiliation></author><author><name sortKey="Rioux, Jean Aptiste" sort="Rioux, Jean Aptiste" uniqKey="Rioux J" first="Jean-Baptiste" last="Rioux">Jean-Baptiste Rioux</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation></author><author><name sortKey="Ginet, Nicolas" sort="Ginet, Nicolas" uniqKey="Ginet N" first="Nicolas" last="Ginet">Nicolas Ginet</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation></author><author><name sortKey="Sabaty, Monique" sort="Sabaty, Monique" uniqKey="Sabaty M" first="Monique" last="Sabaty">Monique Sabaty</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation></author><author><name sortKey="Mangenot, Sophie" sort="Mangenot, Sophie" uniqKey="Mangenot S" first="Sophie" last="Mangenot">Sophie Mangenot</name><affiliation><mods:affiliation>Laboratoire de Finition, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, CP 5706 – 91057, Evry cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Pradel, Nathalie" sort="Pradel, Nathalie" uniqKey="Pradel N" first="Nathalie" last="Pradel">Nathalie Pradel</name><affiliation><mods:affiliation>Aix‐Marseille Université, Université du Sud Toulon‐Var, CNRS/INSU, IRD, MIO, UM110, F‐13288, Marseille, France</mods:affiliation></affiliation></author><author><name sortKey="Tian, Jiesheng" sort="Tian, Jiesheng" uniqKey="Tian J" first="Jiesheng" last="Tian">Jiesheng Tian</name><affiliation><mods:affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</mods:affiliation></affiliation></author><author><name sortKey="Yang, Jing" sort="Yang, Jing" uniqKey="Yang J" first="Jing" last="Yang">Jing Yang</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</mods:affiliation></affiliation></author><author><name sortKey="Zhang, Lichen" sort="Zhang, Lichen" uniqKey="Zhang L" first="Lichen" last="Zhang">Lichen Zhang</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Zhang, Wenyan" sort="Zhang, Wenyan" uniqKey="Zhang W" first="Wenyan" last="Zhang">Wenyan Zhang</name><affiliation><mods:affiliation>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</mods:affiliation></affiliation></author><author><name sortKey="Pan, Hongmiao" sort="Pan, Hongmiao" uniqKey="Pan H" first="Hongmiao" last="Pan">Hongmiao Pan</name><affiliation><mods:affiliation>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</mods:affiliation></affiliation></author><author><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name><affiliation><mods:affiliation>Architecture et Fonction des Macromolécules Biologiques, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, F‐13288, Marseille Cedex 9, France</mods:affiliation></affiliation></author><author><name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M." last="Coutinho">Pedro M. Coutinho</name><affiliation><mods:affiliation>Architecture et Fonction des Macromolécules Biologiques, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, F‐13288, Marseille Cedex 9, France</mods:affiliation></affiliation></author><author><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name><affiliation><mods:affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</mods:affiliation></affiliation><affiliation><mods:affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Xiao, Tian" sort="Xiao, Tian" uniqKey="Xiao T" first="Tian" last="Xiao">Tian Xiao</name><affiliation><mods:affiliation>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</mods:affiliation></affiliation><affiliation><mods:affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Medigue, Claudine" sort="Medigue, Claudine" uniqKey="Medigue C" first="Claudine" last="Médigue">Claudine Médigue</name><affiliation><mods:affiliation>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, F‐91057, Evry, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Centre National de la Recherche Scientifique, Unité Mixte de Recherche 80302 rue Gaston Crémieux, F‐91057, Evry, France</mods:affiliation></affiliation><affiliation><mods:affiliation>UEVE, Université d'Evry, boulevard François Mitterrand, F‐91025, Evry, France</mods:affiliation></affiliation></author><author><name sortKey="Barbe, Valerie" sort="Barbe, Valerie" uniqKey="Barbe V" first="Valérie" last="Barbe">Valérie Barbe</name><affiliation><mods:affiliation>Laboratoire de Finition, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, CP 5706 – 91057, Evry cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Pignol, David" sort="Pignol, David" uniqKey="Pignol D" first="David" last="Pignol">David Pignol</name><affiliation><mods:affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</mods:affiliation></affiliation></author><author><name sortKey="Talla, Emmanuel" sort="Talla, Emmanuel" uniqKey="Talla E" first="Emmanuel" last="Talla">Emmanuel Talla</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: wu@imm.cnrs.fr</mods:affiliation></affiliation></author><author><name sortKey="Wu, Long Ei" sort="Wu, Long Ei" uniqKey="Wu L" first="Long-Fei" last="Wu">Long-Fei Wu</name><affiliation><mods:affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Environmental Microbiology</title><title level="j" type="alt">ENVIRONMENTAL MICROBIOLOGY</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><biblScope unit="vol">16</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="525">525</biblScope><biblScope unit="page" to="544">544</biblScope><biblScope unit="page-count">20</biblScope><date type="published" when="2014-02">2014-02</date></imprint><idno type="ISSN">1462-2912</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1462-2912</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract">Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane‐bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH‐2. The high number of repeats and transposable elements account for the differences in QH‐2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH‐2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium‐quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH‐2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH‐2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH‐2 neither has TonB and TonB‐dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH‐2 to marine sediments in comparison with its closely related freshwater counterparts.