Viral and microbial community dynamics in four aquatic environments
暂无分享,去创建一个
Peter Salamon | Forest Rohwer | Florent E. Angly | Beltran Rodriguez-Brito | Mya Breitbart | Ben Felts | Merry Youle | Robert Edwards | Dana Willner | Mike Furlan | Matthew Haynes | Linda Wegley | Elizabeth Dinsdale | Joseph Mahaffy | Steve Rayhawk | P. Salamon | M. Breitbart | D. Willner | R. Edwards | C. Desnues | E. Dinsdale | M. Haynes | L. Wegley | F. Rohwer | Linlin Li | R. V. Thurber | Beltran Rodriguez-Brito | Steve Rayhawk | T. Tran | Hong Liu | F. Rodríguez-Valera | B. Felts | J. Mahaffy | J. Nulton | A. Mira | D. Lipson | L. Pasic | T. Thingstad | M. Youle | Jim Nulton | Jennifer Rodriguez-Mueller | Francisco Rodriguez-Valera | LinLin Li | Florent Angly | John Buchanan | Christelle Desnues | Hong Liu | David Lipson | Anna Belen Martin-Cuadrado | Alex Mira | Lejla Pašić | Jennifer Rodriguez-Mueller | Shailaja Srinagesh | Tron Frede Thingstad | Tuong Tran | Rebecca Vega Thurber | S. Srinagesh | Mike Furlan | John Buchanan | Matthew Haynes
[1] I. Hewson,et al. Annually reoccurring bacterial communities are predictable from ocean conditions , 2006, Proceedings of the National Academy of Sciences.
[2] Mathias Middelboe,et al. Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties. , 2009, Environmental microbiology.
[3] S. Karthikeyan,et al. Pseudomonas aeruginosa biofilms react with and precipitate toxic soluble gold. , 2002, Environmental microbiology.
[4] P. Salamon,et al. Metagenomic Analyses of an Uncultured Viral Community from Human Feces , 2003, Journal of bacteriology.
[5] Forest Rohwer,et al. An application of statistics to comparative metagenomics , 2006, BMC Bioinformatics.
[6] T. Yokoyama,et al. Thermus thermophilus TMY isolated from silica scale taken from a geothermal power plant , 2007, Journal of applied microbiology.
[7] M. Marston,et al. Selection and Characterization of Cyanophage Resistance in Marine Synechococcus Strains , 2007, Applied and Environmental Microbiology.
[8] Naryttza N. Diaz,et al. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.
[9] Florent E. Angly,et al. The Marine Viromes of Four Oceanic Regions , 2006, PLoS biology.
[10] A. Mills,et al. Classification and Characterization of Heterotrophic Microbial Communities on the Basis of Patterns of Community-Level Sole-Carbon-Source Utilization , 1991, Applied and environmental microbiology.
[11] E. Groisman,et al. Regulation of polymyxin resistance and adaptation to low-Mg2+ environments , 1997, Journal of bacteriology.
[12] K. Linton,et al. The Escherichia coli ATP‐binding cassette (ABC) proteins , 1998, Molecular microbiology.
[13] F. Rohwer,et al. Explaining microbial population genomics through phage predation , 2009, Nature Reviews Microbiology.
[14] C. M. Short,et al. Quantitative PCR reveals transient and persistent algal viruses in Lake Ontario, Canada. , 2009, Environmental microbiology.
[15] J. Sambrook,et al. Molecular Cloning: A Laboratory Manual , 2001 .
[16] T. Yokoyama,et al. Stimulation of Expression of a Silica-Induced Protein (Sip) in Thermus thermophilus by Supersaturated Silicic Acid , 2009, Applied and Environmental Microbiology.
[17] J. Ravel,et al. Population Dynamics of Chesapeake Bay Virioplankton: Total-Community Analysis by Pulsed-Field Gel Electrophoresis , 1999, Applied and Environmental Microbiology.
[18] T. Thingstad. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems , 2000 .
