The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea

[1]  H. Brinkmann,et al.  Diversity and evolution of repABC type plasmids in Rhodobacterales. , 2009, Environmental microbiology.

[2]  C. Wittmann,et al.  Bmc Microbiology , 2004 .

[3]  Adrian P. Martin,et al.  Viral infection as a regulator of oceanic phytoplankton populations , 2008 .

[4]  M. Weinbauer,et al.  Major viral impact on the functioning of benthic deep-sea ecosystems , 2008, Nature.

[5]  D. Hutchins,et al.  Potential cobalt limitation of vitamin B12 synthesis in the North Atlantic Ocean , 2008 .

[6]  M. Weinbauer,et al.  Global-scale processes with a nanoscale drive: the role of marine viruses , 2008, The ISME Journal.

[7]  Michael Kühl,et al.  Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat , 2008, The ISME Journal.

[8]  F. Chen,et al.  Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton , 2008, Applied and Environmental Microbiology.

[9]  F. Azam,et al.  Cultivation and Ecosystem Role of a Marine Roseobacter Clade-Affiliated Cluster Bacterium , 2008, Applied and Environmental Microbiology.

[10]  Maurizio Labbate,et al.  AHL-driven quorum-sensing circuits: their frequency and function among the Proteobacteria , 2008, The ISME Journal.

[11]  M. Simon,et al.  Diversity, ecology, and genomics of the Roseobacter clade: a short overview , 2008, Archives of Microbiology.

[12]  J. Poggiale,et al.  Imaging Oxygen Distribution in Marine Sediments. The Importance of Bioturbation and Sediment Heterogeneity , 2008, Acta biotheoretica.

[13]  A. Halpern,et al.  The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples , 2008, PloS one.

[14]  R. Belas,et al.  Genetic Dissection of Tropodithietic Acid Biosynthesis by Marine Roseobacters , 2008, Applied and Environmental Microbiology.

[15]  Hanh H. Hoang,et al.  Regulation of Motility by the ExpR/Sin Quorum-Sensing System in Sinorhizobium meliloti , 2007, Journal of bacteriology.

[16]  J. Banfield,et al.  Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. , 2007, Environmental microbiology.

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

[18]  Jennifer L. Martin,et al.  Microbial community diversity in the phycosphere of natural populations of the toxic alga, Alexandrium fundyense. , 2007, Environmental microbiology.

[19]  C. Gobler,et al.  Effect of B-vitamins (B1, B12) and inorganic nutrients on algal bloom dynamics in a coastal ecosystem , 2007 .

[20]  M. Parsons,et al.  A survey of epiphytic dinoflagellates from the coastal waters of the island of Hawai'i , 2007 .

[21]  M. Moran,et al.  Resourceful heterotrophs make the most of light in the coastal ocean , 2007, Nature Reviews Microbiology.

[22]  Kenneth H Nealson,et al.  Metagenomics and the global ocean survey: what's in it for us, and why should we care? , 2007, The ISME Journal.

[23]  G. Thomas,et al.  Tripartite ATP-Independent Periplasmic Transporters: Application of a Relational Database for Genome-Wide Analysis of Transporter Gene Frequency and Organization , 2007, Journal of Molecular Microbiology and Biotechnology.

[24]  M. Hoppenrath,et al.  Seasonal changes of benthic and epiphytic dinoflagellates in the Veracruz reef zone, Gulf of Mexico , 2007 .

[25]  Luke E. Ulrich,et al.  Ecological Genomics of Marine Roseobacters , 2007, Applied and Environmental Microbiology.

[26]  Ibtissem Grissa,et al.  The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats , 2007, BMC Bioinformatics.

[27]  M. Saito,et al.  Vitamin B12 and iron colimitation of phytoplankton growth in the Ross Sea , 2007 .

[28]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[29]  S. Kravitz,et al.  CAMERA: A Community Resource for Metagenomics , 2007, PLoS biology.

[30]  Michael R Droop Vitamins, Phytoplankton and Bacteria: Symbiosis or Scavenging? , 2007 .

[31]  M. Choudhary,et al.  Genome Analyses of Three Strains of Rhodobacter sphaeroides: Evidence of Rapid Evolution of Chromosome II , 2006, Journal of bacteriology.

[32]  Maeve O’Huallachain,et al.  The Complete Genome Sequence of Roseobacter denitrificans Reveals a Mixotrophic Rather than Photosynthetic Metabolism , 2006, Journal of bacteriology.

[33]  B. Ryall,et al.  Oxygen, cyanide and energy generation in the cystic fibrosis pathogen Pseudomonas aeruginosa. , 2007, Advances in microbial physiology.

[34]  Nikos Kyrpides,et al.  CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats , 2007, BMC Bioinformatics.

[35]  C. Duarte,et al.  B vitamins as regulators of phytoplankton dynamics , 2006 .

[36]  Alison Buchan,et al.  Bacterial Taxa That Limit Sulfur Flux from the Ocean , 2006, Science.

