Complete genome sequence of Desulfohalobium retbaense type strain (HR100T)

Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H2 and a limited range of organic substrates, which are incompletely oxidized to acetate and CO2, for growth. The type strain ${\rm HR}_{100}^{\rm T}$ was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the GenomicEncyclopedia ofBacteria andArchaea project.

[1]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[2]  Lynne A. Goodwin,et al.  Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T) , 2009, Standards in genomic sciences.

[3]  I-Min A. Chen,et al.  IMG ER: a system for microbial genome annotation expert review and curation , 2009, Bioinform..

[4]  S. Spring,et al.  Complete genome sequence of Desulfomicrobium baculatum type strain (XT) , 2009, Standards in genomic sciences.

[5]  Lynne A. Goodwin,et al.  Complete genome sequence of Kytococcus sedentarius type strain (541T) , 2009, Standards in genomic sciences.

[6]  Kimberly L. Keller,et al.  A Molybdopterin Oxidoreductase Is Involved in H2 Oxidation in Desulfovibrio desulfuricans G20 , 2009, Journal of bacteriology.

[7]  S. Kawasaki,et al.  O2 and Reactive Oxygen Species Detoxification Complex, Composed of O2-Responsive NADH:Rubredoxin Oxidoreductase-Flavoprotein A2-Desulfoferrodoxin Operon Enzymes, Rubperoxin, and Rubredoxin, in Clostridium acetobutylicum , 2009, Applied and Environmental Microbiology.

[8]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[9]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[10]  Nikos Kyrpides,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[11]  J. Euzéby Validation List no. 117. List of new names and new combinations previously effectively, but not validly, published. , 2007, International journal of systematic and evolutionary microbiology.

[12]  M. Wagner,et al.  Diversity of sulfate-reducing bacteria from an extreme hypersaline sediment, Great Salt Lake (Utah). , 2007, FEMS microbiology ecology.

[13]  K. U. Kjeldsen,et al.  Desulfohalobium utahense sp. nov., a moderately halophilic, sulfate-reducing bacterium isolated from Great Salt Lake. , 2006, International journal of systematic and evolutionary microbiology.

[14]  A. Lysenko,et al.  The new facultatively chemolithoautotrophic, moderately halophilic, sulfate-reducing bacterium Desulfovermiculus halophilus gen. nov., sp. nov., isolated from an oil field , 2006, Microbiology.

[15]  M. Teixeira,et al.  Characterization of the Desulfovibrio desulfuricans ATCC 27774 DsrMKJOP complex--a membrane-bound redox complex involved in the sulfate respiratory pathway. , 2006, Biochemistry.

[16]  C. Soares,et al.  Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview. , 2005, Progress in biophysics and molecular biology.

[17]  M. Teixeira,et al.  A novel membrane-bound respiratory complex from Desulfovibrio desulfuricans ATCC 27774. , 2003, Biochimica et biophysica acta.

[18]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[19]  N. Shenvi,et al.  Rubrerythrin and Rubredoxin Oxidoreductase in Desulfovibrio vulgaris: a Novel Oxidative Stress Protection System , 2001 .

[20]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[21]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[22]  Aharon Oren,et al.  Bioenergetic Aspects of Halophilism , 1999, Microbiology and Molecular Biology Reviews.

[23]  J. Euzéby List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. , 1997, International journal of systematic bacteriology.

[24]  J. Hannan,et al.  Identification of trehalose and glycine betaine as compatible solutes in the moderately halophilic sulfate reducing bacterium, Desulfovibrio halophilus , 1996 .

[25]  H. Cypionka,et al.  Influence of oxygen on sulfate reduction and growth of sulfate-reducing bacteria , 1993, Archives of Microbiology.

[26]  I. Wilson,et al.  The cellular location and specificity of bacterial cytochrome c peroxidases. , 1990, The Biochemical journal.

[27]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[28]  G. Garrity Bergey’s Manual® of Systematic Bacteriology , 2012, Springer New York.

[29]  Lynne A. Goodwin,et al.  Complete genome sequence of Kytococcus sedentarius type strain (541 T ) , 2009 .

[30]  T. Hansen Bergey's Manual of Systematic Bacteriology , 2005 .

[31]  H. Cypionka,et al.  Oxygen respiration by desulfovibrio species. , 2000, Annual review of microbiology.

[32]  B. Ollivier,et al.  Desulfohalobium retbaense gen. nov., sp. nov., a Halophilic Sulfate-Reducing Bacterium from Sediments of a Hypersaline Lake in Senegal , 1991 .