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Boyang Ji</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string></affiliations></json:item><json:item><name>Sheng‐Da Zhang</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string></affiliations></json:item><json:item><name>Pascal Arnoux</name><affiliations><json:string>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</json:string></affiliations></json:item><json:item><name>Zoe Rouy</name><affiliations><json:string>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, F‐91057, Evry, France</json:string><json:string>Centre National de la Recherche Scientifique, Unité Mixte de Recherche 80302 rue Gaston Crémieux, F‐91057, Evry, France</json:string><json:string>UEVE, Université d'Evry, boulevard François Mitterrand, F‐91025, Evry, France</json:string></affiliations></json:item><json:item><name>François Alberto</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string></affiliations></json:item><json:item><name>Nadège Philippe</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string><json:string>Current Address: Information Génomique et Structurale, UMR7256, CNRS, Aix‐Marseille Université, 13288 Marseille Cedex 09, IMM, FR3479, France</json:string></affiliations></json:item><json:item><name>Dorothée Murat</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string></affiliations></json:item><json:item><name>Wei‐Jia Zhang</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string><json:string>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</json:string><json:string>Current Address: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</json:string></affiliations></json:item><json:item><name>Jean‐Baptiste Rioux</name><affiliations><json:string>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</json:string></affiliations></json:item><json:item><name>Nicolas Ginet</name><affiliations><json:string>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</json:string></affiliations></json:item><json:item><name>Monique Sabaty</name><affiliations><json:string>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</json:string></affiliations></json:item><json:item><name>Sophie Mangenot</name><affiliations><json:string>Laboratoire de Finition, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, CP 5706 – 91057, Evry cedex, France</json:string></affiliations></json:item><json:item><name>Nathalie Pradel</name><affiliations><json:string>Aix‐Marseille Université, Université du Sud Toulon‐Var, CNRS/INSU, IRD, MIO, UM110, F‐13288, Marseille, France</json:string></affiliations></json:item><json:item><name>Jiesheng Tian</name><affiliations><json:string>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</json:string></affiliations></json:item><json:item><name>Jing Yang</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string><json:string>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</json:string></affiliations></json:item><json:item><name>Lichen Zhang</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string></affiliations></json:item><json:item><name>Wenyan Zhang</name><affiliations><json:string>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</json:string></affiliations></json:item><json:item><name>Hongmiao Pan</name><affiliations><json:string>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</json:string></affiliations></json:item><json:item><name>Bernard Henrissat</name><affiliations><json:string>Architecture et Fonction des Macromolécules Biologiques, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, F‐13288, Marseille Cedex 9, France</json:string></affiliations></json:item><json:item><name>Pedro M. Coutinho</name><affiliations><json:string>Architecture et Fonction des Macromolécules Biologiques, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, F‐13288, Marseille Cedex 9, France</json:string></affiliations></json:item><json:item><name>Ying Li</name><affiliations><json:string>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</json:string><json:string>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</json:string></affiliations></json:item><json:item><name>Tian Xiao</name><affiliations><json:string>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</json:string><json:string>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</json:string></affiliations></json:item><json:item><name>Claudine Médigue</name><affiliations><json:string>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, F‐91057, Evry, France</json:string><json:string>Centre National de la Recherche Scientifique, Unité Mixte de Recherche 80302 rue Gaston Crémieux, F‐91057, Evry, France</json:string><json:string>UEVE, Université d'Evry, boulevard François Mitterrand, F‐91025, Evry, France</json:string></affiliations></json:item><json:item><name>Valérie Barbe</name><affiliations><json:string>Laboratoire de Finition, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, CP 5706 – 91057, Evry cedex, France</json:string></affiliations></json:item><json:item><name>David Pignol</name><affiliations><json:string>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</json:string><json:string>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</json:string></affiliations></json:item><json:item><name>Emmanuel Talla</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string><json:string>E-mail: wu@imm.cnrs.fr</json:string></affiliations></json:item><json:item><name>Long‐Fei Wu</name><affiliations><json:string>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</json:string><json:string>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</json:string></affiliations></json:item></author><articleId><json:string>EMI12180</json:string></articleId><arkIstex>ark:/67375/WNG-T71MC176-8</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane‐bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH‐2. The high number of repeats and transposable elements account for the differences in QH‐2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH‐2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium‐quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH‐2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH‐2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH‐2 neither has TonB and TonB‐dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH‐2 to marine sediments in comparison with its closely related freshwater counterparts.