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

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, July 2006, p. 4829-4838, Vol. 72, No. 7
0099-2240/06/$08.00+0     doi:10.1128/AEM.02949-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities

Jörg Peplies,^1* Christine Lachmund,² Frank Oliver Glöckner,¹ and Werner Manz²

Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Microbial Genomics Group, Celsiusstrasse 1, 28359 Bremen, Germany,¹ Federal Institute of Hydrology, Department of Biochemistry and Ecotoxicology, Am Mainzer Tor 1, 56068 Koblenz, Germany²

Received 14 December 2005/ Accepted 13 April 2006

A DNA microarray platform for the characterization of bacterial communities in freshwater sediments based on a heterogeneous set of 70 16S rRNA-targeted oligonucleotide probes and directly labeled environmental RNA was developed and evaluated. Application of a simple protocol for the efficient background blocking of aminosilane-coated slides resulted in an improved signal-to-noise ratio and a detection limit of 10 ng for particular 16S rRNA targets. An initial specificity test of the system using RNA from pure cultures of different phylogenetic lineages showed a fraction of false-positive signals of 5% after protocol optimization and a marginal loss of correct positive signals. Subsequent microarray analysis of sediment-related community RNA from four different German river sites suggested low diversity for the groups targeted but indicated distinct differences in community composition. The results were supported by parallel fluorescence in situ hybridization in combination with sensitive catalyzed reporter deposition (CARD-FISH). In comparisons of the data of different sampling sites, specific detection of populations with relative cellular abundances down to 2% as well as a correlation of microarray signal intensities and population size is suggested. Our results demonstrate that DNA microarray technology allows for the fast and efficient precharacterization of complex bacterial communities by the use of standard single-cell hybridization probes and the direct detection of environmental rRNA, also in methodological challenging habitats such as heterogeneous lotic freshwater sediments.

---

* Corresponding author. Present address: Ribocon GmbH, Fahrenheitstrasse 1, 28359 Bremen, Germany. Phone: 49 421 24 87 053. Fax: 49 421 2208 150. E-mail: jpeplies{at}ribocon.com.

---

Applied and Environmental Microbiology, July 2006, p. 4829-4838, Vol. 72, No. 7
0099-2240/06/$08.00+0     doi:10.1128/AEM.02949-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

This article has been cited by other articles:

• Militon, C., Rimour, S., Missaoui, M., Biderre, C., Barra, V., Hill, D., Mone, A., Gagne, G., Meier, H., Peyretaillade, E., Peyret, P. (2007). PhylArray: phylogenetic probe design algorithm for microarray. Bioinformatics 23: 2550-2557 [Abstract] [Full Text]  
• Han, W., Liu, B., Cao, B., Beutin, L., Kruger, U., Liu, H., Li, Y., Liu, Y., Feng, L., Wang, L. (2007). DNA Microarray-Based Identification of Serogroups and Virulence Gene Patterns of Escherichia coli Isolates Associated with Porcine Postweaning Diarrhea and Edema Disease. Appl. Environ. Microbiol. 73: 4082-4088 [Abstract] [Full Text]