[37]  H. Biebl,et al.  Growth and bacteriochlorophyll a formation in taxonomically diverse aerobic anoxygenic phototrophic bacteria in chemostat culture: Influence of light regimen and starvation , 2006 .

[38]  H. Biebl,et al.  Environmental biology of the marine Roseobacter lineage. , 2006, Annual review of microbiology.

[39]  Todd R. Miller,et al.  Motility is involved in Silicibacter sp. TM1040 interaction with dinoflagellates. , 2006, Environmental microbiology.

[40]  F. Chen,et al.  Induction of Multiple Prophages from a Marine Bacterium: a Genomic Approach , 2006, Applied and Environmental Microbiology.

[41]  N. Grishin,et al.  A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action , 2006, Biology Direct.

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

[43]  J. S. Godde,et al.  The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes , 2006, Journal of Molecular Evolution.

[44]  R. Pukall,et al.  Discovery of Complex Mixtures of Novel Long‐Chain Quorum Sensing Signals in Free‐Living and Host‐Associated Marine Alphaproteobacteria , 2005, Chembiochem : a European journal of chemical biology.

[45]  Dieter Jahn,et al.  Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes , 2005, Bioinform..

[46]  Martin J. Warren,et al.  Algae acquire vitamin B12 through a symbiotic relationship with bacteria , 2005, Nature.

[47]  L. Gram,et al.  Ecology, Inhibitory Activity, and Morphogenesis of a Marine Antagonistic Bacterium Belonging to the Roseobacter Clade , 2005, Applied and Environmental Microbiology.

[48]  Daniel H. Haft,et al.  A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes , 2005, PLoS Comput. Biol..

[49]  M. Moran,et al.  Overview of the Marine Roseobacter Lineage , 2005, Applied and Environmental Microbiology.

[50]  D. Gevers,et al.  Re-evaluating prokaryotic species , 2005, Nature Reviews Microbiology.

[51]  K. Nagasaki,et al.  [Molecular ecology of microalgal viruses]. , 2005, Uirusu.

[52]  R. Pukall,et al.  Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates. , 2005, International journal of systematic and evolutionary microbiology.

[53]  S. Sañudo-Wilhelmy,et al.  Direct determination of vitamin B1 in seawater by solid‐phase extraction and high‐performance liquid chromatography quantification , 2005 .

[54]  D. Scanlan,et al.  Genetic diversity of marine Synechococcus and co-occurring cyanophage communities: evidence for viral control of phytoplankton. , 2005, Environmental microbiology.

[55]  C. Miles,et al.  Yessotoxins in Norwegian blue mussels (Mytilus edulis): uptake from Protoceratium reticulatum, metabolism and depuration. , 2005, Toxicon : official journal of the International Society on Toxinology.

[56]  S. Santabarbara,et al.  Identification and Characterization of a Novel Vitamin B12 (Cobalamin) Biosynthetic Enzyme (CobZ) from Rhodobacter capsulatus, Containing Flavin, Heme, and Fe-S Cofactors* , 2005, Journal of Biological Chemistry.

[57]  Tom Coenye,et al.  Opinion: Re-evaluating prokaryotic species. , 2005, Nature reviews. Microbiology.

[58]  R. Genovese The cultural heritage for the man , 2005 .

[59]  Ian T. Paulsen,et al.  Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment , 2004, Nature.

[60]  Todd R. Miller,et al.  Chemotaxis of Silicibacter sp. Strain TM1040 toward Dinoflagellate Products , 2004, Applied and Environmental Microbiology.

[61]  J. Buer,et al.  Long-Term Anaerobic Survival of the Opportunistic Pathogen Pseudomonas aeruginosa via Pyruvate Fermentation , 2004, Journal of bacteriology.

[62]  Todd R. Miller,et al.  Dimethylsulfoniopropionate Metabolism by Pfiesteria-Associated Roseobacter spp , 2004, Applied and Environmental Microbiology.

[63]  E. Stackebrandt,et al.  Genome Organization and Localization of the pufLM Genes of the Photosynthesis Reaction Center in Phylogenetically Diverse Marine Alphaproteobacteria , 2004, Applied and Environmental Microbiology.

[64]  M. Weinbauer Ecology of prokaryotic viruses. , 2004, FEMS microbiology reviews.

[65]  T. Heidorn,et al.  Antibiotic Production by a Roseobacter Clade-Affiliated Species from the German Wadden Sea and Its Antagonistic Effects on Indigenous Isolates , 2004, Applied and Environmental Microbiology.

[66]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[67]  K. Nagasaki,et al.  Widespread occurrence of viruses lytic to the bivalve-killing dinoflagellate Heterocapsa circularisquama along the western coast of Japan , 2004 .

[68]  M. Simon,et al.  A newly discovered Roseobacter cluster in temperate and polar oceans , 2004, Nature.