</abstract><qualityIndicators><score>9.364</score><pdfWordCount>11157</pdfWordCount><pdfCharCount>72928</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>20</pdfPageCount><pdfPageSize>595.276 x 782.333 pts</pdfPageSize><pdfWordsPerPage>558</pdfWordsPerPage><pdfText>true</pdfText><refBibsNative>true</refBibsNative><abstractWordCount>197</abstractWordCount><abstractCharCount>1438</abstractCharCount><keywordCount>0</keywordCount></qualityIndicators><title>Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH‐2 strain</title><genre><json:string>article</json:string></genre><host><title>Environmental Microbiology</title><language><json:string>unknown</json:string></language><doi><json:string>10.1111/(ISSN)1462-2920</json:string></doi><issn><json:string>1462-2912</json:string></issn><eissn><json:string>1462-2920</json:string></eissn><publisherId><json:string>EMI</json:string></publisherId><volume>16</volume><issue>2</issue><pages><first>525</first><last>544</last><total>20</total></pages><genre><json:string>journal</json:string></genre><subject><json:item><value>Research articles</value></json:item><json:item><value>Research article</value></json:item></subject></host><ark><json:string>ark:/67375/WNG-T71MC176-8</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - microbiology</json:string></wos><scienceMetrix><json:string>1 - health sciences</json:string><json:string>2 - biomedical research</json:string><json:string>3 - microbiology</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Agricultural and Biological Sciences</json:string><json:string>3 - Ecology, Evolution, Behavior and Systematics</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Immunology and Microbiology</json:string><json:string>3 - Microbiology</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string></inist></categories><publicationDate>2014</publicationDate><copyrightDate>2014</copyrightDate><doi><json:string>10.1111/1462-2920.12180</json:string></doi><id>C0D72C039B1913DF00DDF28B0AD54DB8B082BE3F</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-T71MC176-8/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-T71MC176-8/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/WNG-T71MC176-8/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main">Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. 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QH‐2 strain</title><title level="a" type="short">Comparative genomics of magnetotactic spirilla</title><author xml:id="author-0000"><persName><forename type="first">Boyang</forename><surname>Ji</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">Sheng‐Da</forename><surname>Zhang</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0002"><persName><forename type="first">Pascal</forename><surname>Arnoux</surname></persName><affiliation><orgName type="division">Laboratoire de Bioénergétique Cellulaire</orgName><orgName type="division">Université Aix‐Marseille</orgName><orgName type="institution">CEA/DSV/IBEB, UMR 7265 CNRS/CEA</orgName><address><settlement>Saint‐Paul‐lez‐Durance</settlement><postCode>F‐13180</postCode><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0003"><persName><forename type="first">Zoe</forename><surname>Rouy</surname></persName><affiliation><orgName type="division">Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme</orgName><orgName type="institution">Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope</orgName><address><street>2 rue Gaston Crémieux</street><postCode>F‐91057</postCode><settlement>Evry</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation><affiliation><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 8030</street><street>2 rue Gaston Crémieux</street><postCode>F‐91057</postCode><settlement>Evry</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation><affiliation><orgName type="institution">UEVE, Université d'Evry</orgName><address><street>boulevard François Mitterrand</street><postCode>F‐91025</postCode><settlement>Evry</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0004"><persName><forename type="first">François</forename><surname>Alberto</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0005"><persName><forename type="first">Nadège</forename><surname>Philippe</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation><affiliation><orgName type="division">Information Génomique et Structurale</orgName><orgName type="division">UMR7256, CNRS</orgName><orgName type="institution">Aix‐Marseille Université</orgName><address><postCode>IMM, FR3479</postCode><street>13288 Marseille Cedex 09</street><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0006"><persName><forename type="first">Dorothée</forename><surname>Murat</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0007"><persName><forename type="first">Wei‐Jia</forename><surname>Zhang</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation><affiliation><orgName type="division">State Key Laboratories for Agro‐biotechnology</orgName><orgName type="institution">College of Biological Sciences</orgName><address><street>China Agricultural University</street><settlement>Beijing</settlement><postCode>100193</postCode><country key="CN" xml:lang="en">CHINA</country></address></affiliation><affiliation><orgName type="division">MOH Key Laboratory of Systems Biology of Pathogens</orgName><orgName type="division">Institute of Pathogen Biology</orgName><orgName type="institution">Chinese Academy of Medical Sciences and Peking Union Medical College</orgName><address><settlement>Beijing</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0008"><persName><forename type="first">Jean‐Baptiste</forename><surname>Rioux</surname></persName><affiliation><orgName type="division">Laboratoire de Bioénergétique Cellulaire</orgName><orgName type="division">Université Aix‐Marseille</orgName><orgName type="institution">CEA/DSV/IBEB, UMR 7265 CNRS/CEA</orgName><address><settlement>Saint‐Paul‐lez‐Durance</settlement><postCode>F‐13180</postCode><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0009"><persName><forename type="first">Nicolas</forename><surname>Ginet</surname></persName><affiliation><orgName type="division">Laboratoire de Bioénergétique Cellulaire</orgName><orgName type="division">Université Aix‐Marseille</orgName><orgName type="institution">CEA/DSV/IBEB, UMR 7265 CNRS/CEA</orgName><address><settlement>Saint‐Paul‐lez‐Durance</settlement><postCode>F‐13180</postCode><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0010"><persName><forename type="first">Monique</forename><surname>Sabaty</surname></persName><affiliation><orgName type="division">Laboratoire de Bioénergétique Cellulaire</orgName><orgName type="division">Université Aix‐Marseille</orgName><orgName type="institution">CEA/DSV/IBEB, UMR 7265 CNRS/CEA</orgName><address><settlement>Saint‐Paul‐lez‐Durance</settlement><postCode>F‐13180</postCode><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0011"><persName><forename type="first">Sophie</forename><surname>Mangenot</surname></persName><affiliation><orgName type="division">Laboratoire de Finition</orgName><orgName type="institution">Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope</orgName><address><street>2 rue Gaston Crémieux</street><postCode>CP 5706 – 91057</postCode><settlement>Evry cedex</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0012"><persName><forename type="first">Nathalie</forename><surname>Pradel</surname></persName><affiliation><orgName type="institution">Aix‐Marseille Université, Université du Sud Toulon‐Var, CNRS/INSU, IRD, MIO, UM110</orgName><address><settlement>Marseille</settlement><postCode>F‐13288</postCode><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0013"><persName><forename type="first">Jiesheng</forename><surname>Tian</surname></persName><affiliation><orgName