[19] Florent E. Angly,et al. Biodiversity and biogeography of phages in modern stromatolites and thrombolites , 2008, Nature.
[20] J. Lennon,et al. Rapid evolution buffers ecosystem impacts of viruses in a microbial food web. , 2008, Ecology letters.
[21] K. Konhauser,et al. Benefits of bacterial biomineralization , 2008, Geobiology.
[22] S. Lewenza,et al. Extracellular DNA Chelates Cations and Induces Antibiotic Resistance in Pseudomonas aeruginosa Biofilms , 2008, PLoS pathogens.
[23] K. Konhauser,et al. The effect of cyanobacteria on silica precipitation at neutral pH: implications for bacterial silicification in geothermal hot springs , 2003 .
[24] D. Lowe,et al. Silicified Microbial Community at Steep Cone Hot Spring,Yellowstone National Park , 2001 .
[25] Jakob Fredslund,et al. PHY·FI: fast and easy online creation and manipulation of phylogeny color figures , 2006, BMC Bioinformatics.
[26] Eoin L. Brodie,et al. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.
[27] J. Fuhrman,et al. Viral Influence on Aquatic Bacterial Communities , 2003, The Biological Bulletin.
[28] T. Z. DeSantis,et al. Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA , 2003, Bioinform..
[29] M. Breitbart,et al. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. , 2005, BioTechniques.
[30] F. Chen,et al. Phylogenetic Diversity of Marine Cyanophage Isolates and Natural Virus Communities as Revealed by Sequences of Viral Capsid Assembly Protein Gene g20 , 2002, Applied and Environmental Microbiology.
[31] Eric W. Triplett,et al. Geographic and Environmental Sources of Variation in Lake Bacterial Community Composition , 2005, Applied and Environmental Microbiology.
[32] R. Edwards,et al. The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage , 2002, Journal of bacteriology.
[33] Frede Thingstad,et al. Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. , 2002, Environmental microbiology.
[34] Florent E. Angly,et al. Microbial Ecology of Four Coral Atolls in the Northern Line Islands , 2008, PloS one.
[35] K. Campbell,et al. Silicifying biofilm exopolymers on a hot-spring microstromatolite: templating nanometer-thick laminae. , 2008, Astrobiology.
[36] Henk Bolhuis,et al. Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species , 2006, BMC Genomics.
[37] W. Whitman,et al. Prokaryotes: the unseen majority. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[38] J. Fuhrman,et al. Virus decay and its causes in coastal waters , 1997, Applied and environmental microbiology.
[39] T J Beveridge,et al. Participation of a cyanobacterial S layer in fine-grain mineral formation , 1992, Journal of bacteriology.
[40] D. Moreira,et al. Archaeal and bacterial community composition of sediment and plankton from a suboxic freshwater pond. , 2007, Research in microbiology.
[41] J. Fuhrman,et al. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria , 1998 .
[42] R. Edwards,et al. Viral metagenomics , 2005, Nature Reviews Microbiology.
[43] Jonathan P Zehr,et al. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. , 2003, Environmental microbiology.
[44] M. G. Lorenz,et al. Effects of Bacteriophages on the Population Dynamics of Four Strains of Pelagic Marine Bacteria , 2001, Microbial Ecology.
[45] A. Buckling,et al. Local Adaptation of Bacteriophages to Their Bacterial Hosts in Soil , 2009, Science.
[46] E. Groisman,et al. Identification of the lipopolysaccharide modifications controlled by the Salmonella PmrA/PmrB system mediating resistance to Fe(III) and Al(III) , 2006, Molecular microbiology.
[47] D. Andersson,et al. Genetic Analysis of Colistin Resistance in Salmonella enterica Serovar Typhimurium , 2009, Antimicrobial Agents and Chemotherapy.
[49] H. Wichman,et al. Evolutionary Feedback Mediated through Population Density, Illustrated with Viruses in Chemostats , 2005, The American Naturalist.
[50] F. Chen,et al. Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences. , 2009, Environmental microbiology.
[51] J. Banfield,et al. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. , 2007, Environmental microbiology.
