Community-wide plasmid gene mobilization and selection

ISME Journal

Volumn 7, Issue 6, 2013, Pages 1173-1186

  Sentchilo, Vladimir ^a   Mayer, Antonia P ^a,e   Guy, Lionel ^b   Miyazaki, Ryo ^a   Tringe, Susannah Green ^c   Barry, Kerrie ^c   Malfatti, Stephanie ^c   Goessmann, Alexander ^d   Robinson Rechavi, Marc ^a,e   Van Der Meer, Jan R ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b UPPSALA UNIVERSITY   (Sweden)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d BIELEFELD UNIVERSITY   (Germany)

^e SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

Metagenomic studies; Mobilome

Indexed keywords

ACTIVATED SLUDGE; ADAPTATION; ANTIBIOTIC RESISTANCE; CHROMOSOME; EVOLUTIONARY BIOLOGY; FUNCTIONAL ROLE; GENE EXPRESSION; GENE TRANSFER; GENETIC STRUCTURE; GENOME; GENOMICS; HYPOTHESIS TESTING; METABOLISM; MICROBIAL COMMUNITY; NATURAL SELECTION; PLASMID; POLLUTION TOLERANCE;

ARTICLE; BACTERIUM; GENETICS; METAGENOME; MICROBIOLOGY; PHYLOGENY; PLASMID; SEWAGE;

BACTERIA; METAGENOME; PHYLOGENY; PLASMIDS; SEWAGE;

PROKARYOTA;

EID: 84878275176     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.13     Document Type: Article

References (52)

1. Albertsen M, Hansen LB, Saunders AM, Nielsen PH, Nielsen KL. (2012). A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. ISME J 6: 1094-1106.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
3. Anisimova M, Gascuel O. (2006). Approximate likelihoodratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 55: 539-552.
4. Arber W. (2000). Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 24: 1-7.
5. Bench SR, Hanson TE, Williamson KE, Ghosh D, Radosovich M, Wang K et al. (2007). Metagenomic characterization of Chesapeake Bay virioplankton. Appl Environ Microbiol 73: 7629-7641.
6. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. (2001). Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125: 279-284.
7. Birnboim HC, Doly J. (1979). A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7: 1513-1523.
8. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D et al. (2002). Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 99: 14250-14255.
9. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. (2009). DNA Plotter: circular and linear interactive genome visualization. Bioinformatics 25: 119-120.
10. Chevreux B, Wetter T, Suhai S. (1999). Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, German Conference on Bioinformatics: Hannover, Germany, pp 45-56, Available at, http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title= Main-Page#Papers.
11. Chou H-H, Holmes MH. (2001). DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104.
12. Cortez D, Forterre P, Gribaldo S. (2009). A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biol 10: R65.
13. Daims H, Taylor MW, Wagner M. (2006). Wastewater treatment: a model system for microbial ecology. Trends Biotechnol 24: 483-489.
14. Fondi M, Bacci G, Brilli M, Papaleo M, Mengoni A, Vaneechoutte M et al. (2010). Exploring the evolutionary dynamics of plasmids: the Acinetobacter panplasmidome. BMC Evol Biol 10: 59.
15. Frost LS, Leplae R, Summers AO, Toussaint A. (2005). Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3: 722-732.
16. Guindon S, Gascuel O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
17. Huson DH, Auch AF, Qi J, Schuster SC. (2007). MEGAN analysis of metagenomic data. Genome Res 17: 377-386.
18. Jones BV, Marchesi JR. (2007). Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods 4: 55-61.
19. Jones BV, Sun F, Marchesi JR. (2010). Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome. BMC Genomics 11: 46.
20. Kav AB, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, Mizrahi I. (2012). Insights into the bovine rumen plasmidome. Proc Natl Acad Sci USA 109: 5452-5457.
21. Kieser T. (1984). Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli. Plasmid 12: 19-36.
22. Kloesges T, Popa O, Martin W, Dagan T. (2011). Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28: 1057-1074.
23. Koonin EV, Wolf YI. (2008). Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36: 6688-6719.
24. Li W. (2009). Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinformatics 10: 359.
25. Loytynoja A, Goldman N. (2005). An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci USA 102: 10557-10562.
26. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
27. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D et al. (2008). IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 36: D534-D538.
28. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. (2009). IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25: 2271-2278.
29. Mazel D, Davies J. (1999). Antibiotic resistance in microbes. Cell Mol Life Sci 56: 742-754.
30. McDaniel L, Breitbart M, Mobberley J, Long A, Haynes M, Rohwer F et al. (2008). Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression. PLoS One 3: e3263.
31. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J et al. (2003). GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31: 2187-2195.
32. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M et al. (2008). The metagenomics RAST server-A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
33. Miyazaki R, Sato Y, Ito M, Ohtsubo Y, Nagata Y, Tsuda M. (2006). Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gammahexachlorocyclohexane degradation. Appl Environ Microbiol 72: 6923-6933.
34. Noguchi H, Park J, Takagi T. (2006). Meta Gene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Research 34: 5623-5630.
35. Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EP. (2009). Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr Biol 19: 1683-1691.
36. Ochman H, Lawrence JG, Groisman EA. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
37. Parks DH, Beiko RG. (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715-721.
38. Rankin DJ, Rocha EP, Brown SP. (2011). What traits are carried on mobile genetic elements, and why? Heredity (Edinb) 106: 1-10.
39. Robicsek A, Jacoby GA, Hooper DC. (2006). The worldwide emergence of plasmid-mediated quinolone resistance. Lancet Infect Dis 6: 629-640.
40. Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M. (2009). Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 11: 2806-2820.
41. Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM. (2009). Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. Appl Environ Microbiol 75: 1688-1696.
42. Schlü ter A, Heuer H, Szczepanowski R, Forney LJ, Thomas CM, Pü hler A et al. (2003). The 64 508 bp IncP-1b antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1b group. Microbiology 149: 3139-3153.
43. Schlü ter A, Krause L, Szczepanowski R, Goesmann A, Pü hler A. (2008). Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. J Biotechnol 136: 65-76.
44. Schlü ter A, Szczepanowski R, Pü hler A, Top EM. (2007). Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol Rev 31: 449-477.
45. Siefert JL. (2009). Defining the mobilome. Methods Mol Biol 532: 13-27.
46. Stepanauskas R, Sieracki ME. (2007). Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Natl Acad Sci USA 104: 9052-9057.
47. Storey JD, Tibshirani R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440-9445.
48. Szczepanowski R, Bekel T, Goesmann A, Krause L, Kromeke H, Kaiser O et al. (2008). Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology. J Biotechnol 136: 54-64.
49. Thomas CM, Nielsen KM. (2005). Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3: 711-721.
50. Top E, De Smet I, Verstraete W, Dijkmans R, Mergeay M. (1994). Exogenous isolation of mobilizing plasmids from polluted soils and sludges. Appl Environ Microbiol 60: 831-839.
51. Warren R, Hsiao WW, Kudo H, Myhre M, Dosanjh M, Petrescu A et al. (2004). Functional characterization of a catabolic plasmid from polychlorinated- biphenyldegrading Rhodococcus sp. strain RHA1. J Bacteriol 186: 7783-7795.
52. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM et al. (2002). Cultivating the uncultured. Proc Natl Acad Sci USA 99: 15681-15686.