type="division">State Key Laboratories for Agro‐biotechnology</orgName><orgName type="institution">College of Biological Sciences</orgName><address><street>China Agricultural University</street><settlement>Beijing</settlement><postCode>100193</postCode><country key="CN" xml:lang="en">CHINA</country></address></affiliation></author><author xml:id="author-0014"><persName><forename type="first">Jing</forename><surname>Yang</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation><affiliation><orgName type="division">State Key Laboratories for Agro‐biotechnology</orgName><orgName type="institution">College of Biological Sciences</orgName><address><street>China Agricultural University</street><settlement>Beijing</settlement><postCode>100193</postCode><country key="CN" xml:lang="en">CHINA</country></address></affiliation></author><author xml:id="author-0015"><persName><forename type="first">Lichen</forename><surname>Zhang</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0016"><persName><forename type="first">Wenyan</forename><surname>Zhang</surname></persName><affiliation><orgName type="division">Key Laboratory of Marine Ecology & Environmental Sciences</orgName><orgName type="institution">Institute of Oceanology, Chinese Academy of Sciences</orgName><address><settlement>Qingdao</settlement><postCode>266071</postCode><country key="CN" xml:lang="en">CHINA</country></address></affiliation></author><author xml:id="author-0017"><persName><forename type="first">Hongmiao</forename><surname>Pan</surname></persName><affiliation><orgName type="division">Key Laboratory of Marine Ecology & Environmental Sciences</orgName><orgName type="institution">Institute of Oceanology, Chinese Academy of Sciences</orgName><address><settlement>Qingdao</settlement><postCode>266071</postCode><country key="CN" xml:lang="en">CHINA</country></address></affiliation></author><author xml:id="author-0018"><persName><forename type="first">Bernard</forename><surname>Henrissat</surname></persName><affiliation><orgName type="division">Architecture et Fonction des Macromolécules Biologiques</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7257</street><postCode>F‐13288</postCode><settlement>Marseille Cedex 9</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0019"><persName><forename type="first">Pedro M.</forename><surname>Coutinho</surname></persName><affiliation><orgName type="division">Architecture et Fonction des Macromolécules Biologiques</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7257</street><postCode>F‐13288</postCode><settlement>Marseille Cedex 9</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0020"><persName><forename type="first">Ying</forename><surname>Li</surname></persName><affiliation><orgName type="division">State Key Laboratories for Agro‐biotechnology</orgName><orgName type="institution">College of Biological Sciences</orgName><address><street>China Agricultural University</street><settlement>Beijing</settlement><postCode>100193</postCode><country key="CN" xml:lang="en">CHINA</country></address></affiliation><affiliation><orgName type="division">Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL)</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><postCode>F‐13402</postCode><settlement>Marseille cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0021"><persName><forename type="first">Tian</forename><surname>Xiao</surname></persName><affiliation><orgName type="division">Key Laboratory of Marine Ecology & Environmental Sciences</orgName><orgName type="institution">Institute of Oceanology, Chinese Academy of Sciences</orgName><address><settlement>Qingdao</settlement><postCode>266071</postCode><country key="CN" xml:lang="en">CHINA</country></address></affiliation><affiliation><orgName type="division">Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL)</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><postCode>F‐13402</postCode><settlement>Marseille cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0022"><persName><forename type="first">Claudine</forename><surname>Médigue</surname></persName><affiliation><orgName type="division">Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme</orgName><orgName type="institution">Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope</orgName><address><street>2 rue Gaston Crémieux</street><postCode>F‐91057</postCode><settlement>Evry</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation><affiliation><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 8030</street><street>2 rue Gaston Crémieux</street><postCode>F‐91057</postCode><settlement>Evry</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation><affiliation><orgName type="institution">UEVE, Université d'Evry</orgName><address><street>boulevard François Mitterrand</street><postCode>F‐91025</postCode><settlement>Evry</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0023"><persName><forename type="first">Valérie</forename><surname>Barbe</surname></persName><affiliation><orgName type="division">Laboratoire de Finition</orgName><orgName type="institution">Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope</orgName><address><street>2 rue Gaston Crémieux</street><postCode>CP 5706 – 91057</postCode><settlement>Evry cedex</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0024"><persName><forename type="first">David</forename><surname>Pignol</surname></persName><affiliation><orgName type="division">Laboratoire de Bioénergétique Cellulaire</orgName><orgName type="division">Université Aix‐Marseille</orgName><orgName type="institution">CEA/DSV/IBEB, UMR 7265 CNRS/CEA</orgName><address><settlement>Saint‐Paul‐lez‐Durance</settlement><postCode>F‐13180</postCode><country key="FR" xml:lang="en">FRANCE</country></address></affiliation><affiliation><orgName type="division">Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL)</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><postCode>F‐13402</postCode><settlement>Marseille cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0025" role="corresp"><persName><forename type="first">Emmanuel</forename><surname>Talla</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0026"><persName><forename type="first">Long‐Fei</forename><surname>Wu</surname></persName><affiliation><orgName type="division">Laboratoire de Chimie Bactérienne</orgName><orgName type="division">Aix‐Marseille Université</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><settlement>Marseille Cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation><affiliation><orgName type="division">Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL)</orgName><orgName type="institution">Centre National de la Recherche Scientifique</orgName><address><postCode>F‐13402</postCode><settlement>Marseille cedex 