Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing

Journal of Microbiology

Volumn 46, Issue 4, 2008, Pages 357-363

  Kim, Bong Soo ^a   Kim, Byung Kwon ^a   Lee, Jae Hak ^a   Kim, Myungjin ^a   Lim, Young Woon ^b   Chun, Jongsik ^a  

^a Seoul National University   (South Korea)

^b National Institute of Biological Resources   (South Korea)

Author keywords

Prokaryotic community; Pyrosequencing; Taxonomic assignment; Tidal flat

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); DELTAPROTEOBACTERIA; EURYARCHAEOTA; PROKARYOTA; PROTEOBACTERIA; UNCLASSIFIED EURYARCHAEOTA;

ARCHAEAL DNA; BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; DNA SEQUENCE; ECONOMICS; EVALUATION; GENETICS; KOREA; METHODOLOGY; MICROBIOLOGY; PHYLOGENY; SEDIMENT;

ARCHAEA; BACTERIA; BIODIVERSITY; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; GEOLOGIC SEDIMENTS; KOREA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 56149109448     PISSN: 12258873     EISSN: 12258873     Source Type: Journal    
DOI: 10.1007/s12275-008-0071-9     Document Type: Article

References (46)

1. Z. Abdo U.M. Schuette S.J. Bent C.J. Williams L.J. Forney P. Joyce 2006 Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes Environ. Microbiol. 8 929 938
2. S.G. Acinas R. Sarma-Rupavtarm V. Klepac-Ceraj M.F. Polz 2005 PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample Appl. Environ. Microbiol. 71 8966 8969
3. S.F. Altschul W. Gish W. Miller E.W. Myers D.J. Lipman 1990 Basic local alignment search tool J. Mol. Biol. 215 403 410
4. J. Borneman E.W. Triplett 1997 Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation Appl. Environ. Microbiol. 63 2647 2653
5. P.A. Carling 1982 Temporal and spatial variation in intertidal sedimentation rates Sedimentology 29 17 23
6. A. Chao 1984 Nonparametric-estimation of the number of classes in a population Scand. J. Stat. 11 265 270
7. A. Chao S.M. Lee 1992 Estimating the number of classes via sample coverage J. Am. Stat. Assoc. 87 210 217
8. J. Chun J.H. Lee Y. Jung M. Kim S. Kim B.K. Kim Y.W. Lim 2007 EzTaxon: A web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequence Int. J. Syst. Evol. Microbiol. 57 2259 2261
9. S.A. Dar J.G. Kuenen G. Muyzer 2005 Nested PCR-dena-turing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities Appl. Environ. Microbiol. 71 2325 2330
10. M.A. Dojka P. Hugenholtz S.K. Haack N.R. Pace 1998 Microbial diversity in a hydrocarbon-and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation Appl. Environ. Microbiol. 64 3869 3877
11. W. Eder M. Schmidt M. Koch D. Garbe-Schonberg R. Huber 2002 Prokaryotic phylogenetic diversity and corresponding geochemical data of the brine-seawater interface of the Shaban Deep, Red Sea Environ. Microbiol. 4 758 763
12. Edwards, R.A., B. Rodriguez-Brito, L. Wegley, M. Haynes, M. Breitbart, D.M. Peterson, M.O. Saar, S. Alexander, E.C. Alexander, Jr., and F. Rohwer. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7, Art No. 57.
13. B. Gharizadeh T. Nordstrom A. Ahmadian M. Ronaghi P. Nyren 2002 Long-read pyrosequencing using pure 2'-deoxy-adenosine-5'-O'-(1-thiotriphosphate) Sp-isomer Anal. Biochem. 301 82 90
14. J.P. Gray R.P. Herwig 1996 Phylogenetic analysis of the bacterial communities in marine sediments Appl. Environ. Microbiol. 62 4049 4059
15. I.M. Head J.R. Saunders R.W. Pickup 1998 Microbial evolution, diversity, and ecology: A decade of ribosomal RNA analysis of uncultivated microorganisms Microb. Ecol. 35 1 21
16. J.A. Huber D.B. Welch H.G. Morrison S.M. Huse P.R. Neal D.A. Butterfield M.L. Sogin 2007 Microbial population structures in the deep marine biosphere Science 318 97 100
17. P. Hugenholtz C. Pitulle K.L. Hershberger N.R. Pace 1998 Novel division level bacterial diversity in a Yellowstone hot spring J. Bacteriol. 180 366 376
18. S.M. Huse J.A. Huber H.G. Morrison M.L. Sogin D.M. Welch 2007 Accuracy and quality of massively parallel DNA pyrosequencing Genome Biol. 8 R143
19. D. Isola M. Pardini F. Varaine S. Niemann S. Rusch-Gerdes L. Fattorini G. Orefici F. Meacci C. Trappetti M. Rinaldo Oggioni G. Orru 2005 A pyrosequencing assay for rapid recognition of SNPs in Mycobacterium tuberculosis embB306 region J. Microbiol. Methods 62 113 120
20. J. Jonasson M. Olofsson H.J. Monstein 2002 Classification, identification and subsyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments PMIS 110 263 272
21. T. Kanagawa 2003 Bias and artifacts in multitemplate polymerase chain reactions (PCR) J. Biosci. Bioeng. 96 317 323
22. B.S. Kim H.M. Oh H. Kang S.S. Pack J. Chun 2004 Remarkable bacterial diversity in the tidal flat sediment as revealed by 16S rDNA analysis J. Microbiol. Biotechnol. 14 205 211
