Community-wide plasmid gene mobilization and selection

[1]  John R. Lawrence,et al.  Next-generation sequencing of microbial communities in the Athabasca River 1 and its tributaries in relation to oil sands mining activities 2 3 , 2012 .

[2]  E. Douzery,et al.  Environment drives high phylogenetic turnover among oceanic bacterial communities , 2012, Biology Letters.

[3]  N. Fierer,et al.  Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes , 2012 .

[4]  Adi Doron-Faigenboim,et al.  Insights into the bovine rumen plasmidome , 2012, Proceedings of the National Academy of Sciences.

[5]  M. Schloter,et al.  Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments , 2012, The ISME Journal.

[6]  K. Konstantinidis,et al.  Bacterial species may exist, metagenomics reveal. , 2012, Environmental microbiology.

[7]  Etienne Yergeau,et al.  Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils , 2012, PloS one.

[8]  Per Halkjær Nielsen,et al.  A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal , 2011, The ISME Journal.

[9]  Peter Zuber,et al.  Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient , 2011, The ISME Journal.

[10]  Jizhong Zhou,et al.  Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments , 2011, The ISME Journal.

[11]  M. Bradford,et al.  The effect of resource history on the functioning of soil microbial communities is maintained across time , 2011 .

[12]  Folker Meyer,et al.  37. The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes , 2011 .

[13]  É. Yergeau,et al.  Identification of Nitrogen-Incorporating Bacteria in Petroleum-Contaminated Arctic Soils by Using [15N]DNA-Based Stable Isotope Probing and Pyrosequencing , 2011, Applied and Environmental Microbiology.

[14]  S. Ghoshal,et al.  Petroleum hydrocarbon biodegradation under seasonal freeze-thaw soil temperature regimes in contaminated soils from a sub-Arctic site. , 2011, Environmental science & technology.

[15]  S. Bertilsson,et al.  Function-specific response to depletion of microbial diversity , 2011, The ISME Journal.

[16]  A. Magurran,et al.  Temporal turnover and the maintenance of diversity in ecological assemblages , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[17]  W. Martin,et al.  Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths , 2010, Molecular biology and evolution.

[18]  J. Bowman,et al.  The importance of soil characteristics to the structure of alkane-degrading bacterial communities on sub-Antarctic Macquarie Island , 2010 .

[19]  Rob Knight,et al.  Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. , 2010, Environmental microbiology.

[20]  C. Violle,et al.  Experimental demonstration of the importance of competition under disturbance , 2010, Proceedings of the National Academy of Sciences.

[21]  Robert G. Beiko,et al.  Identifying biologically relevant differences between metagenomic communities , 2010, Bioinform..

[22]  Matteo Brilli,et al.  Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome , 2010, BMC Evolutionary Biology.

[23]  Woojun Park,et al.  Protection against diesel oil toxicity by sodium chloride-induced exopolysaccharides in Acinetobacter sp. strain DR1. , 2010, Journal of bioscience and bioengineering.

[24]  Ye Deng,et al.  Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community , 2010, The ISME Journal.

[25]  J. Marchesi,et al.  Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome , 2010, BMC Genomics.

[26]  C. Greer.  Bioremediation of Contaminated Sites in the Canadian Arctic: Monitoring Performance and the Effects of Biostimulation Using Molecular Methods , 2009 .

[27]  R. Knight,et al.  Bacterial Community Variation in Human Body Habitats Across Space and Time , 2009, Science.

[28]  X. Le Roux,et al.  Community niche predicts the functioning of denitrifying bacterial assemblages. , 2009, Ecology.

[29]  Sam P. Brown,et al.  Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence , 2009, Current Biology.

[30]  Yan Wei Lim,et al.  Metagenomic analysis of viruses in reclaimed water. , 2009, Environmental microbiology.

[31]  Weizhong Li,et al.  Analysis and comparison of very large metagenomes with fast clustering and functional annotation , 2009, BMC Bioinformatics.

[32]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[33]  W. D. de Vos,et al.  Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine , 2009, PloS one.

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

[35]  É. Yergeau,et al.  Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments , 2009, Applied and Environmental Microbiology.

[36]  P. Forterre,et al.  A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes , 2009, Genome Biology.

[37]  R. Knight,et al.  Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale , 2009, Applied and Environmental Microbiology.

[38]  Alicja Szulc,et al.  Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218 microbial consortia are not correlated to cell surface hydrophobicity , 2009, Applied Microbiology and Biotechnology.

[39]  A. Fodor,et al.  Molecular Diversity of a North Carolina Wastewater Treatment Plant as Revealed by Pyrosequencing , 2008, Applied and Environmental Microbiology.

[40]  Matthew Berriman,et al.  DNAPlotter: circular and linear interactive genome visualization , 2008, Bioinform..

