SEARCH

SEARCH BY CITATION

References

  • Bentley SD & Parkhill J (2004) Comparative genomic structure of prokaryotes. Annu Rev Genet 38: 771792.
  • Bergstrom CT, Lipsitch M & Levin BR (2000) Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155: 15051519.
  • Bjorkman J & Andersson DI (2000) The cost of antibiotic resistance from a bacterial perspective. Drug Resist Updates 3: 237245.
  • Bouma JE & Lenski RE (1988) Evolution of a bacteria/plasmid association. Nature 335: 351352.
  • Buckling A, Kassen R, Bell G & Rainey PB (2000) Disturbance and diversity in experimental microcosms. Nature 408: 961964.
  • Chain PSG, Denef VJ, Konstantinidis KT et al. (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73 Mbp genome shaped for versatility. Proc Natl Acad Sci USA 103: 1528015287.
  • Chao L & Levin BR (1981) Structured habitats and the evolution of anticompetitor toxins in bacteria. Proc Natl Acad Sci USA 78: 63246328.
  • Chaslusdancla E, Gerbaud G, Lagorce M, Lafont JP & Courvalin P (1987) Persistence of an antibiotic-resistance plasmid in intestinal Escherichia coli of chickens in the absence of selective pressure. Antimicrob Agents Chemother 31: 784788.
  • Corchero JL & Villaverde A (1998) Plasmid maintenance in Escherichia coli recombinant cultures is dramatically, steadily and specifically influenced by features of the encoded proteins. Biotechnol Bioeng 58: 625632.
  • Costerton JW, Lewandowski Z, Debeer D, Caldwell D, Korber D & James G (1994) Biofilms, the customized microniche. J Bacteriol 176: 21372142.
  • Dahlberg C & Chao L (2003) Amelioration of the cost of conjugative plasmid carriage in Escherichia coli K12. Genetics 165: 16411649.
  • Dale C & Moran NA (2006) Molecular interactions between bacterial symbionts and their hosts. Cell 126: 453465.
  • De Gelder L, Ponciano JM, Joyce P & Top EM (2007) Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiol-SGM 153: 452463.
  • Del Solar G, Giraldo R, Ruiz-Echevarria MJ, Espinosa M & Diaz-Orejas R (1998) Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62: 434464.
  • De Nettancourt D (1977) Incompatibility in Angiosperms. Springer-Verlag, Berlin.
  • Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284: 21242128.
  • Doucet-Populaire F, Trieu-Cuot P, Andremont A & Courvalin P (1992) Conjugal transfer of plasmid DNA from Enterococcus faecalis to Escherichia coli in digestive tracts of gnotobiotic mice. Antimicrob Agents Chemother 36: 502504.
  • Dronen AK, Torsvik V, Goksoyr J & Top EM (1998) Effect of mercury addition on plasmid incidence and gene mobilizing capacity in bulk soil. FEMS Microbiol Ecol 27: 381394.
  • Dugatkin LA, Perlin M, Lucas JS & Atlas R (2005) Group-beneficial traits, frequency-dependent selection and genotypic diversity: an antibiotic resistance paradigm. Proc R Soc Lond B Biol Sci 272: 7983.
  • Eberhard WG (1990) Evolution in bacterial plasmids and levels of selection. Q Rev Biol 65: 322.
  • Ebersbach G & Gerdes K (2005) Plasmid segregation mechanisms. Annu Rev Genet 39: 453479.
  • Egan ES, Fogel MA & Waldor MK (2005) Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol Microbiol 56: 11291138.
  • Eisen JA (2000) Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genet Dev 10: 606611.
  • El Yacoubi B, Brunings AM, Yuan Q, Shankar S & Gabriel DW (2007) In planta horizontal transfer of a major pathogenicity effector gene. Appl Environ Microbiol 73: 16121621.
