Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1)

1 Department of Biological Sciences and Research School Chemical Biology, University of Konstanz, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia

[1]  Liping Wang,et al.  Parvibaculum indicum sp. nov., isolated from deep-sea water. , 2011, International journal of systematic and evolutionary microbiology.

[2]  D. Prieur,et al.  Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches , 2010, Extremophiles.

[3]  A. M. Solanas,et al.  Chemical and microbial community analysis during aerobic biostimulation assays of non-sulfonated alkyl-benzene-contaminated groundwater , 2010, Applied Microbiology and Biotechnology.

[4]  Marc Viñas,et al.  Degradation of 4-n-nonylphenol under nitrate reducing conditions , 2010, Biodegradation.

[5]  E. G. Lemos,et al.  Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation , 2010 .

[6]  Zongze Shao,et al.  Gene diversity of CYP153A and AlkB alkane hydroxylases in oil-degrading bacteria isolated from the Atlantic Ocean. , 2010, Environmental microbiology.

[7]  F. Rainey,et al.  Tepidamorphus gemmatus gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria. , 2010, Systematic and applied microbiology.

[8]  E. Roden,et al.  Composition and Activity of an Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture , 2009, Applied and Environmental Microbiology.

[9]  G. Fuchs,et al.  (2S)‐Methylsuccinyl‐CoA dehydrogenase closes the ethylmalonyl‐CoA pathway for acetyl‐CoA assimilation , 2009, Molecular microbiology.

[10]  A. M. Solanas,et al.  Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill , 2009, Applied and Environmental Microbiology.

[11]  Jessica Rehdorf,et al.  Cloning, Expression, Characterization, and Biocatalytic Investigation of the 4-Hydroxyacetophenone Monooxygenase from Pseudomonas putida JD1 , 2009, Applied and Environmental Microbiology.

[12]  Zhang De-min.  Dynamics of Petroleum-degrading Bacterial Community with Biodegradation of Petroleum Contamination in Seawater , 2009 .

[13]  K. Yrjälä,et al.  High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil , 2008, The ISME Journal.

[14]  Tianfeng Tan,et al.  A pyrene-degrading consortium from deep-sea sediment of the West Pacific and its key member Cycloclasticus sp. P1. , 2008, Environmental microbiology.

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

[16]  I-Min A. Chen,et al.  The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions , 2007, Nucleic Acids Res..

[17]  Notification that new names and new combinations have appeared in volume 57, part 10, of the IJSEM. , 2008, International journal of systematic and evolutionary microbiology.

[18]  R. Hill,et al.  Enrichment, Isolation, and Phylogenetic Identification of Polycyclic Aromatic Hydrocarbon-Degrading Bacteria from Elizabeth River Sediments , 2007, Applied and Environmental Microbiology.

[19]  Daniel H. Huson,et al.  Dendroscope: An interactive viewer for large phylogenetic trees , 2007, BMC Bioinformatics.

[20]  M. Höfle,et al.  Anderseniella baltica gen. nov., sp. nov., a novel marine bacterium of the Alphaproteobacteria isolated from sediment in the central Baltic Sea. , 2007, International journal of systematic and evolutionary microbiology.

[21]  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.

[22]  K. Timmis,et al.  Widespread capacity to metabolize polychlorinated biphenyls by diverse microbial communities in soils with no significant exposure to PCB contamination. , 2007, Environmental microbiology.

[23]  K. Egli,et al.  Phylogenetic and functional diversity of bacteria in biofilms from metal surfaces of an alkaline district heating system. , 2007, FEMS microbiology ecology.

[24]  V. Brecht,et al.  Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: The ethylmalonyl-CoA pathway , 2007, Proceedings of the National Academy of Sciences.

[25]  T. Knepper,et al.  Parvibaculum lavamentivorans DS-1T Degrades Centrally Substituted Congeners of Commercial Linear Alkylbenzenesulfonate to Sulfophenyl Carboxylates and Sulfophenyl Dicarboxylates , 2007, Applied and Environmental Microbiology.

[26]  Steven Salzberg,et al.  Identifying bacterial genes and endosymbiont DNA with Glimmer , 2007, Bioinform..

[27]  Philip Hugenholtz,et al.  NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes , 2006, Nucleic Acids Res..

[28]  B. Schink,et al.  Cell aggregation of Pseudomonas aeruginosa strain PAO1 as an energy-dependent stress response during growth with sodium dodecyl sulfate , 2006, Archives of Microbiology.

[29]  Patrick Chain,et al.  Finishing Repetitive Regions Automatically with Dupfinisher , 2006, BIOCOMP.

[30]  J. Mas,et al.  Molecular Characterization of an Oil-Degrading Cyanobacterial Consortium , 2005, Microbial Ecology.

[31]  D. Schleheck,et al.  ω-Oxygenation of the alkyl sidechain of linear alkylbenzenesulfonate (LAS) surfactant in Parvibaculum lavamentivoransT , 2005, Archives of Microbiology.

[32]  J. Euzéby.  Notification that new names and new combinations have appeared in volume 54, part 5, of the IJSEM. , 2005, International journal of systematic and evolutionary microbiology.

[33]  B. Tindall,et al.  Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate. , 2004, International journal of systematic and evolutionary microbiology.

[34]  S. Brunak,et al.  Improved prediction of signal peptides: SignalP 3.0. , 2004, Journal of molecular biology.

[35]  T. Knepper,et al.  Mineralization of Individual Congeners of Linear Alkylbenzenesulfonate by Defined Pairs of Heterotrophic Bacteria , 2004, Applied and Environmental Microbiology.

[36]  T. Knepper,et al.  Parvibaculum lavamentivorans converts linear alkylbenzenesulphonate surfactant to sulphophenylcarboxylates, α,β‐unsaturated sulphophenylcarboxylates and sulphophenyldicarboxylates, which are degraded in communities , 2004, Journal of applied microbiology.

[37]  D. Schleheck,et al.  Desulfonation and Degradation of the Disulfodiphenylethercarboxylates from Linear Alkyldiphenyletherdisulfonate Surfactants , 2003, Applied and Environmental Microbiology.

[38]  R. Amann,et al.  Isolation of Novel Pelagic Bacteria from the German Bight and Their Seasonal Contributions to Surface Picoplankton , 2001, Applied and Environmental Microbiology.

[39]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[40]  E. Heinzle,et al.  An α-Proteobacterium Converts Linear Alkylbenzenesulfonate Surfactants into Sulfophenylcarboxylates and Linear Alkyldiphenyletherdisulfonate Surfactants into Sulfodiphenylethercarboxylates , 2000, Applied and Environmental Microbiology.

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

[42]  G. Olsen,et al.  CRITICA: coding region identification tool invoking comparative analysis. , 1999, Molecular biology and evolution.

[43]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[44]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[45]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[46]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[47]  C. Walsh,et al.  Acinetobacter cyclohexanone monooxygenase: gene cloning and sequence determination , 1988, Journal of bacteriology.

[48]  I. C. Gunsalus,et al.  Mixed function oxidation. IV. An induced methylene hydroxylase in camphor oxidation. , 1965, The Journal of biological chemistry.