20</settlement><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><idno type="istex">C0D72C039B1913DF00DDF28B0AD54DB8B082BE3F</idno><idno type="ark">ark:/67375/WNG-T71MC176-8</idno><idno type="DOI">10.1111/1462-2920.12180</idno><idno type="unit">EMI12180</idno><idno type="toTypesetVersion">file://EMI.EMI12180.pdf</idno></analytic><monogr><title level="j" type="main">Environmental Microbiology</title><title level="j" type="alt">ENVIRONMENTAL MICROBIOLOGY</title><idno type="pISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><idno type="book-DOI">10.1111/(ISSN)1462-2920</idno><idno type="book-part-DOI">10.1111/emi.2014.16.issue-2</idno><idno type="product">EMI</idno><imprint><biblScope unit="vol">16</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="525">525</biblScope><biblScope unit="page" to="544">544</biblScope><biblScope unit="page-count">20</biblScope><date type="published" when="2014-02"></date></imprint></monogr></biblStruct></sourceDesc></fileDesc><encodingDesc><schemaRef type="ODD" url="https://xml-schema.delivery.istex.fr/tei-istex.odd"></schemaRef><appInfo><application ident="pub2tei" version="1.0.10" when="2019-12-20"><label>pub2TEI-ISTEX</label><desc>A set of style sheets for converting XML documents encoded in various scientific publisher formats into a common TEI format.
<ref target="http://www.tei-c.org/">We use TEI</ref></desc></application></appInfo></encodingDesc><profileDesc><abstract style="main"><head>Summary</head><p>Magnetotactic bacteria (<hi rend="fc">MTB</hi>) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane‐bounded magnetite or greigite crystals arranged in chains. Although <hi rend="fc">MTB</hi> are widely spread in various ecosystems, few axenic cultures are available, and only freshwater <hi rend="italic"><hi rend="fc">M</hi>agnetospirillum</hi> spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, <hi rend="italic"><hi rend="fc">M</hi>agnetospira</hi> sp. <hi rend="fc">QH</hi>‐2. The high number of repeats and transposable elements account for the differences in <hi rend="fc">QH</hi>‐2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the <hi rend="fc">QH</hi>‐2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium‐quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of <hi rend="italic"><hi rend="fc">M</hi>agnetospira</hi> sp. <hi rend="fc">QH</hi>‐2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the <hi rend="fc">QH</hi>‐2 genome. Unlike freshwater <hi rend="italic"><hi rend="fc">M</hi>agnetospirillum</hi> spp., marine <hi rend="italic"><hi rend="fc">M</hi>agnetospira</hi> sp. <hi rend="fc">QH</hi>‐2 neither has <hi rend="fc">TonB</hi> and <hi rend="fc">TonB</hi>‐dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of <hi rend="italic"><hi rend="fc">M</hi>agnetospira</hi> sp. <hi rend="fc">QH</hi>‐2 to marine sediments in comparison with its closely related freshwater counterparts.</p></abstract><textClass><keywords rend="tocHeading1"><term>Research articles</term></keywords><keywords rend="articleCategory"><term>Research article</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2019-12-20" who="#istex" xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-T71MC176-8/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component type="serialArticle" version="2.0" xml:id="emi12180" xml:lang="en"><header><publicationMeta level="product"><doi origin="wiley">10.1111/(ISSN)1462-2920</doi><issn type="print">1462-2912</issn><issn type="electronic">1462-2920</issn><idGroup><id type="product" value="EMI"></id></idGroup><titleGroup><title sort="ENVIRONMENTAL MICROBIOLOGY" type="main">Environmental Microbiology</title><title type="short">Environ Microbiol</title></titleGroup></publicationMeta><publicationMeta level="part" position="02102"><doi>10.1111/emi.2014.16.issue-2</doi><titleGroup><title type="main">Thematic Issue: Protists</title></titleGroup><copyright ownership="publisher">Copyright © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd</copyright><numberingGroup><numbering number="16" type="journalVolume">16</numbering><numbering type="journalIssue">2</numbering></numberingGroup><coverDate startDate="2014-02">February 2014</coverDate></publicationMeta><publicationMeta level="unit" status="forIssue" type="article" position="160"><doi>10.1111/1462-2920.12180</doi><idGroup><id type="unit" value="EMI12180"></id></idGroup><countGroup><count number="20" type="pageTotal"></count></countGroup><titleGroup><title type="tocHeading1">Research articles</title><title type="articleCategory">Research article</title></titleGroup><copyright ownership="joint">© 2013 Society for Applied Microbiology and John Wiley & Sons Ltd</copyright><eventGroup><event agent="bestset" date="2013-06-14" type="xmlCreated"></event><event date="2013-03-11" type="manuscriptReceived"></event><event date="2013-05-17" type="manuscriptRevised"></event><event date="2013-06-02" type="manuscriptAccepted"></event><event type="publishedOnlineAccepted" date="2013-06-11"></event><event type="publishedOnlineEarlyUnpaginated" date="2013-07-10"></event><event type="publishedOnlineFinalForm" date="2014-01-27"></event><event type="firstOnline" date="2013-07-10"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.6.4 mode:FullText" date="2015-10-07"></event></eventGroup><numberingGroup><numbering type="pageFirst">525</numbering><numbering type="pageLast">544</numbering></numberingGroup><correspondenceTo>For correspondence. E‐mail <email>wu@imm.cnrs.fr</email>; <email>talla@imm.cnrs.fr</email>; Tel. (+33) 4 91 16 41 57; Fax (+33) 4 91 71 89 14.</correspondenceTo><linkGroup><link type="toTypesetVersion" href="file://EMI.EMI12180.pdf"></link></linkGroup></publicationMeta><contentMeta><titleGroup><title type="short">Comparative genomics of magnetotactic spirilla</title><title type="shortAuthors">B. <fc>J</fc>i <i>et al</i>.