  • Ellis RJ, Lilley AK, Lacey SJ, Murrell D & Godfray HCJ (2007) Frequency-dependent advantages of plasmid carriage by Pseudomonas in homogeneous and spatially structured environments. ISME J 1: 9295.
  • Fagerli IL & Svenning MM (2005) Arctic and subarctic soil populations of Rhizobium leguminosarum biovar trifolii nodulating three different clover species: characterisation by diversity at chromosomal and symbiosis loci. Plant Soil 275: 371381.
  • Fitzpatrick MJ, Feder E, Rowe L & Sokolowski MB (2007) Maintaining a behaviour polymorphism by frequency-dependent selection on a single gene. Nature 447: 210212.
  • Freter R, Freter RR & Brickner H (1983) Experimental and mathematical models of Escherichia coli plasmid transfer in vitro and in vivo. Infect Immun 39: 6084.
  • Galibert F, Finan TM, Long SR et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293: 668672.
  • Gogarten JP & Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3: 679687.
  • Hardin G (1968) The tragedy of the commons. Science 162: 12431248.
  • Hayes F (2003) Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301: 14961499.
  • Hill P, Saunders DS & Campbell JA (1973) Production of symbiont-free Glossina morsitans and an associated loss of female fertility. Trans R Soc Trop Med Hyg 67: 727728.
  • Jain R, Rivera MC, Moore JE & Lake JA (2002) Horizontal gene transfer in microbial genome evolution. Theor Popul Biol 61: 489495.
  • Jayaratne A, Collins-Thompson DL & Trevors JT (1989) In vitro and in situ conjugal transfer of an R-plasmid among Enterobacteriaceae species isolated from meat samples. FEMS Microbiol Ecol 62: 7986.
  • Johnsen PJ, Osterhus JI, Sletvold H, Sorum M, Kruse H, Nielsen K, Simonsen GS & Sundsfjord A (2005) Persistence of animal and human glycopeptide-resistant Enterococci on two Norwegian poultry farms formerly exposed to avoparcin is associated with a widespread plasmid-mediated vanA element within a polyclonal Enterococcus faecium population. Appl Environ Microbiol 71: 159168.
  • Kado CI (1998) Origin and evolution of plasmids. Antonie van Leeuwenhoek 73: 117126.
  • Kozlowicz BK, Dworkin M & Dunny GM (2006) Pheromone-inducible conjugation in Enterococcus faecalis: a model for the evolution of biological complexity? Int J Med Microbiol 296: 141147.
  • Krone SM, Lu R, Fox R, Suzuki H & Top EM (2007) Modelling the spatial dynamics of plasmid transfer and persistence. Microbiol-SGM 153: 28032816.
  • Lagido C, Wilson IJ, Glover LA & Prosser JI (2003) A model for bacterial conjugal gene transfer on solid surfaces. FEMS Microbiol Ecol 44: 6778.
  • Lawrence JG & Ochman H (1997) Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44: 383397.
  • Lawrence JG & Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95: 94139417.
  • Levin BR (1988) Frequency-dependent selection in bacterial populations. Philos Trans R Soc Lond B Biol Sci 319: 459472.
  • Levin BR & Stewart FM (1980) The population biology of bacterial plasmids: a priori conditions for the existence of mobilizable nonconjugative factors. Genetics 94: 425443.
  • Levin BR, Stewart FM & Rice VA (1979) Kinetics of conjugative plasmid transmission: fit of a simple mass action model. Plasmid 2: 247260.
  • Lilley AK, Bailey MJ, Day MJ & Fry JC (1996) Diversity of mercury resistance plasmids obtained by exogenous isolation from the bacteria of sugar beet in three successive years. FEMS Microbiol Ecol 20: 211227.
  • Lotka AJ (1925) Elements of Physical Biology. Williams and Wilkins Co., Baltimore.
  • Lundquist PD & Levin BR (1986) Transitory derepression and the maintenance of conjugative plasmids. Genetics 113: 483497.
