- Rappé, M. S. & Giovannoni, S. J. The uncultured microbial majority. Annu. Rev. Microbiol. 57, 369–394 (2003)
Article PubMed Google Scholar
- Curtis, T. P., Sloan, W. T. & Scannell, J. W. Estimating prokaryotic diversity and its limits. Proc. Natl Acad. Sci. USA 99, 10494–10499 (2002)
Article ADS CAS PubMed PubMed Central Google Scholar
- Rosselló-Mora, R. & Amann, R. The species concept for prokaryotes. FEMS Microbiol. Rev. 25, 39–67 (2001)
Article PubMed Google Scholar
- Cohan, F. M. What are bacterial species. Annu. Rev. Microbiol. 56, 457–487 (2002)
Article CAS PubMed Google Scholar
- 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)
Article CAS PubMed Google Scholar
- Venter, C. J. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004)
Article ADS CAS PubMed Google Scholar
- 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)
Article CAS PubMed PubMed Central Google Scholar
- Martin, A. P. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68, 3673–3682 (2002)
Article CAS PubMed PubMed Central Google Scholar
- 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)
Article CAS PubMed PubMed Central Google Scholar
- 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)
Article CAS PubMed PubMed Central Google Scholar
- 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)
Article CAS PubMed PubMed Central Google Scholar
- 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)
Article CAS PubMed Google Scholar
- 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)
Article ADS CAS PubMed PubMed Central Google Scholar
- Daubin, V., Moran, N. A. & Ochman, H. Phylogenetics and the cohesion of bacterial genomes. Science 301, 829–832 (2003)
Article ADS CAS PubMed Google Scholar
- Rocap, G. et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042–1047 (2003)
Article ADS CAS PubMed Google Scholar
- 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)
CAS PubMed PubMed Central Google Scholar
- 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)
Article PubMed PubMed Central Google Scholar
- 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)
Article ADS Google Scholar
- Lan, R. T. & Reeves, P. R. Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8, 396–401 (2000)
Article CAS PubMed Google Scholar
- 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)
- 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)
Article Google Scholar
- 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)
CAS PubMed PubMed Central Google Scholar
- 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)
Article CAS PubMed PubMed Central Google Scholar
- 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)
Article CAS PubMed PubMed Central Google Scholar
- 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)
Article CAS PubMed Google Scholar
- Field, K. G. et al. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl. Environ. Microbiol. 63, 63–70 (1997)
CAS PubMed PubMed Central Google Scholar
- Pybus, O. G. & Rambaut, A. GENIE: Estimating demographic history from molecular phylogenies. Bioinformatics 18, 1404–1405 (2003)
Article Google Scholar
- Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004)
Article CAS PubMed PubMed Central Google Scholar
- Swofford, D. L. PAUP*. Phylogenetic Analysis Using Parsimony (*And Other Methods) Version 4 (Sinauer Associates, Sunderland, Massachusetts, 2002)
Google Scholar