</title><title type="main">Comparative genomic analysis provides insights into the evolution and niche adaptation of marine <i><fc>M</fc>agnetospira</i> sp. <fc>QH</fc>‐2 strain</title></titleGroup><creators><creator affiliationRef="#emi12180-aff-0003" creatorRole="author" noteRef="#emi12180-note-0001" xml:id="emi12180-cr-0001"><personName><givenNames>Boyang</givenNames><familyName>Ji</familyName></personName></creator><creator affiliationRef="#emi12180-aff-0003" creatorRole="author" noteRef="#emi12180-note-0001" xml:id="emi12180-cr-0002"><personName><givenNames>Sheng‐Da</givenNames><familyName>Zhang</familyName></personName></creator><creator 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#emi12180-aff-0013" creatorRole="author" xml:id="emi12180-cr-0027"><personName><givenNames>Long‐Fei</givenNames><familyName>Wu</familyName></personName></creator></creators><affiliationGroup><affiliation countryCode="FR" xml:id="emi12180-aff-0001"><orgDiv>Information Génomique et Structurale</orgDiv><orgDiv>UMR7256, CNRS</orgDiv><orgName>Aix‐Marseille Université</orgName><address><postCode>IMM, FR3479</postCode><street>13288 Marseille Cedex 09</street><country>France</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0002"><orgDiv>MOH Key Laboratory of Systems Biology of Pathogens</orgDiv><orgDiv>Institute of Pathogen Biology</orgDiv><orgName>Chinese Academy of Medical Sciences and Peking Union Medical College</orgName><address><city>Beijing</city><country>China</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0003"><orgDiv>Laboratoire de Chimie Bactérienne</orgDiv><orgDiv>Aix‐Marseille Université</orgDiv><orgName>Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7283</street><postCode>F‐13402</postCode><city>Marseille Cedex 20</city><country>France</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0004"><orgDiv>Laboratoire de Bioénergétique Cellulaire</orgDiv><orgDiv>Université Aix‐Marseille</orgDiv><orgName>CEA/DSV/IBEB, UMR 7265 CNRS/CEA</orgName><address><city>Saint‐Paul‐lez‐Durance</city><postCode>F‐13180</postCode><country>France</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0005"><orgDiv>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme</orgDiv><orgName>Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope</orgName><address><street>2 rue Gaston Crémieux</street><postCode>F‐91057</postCode><city>Evry</city><country>France</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0006"><orgName>Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 8030</street><street>2 rue Gaston Crémieux</street><postCode>F‐91057</postCode><city>Evry</city><country>France</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0007"><orgName>UEVE, Université d'Evry</orgName><address><street>boulevard François Mitterrand</street><postCode>F‐91025</postCode><city>Evry</city><country>France</country></address></affiliation><affiliation countryCode="CN" xml:id="emi12180-aff-0008"><orgDiv>State Key Laboratories for Agro‐biotechnology</orgDiv><orgName>College of Biological Sciences</orgName><address><street>China Agricultural University</street><city>Beijing</city><postCode>100193</postCode><country>China</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0009"><orgDiv>Laboratoire de Finition</orgDiv><orgName>Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope</orgName><address><street>2 rue Gaston Crémieux</street><postCode>CP 5706 – 91057</postCode><city>Evry cedex</city><country>France</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0010"><orgName>Aix‐Marseille Université, Université du Sud Toulon‐Var, CNRS/INSU, IRD, MIO, UM110</orgName><address><city>Marseille</city><postCode>F‐13288</postCode><country>France</country></address></affiliation><affiliation countryCode="CN" xml:id="emi12180-aff-0011"><orgDiv>Key Laboratory of Marine Ecology & Environmental Sciences</orgDiv><orgName>Institute of Oceanology, Chinese Academy of Sciences</orgName><address><city>Qingdao</city><postCode>266071</postCode><country>China</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0012"><orgDiv>Architecture et Fonction des Macromolécules Biologiques</orgDiv><orgDiv>Aix‐Marseille Université</orgDiv><orgName>Centre National de la Recherche Scientifique</orgName><address><street>Unité Mixte de Recherche 7257</street><postCode>F‐13288</postCode><city>Marseille Cedex 9</city><country>France</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12180-aff-0013"><orgDiv>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL)</orgDiv><orgName>Centre National de la Recherche Scientifique</orgName><address><postCode>F‐13402</postCode><city>Marseille cedex 20</city><country>France</country></address></affiliation></affiliationGroup><fundingInfo><fundingAgency>Grands Projets de Séquençage, Agence Nationale de la Recherche</fundingAgency><fundingNumber>ANR‐2010‐BLAN‐1320‐01</fundingNumber></fundingInfo><fundingInfo><fundingAgency>National Science Fundation of China</fundingAgency><fundingNumber>NSFC40776094</fundingNumber><fundingNumber>41276170</fundingNumber></fundingInfo><fundingInfo><fundingAgency>Centre National de la Recherche Scientifique</fundingAgency></fundingInfo><fundingInfo><fundingAgency>Chinese Scholarship Council fellowship</fundingAgency></fundingInfo><supportingInformation><supportingInfoItem><mediaResource alt="docx" href="urn-x:wiley:14622912:media:emi12180:emi12180-sup-0001-si"></mediaResource><caption><p><b>Fig. S1.</b> The comparison of CRISPR locus between the marine <i>Magnetospira</i> sp. QH‐2 and one of <i>R. rubrum</i>.</p><p><b>Fig. S2.</b> The genome alignment between the marine <i>Magnetospira</i> sp. QH‐2 and other related genomes.</p><p>A, C and E graphs are based on nucleotide alignments while B, D and F are from amino acid alignments.</p><p><b>Fig. S3.</b> A. The phylogenetic analysis of marine <i>Magnetospira</i> sp. QH‐2 based on the 16S rRNA sequences. Numbers indicate node branch support; only values greater than 50 were shown. Clades I, II, III, IV and V, indicated <i>Alphaproteobacteria</i>, <i>Magnetococcus</i>, <i>Gammaproteobacteria</i>, <i>Deltaproteobacteria</i>, <i>Nitrospira</i> respectively. Red squares indicated the magnetotactic bacteria, and axenic cultures were marked by blue squares; complete genome sequences available strains is indicated with green squares; Non MTB, non axenic cultures or no complete genome bacteria is indicated by a grey square. B. The phylogenetic analysis of the marine <i>Magnetospira</i> sp. QH‐2 based on concatenated protein sequences of 28 housekeeping genes. C. The genome content tree based on the presence/absence of orthologous groups.</p><p><b>Fig. S4.</b> Repeat sequence elements (> 200 bp) (dots) in MAI regions. Red (for direct repeats) and blue (opposite orientation repeats) dots.</p><p><b>Fig. S5.</b> Presence (+)/Absence (–) of <i>mamCDFG</i>, <i>mamAB</i> or <i>mamXYZ</i> clusters in MTB with the total number (##) of <i>mam</i> genes in the MAI region. Red arrows indicated the MAI insertion event. See also <url href="http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12180/suppinfo">Fig. S1</url>.</p><p><b>Fig. S6.</b> The overview of sulfur metabolism in the marine <i>Magnetospira</i> sp. QH‐2 and related genomes.</p><p><b>Fig. S7.</b> The overview of nitrogen metabolism in the marine <i>Magnetospira</i> sp. QH‐2 and related genomes.</p><p><b>Table S1.</b> The distribution of the COG functional classes in the QH‐2 chromosome and plasmid.</p><p><b>Table S2.</b> Putative genomic islands (GI) in the marine <i>Magnetospira</i> sp. QH‐2.</p><p><b>Table S3.</b> List of proteins with length greater than 2000aa in marine <i>Magnetospira</i> sp. QH‐2 and related genomes.</p><p><b>Table S4.</b> Classification of IS family in the marine <i>Magnetospira</i> sp. QH‐2.</p><p><b>Table S5.