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Molecular musings in microbial ecology and evolution 원문보기

Biology direct, v.6, 2011년, pp.58 - 58  

Case, Rebecca J (Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada) ,  Boucher, Yan (Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada)

Abstract AI-Helper 아이콘AI-Helper

A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking ...

주제어

참고문헌 (66)

  1. Taylor MW Schupp PJ de Nys R Kjelleberg S Steinberg PD Biogeography of bacteria associated with the marine sponge Cymbastela concentrica Environ Microbiol 2005 7 3 419 433 10.1111/j.1462-2920.2004.00711.x 15683402 

  2. Peterson CN Day S Wolfe BE Ellison AM Kolter R Pringle A A keystone predator controls bacterial diversity in the pitcher-plant ( Sarracenia purpurea ) microecosystem Environ Microbiol 2008 10 9 2257 2266 10.1111/j.1462-2920.2008.01648.x 18479443 

  3. Keymer JE Galajda P Muldoon C Park S Austin RH Bacterial metapopulations in nanofabricated landscapes Proc Natl Acad Sci USA 2006 103 46 17290 17295 10.1073/pnas.0607971103 17090676 

  4. Burke C Steinberg P Rusch D Kjelleberg S Thomas T Bacterial community assembly based on functional genes rather than species Proc Natl Acad Sci USA 2011 108 34 14288 14293 10.1073/pnas.1101591108 21825123 

  5. Reno ML Held NL Fields CJ Burke PV Whitaker RJ Biogeography of the Sulfolobus islandicus pan-genome Proc Natl Acad Sci USA 2009 106 21 8605 8610 10.1073/pnas.0808945106 19435847 

  6. Thompson JR Pacocha S Pharino C Klepac-Ceraj V Hunt DE Benoit J Sarma-Rupavtarm R Distel DL Polz MF Genotypic diversity within a natural coastal bacterioplankton population Science 2005 307 5713 1311 1313 10.1126/science.1106028 15731455 

  7. Woese CR The Phylogeny of Prokaryotes Science 1980 209 457 10.1126/science.6771870 6771870 

  8. Woese CR Magrum LJ Fox GE Archaebacteria J Mol Evol 1978 11 3 245 251 10.1007/BF01734485 691075 

  9. Woese CR Bacterial evolution Microbiol Rev 1987 51 2 221 271 2439888 

  10. Stanier RY Van Niel CB The Main Outlines of Bacterial Classification J Bacteriol 1941 42 4 437 466 16560462 

  11. Weisburg WG Oyaizu Y Oyaizu H Woese CR Natural relationship between bacteroides and flavobacteria J Bacteriol 1985 164 1 230 236 2413007 

  12. Weisburg WG Giovannoni SJ Woese CR The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction Syst Appl Microbiol 1989 11 128 134 11542160 

  13. Bonen L Doolittle WF On the prokaryotic nature of red algal chloroplasts Proc Natl Acad Sci USA 1975 72 6 2310 2314 10.1073/pnas.72.6.2310 1056032 

  14. Yang D Oyaizu Y Oyaizu H Olsen GJ Woese CR Mitochondrial origins Proc Natl Acad Sci USA 1985 82 13 4443 4447 10.1073/pnas.82.13.4443 3892535 

  15. Achenbach-Richter L Gupta R Stetter KO Woese CR Were the original eubacteria thermophiles? Syst Appl Microbiol 1987 9 34 39 10.1016/S0723-2020(87)80053-X 11542087 

  16. Dagan T Martin W The tree of one percent Genome Biol 2006 7 10 118 10.1186/gb-2006-7-10-118 17081279 

  17. Giovannoni SJ Britschgi TB Moyer CL Field KG Genetic diversity in Sargasso Sea bacterioplankton Nature 1990 345 6270 60 63 10.1038/345060a0 2330053 

  18. Ward DM Weller R Bateson MM 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community Nature 1990 345 6270 63 65 10.1038/345063a0 1691827 

  19. Hugenholtz P Goebel BM Pace NR Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity J Bacteriol 1998 180 18 4765 4774 9733676 

  20. Hugenholtz P Pitulle C Hershberger KL Pace NR Novel division level bacterial diversity in a Yellowstone hot spring J Bacteriol 1998 180 2 366 376 9440526 

