Fine-scale phylogenetic architecture of a complex bacterial community

Nature

Volumn 430, Issue 6999, 2004, Pages 551-554

  Acinas, Silvia G ^a   Klepac Ceraj, Vanja ^a   Hunt, Dana E ^a   Pharino, Chanathip ^a   Ceraj, Ivica ^b   Distel, Daniel L ^c   Polz, Martin F ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b Bugaco   (United States)

^c UNIVERSITY OF MAINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLONING; EXTRAPOLATION; MICROORGANISMS; RNA;

ECOLOGICAL SIGNIFICANCE; MICROBIAL DIVERSITY;

BACTERIA;

RIBOSOME RNA; RNA 16S; SEA WATER;

BACTERIUM; COMMUNITY STRUCTURE; PHYLOGENY;

ARTICLE; ARTIFACT; BACTERIOPLANKTON; BACTERIUM; BACTERIUM IDENTIFICATION; ECOLOGY; MICROBIAL DIVERSITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RIBOTYPING; RNA SEQUENCE; TAXONOMY; UNINDEXED SEQUENCE; BACTERIAL GENE; BACTERIAL GENOME; CLASSIFICATION; ECOSYSTEM; GENE LIBRARY; GENETIC VARIABILITY; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; PHYSIOLOGY; PLANKTON; UNITED STATES;

BACTERIA (MICROORGANISMS); PROKARYOTA;

ARTIFACTS; BACTERIA; ECOSYSTEM; GENE LIBRARY; GENES, BACTERIAL; GENOME, BACTERIAL; MASSACHUSETTS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANKTON; RIBOTYPING; RNA, RIBOSOMAL, 16S; SEAWATER; VARIATION (GENETICS);

EID: 3242884054     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02649     Document Type: Article

References (29)

1. Rappé, M. S. & Giovannoni, S. J. The uncultured microbial majority. Annu. Rev. Microbiol. 57, 369-394 (2003).
2. Curtis, T. P., Sloan, W. T. & Scannell, J. W. Estimating prokaryotic diversity and its limits. Proc. Natl Acad. Sci. USA 99, 10494-10499 (2002).
3. Rosselló-Mora, R. & Amann, R. The species concept for prokaryotes. FEMS Microbiol. Rev. 25, 39-67 (2001).
4. Cohan, F. M. What are bacterial species. Annu. Rev. Microbiol. 56, 457-487 (2002).
5. Palys, T., Nakamura, L. K. & Cohan, F. M. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47, 1145-1156 (1997).
6. Venter, C. J. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74 (2004).
7. Hughes, J. B., Hellmann, J. J., Ricketts, T. H. & Bohannan, B. J. M. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67, 4399-4406 (2001).
8. Martin, A. P. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68, 3673-3682 (2002).
9. Acinas, S. G., Marcelino, L. A., Klepac-Ceraj, V. & Polz, M. F. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186, 2629-2635 (2004).
10. Klappenbach, J. A., Dunbar, J. M. & Schmidt, T. M. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66, 1328-1333 (2000).
11. Hacker, J. & Carniel, E. Ecological fitness, genomic islands and bacterial pathogenicity-a Darwinian view of the evolution of microbes. EMBO Rep. 2, 376-381 (2001).
12. Lan, R. T. & Reeves, P. R. When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9, 419-424 (2001).
13. Welch, R. A. et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl Acad. Sci. USA 99, 17020-17024 (2002).
14. Daubin, V., Moran, N. A. & Ochman, H. Phylogenetics and the cohesion of bacterial genomes. Science 301, 829-832 (2003).
15. Rocap, G. et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042-1047 (2003).
16. Schleper, C. A. et al. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Crenarchaeum symbiosum. J. Bacteriol. 180, 5003-5009 (1998).
17. Béja, O. et al. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68, 335-345 (2002).
18. Thingstad, T. F. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol. Oceanogr. 45, 1320-1328 (2000).
19. Lan, R. T. & Reeves, P. R. Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8, 396-401 (2000).
20. Klepac-Ceraj, V. et al. High overall diversity and dominance of microdiverse relationships in salt marsh sulfate-reducing bacteria. Environ. Microbiol. doi: 10.1111/j.1462-2920.2004.00600.x (2004).
21. Connon, S. A. & Giovannoni, S. J. High-throughput method for culturing microorganisms in very low nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 768, 3878-3885 (2002).
22. Vergin, K. L. et al. Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl. Environ. Microbiol. 64, 3075-3078 (1998).
23. Thompson, J. R., Marcelino, L. A. & Polz, M. F. Heteroduplexes in mixed-template amplifications: formation, consequences and elimination by 'reconditioning PCR'. Nucleic Acids Res. 30, 2083-2088 (2002).
24. Cole, J. R. et al. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31, 442-443 (2003).
25. Hugenholtz, P. & Huber, T. Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int. J. Syst. Evol. Microbiol. 53, 289-293 (2003).
26. Field, K. G. et al. Diversity and depth-specific distribution of SARI I cluster rRNA genes from marine planktonic bacteria. Appl. Environ. Microbiol. 63, 63-70 (1997).
27. Pybus, O. G. & Rambaut, A. GENIE: Estimating demographic history from molecular phylogenies. Bioinformatics 18, 1404-1405 (2003).
28. Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363-1371 (2004).
29. Swofford, D. L. PAUP*. Phylogenetic Analysis Using Parsimony (*And Other Methods) Version 4 (Sinauer Associates, Sunderland, Massachusetts, 2002).