</b> The CRISPR (clustered regularly interspaced short palindromic repeats) in selected genomes.</p><p><b>Table S6.</b> List of the 13 marine <i>Alphaproteobacteria</i> genomes used in comparative analysis.</p><p><b>Table S7.</b> The presence (+)/absence (–) of magnetosome island genes in completely/partially sequenced MTB.</p><p><b>Table S8.</b> The correlation coefficients between <i>dsr</i> genes.</p><p><b>Table S9.</b> The correlation coefficient between <i>mam</i> genes.</p><p><b>Table S10.</b> Amino acid substitution rates of different Mam proteins in AMB‐1, MS‐1, MSR‐1, MV‐1 and QH‐2, with MC‐1 as the out‐group. Mean (without or with 2SD) is the average of AMB‐1, MS‐1 and MSR‐1 rates.</p><p><b>Table S11.</b> The comparison of CAZymes between QH‐2 and AMB‐1, MSR‐1.</p><p><b>Table S12.</b> List of genomes used in the phylogenetic study.</p><p><b>Table S13.</b> List of 16S rRNA sequences used in this study.</p></caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main"><title type="main">Summary</title><p>Magnetotactic bacteria (<fc>MTB</fc>) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane‐bounded magnetite or greigite crystals arranged in chains. Although <fc>MTB</fc> are widely spread in various ecosystems, few axenic cultures are available, and only freshwater <i><fc>M</fc>agnetospirillum</i> spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, <i><fc>M</fc>agnetospira</i> sp. <fc>QH</fc>‐2. The high number of repeats and transposable elements account for the differences in <fc>QH</fc>‐2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the <fc>QH</fc>‐2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium‐quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of <i><fc>M</fc>agnetospira</i> sp. <fc>QH</fc>‐2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the <fc>QH</fc>‐2 genome. Unlike freshwater <i><fc>M</fc>agnetospirillum</i> spp., marine <i><fc>M</fc>agnetospira</i> sp. <fc>QH</fc>‐2 neither has <fc>TonB</fc> and <fc>TonB</fc>‐dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of <i><fc>M</fc>agnetospira</i> sp. <fc>QH</fc>‐2 to marine sediments in comparison with its closely related freshwater counterparts.</p></abstract></abstractGroup></contentMeta><noteGroup><note numbered="no" xml:id="emi12180-note-0001">B.J. and S.D.Z. contributed equally to this work.</note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH‐2 strain</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Comparative genomics of magnetotactic spirilla</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH‐2 strain</title></titleInfo><name type="personal"><namePart type="given">Boyang</namePart><namePart type="family">Ji</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><description>B.J. and S.D.Z. contributed equally to this work.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Sheng‐Da</namePart><namePart type="family">Zhang</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><description>B.J. and S.D.Z. contributed equally to this work.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Pascal</namePart><namePart type="family">Arnoux</namePart><affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Zoe</namePart><namePart type="family">Rouy</namePart><affiliation>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, F‐91057, Evry, France</affiliation><affiliation>Centre National de la Recherche Scientifique, Unité Mixte de Recherche 80302 rue Gaston Crémieux, F‐91057, Evry, France</affiliation><affiliation>UEVE, Université d'Evry, boulevard François Mitterrand, F‐91025, Evry, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">François</namePart><namePart type="family">Alberto</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Nadège</namePart><namePart type="family">Philippe</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><affiliation>Current Address: Information Génomique et Structurale, UMR7256, CNRS, Aix‐Marseille Université, 13288 Marseille Cedex 09, IMM, FR3479, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Dorothée</namePart><namePart type="family">Murat</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Wei‐Jia</namePart><namePart type="family">Zhang</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</affiliation><affiliation>Current Address: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jean‐Baptiste</namePart><namePart type="family">Rioux</namePart><affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Nicolas</namePart><namePart type="family">Ginet</namePart><affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Monique</namePart><namePart type="family">Sabaty</namePart><affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Sophie</namePart><namePart type="family">Mangenot</namePart><affiliation>Laboratoire de Finition, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, CP 5706 – 91057, Evry cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Nathalie</namePart><namePart type="family">Pradel</namePart><affiliation>Aix‐Marseille Université, Université du Sud Toulon‐Var, CNRS/INSU, IRD, MIO, UM110, F‐13288, Marseille, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jiesheng</namePart><namePart type="family">Tian</namePart><affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jing</namePart><namePart type="family">Yang</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Lichen</namePart><namePart type="family">Zhang</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Wenyan</namePart><namePart type="family">Zhang</namePart><affiliation>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Hongmiao</namePart><namePart type="family">Pan</namePart><affiliation>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Bernard</namePart><namePart type="family">Henrissat</namePart><affiliation>Architecture et Fonction des Macromolécules Biologiques, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, F‐13288, Marseille Cedex 9, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Pedro M.