[41]  E. Koonin,et al.  Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world , 2008, Nucleic acids research.

[42]  Amy Long,et al.  Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression , 2008, PloS one.

[43]  Andreas Wilke,et al.  phylogenetic and functional analysis of metagenomes , 2022 .

[44]  J. Nielsen,et al.  Method for measuring substrate preferences by individual members of microbial consortia proposed for bioaugmentation , 2008, Biodegradation.

[45]  A. Goesmann,et al.  Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology. , 2008, Journal of Biotechnology.

[46]  Alexander Goesmann,et al.  Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. , 2008, Journal of biotechnology.

[47]  K. L. Cottingham,et al.  Microbial productivity in variable resource environments. , 2008, Ecology.

[48]  M. Holyoak,et al.  Species' traits predict the effects of disturbance and productivity on diversity. , 2008, Ecology letters.

[49]  Dhritiman Ghosh,et al.  Metagenomic Characterization of Chesapeake Bay Virioplankton , 2007, Applied and Environmental Microbiology.

[50]  I-Min A. Chen,et al.  IMG/M: a data management and analysis system for metagenomes , 2007, Nucleic Acids Res..

[51]  S. Allison,et al.  Nitrogen fertilization reduces diversity and alters community structure of active fungi in boreal ecosystems , 2007 .

[52]  A. Pühler,et al.  Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. , 2007, FEMS microbiology reviews.

[53]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[54]  R. B. Jackson,et al.  Toward an ecological classification of soil bacteria. , 2007, Ecology.

[55]  R. Stepanauskas,et al.  Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time , 2007, Proceedings of the National Academy of Sciences.

[56]  Michel Loreau,et al.  From selection to complementarity: shifts in the causes of biodiversity–productivity relationships in a long-term biodiversity experiment , 2007, Proceedings of the Royal Society B: Biological Sciences.

[57]  Alexander F. Auch,et al.  MEGAN analysis of metagenomic data. , 2007, Genome research.

[58]  Michael Wagner,et al.  Wastewater treatment: a model system for microbial ecology. , 2006, Trends in biotechnology.

[59]  T. Takagi,et al.  MetaGene: prokaryotic gene finding from environmental genome shotgun sequences , 2006, Nucleic acids research.

[60]  A. Robicsek,et al.  The worldwide emergence of plasmid-mediated quinolone resistance. , 2006, The Lancet. Infectious diseases.

[61]  R. Aerts,et al.  Size and structure of bacterial, fungal and nematode communities along an Antarctic environmental gradient. , 2006, FEMS microbiology ecology.

[62]  Yukari Sato,et al.  Complete Nucleotide Sequence of an Exogenously Isolated Plasmid, pLB1, Involved in γ-Hexachlorocyclohexane Degradation , 2006, Applied and Environmental Microbiology.

[63]  I. Hewson,et al.  Annually reoccurring bacterial communities are predictable from ocean conditions , 2006, Proceedings of the National Academy of Sciences.

[64]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[65]  O. Gascuel,et al.  Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. , 2006, Systematic biology.

[66]  J. Aburto,et al.  Carbazole biodegradation in gas oil/water biphasic media by a new isolated bacterium Burkholderia sp. strain IMP5GC , 2006, Journal of applied microbiology.

[67]  J. Aislabie,et al.  Bioremediation of hydrocarbon-contaminated polar soils , 2006, Extremophiles.

[68]  Z. Shao,et al.  Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer. , 2006, Environmental microbiology.

[69]  R. B. Jackson,et al.  The diversity and biogeography of soil bacterial communities. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[70]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[71]  Christopher M Thomas,et al.  Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria , 2005, Nature Reviews Microbiology.

[72]  Laura S. Frost,et al.  Mobile genetic elements: the agents of open source evolution , 2005, Nature Reviews Microbiology.

[73]  B. Silverman,et al.  The contribution of species richness and composition to bacterial services , 2005, Nature.

[74]  Ari Löytynoja,et al.  An algorithm for progressive multiple alignment of sequences with insertions. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[75]  L. Ciric,et al.  Bioaugmentation for bioremediation: the challenge of strain selection. , 2005, Environmental microbiology.

[76]  M. Marra,et al.  Functional Characterization of a Catabolic Plasmid from Polychlorinated- Biphenyl-Degrading Rhodococcus sp. Strain RHA1 , 2004, Journal of Bacteriology.

[77]  K. McCarthy,et al.  Remediation of spilled petroleum hydrocarbons by in situ landfarming at an arctic site , 2004 .

[78]  B. Bohannan,et al.  An ecological perspective on bacterial biodiversity , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[79]  D. Cowan,et al.  Review and re-analysis of domain-specific 16S primers. , 2003, Journal of microbiological methods.