  21. Rappe MS Connon SA Vergin KL Giovannoni SJ Cultivation of the ubiquitous SAR11 marine bacterioplankton clade Nature 2002 418 6898 630 633 10.1038/nature00917 12167859 

  22. Ludwig W Strunk O Westram R Richter L Meier H Yadhukumar Buchner A Lai T Steppi S Jobb G Forster W Brettske I Gerber S Ginhart AW Gross O Grumann S Hermann S Jost R Konig A Liss T Lussmann R May M Nonhoff B Reichel B Strehlow R Stamatakis A Stuckmann N Vilbig A Lenke M Ludwig T Bode A Schleifer KH ARB: a software environment for sequence data Nucleic Acids Res 2004 32 4 1363 1371 10.1093/nar/gkh293 14985472 

  23. Schmidt TM DeLong EF Pace NR Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing J Bacteriol 1991 173 14 4371 4378 2066334 

  24. Rolleke S Muyzer G Wawer C Wanner G Lubitz W Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA Appl Environ Microbiol 1996 62 6 2059 2065 8787403 

  25. Whitman WB Coleman DC Wiebe WJ Prokaryotes: the unseen majority Proc Natl Acad Sci USA 1998 95 12 6578 6583 10.1073/pnas.95.12.6578 9618454 

  26. Watanabe T Infective heredity of multiple drug resistance in bacteria Bacteriol Rev 1963 27 87 115 13999115 

  27. Deppenmeier U Johann A Hartsch T Merkl R Schmitz RA Martinez-Arias R Henne A Wiezer A Baumer S Jacobi C Bruggemann H Lienard T Christmann A Bomeke M Steckel S Bhattacharyya A Lykidis A Overbeek R Klenk HP Gunsalus RP Fritz HJ Gottschalk G The genome of Methanosarcina mazei : evidence for lateral gene transfer between bacteria and archaea J Mol Microbiol Biotechnol 2002 4 4 453 461 12125824 

  28. Nelson KE Clayton RA Gill SR Gwinn ML Dodson RJ Haft DH Hickey EK Peterson JD Nelson WC Ketchum KA McDonald L Utterback TR Malek JA Linher KD Garrett MM Stewart AM Cotton MD Pratt MS Phillips CA Richardson D Heidelberg J Sutton GG Fleischmann RD Eisen JA White O Salzberg SL Smith HO Venter JC Fraser CM Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima Nature 1999 399 6734 323 329 10.1038/20601 10360571 

  29. Bapteste E Boucher Y Lateral gene transfer challenges principles of microbial systematics Trends Microbiol 2008 16 5 200 207 10.1016/j.tim.2008.02.005 18420414 

  30. Beauregard-Racine J Bicep C Schliep K Lopez P Lapointe FJ Bapteste E Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli Biol Direct 2011 6 1 39 10.1186/1745-6150-6-39 21774799 

  31. Konstantinidis KT Tiedje JM Genomic insights that advance the species definition for prokaryotes Proc Natl Acad Sci USA 2005 102 7 2567 2572 10.1073/pnas.0409727102 15701695 

  32. Konstantinidis KT Tiedje JM Towards a genome-based taxonomy for prokaryotes J Bacteriol 2005 187 18 6258 6264 10.1128/JB.187.18.6258-6264.2005 16159757 

  33. Bapteste E Boucher Y Lateral gene transfer challenges principles of microbial systematics Trends Microbiol 2008 16 5 200 207 10.1016/j.tim.2008.02.005 18420414 

  34. Feil EJ Small change: keeping pace with microevolution Nat Rev Microbiol 2004 2 6 483 495 10.1038/nrmicro904 15152204 

  35. Fox GE Wisotzkey JD Jurtshuk P How close is close - 16S ribosomal-RNA sequence identity may not be sufficient to guarantee species identity Int J Syst Bact 1992 42 1 166 170 10.1099/00207713-42-1-166 

  36. Kurland CG What tangled web: barriers to rampant horizontal gene transfer Bioessays 2005 27 7 741 747 10.1002/bies.20258 15954096 