[52] J. Imhoff,et al. Variation of environmental features and microbial populations with salt concentrations in a multi-pond saltern , 1985, Microbial Ecology.
[53] J. Hughes,et al. A taxa–area relationship for bacteria , 2004, Nature.
[54] S. Miller,et al. Lipid A Modifications in Polymyxin-resistant Salmonella typhimurium , 2001, The Journal of Biological Chemistry.
[55] J. Costerton,et al. Bacterial biofilms: a common cause of persistent infections. , 1999, Science.
[56] G. Zwart,et al. Distribution of Typical Freshwater Bacterial Groups Is Associated with pH, Temperature, and Lake Water Retention Time , 2005, Applied and Environmental Microbiology.
[57] Florent E. Angly,et al. Genomic analysis of multiple Roseophage SIO1 strains. , 2009, Environmental microbiology.
[58] Peter Salamon,et al. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information , 2005, BMC Bioinformatics.
[59] E. Mardis,et al. An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.
[60] Florent E. Angly,et al. Power law rank-abundance models for marine phage communities. , 2007, FEMS microbiology letters.
[61] R. Simons,et al. Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage , 2002, Science.
[62] Rick L. Stevens,et al. Functional metagenomic profiling of nine biomes , 2008, Nature.
[63] R. Hancock,et al. Cationic antimicrobial peptides activate a two‐component regulatory system, PmrA‐PmrB, that regulates resistance to polymyxin B and cationic antimicrobial peptides in Pseudomonas aeruginosa , 2003, Molecular microbiology.
[64] Danielle M. Winget,et al. Diel and daily fluctuations in virioplankton production in coastal ecosystems. , 2009, Environmental microbiology.
[65] R. Knight,et al. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities , 2005, Applied and Environmental Microbiology.
[66] James R. Cole,et al. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data , 2006, Nucleic Acids Res..
[67] J. Strominger,et al. Mechanism of action of bacitracin: complexation with metal ion and C 55 -isoprenyl pyrophosphate. , 1971, Proceedings of the National Academy of Sciences of the United States of America.
[68] K. Konhauser,et al. Experimental study of iron and silica immobilization by bacteria in mixed Fe-Si systems: implications for microbial silicification in hot springs , 2003 .
[69] P. Salamon,et al. Diversity and population structure of a near–shore marine–sediment viral community , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[70] D. Willner,et al. Metagenomic signatures of 86 microbial and viral metagenomes. , 2009, Environmental microbiology.
[71] R. Hancock,et al. Induction by Cationic Antimicrobial Peptides and Involvement in Intrinsic Polymyxin and Antimicrobial Peptide Resistance, Biofilm Formation, and Swarming Motility of PsrA in Pseudomonas aeruginosa , 2008, Journal of bacteriology.
[72] Rob Knight,et al. UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context , 2006, BMC Bioinformatics.
[73] J. Tremblay,et al. Swarming motility: a multicellular behaviour conferring antimicrobial resistance. , 2009, Environmental microbiology.
[74] A. Reysenbach,et al. The experimental silicification of Aquificales and their role in hot spring sinter formation , 2005 .
[75] E. Drenkard. Antimicrobial resistance of Pseudomonas aeruginosa biofilms. , 2003, Microbes and infection.
[76] S. Miller,et al. PmrA–PmrB‐regulated genes necessary for 4‐aminoarabinose lipid A modification and polymyxin resistance , 1998, Molecular microbiology.
[77] U. Seydel,et al. Probing the properties of lipopolysaccharide monolayers and their interaction with the antimicrobial peptide polymyxin B by atomic force microscopy. , 2005, Langmuir : the ACS journal of surfaces and colloids.
[78] M. Breitbart,et al. Using pyrosequencing to shed light on deep mine microbial ecology , 2006, BMC Genomics.
[79] C. Higgins,et al. The ABC of channel regulation , 1995, Cell.
[80] V. Kunin,et al. A bacterial metapopulation adapts locally to phage predation despite global dispersal. , 2008, Genome research.
