Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities

Applied and Environmental Microbiology

Volumn 65, Issue 10, 1999, Pages 4630-4636

  Fisher, Madeline M ^a   Triplett, Eric W ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FRESH WATER; RIBOSOME RNA;

BACTERIUM; COMMUNITY COMPOSITION; ESTIMATION METHOD; FRESHWATER ECOSYSTEM; SPECIES DIVERSITY;

ARTICLE; AUTOMATION; BACTERIUM COLONY; BACTERIUM IDENTIFICATION; BIODIVERSITY; ELECTROPHORESIS; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; RNA ANALYSIS;

BACTERIA (MICROORGANISMS);

EID: 0032879764     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.10.4630-4636.1999     Document Type: Article

References (25)

1. Acinas, S. G., J. Anton, and F. Rodriguez-Valera. 1999. Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl. Environ. Microbiol. 65:514-522.
2. Altschul, S. F., T. L. Madden, A. A. Schaffer, 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.
3. Amikam, D., G. Glaser, and S. Razin. 1984. Mycoplasmas (Mollicutes) have a low number of rRNA genes. J. Bacteriol. 158:376-378.
4. Aubel, D., F. N. R. Renaud, and J. Freney. 1997. Genomic diversity of several Corynebacterium species identified by amplification of the 16S-23S rRNA gene spacer regions. Int. J. Syst. Bacteriol. 47:767-772.
5. Borneman, J., P. W. Skroch, K. M. O'Sullivan, J. A. Palus, N. G. Rumjanek, J. L. Jansen, J. Neinhuis, and E. W. Triplett. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62:1935-1943.
6. Borneman, J., and E. W. Triplett. 1997. Molecular microbial diversity in soils from Eastern Amazonia: evidence for unusual microorganisms and population shifts associated with deforestation. Appl. Environ. Microbiol. 63:2647-2653.
7. Garcia-Martinez, J., A. Martinez-Murcia, A. I. Anton, and F. Rodriguez-Valera. 1996. Comparison of the small 16S to 23S intergenic spacer region (ISR) of the rRNA operons of some Escherichia coli strains of the ECOR collection and E. coli K-12. J. Bacteriol. 178:6374-6377.
8. Garnier, T., B. Canard, and S. T. Cole. 1991. Cloning, mapping, and molecular characterization of the rRNA operons of Clostridium perfringens. J. Bacteriol. 173:5431-5438.
9. Gurtler, V., and V. A. Stanisich. 1996. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142:3-16.
10. Hansen, M. C., T. Tolker-Nielsen, M. Givskov, and S. Molin. 1998. Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol. Ecol. 26:141-149.
11. Jensen, M. A., J. A. Webster, and N. Straus. 1993. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl. Environ. Microbiol. 59:945-952.
12. Lindstrom, E. S. 1998. Bacterioplankton community composition in a boreal forest lake. FEMS Microbiol. Ecol. 27:163-174.
13. Liu, W.-T., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63:4516-4522.
14. Maes, N., Y. D. Gheldre, R. D. Rjck, M. Vaneechoutte, H. Meugnier, J. Etienne, and M. J. Struelens. 1997. Rapid and accurate identification of Staphylococcus species by tRNA intergenic spacer length polymorphism analysis. J. Clin. Microbiol. 35:2477-2481.
15. Maguerran, A. E. 1988. Ecological diversity and its measurement. Princeton University Press, Princeton, N.J.
16. McEvoy, C. R. E., R. Seshadri, and F. A. Firgaira. 1998. Large DNA fragment sizing using native acrylamide gels on an automated DNA sequencer and GENESCAN™ software. BioTechniques 25:464-470.
17. Murray, A. E., J. T. Hollibaugh, and C. Orrego. 1996. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denturing gradient gel electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 62:2676-2680.
18. Murray, A. E., C. M. Preston, R. Massana, L. T. Taylor, B. K. Wu, and E. F. DeLong. 1998. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 64:2585-2595.
19. Nagpal, M. L., K. F. Fox, and A. Fox. 1998. Utility of 16S-23S rRNA spacer region methodology: how similar are interspace regions within a genome and between strains for closely related organisms? J. Microbiol. Methods 33:211-219.
20. Navarro, E., P. Simonet, P. Normand, and R. Bardin. 1992. Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch. Microbiol. 157:107-115.
21. Polz, M. F., and C. M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.
22. Robleto, E. A., J. Borneman, and E. W. Triplett. 1998. Effects of bacterial antibiotic production on rhizosphere microbial communities from a culture-independent perspective. Appl. Environ. Microbiol. 64:5020-5022.
23. Scheinert, P., R. Krausse, U. Ullman, R. Soller, and G. Krupp. 1996. Molecular differentiation of bacteria by PCR amplification of the 16S-23S rRNA spacer. J. Microbiol. Methods 26:103-117.
24. Suzuki, M., M. S. Rappe, and S. J. Giovannoni. 1998. Kinetic bias estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64:4522-4529.
25. Wintzingerode, F. V., U. B. Gobel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.