</namePart><namePart type="family">Coutinho</namePart><affiliation>Architecture et Fonction des Macromolécules Biologiques, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, F‐13288, Marseille Cedex 9, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Ying</namePart><namePart type="family">Li</namePart><affiliation>State Key Laboratories for Agro‐biotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China</affiliation><affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Tian</namePart><namePart type="family">Xiao</namePart><affiliation>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China</affiliation><affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Claudine</namePart><namePart type="family">Médigue</namePart><affiliation>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, F‐91057, Evry, France</affiliation><affiliation>Centre National de la Recherche Scientifique, Unité Mixte de Recherche 80302 rue Gaston Crémieux, F‐91057, Evry, France</affiliation><affiliation>UEVE, Université d'Evry, boulevard François Mitterrand, F‐91025, Evry, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Valérie</namePart><namePart type="family">Barbe</namePart><affiliation>Laboratoire de Finition, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, CP 5706 – 91057, Evry cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">David</namePart><namePart type="family">Pignol</namePart><affiliation>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance, France</affiliation><affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Emmanuel</namePart><namePart type="family">Talla</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><affiliation>E-mail: wu@imm.cnrs.fr</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Long‐Fei</namePart><namePart type="family">Wu</namePart><affiliation>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20, France</affiliation><affiliation>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><dateIssued encoding="w3cdtf">2014-02</dateIssued><dateCreated encoding="w3cdtf">2013-06-14</dateCreated><dateCaptured encoding="w3cdtf">2013-03-11</dateCaptured><dateValid encoding="w3cdtf">2013-06-02</dateValid><copyrightDate encoding="w3cdtf">2014</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract>Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane‐bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH‐2. The high number of repeats and transposable elements account for the differences in QH‐2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH‐2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium‐quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH‐2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH‐2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH‐2 neither has TonB and TonB‐dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH‐2 to marine sediments in comparison with its closely related freshwater counterparts.</abstract><note type="additional physical form">Fig. S1. The comparison of CRISPR locus between the marine Magnetospira sp. QH‐2 and one of R. rubrum. Fig. S2. The genome alignment between the marine Magnetospira sp. QH‐2 and other related genomes. A, C and E graphs are based on nucleotide alignments while B, D and F are from amino acid alignments. Fig. S3. A. The phylogenetic analysis of marine Magnetospira sp. QH‐2 based on the 16S rRNA sequences. Numbers indicate node branch support; only values greater than 50 were shown. Clades I, II, III, IV and V, indicated Alphaproteobacteria, Magnetococcus, Gammaproteobacteria, Deltaproteobacteria, Nitrospira respectively. Red squares indicated the magnetotactic bacteria, and axenic cultures were marked by blue squares; complete genome sequences available strains is indicated with green squares; Non MTB, non axenic cultures or no complete genome bacteria is indicated by a grey square. B. The phylogenetic analysis of the marine Magnetospira sp. QH‐2 based on concatenated protein sequences of 28 housekeeping genes. C. The genome content tree based on the presence/absence of orthologous groups. Fig. S4. Repeat sequence elements (> 200 bp) (dots) in MAI regions. Red (for direct repeats) and blue (opposite orientation repeats) dots. Fig. S5. Presence (+)/Absence (–) of mamCDFG, mamAB or mamXYZ clusters in MTB with the total number (##) of mam genes in the MAI region. Red arrows indicated the MAI insertion event. See also Fig. S1. Fig. S6. The overview of sulfur metabolism in the marine Magnetospira sp. QH‐2 and related genomes. Fig. S7. The overview of nitrogen metabolism in the marine Magnetospira sp. QH‐2 and related genomes. Table S1. The distribution of the COG functional classes in the QH‐2 chromosome and plasmid. Table S2. Putative genomic islands (GI) in the marine Magnetospira sp. QH‐2. Table S3. List of proteins with length greater than 2000aa in marine Magnetospira sp. QH‐2 and related genomes. Table S4. Classification of IS family in the marine Magnetospira sp. QH‐2. Table S5. The CRISPR (clustered regularly interspaced short palindromic repeats) in selected genomes. Table S6. List of the 13 marine Alphaproteobacteria genomes used in comparative analysis. Table S7. The presence (+)/absence (–) of magnetosome island genes in completely/partially sequenced MTB. Table S8. The correlation coefficients between dsr genes. Table S9. The correlation coefficient between mam genes. Table S10. Amino acid substitution rates of different Mam proteins in AMB‐1, MS‐1, MSR‐1, MV‐1 and QH‐2, with MC‐1 as the out‐group. Mean (without or with 2SD) is the average of AMB‐1, MS‐1 and MSR‐1 rates. Table S11. The comparison of CAZymes between QH‐2 and AMB‐1, MSR‐1. Table S12. List of genomes used in the phylogenetic study. Table S13. List of 16S rRNA sequences used in this study.</note><note type="funding">Grands Projets de Séquençage, Agence Nationale de la Recherche - No. ANR‐2010‐BLAN‐1320‐01; </note><note type="funding">National Science Fundation of China - No. NSFC40776094; No. 41276170; </note><note type="funding">Centre National de la Recherche Scientifique</note><note type="funding">Chinese Scholarship Council fellowship</note><relatedItem type="host"><titleInfo><title>Environmental Microbiology</title></titleInfo><titleInfo type="abbreviated"><title>Environ Microbiol</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><subject><genre>article-category</genre><topic>Research articles</topic><topic>Research article</topic></subject><identifier type="ISSN">1462-2912</identifier><identifier type="eISSN">1462-2920</identifier><identifier type="DOI">10.1111/(ISSN)1462-2920</identifier><identifier type="PublisherID">EMI</identifier><part><date>2014</date><detail type="title"><title>Thematic Issue: Protists</title></detail><detail type="volume"><caption>vol.</caption><number>16</number></detail><detail type="issue"><caption>no.</caption><number>2</number></detail><extent unit="pages"><start>525</start><end>544</end><total>20</total></extent></part></relatedItem><relatedItem type="references" displayLabel="emi12180-cit-0001"><titleInfo><title>ProtTest: selection of best‐fit models of protein evolution</title></titleInfo><name type="personal"><namePart type="given">F.</namePart><namePart type="family">Abascal</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R.</namePart><namePart type="family">Zardoya</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">D.</namePart><namePart type="family">Posada</namePart><role><roleTerm type="text">author</roleTerm></role></name><genre>journal-article</genre><note type="citation/reference">Abascal, F., Zardoya, R., and Posada, D. 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