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 Castiglioni, B. Articles by De Bellis, G. Search for Related Content PubMed PubMed Citation Articles by Castiglioni, B. Articles by De Bellis, G. Agricola Articles by Castiglioni, B. Articles by De Bellis, G.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, December 2004, p. 7161-7172, Vol. 70, No. 12
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.12.7161-7172.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Development of a Universal Microarray Based on the Ligation Detection Reaction and 16S rRNA Gene Polymorphism To Target Diversity of Cyanobacteria

Institute of Agricultural Biology and Biotechnology, Italian National Research Council, Milan,¹ Institute of Biomedical Technologies, Italian National Research Council,² Department of Biomedical Sciences and Technology, University of Milan, Segrate,³ Institute of Ecosystem Study, Section of Florence, Italian National Research Council, Sesto Fiorentino, Italy,⁵ Department of Applied Chemistry and Microbiology, Viikki Biocenter, University of Helsinki, Helsinki, Finland,⁴ Center for Protein Engineering, Institute of Chemistry, University of Liege, Liege, Belgium⁶

Received 6 April 2004/ Accepted 3 August 2004

The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds. In eutrophic fresh and brackish waters, their mass occurrences (water blooms) are often toxic and constitute a high potential risk for human health. Therefore, rapid and reliable identification of cyanobacterial species in complex environmental samples is important. Here we describe the development and validation of a microarray for the identification of cyanobacteria in aquatic environments. Our approach is based on the use of a ligation detection reaction coupled to a universal array. Probes were designed for detecting 19 cyanobacterial groups including Anabaena/Aphanizomenon, Calothrix, Cylindrospermopsis, Cylindrospermum, Gloeothece, halotolerants, Leptolyngbya, Palau Lyngbya, Microcystis, Nodularia, Nostoc, Planktothrix, Antarctic Phormidium, Prochlorococcus, Spirulina, Synechococcus, Synechocystis, Trichodesmium, and Woronichinia. These groups were identified based on an alignment of over 300 cyanobacterial 16S rRNA sequences. For validation of the microarrays, 95 samples (24 axenic strains from culture collections, 27 isolated strains, and 44 cloned fragments recovered from environmental samples) were tested. The results demonstrated a high discriminative power and sensitivity to 1 fmol of the PCR-amplified 16S rRNA gene. Accurate identification of target strains was also achieved with unbalanced mixes of PCR amplicons from different cyanobacteria and an environmental sample. Our universal array method shows great potential for rapid and reliable identification of cyanobacteria. It can be easily adapted to future development and could thus be applied both in research and environmental monitoring.

This article has been cited by other articles:

• Huyghe, A., Francois, P., Charbonnier, Y., Tangomo-Bento, M., Bonetti, E.-J., Paster, B. J., Bolivar, I., Baratti-Mayer, D., Pittet, D., Schrenzel, J., and the Geneva Study Group on Noma (GESNOMA), (2008). Novel Microarray Design Strategy To Study Complex Bacterial Communities. Appl. Environ. Microbiol. 74: 1876-1885 [Abstract] [Full Text]  
• Brodie, E. L., DeSantis, T. Z., Joyner, D. C., Baek, S. M., Larsen, J. T., Andersen, G. L., Hazen, T. C., Richardson, P. M., Herman, D. J., Tokunaga, T. K., Wan, J. M., Firestone, M. K. (2006). Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation. Appl. Environ. Microbiol. 72: 6288-6298 [Abstract] [Full Text]  
• DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., Andersen, G. L. (2006). Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB.. Appl. Environ. Microbiol. 72: 5069-5072 [Abstract] [Full Text]  
• Sanguin, H., Remenant, B., Dechesne, A., Thioulouse, J., Vogel, T. M., Nesme, X., Moenne-Loccoz, Y., Grundmann, G. L. (2006). Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities.. Appl. Environ. Microbiol. 72: 4302-4312 [Abstract] [Full Text]  
• Palmer, C., Bik, E. M., Eisen, M. B., Eckburg, P. B., Sana, T. R., Wolber, P. K., Relman, D. A., Brown, P. O. (2006). Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res 34: e5-e5 [Abstract] [Full Text]  
• Szemes, M., Bonants, P., de Weerdt, M., Baner, J., Landegren, U., Schoen, C. D. (2005). Diagnostic application of padlock probes--multiplex detection of plant pathogens using universal microarrays. Nucleic Acids Res 33: e70-e70 [Abstract] [Full Text]