  • Mach PA & Grimes DJ (1982) R-plasmid transfer in a wastewater treatment plant. Appl Environ Microbiol 44: 13951403.
  • Mackenzie C, Kaplan S & Choudhary M (2004) Multiple chromosomes. Microbial Evolution: Gene Establishment, Survival and Exchange (MillerRV & DayMJ, eds), pp. 82101. ASM Press, Washington, DC.
  • Maclellan SR, Sibley CD & Finan TM (2004) Second chromosomes and megaplasmids in bacteria. Plasmid Biology (FunnellBE & PhillipsGJ, eds), pp. 529542. ASM Press, Washington, DC.
  • Martinez-Romero E & Caballero-Mellado J (1996) Rhizobium phylogenies and bacterial genetic diversity. Crit Rev Plant Sci 15: 113140.
  • Modi RI & Adams J (1991) Coevolution in bacterial plasmid populations. Evolution 45: 656667.
  • Molbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M & Field D (2003) The plasmid genome database. Microbiol-SGM 149: 30433045.
  • Molin S & Tolker-Nielsen T (2003) Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr Opin Biotechnol 14: 255261.
  • Moran NA (2002) Microbial minimalism: genome reduction in bacterial pathogens. Cell 108: 583586.
  • Moran NA, Russell JA, Koga R & Fukatsu T (2005) Evolutionary relationships of three new species of Enterobacteriaceae living as symbionts of aphids and other insects. Appl Environ Microbiol 71: 33023310.
  • Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA & Hattori M (2006) The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314: 267267.
  • Nesbo CL, Dlutek M & Doolittle WF (2006) Recombination in Thermotoga: implications for species concepts and biogeography. Genetics 172: 759769.
  • Ochman H & Moran NA (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292: 10961098.
  • Ochman H, Lawrence JG & Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299304.
  • Oger P & Farrand SK (2002) Two opines control conjugal transfer of an Agrobacterium plasmid by regulating expression of separate copies of the quorurn-sensing activator gene traR. J Bacteriol 184: 11211131.
  • Oliver KM, Russell JA, Moran NA & Hunter MS (2003) Facultative bacterial symbionts in aphids confer resistance to parasitic wasps. Proc Natl Acad Sci USA 100: 18031807.
  • Oliver KM, Moran NA & Hunter MS (2006) Costs and benefits of a superinfection of facultative symbionts in aphids. Proc Royal Soc B-Biol Sci 273: 12731280.
  • Oresnik IJ, Liu SL, Yost CK & Hynes MF (2000) Megaplasmid pRme2011a of Sinorhizobium meliloti is not required for viability. J Bacteriol 182: 35823586.
  • Perez-Mendoza D, Sepulveda E, Pando V et al. (2005) Identification of the rctA gene, which is required for repression of conjugative transfer of rhizobial symbiotic megaplasmids. J Bacteriol 187: 73417350.
  • Petridis M, Bagdasarian M, Waldor MK & Walker E (2006) Horizontal transfer of shiga toxin and antibiotic resistance genes among Escherichia coli strains in house fly (Diptera muscidae) gut. J Med Entomol 43: 288295.
  • Ponciano JM, De Gelder L, Top EM & Joyce P (2007) The population biology of bacterial plasmids: a hidden Markov model approach. Genetics 176: 957968.
  • Postgate J (1978) Nitrogen Fixation. Edward Arnold, London.
  • Prieur D, Erauso G, Geslin C et al. (2004) Genetic elements of Thermococcales. Biochem Soc Trans 32: 184187.
  • Prosser JI, Bohannan BJM, Curtis TP et al. (2007) Essay: the role of ecological theory in microbial ecology. Nat Rev Microbiol 5: 384392.
  • Raes J, Korbel JO, Lercher MJ, Von Mering C & Bork P (2007) Prediction of effective genome size in metagenomic samples. Genome Biol 8: R10.
  • Rainey PB & Travisano M (1998) Adaptive radiation in a heterogeneous environment. Nature 394: 6972.