[80]  A. Pühler,et al.  The 64 508 bp IncP-1beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1beta group. , 2003, Microbiology.

[81]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[82]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[83]  R. Giegerich,et al.  GenDB--an open source genome annotation system for prokaryote genomes. , 2003, Nucleic acids research.

[84]  K. Zengler,et al.  Cultivating the uncultured , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[85]  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.

[86]  Hui-Hsien Chou,et al.  DNA sequence quality trimming and vector removal , 2001, Bioinform..

[87]  Y. Benjamini,et al.  Controlling the false discovery rate in behavior genetics research , 2001, Behavioural Brain Research.

[88]  J. Walworth,et al.  Nutrient and temperature interactions in bioremediation of cryic soils , 2001 .

[89]  J. Neff,et al.  Effects of weathering on the toxicity of three offshore australian crude oils and a diesel fuel to marine animals , 2000 .

[90]  H. Ochman,et al.  Lateral gene transfer and the nature of bacterial innovation , 2000, Nature.

[91]  B. Finlay,et al.  Segmented filamentous bacteria prevent colonization of enteropathogenic Escherichia coli O103 in rabbits. , 2000, The Journal of infectious diseases.

[92]  J. Salanitro,et al.  Temporal ecological assessment of oil contaminated soils before and after bioremediation. , 2000, Chemosphere.

[93]  D. Mazel,et al.  Antibiotic resistance in microbes , 1999, Cellular and Molecular Life Sciences CMLS.

[94]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[95]  L. Whyte,et al.  Biodegradation of petroleum hydrocarbons by psychrotrophic Pseudomonas strains possessing both alkane (alk) and naphthalene (nah) catabolic pathways , 1997, Applied and environmental microbiology.

[96]  J. Walworth,et al.  Enhancement and inhibition of soil petroleum biodegradation through the use of fertilizer nitrogen: An approach to determining optimum levels , 1997 .

[97]  W. Verstraete,et al.  Exogenous Isolation of Mobilizing Plasmids from Polluted Soils and Sludges , 1994, Applied and environmental microbiology.

[98]  R. Atlas.  Fate of Petroleum Pollutants in Arctic Ecosystems , 1986 .

[99]  T. Kieser,et al.  Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli. , 1984, Plasmid.

[100]  H. Birnboim,et al.  A rapid alkaline extraction procedure for screening recombinant plasmid DNA. , 1979, Nucleic acids research.

[101]  Sam P. Brown,et al.  What traits are carried on mobile genetic elements, and why? , 2011, Heredity.

[102]  Bozhong Mu,et al.  Microbial communities involved in anaerobic degradation of alkanes , 2011 .

[103]  L. Whyte,et al.  Microbial Communities in Hydrocarbon-Contaminated Temperate, Tropical, Alpine, and Polar Soils , 2010 .

[104]  J. Siefert,et al.  Defining the mobilome. , 2009, Methods in molecular biology.

[105]  Alessandra Conversi,et al.  Comparative Analysis , 2009, Encyclopedia of Database Systems.

[106]  M. Andersson,et al.  Temporal variation in soil microbial communities in Alpine tundra , 2008 .

[107]  J. Marchesi,et al.  Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome , 2007, Nature Methods.

[108]  S. Wuertz,et al.  Effect of bioaugmentation and supplementary carbon sources on degradation of polycyclic aromatic hydrocarbons by a soil-derived culture. , 2006, FEMS microbiology ecology.

[109]  R. Fani,et al.  Long-term analysis of diesel fuel consumption in a co-culture of Acinetobacter venetianus, Pseudomonas putida and Alcaligenes faecalis , 2004, Antonie van Leeuwenhoek.

[110]  A. Pühler,et al.  The 64508 bp IncP-1 b antibiotic multiresistance plasmid pB 10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1 b group , 2003 .

[111]  Noah Fierer,et al.  Variations in microbial community composition through two soil depth profiles , 2003 .

[112]  K. Reimer,et al.  Biostimulation and bioaugmentation for on-site treatment of weathered diesel fuel in Arctic soil , 2002, Applied Microbiology and Biotechnology.

[113]  Ana Segura,et al.  Mechanisms of solvent tolerance in gram-negative bacteria. , 2002, Annual review of microbiology.

[114]  W Arber,et al.  Genetic variation: molecular mechanisms and impact on microbial evolution. , 2000, FEMS microbiology reviews.

[115]  Thomas Wetter,et al.  Genome Sequence Assembly Using Trace Signals and Additional Sequence Information , 1999, German Conference on Bioinformatics.

[116]  B. Griffiths,et al.  Soil microbial community structure: Effects of substrate loading rates , 1998 .