[69]  M. Gelfand,et al.  Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes* , 2003, Journal of Biological Chemistry.

[70]  M. Allgaier,et al.  Aerobic Anoxygenic Photosynthesis in Roseobacter Clade Bacteria from Diverse Marine Habitats , 2003, Applied and Environmental Microbiology.

[71]  R. Amann,et al.  An Improved Protocol for Quantification of Freshwater Actinobacteria by Fluorescence In Situ Hybridization , 2003, Applied and Environmental Microbiology.

[72]  M. Levasseur,et al.  Pelagic and epiphytic summer distributions of Prorocentrum lima and P. mexicanum at two mussel farms in the Gulf of St. Lawrence, Canada , 2003 .

[73]  A. Tomaszewski Tangible and intangible values of cultural property in Western tradition and science , 2003 .

[74]  D. C. Yoch Dimethylsulfoniopropionate: Its Sources, Role in the Marine Food Web, and Biological Degradation to Dimethylsulfide , 2002, Applied and Environmental Microbiology.

[75]  J. Escalante‐Semerena,et al.  The Biosynthesis of Adenosylcobalamin (Vitamin B12) , 2002 .

[76]  A. Eberhard,et al.  Characterization of the Sinorhizobium meliloti sinR/sinI Locus and the Production of Novel N-Acyl Homoserine Lactones , 2002, Journal of bacteriology.

[77]  Rudolf Amann,et al.  Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria , 2002, Applied and Environmental Microbiology.

[78]  W. Whitman,et al.  Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. , 2002, International journal of systematic and evolutionary microbiology.

[79]  C. Roessner,et al.  Biosynthesis of cobalamin (vitamin B(12)). , 2001, Biochemical Society transactions.

[80]  Robert F. Chen,et al.  Chemical composition and cycling of dissolved organic matter in the Mid-Atlantic Bight , 2002 .

[81]  R. Amann,et al.  The species concept for prokaryotes. , 2013, FEMS microbiology reviews.

[82]  D. Jahn,et al.  Microbial production of vitamin B12 , 2002, Applied Microbiology and Biotechnology.

[83]  G. Chaconas,et al.  The circle is broken: telomere resolution in linear replicons. , 2001, Current opinion in microbiology.

[84]  Todd R. Miller,et al.  Bacterial community associated with Pfiesteria-like dinoflagellate cultures. , 2001, Environmental microbiology.

[85]  U. Zielenkiewicz,et al.  Mechanisms of plasmid stable maintenance with special focus on plasmid addiction systems. , 2001, Acta biochimica Polonica.

[86]  M. Saier,et al.  TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters. , 1999, Microbiology.

[87]  A. Cembella,et al.  Cell cycle and toxin production in the benthic dinoflagellate Prorocentrum lima , 1999 .

[88]  J. Fuhrman Marine viruses and their biogeochemical and ecological effects , 1999, Nature.

[89]  G. Gerdts,et al.  Bacteria of the Genus Roseobacter Associated with the Toxic Dinoflagellate Prorocentrum lima. , 1998, Protist.

[90]  R. Benner,et al.  Carbohydrates in phytoplankton and freshly produced dissolved organic matter , 1998 .

[91]  N. Revsbech,et al.  Biosensor Determination of the Microscale Distribution of Nitrate, Nitrate Assimilation, Nitrification, and Denitrification in a Diatom-Inhabited Freshwater Sediment , 1998, Applied and Environmental Microbiology.

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

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

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

[95]  D. Kelly,et al.  TRAP transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse gram-negative bacteria , 1997, Journal of bacteriology.

[96]  A. Douglas,et al.  Nutrients, Signals, and Photosynthate Release by Symbiotic Algae (The Impact of Taurine on the Dinoflagellate Alga Symbiodinium from the Sea Anemone Aiptasia pulchella) , 1997, Plant physiology.

[97]  F. Meinhardt,et al.  Microbial linear plasmids , 1997, Applied Microbiology and Biotechnology.

[98]  T. Bobik,et al.  Cobalamin (coenzyme B12): synthesis and biological significance. , 1996, Annual review of microbiology.

[99]  R. Christen,et al.  Roseobacter algicola sp. nov., a new marine bacterium isolated from the phycosphere of the toxin-producing dinoflagellate Prorocentrum lima. , 1995, International journal of systematic bacteriology.

[100]  R. Guillard,et al.  Stichochrysis immobilis is a diatom, not a chrysophyte , 1993 .

[101]  V. Stewart,et al.  Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12 , 1993, Journal of Bacteriology.

[102]  Tsuneo Shiba,et al.  Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., Aerobic Pink-Pigmented Bacteria which Contain Bacteriochlorophyll a , 1991 .

[103]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[104]  J. G. Field,et al.  The Ecological Role of Water-Column Microbes in the Sea* , 1983 .

[105]  K. Kowallik The crystal lattice of the pyrenoid matrix of Prorocentrum micans. , 1969, Journal of cell science.