[81] G. O’Toole,et al. Mechanisms of biofilm resistance to antimicrobial agents. , 2001, Trends in microbiology.
[82] E. Groisman,et al. A Signal Transduction System that Responds to Extracellular Iron , 2000, Cell.
[83] Alexander F. Auch,et al. MEGAN analysis of metagenomic data. , 2007, Genome research.
[84] K. Holmfeldt,et al. Large Variabilities in Host Strain Susceptibility and Phage Host Range Govern Interactions between Lytic Marine Phages and Their Flavobacterium Hosts , 2007, Applied and Environmental Microbiology.
[85] D. Prieur,et al. Experimental silicification of the extremophilic Archaea Pyrococcus abyssi and Methanocaldococcus jannaschii: applications in the search for evidence of life in early Earth and extraterrestrial rocks , 2009, Geobiology.
[86] S. Tringe,et al. Comparative Metagenomics of Microbial Communities , 2004, Science.
[87] D. Stakes,et al. Biogeological Mineralization in Deep-Sea Hydrothermal Deposits , 1995, Science.
[88] E. Groisman,et al. The PmrA-Regulated pmrC Gene Mediates Phosphoethanolamine Modification of Lipid A and Polymyxin Resistance in Salmonella enterica , 2004, Journal of bacteriology.
[89] A theoretical approach to structuring mechanisms in the pelagic food web , 1998 .
[90] J. Zhou,et al. Sequence diversity within the argF, fbp and recA genes of natural isolates of Neisseria meningitidis: interspecies recombination within the argF gene , 1992, Molecular microbiology.
[91] J. Fuhrman,et al. Rapid Virus Production and Removal as Measured with Fluorescently Labeled Viruses as Tracers , 2000, Applied and Environmental Microbiology.
[92] P. Klesius,et al. Genetic fingerprinting of Flavobacterium columnare isolates from cultured fish , 2004, Journal of applied microbiology.
[93] T. Yokoyama,et al. Bio-deposition of Amorphous Silica by an Extremely Thermophilic Bacterium, Thermus spp. , 1998, Bioscience, biotechnology, and biochemistry.
[94] B. Rodriguez-Mueller,et al. Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber , 2009, BMC Genomics.
[95] O. White,et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.
[96] M. Middelboe,et al. Bacterial Growth Rate and Marine Virus–Host Dynamics , 2000, Microbial Ecology.
[97] J. Banfield,et al. Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.
[98] D. Sigee. Freshwater Microbiology: Biodiversity and Dynamic Interactions of Microorganisms in the Aquatic Environment , 2005 .
[99] F. Rodríguez-Valera,et al. Genomic plasticity in prokaryotes: the case of the square haloarchaeon , 2007, The ISME Journal.
[100] Rick L. Stevens,et al. The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.
[101] F. Inagaki,et al. Microbial silica deposition in geothermal hot waters , 2003, Applied Microbiology and Biotechnology.
[102] J. J. Bull,et al. Impact of Phages on Two-Species Bacterial Communities , 2005, Applied and Environmental Microbiology.
[103] Anders F. Andersson,et al. Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities , 2008, Science.
[104] R. Kolter,et al. ABC transporters: bacterial exporters , 1993, Microbiological reviews.
[105] S. Lory,et al. The chaperone/usher pathways of Pseudomonas aeruginosa: Identification of fimbrial gene clusters (cup) and their involvement in biofilm formation , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[106] R. Lenski,et al. Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage , 2000 .
[107] J. Elphinstone,et al. Dickeya species relatedness and clade structure determined by comparison of recA sequences. , 2009, International journal of systematic and evolutionary microbiology.
[108] Andrew Steele,et al. The simulated silicification of bacteria--new clues to the modes and timing of bacterial preservation and implications for the search for extraterrestrial microfossils. , 2002, Astrobiology.
[109] B. Andresen,et al. Genomic analysis of uncultured marine viral communities , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[110] S. Lalonde,et al. Bacterial biomineralization: Where to from here? , 2008, Geobiology.