  37. Rossello-Mora R Amann R The species concept for prokaryotes FEMS Microbiol Rev 2001 25 1 39 67 11152940 

  38. Allgaier M Uphoff H Felske A Wagner-Dobler I Aerobic anoxygenic photosynthesis in Roseobacter clade bacteria from diverse marine habitats Appl Environ Microbiol 2003 69 9 5051 5059 10.1128/AEM.69.9.5051-5059.2003 12957886 

  39. Amann RI Ludwig W Schleifer KH Phylogenetic identification and in situ detection of individual microbial cells without cultivation Microbiol Rev 1995 59 1 143 169 7535888 

  40. Balskus EP Case RJ Walsh CT The biosynthesis of cyanobacterial sunscreen scytonemin in intertidal microbial mat communities FEMS Microbiol Ecol 2011 77 2 322 332 10.1111/j.1574-6941.2011.01113.x 21501195 

  41. Hendrickx B Dejonghe W Faber F Boenne W Bastiaens L Verstraete W Top EM Springael D PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites FEMS Microbiol Ecol 2006 55 2 262 273 10.1111/j.1574-6941.2005.00018.x 16420634 

  42. Jabado OJ Palacios G Kapoor V Hui J Renwick N Zhai J Briese T Lipkin WI Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments Nucleic Acids Res 2006 34 22 6605 6611 10.1093/nar/gkl966 17135211 

  43. Tyson GW Chapman J Hugenholtz P Allen EE Ram RJ Richardson PM Solovyev VV Rubin EM Rokhsar DS Banfield JF Community structure and metabolism through reconstruction of microbial genomes from the environment Nature 2004 428 6978 37 43 10.1038/nature02340 14961025 

  44. Beja O Aravind L Koonin EV Suzuki MT Hadd A Nguyen LP Jovanovich SB Gates CM Feldman RA Spudich JL Spudich EN DeLong EF Bacterial rhodopsin: evidence for a new type of phototrophy in the sea Science 2000 289 5486 1902 1906 10.1126/science.289.5486.1902 10988064 

  45. Frias-Lopez J Shi Y Tyson GW Coleman ML Schuster SC Chisholm SW Delong EF Microbial community gene expression in ocean surface waters Proc Natl Acad Sci USA 2008 105 10 3805 3810 10.1073/pnas.0708897105 18316740 

  46. VerBerkmoes NC Denef VJ Hettich RL Banfield JF Systems biology: Functional analysis of natural microbial consortia using community proteomics Nat Rev Microbiol 2009 7 3 196 205 10.1038/nrmicro2080 19219053 

  47. Fraser C Alm EJ Polz MF Spratt BG Hanage WP The bacterial species challenge: making sense of genetic and ecological diversity Science 2009 323 5915 741 746 10.1126/science.1159388 19197054 

  48. Huse SM Dethlefsen L Huber JA Mark Welch D Relman DA Sogin ML Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing PLoS Genet 2008 4 11 e1000255 10.1371/journal.pgen.1000255 19023400 

  49. Konstantinidis KT Ramette A Tiedje JM The bacterial species definition in the genomic era Philos Trans R Soc Lond B Biol Sci 2006 361 1475 1929 1940 10.1098/rstb.2006.1920 17062412 

  50. Welch RA Burland V Plunkett G Redford P Roesch P Rasko D Buckles EL Liou SR Boutin A Hackett J Stroud D Mayhew GF Rose DJ Zhou S Schwartz DC Perna NT Mobley HL Donnenberg MS Blattner FR Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli Proc Natl Acad Sci USA 2002 99 26 17020 17024 10.1073/pnas.252529799 12471157 

  51. Thompson JR Pacocha S Pharino C Klepac-Ceraj V Hunt DE Benoit J Sarma-Rupavtarm R Distel DL Polz MF Genotypic diversity within a natural coastal bacterioplankton population Science 2005 307 5713 1311 1313 10.1126/science.1106028 15731455 

  52. Gevers D Cohan FM Lawrence JG Spratt BG Coenye T Feil EJ Stackebrandt E Van de Peer Y Vandamme P Thompson FL Swings J Opinion: Re-evaluating prokaryotic species Nat Rev Microbiol 2005 3 9 733 739 10.1038/nrmicro1236 16138101 

