title: Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200.
abstract: Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantial eco-physiological diversity including free-living, symbiotic and piezophilic life styles. Genomic characteristics underlying this variability across species are poorly understood. Here we carried out genomic and physiological analysis of Photobacterium phosphoreum strain ANT-2200, the first deep-sea luminous bacterium of which the genome has been sequenced. Using optical mapping we updated the genomic data and reassembled it into two chromosomes and a large plasmid. Genomic analysis revealed a versatile energy metabolic potential and physiological analysis confirmed its growth capacity by deriving energy from fermentation of glucose or maltose, by respiration with formate as electron donor and trimethlyamine N-oxide (TMAO), nitrate or fumarate as electron acceptors, or by chemo-organo-heterotrophic growth in rich media. Despite that it was isolated at a site with saturated dissolved oxygen, the ANT-2200 strain possesses four gene clusters coding for typical anaerobic enzymes, the TMAO reductases. Elevated hydrostatic pressure enhances the TMAO reductase activity, mainly due to the increase of isoenzyme TorA1. The high copy number of the TMAO reductase isoenzymes and pressure-enhanced activity might imply a strategy developed by bacteria to adapt to deep-sea habitats where the instant TMAO availability may increase with depth.
authors.affiliation: Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.|France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China.
authors.forename: Sheng-Da
authors.initials: SD
authors.lastname: Zhang
authors.affiliation: LCB UMR 7257, Aix-Marseille Université, CNRS, IMM, 31, Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.|France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China.
authors.forename: Claire-Lise
authors.initials: CL
authors.lastname: Santini
authors.affiliation: Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.|France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China.
authors.forename: Wei-Jia
authors.initials: WJ
authors.lastname: Zhang
authors.affiliation: DSV/IG/Genoscope/LF, CEA, Evry, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.affiliation: DSV/IG/Genoscope/LF, CEA, Evry, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Mangenot
authors.affiliation: LCB UMR 7257, Aix-Marseille Université, CNRS, IMM, 31, Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.|France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Guyomar
authors.affiliation: Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM110, 13288, Marseille, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Garel
authors.affiliation: Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.|France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China.
authors.forename: Hai-Tao
authors.initials: HT
authors.lastname: Chen
authors.affiliation: Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.|France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China.
authors.forename: Xue-Gong
authors.initials: XG
authors.lastname: Li
authors.affiliation: Deep-Sea Microbial Cell Biology, Department of Deep Sea Sciences, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.|France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China.
authors.forename: Qun-Jian
authors.initials: QJ
authors.lastname: Yin
authors.affiliation: Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: DSV, iBEB/SBTN, CEA, Bagnols-sur-Cèze, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Armengaud
authors.affiliation: DSV, iBEB/SBTN, CEA, Bagnols-sur-Cèze, France.
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Gaillard
authors.affiliation: Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM110, 13288, Marseille, France.
authors.forename: Séverine
authors.initials: S
authors.lastname: Martini
authors.affiliation: Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM110, 13288, Marseille, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Pradel
authors.affiliation: DSV, iBEB/SBTN, CEA, Bagnols-sur-Cèze, France.
authors.forename: Claude
authors.initials: C
authors.lastname: Vidaud
authors.affiliation: LCB UMR 7257, Aix-Marseille Université, CNRS, IMM, 31, Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.|France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China.
authors.forename: François
authors.initials: F
authors.lastname: Alberto
authors.affiliation: Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, CEA/DSV/IG/Genoscope and CNRS-UMR 8030 and Univ. Evry Val d'Esssone, Evry, France.
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.affiliation: Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM110, 13288, Marseille, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Tamburini
authors.affiliation: LCB UMR 7257, Aix-Marseille Université, CNRS, IMM, 31, Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France. wu@imm.cnrs.fr.|France-China Bio-Mineralization and Nano-Structure Laboratory (LIA-BioMNSL), LCB-CNRS, Marseille, France/SIDSSE-CAS, Sanya, China. wu@imm.cnrs.fr.
authors.forename: Long-Fei
authors.initials: LF
authors.lastname: Wu
mesh_terms: D000222:Adaptation, Physiological; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D004579:Electron Transport; D004734:Energy Metabolism; D016680:Genome, Bacterial; D005947:Glucose / Q000378:metabolism; D006874:Hydrostatic Pressure; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D008320:Maltose / Q000378:metabolism; D008744:Methylamines / Q000378:metabolism; D010089:Oxidoreductases, N-Demethylating / Q000235:genetics / Q000378:metabolism; D010776:Photobacterium / Q000235:genetics* / Q000378:metabolism; D012623:Seawater / Q000382:microbiology
chemical_list: D001426:Bacterial Proteins; D007527:Isoenzymes; D008744:Methylamines; D008320:Maltose; D010089:Oxidoreductases, N-Demethylating; C023186:trimethylamine dehydrogenase; C005855:trimethyloxamine; D005947:Glucose
keywords: Anaerobic respiration; Bioluminescence; Deep-sea adaptation; Hydrostatic pressure; TMAO reductase