This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Case, R. J.
Right arrow Articles by Kjelleberg, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Case, R. J.
Right arrow Articles by Kjelleberg, S.
Agricola
Right arrow Articles by Case, R. J.
Right arrow Articles by Kjelleberg, S.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, January 2007, p. 278-288, Vol. 73, No. 1
0099-2240/07/$08.00+0     doi:10.1128/AEM.01177-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies{triangledown}

Rebecca J. Case,1,2 Yan Boucher,3,{dagger} Ingela Dahllöf,4 Carola Holmström,1,2 W. Ford Doolittle,3 and Staffan Kjelleberg1,2*

School of Biotechnology and Biomolecular Sciences,1 The Centre for Marine Biofouling and Bio-Innovation, University of New South Wales, Sydney 2052, Australia,2 Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, 5859 University Avenue, Halifax B3H 4H7, Canada,3 The National Environmental Research Institute, Roskilde, Denmark4

Received 22 May 2006/ Accepted 21 October 2006

Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such "heterogeneity hot spots" occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.

* Corresponding author. Mailing address: School of Biotechnology and Biomolecular Sciences and Centre for Marine Biofouling and Bio-Innovation, University of New South Wales, Randwick, Sydney NSW 2052, Australia. Phone: 61 2 9385 2102. Fax: 61 2 9385 1779. E-mail: s.kjelleberg{at}unsw.edu.au.

{triangledown} Published ahead of print on 27 October 2006.

{dagger} Present address: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia.

Applied and Environmental Microbiology, January 2007, p. 278-288, Vol. 73, No. 1
0099-2240/07/$08.00+0     doi:10.1128/AEM.01177-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Pereira, C. S., de Regt, A. K., Brito, P. H., Miller, S. T., Xavier, K. B. (2009). Identification of Functional LsrB-Like Autoinducer-2 Receptors. J. Bacteriol. 191: 6975-6987 [Abstract] [Full Text]  
  • Sorrels, C. M., Proteau, P. J., Gerwick, W. H. (2009). Organization, Evolution, and Expression Analysis of the Biosynthetic Gene Cluster for Scytonemin, a Cyanobacterial UV-Absorbing Pigment. Appl. Environ. Microbiol. 75: 4861-4869 [Abstract] [Full Text]  
  • Rahalkar, M., Deutzmann, J., Schink, B., Bussmann, I. (2009). Abundance and Activity of Methanotrophic Bacteria in Littoral and Profundal Sediments of Lake Constance (Germany). Appl. Environ. Microbiol. 75: 119-126 [Abstract] [Full Text]  
  • Adekambi, T., Shinnick, T. M., Raoult, D., Drancourt, M. (2008). Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus delineation. Int. J. Syst. Evol. Microbiol. 58: 1807-1814 [Abstract] [Full Text]  
  • Quemeneur, M., Heinrich-Salmeron, A., Muller, D., Lievremont, D., Jauzein, M., Bertin, P. N., Garrido, F., Joulian, C. (2008). Diversity Surveys and Evolutionary Relationships of aoxB Genes in Aerobic Arsenite-Oxidizing Bacteria. Appl. Environ. Microbiol. 74: 4567-4573 [Abstract] [Full Text]  
  • Pineiro, S. A., Williams, H. N., Stine, O. C. (2008). Phylogenetic relationships amongst the saltwater members of the genus Bacteriovorax using rpoB sequences and reclassification of Bacteriovorax stolpii as Bacteriolyticum stolpii gen. nov., comb. nov.. Int. J. Syst. Evol. Microbiol. 58: 1203-1209 [Abstract] [Full Text]  
  • Scheirlinck, I., Van der Meulen, R., Van Schoor, A., Vancanneyt, M., De Vuyst, L., Vandamme, P., Huys, G. (2008). Taxonomic Structure and Stability of the Bacterial Community in Belgian Sourdough Ecosystems as Assessed by Culture and Population Fingerprinting. Appl. Environ. Microbiol. 74: 2414-2423 [Abstract] [Full Text]  
  • Downes, J., Sutcliffe, I. C., Booth, V., Wade, W. G. (2007). Prevotella maculosa sp. nov., isolated from the human oral cavity. Int. J. Syst. Evol. Microbiol. 57: 2936-2939 [Abstract] [Full Text]  
  • Enache, M., Itoh, T., Fukushima, T., Usami, R., Dumitru, L., Kamekura, M. (2007). Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB' gene and protein sequences. Int. J. Syst. Evol. Microbiol. 57: 2289-2295 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»