  53. Spratt BG Hanage WP Feil EJ The relative contributions of recombination and point mutation to the diversification of bacterial clones Curr Opin Microbiol 2001 4 5 602 606 10.1016/S1369-5274(00)00257-5 11587939 

  54. Nakayama K Yamashita A Kurokawa K Morimoto T Ogawa M Fukuhara M Urakami H Ohnishi M Uchiyama I Ogura Y Ooka T Oshima K Tamura A Hattori M Hayashi T The Whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution DNA Res 2008 15 4 185 199 10.1093/dnares/dsn011 18508905 

  55. Chun J Grim CJ Hasan NA Lee JH Choi SY Haley BJ Taviani E Jeon YS Kim DW Lee JH Brettin TS Bruce DC Challacombe JF Detter JC Han CS Munk AC Chertkov O Meincke L Saunders E Walters RA Huq A Nair GB Colwell RR Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae Proc Natl Acad Sci USA 2009 106 36 15442 15447 10.1073/pnas.0907787106 19720995 

  56. Moran NA McLaughlin HJ Sorek R The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria Science 2009 323 5912 379 382 10.1126/science.1167140 19150844 

  57. Torsvik V Goksoyr J Daae FL High diversity in DNA of soil bacteria Appl Environ Microbiol 1990 56 3 782 787 2317046 

  58. Gevers D Cohan FM Lawrence JG Spratt BG Coenye T Feil EJ Stackebrandt E Van de Peer Y Vandamme P Thompson FL Swings J Opinion: Re-evaluating prokaryotic species Nat Rev Microbiol 2005 3 9 733 739 10.1038/nrmicro1236 16138101 

  59. Acinas SG Klepac-Ceraj V Hunt DE Pharino C Ceraj I Distel DL Polz MF Fine-scale phylogenetic architecture of a complex bacterial community Nature 2004 430 6999 551 554 10.1038/nature02649 15282603 

  60. Schloss PD Westcott SL Ryabin T Hall JR Hartmann M Hollister EB Lesniewski RA Oakley BB Parks DH Robinson CJ Sahl JW Stres B Thallinger GG Van Horn DJ Weber CF Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities Appl Environ Microbiol 2009 75 23 7537 7541 10.1128/AEM.01541-09 19801464 

  61. Huse SM Dethlefsen L Huber JA Mark Welch D Relman DA Sogin ML Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing PLoS Genet 2008 4 11 e1000255 10.1371/journal.pgen.1000255 19023400 

  62. Touchon M Hoede C Tenaillon O Barbe V Baeriswyl S Bidet P Bingen E Bonacorsi S Bouchier C Bouvet O Calteau A Chiapello H Clermont O Cruveiller S Danchin A Diard M Dossat C Karoui ME Frapy E Garry L Ghigo JM Gilles AM Johnson J Le Bouguenec C Lescat M Mangenot S Martinez-Jehanne V Matic I Nassif X Oztas S Petit MA Pichon C Rouy Z Ruf CS Schneider D Tourret J Vacherie B Vallenet D Medigue C Rocha EP Denamur E Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths PLoS Genet 2009 5 1 e1000344 10.1371/journal.pgen.1000344 19165319 

  63. Pupo GM Lan R Reeves PR Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics Proc Natl Acad Sci USA 2000 97 19 10567 10572 10954745 

  64. Kettler GC Martiny AC Huang K Zucker J Coleman ML Rodrigue S Chen F Lapidus A Ferriera S Johnson J Steglich C Church GM Richardson P Chisholm SW Patterns and implications of gene gain and loss in the evolution of Prochlorococcus PLoS Genet 2007 3 12 e231 10.1371/journal.pgen.0030231 18159947 

  65. O'Malley MA Boucher Y Paradigm change in evolutionary microbiology Stud Hist Philos Biol Biomed Sci 2005 36 1 183 208 16120264 

  66. Huse SM Huber JA Morrison HG Sogin ML Welch DM Accuracy and quality of massively parallel DNA pyrosequencing Genome Biol 2007 8 7 R143 10.1186/gb-2007-8-7-r143 17659080 

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