  • Ricci JCD & Hernandez ME (2000) Plasmid effects on Escherichia coli metabolism. Crit Rev Biotechnol 20: 79108.
  • Rozkov A, Avignone-Rossa CA, Ertl PF, Jones P, O'Kennedy RD, Smith JJ, Dale JW & Bushell ME (2004) Characterization of the metabolic burden on Escherichia coli DH1 cells imposed by the presence of a plasmid containing a gene therapy sequence. Biotechnol Bioeng 88: 909915.
  • Salanoubat M, Genin S, Artiguenave F et al. (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415: 497502.
  • Schneiker S, Perlova O, Kaiser O et al. (2007) Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol 25: 12811289.
  • Sherburne CK, Lawley TD, Gilmour MW, Blattner FR, Burland V, Grotbeck E, Rose DJ & Taylor DE (2000) The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer. Nucleic Acids Res 28: 21772186.
  • Simonsen L (1990) Dynamics of plasmid transfer on surfaces. J Gen Microbiol 136: 10011007.
  • Simonsen L, Gordon DM, Stewart FM & Levin BR (1990) Estimating the rate of plasmid transfer: an end-point method. J Gen Microbiol 136: 23192325.
  • Smit E, Wolters A & Van Elsas JD (1998) Self-transmissible mercury resistance plasmids with gene-mobilizing capacity in soil bacterial populations: influence of wheat roots and mercury addition. Appl Environ Microbiol 64: 12101219.
  • Smith J (2001) The social evolution of bacterial pathogenesis. Proc R Soc Lond B Biol Sci 268: 6169.
  • Sorensen SJ, Bailey M, Hansen LH, Kroer N & Wuertz S (2005) Studying plasmid horizontal transfer in situ: a critical review. Nat Rev Microbiol 3: 700710.
  • Stewart FM & Levin BR (1977) Population biology of bacterial plasmids: a priori conditions for existence of conjugationally transmitted factors. Genetics 87: 209228.
  • Stouthamer R, Breeuwer JAJ & Hurst GDD (1999) Wolbachia pipientis: microbial manipulator of arthropod reproduction. Annu Rev Microbiol 53: 71102.
  • Summers D (1998) Timing, self-control and a sense of direction are the secrets of multicopy plasmid stability. Mol Microbiol 29: 11371145.
  • Tett A, Spiers AJ, Crossman LC et al. (2007) Sequence-based analysis of pQBR103: a representative of a unique, transfer-proficient megaplasmid resident in the microbial community of sugar beet. ISME J 1: 331340.
  • Thao ML, Clark MA, Baumann L, Brennan EB, Moran NA & Baumann P (2000) Secondary endosymbionts of psyllids have been acquired multiple times. Curr Microbiol 41: 300304.
  • Thomas CM & Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3: 711721.
  • Toh H, Weiss BL, Perkin SAH, Yamashita A, Oshima K, Hattori M & Aksoy S (2006) Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res 16: 149156.
  • Turner PE, Cooper VS & Lenski RE (1998) Tradeoff between horizontal and vertical modes of transmission in bacterial plasmids. Evolution 52: 315329.
  • Van Elsas JD & Bailey MJ (2002) The ecology of transfer of mobile genetic elements. FEMS Microbiol Ecol 42: 187197.
  • Van Elsas JD, Turner S & Bailey MJ (2003) Horizontal gene transfer in the phytosphere. New Phytol 157: 525537.
  • Volterra V (1926) Variazioni e fluttuazioni del numero d'individui in specie animali conviventi. Mem R Accad Naz Lincei 2: 31113.
  • Young IM & Crawford JW (2004) Interactions and self-organization in the soil-microbe complex. Science 304: 16341637.
  • Zund P & Lebek G (1980) Generation time-prolonging R-plasmids: correlation between increases in the generation time of Escherichia coli caused by R-plasmids and their molecular size. Plasmid 3: 6569.