23. B.S. Kim H.M. Oh H. Kang J. Chun 2005 Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis J. Microbiol. 43 144 151
24. I.G. Kim M.H. Lee S.Y. Jung J.J. Song T.K. Oh J.H. Yoon 2005 Exiguobacterium aestuarii sp. nov. and Exiguobac-terium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea Int. J. Syst. Evol. Microbiol. 55 885 889
25. S. Kim H. Jeong S. Kim J. Chun 2006 Clostridium gang-hwense sp. nov., isolated from tidal flat sediment Int. J. Syst. Evol. Microbiol. 56 691 693
26. M. Konneke A.E. Bernhard J.R. De La Torre C.B. Walker J.B. Waterbury D.A. Stahl 2005 Isolation of an autotrophic ammonia-oxidizing marine archaeon Nature 437 543 546
27. S. Kurata T. Kanagawa Y. Magariyama K. Takatsu K. Yamada T. Yokomaku Y. Kamagata 2004 Reevaluation and reduction of a PCR bias caused by reannealing of templates Appl. Environ. Microbiol. 70 7545 7549
28. R.E. Ley J.K. Harris J. Wilcox J.R. Spear S.R. Miller B.M. Bebout J.A. Maresca D.A. Bryant M.L. Sogin N.R. Pace 2006 Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat Appl. Environ. Microbiol. 72 3685 3695
29. M. Margulies M. Egholm W.E. Altman S. Attiya J.S. Bader L.A. Bemben J. Berka M.S. Braverman Y.J. Chen Z. Chen S.B. Dewell L. Du J.M. Fierro X.V. Gomes B.C. Godwin W. He S. Helgesen C.H. Ho G.P. Irzyk S.C. Jando M.L. Alenquer T.P. Jarvie K.B. Jirage J.B. Kim J.R. Knight J.R. Lanza J.H. Leamon S.M. Lefkowitz M. Lei J. Li K.L. Lohman H. Lu V.B. Makhijani K.E. McDade M.P. McKenna E.W. Myers E. Nickerson J.R. Nobile R. Plant B.P. Puc M.T. Ronan G.T. Roth G.J. Sarkis J.F. Simons J.W. Simpson M. Srinivasan K.R. Tartaro A. Tomasz K.A. Vogt G.A. Volkmer S.H. Wang Y. Wang M.P. Weiner P. Yu R.F. Begley J.M. Rothberg 2005 Genome sequencing in mi-crofabricated high-density picolitre reactors Nature 437 376 380
30. R.J. Martinez H.J. Mills S. Story P.A. Sobecky 2006 Prokary-otic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico Environ. Microbiol. 8 1783 1796
31. P. McKenna C. Hoffmann N. Minkah P.A. Pyone A. Lackner Z. Liu C.A. Lozupone M. Hamady R. Knight F.D. Bushman 2008 The macaque gut microbiome in health, lenti-viral infection, and chronic enterocolitis PLoS Pathog. 4 e20
32. M. Mussmann K. Ishii R. Rabus R. Amann 2005 Diversity and vertical distribution of cultured and uncultured Deltapro-teobacteria in an intertidal mud flat of the Wadden Sea Environ Microbiol. 7 405 418
33. E.W. Myers W. Miller 1988 Optimal alignments in linear space Comput. Appl. Biosci. 4 11 17
34. C.L. Nesbo Y. Boucher M. Dlutek W.F. Doolittle 2005 Lateral gene transfer and phylogenetic assignment of environmental fosmid clones Environ. Microbiol. 7 2011 2026
35. D. Papineau J.J. Walker S.J. Mojzsis N.R. Pace 2005 Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia Appl. Environ. Microbiol. 71 4822 4832
36. D.G. Petersen I. Dahllof 2005 Improvements for comparative analysis of changes in diversity of microbial communities using internal standards in PCR-DGGE FEMS Microbiol. Ecol. 53 339 348
37. K. Ravenschlag K. Sahm J. Pernthaler R. Amann 1999 High bacterial diversity in permanently cold marine sediments Appl. Environ. Microbiol. 65 3982 3989
38. M. Ronaghi M. Uhlen P. Nyren 1998 A sequencing method based on real-time pyrophosphate Science 281 363 365
39. M. Ronaghi E. Elahi 2002 Pyrosequencing for microbial typing J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 782 67 72
40. P.D. Schloss J. Handelsman 2005 Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness Appl. Environ. Microbiol. 71 1501 1506
41. M.L. Sogin H.G. Morrison J.A. Huber D.M. Welch S.M. Huse P.R. Neal J.M. Arrieta G.J. Herndl 2006 Microbial diversity in the deep sea and the underexplored "rare biosphere" Proc. Natl. Acad. Sci. USA 103 12115 12120
42. S.G. Tringe C. Von Mering A. Kobayashi A.A. Salamov K. Chen H.W. Chang M. Podar J.M. Short E.J. Mathur J.C. Detter P. Bork P. Hugenholtz E.M. Rubin 2005 Comparative metagenomics of microbial communities Science 308 554 557
43. H. Urakawa K. Kita-Tsukamoto K. Ohwada 1999 Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis Microbiology 145 3305 3315
44. R. Wilms B. Kopke H. Sass T.S. Chang H. Cypionka B. Engelen 2006 Deep biosphere-related bacteria within the subsurface of tidal flat sediments Environ. Microbiol. 8 709 719
45. R. Wilms H. Sass B. Kopke J. Koster H. Cypionka B. Engelen 2006 Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters Appl. Environ. Microbiol. 72 2756 2764
46. J.H. Yoon I.G. Kim K.H. Kang T.K. Oh Y.H. Park 2003 Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea Int. J. Syst. Evol. Microbiol. 53 1297 1303