New Perspective on Uncultured Bacterial Phylogenetic Division OP11

Applied and Environmental Microbiology

Volumn 70, Issue 2, 2004, Pages 845-849

  Harris, J Kirk ^a,b   Kelley, Scott T ^a,c   Pace, Norman R ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLONING; DNA; ENVIRONMENTAL IMPACT; MICROBIOLOGY; MOLECULAR STRUCTURE; RNA;

BACTERIAL DIVISIONS; MOLECULAR SIGNATURES;

BACTERIA;

DNA; RIBOSOME RNA;

MICROBIOLOGY;

ARTICLE; BACTERIUM; BACTERIUM IDENTIFICATION; BIOGEOCHEMISTRY; CLONE; COMPARATIVE STUDY; ENVIRONMENT; GENETIC VARIABILITY; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLUM; POLYMERASE CHAIN REACTION; RNA SEQUENCE; UNINDEXED SEQUENCE;

BACTERIA; CLONING, MOLECULAR; DNA, BACTERIAL; DNA, RIBOSOMAL; ENVIRONMENTAL MICROBIOLOGY; GENES, RRNA; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 2342531664     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.70.2.845-849.2004     Document Type: Article

References (22)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Borneman, J., and 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.
3. Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2003. The Ribosomal Database Project (RDP-II): previewing a new auto-aligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31:442-443.
4. Dalevi, D., P. Hugenholtz, and L. Blackall. 2001. A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. Int. J. Syst. Evol. Microbiol. 51:385-391.
5. Dojka, M. A., J. K. Harris, and N. R. Pace. 2000. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl. Environ. Microbiol. 66:1617-1621.
6. Dojka, M. A., P. Hugenholtz, S. K. Haack, and N. R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-3877.
7. Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
8. Hillis, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
9. Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux. 1992. Experimental phylogenetics: generation of a known phylogeny. Science 255:589-592.
10. Hillis, D. M., and C. Moritz. 1990. Molecular systematics. Sinauer Associates, Inc., Sunderland, Mass.
11. Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774. (Erratum, 180:6793.)
12. Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366-376.
13. Kuske, C. R., S. M. Barns, and J. D. Busch. 1997. Diverse uncultivated bacterial groups from soils of the and southwestern United States that are present in many geographic regions. Appl. Environ. Microbiol. 63:3614-3621.
14. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, N.Y.
15. Lane, D. J., B. Pace, G. J. Olsen, D. A. Stahl, M. L. Sogin, and N. R. Pace. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82:6955-6959.
16. Li, L., C. Kato, and K. Horikoshi. 1999. Bacterial diversity in deep-sea sediments from different depths. Biodivers. Conserv. 8:659-677.
17. Paster, B. J., S. K. Boches, J. L. Galvin, R. E. Ericson, C. N. Lau, V. A. Levanos, A. Sahasrabudhe, and F. E. Dewhirst. 2001. Bacterial diversity in human subgingival plaque. J. Bacteriol. 183:3770-3783.
18. Pedersen, K., J. Arlinger, S. Ekendahl, and L. Hallbeek. 1996. 16S rRNA gene diversity of attached and unattached bacteria in boreholes along the access tunnel to the Äspö hard rock laboratory, Sweden. FEMS Microbiol. Ecol. 19:249-262.
19. Poe, S. 1998. Sensitivity of phylogeny estimation on taxonomic sampling. Syst. Biol. 47:18-31.
20. Strunk, O., and W. Ludwig. 1999. ARB: a software environment for sequence data. [Online.] http://www.mikro.biologie.tu-muenchen.de.
21. Ueda, T., Y. Suga, and T. Matsuguchi. 1995. Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur. J. Soil Sci. 46:415-421.
22. Wise, M. G., J. V. McArthur, and L. J. Shimkets. 1997. Bacterial diversity of a Carolina bay as determined by 16S rRNA gene analysis: confirmation of novel taxa. Appl. Environ. Microbiol. 63:1505-1514.