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Applied and Environmental Microbiology, October 2002, p. 5064-5081, Vol. 68, No. 10
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.10.5064-5081.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment

Alexander Loy,1 Angelika Lehner,1 Natuschka Lee,1 Justyna Adamczyk,1 Harald Meier,2 Jens Ernst,3 Karl-Heinz Schleifer,1 and Michael Wagner1*

Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising,1 Lehrstuhl für Rechnertechnik und Rechnerorganisation,2 Lehrstuhl für Effiziente Algorithmen, Technische Universität München, D-80290 Munich, Germany3

Received 13 March 2002/ Accepted 5 July 2002

For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of Desulfomicrobium spp. in the tooth pockets and the presence of Desulfonema- and Desulfomonile-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (dsrAB).

* Corresponding author. Mailing address: Lehrstuhl für Mikrobiologie, Technische Universität München, Am Hochanger 4, D-85350 Freising, Germany. Phone: 49 8161 71 5444. Fax: 49 8161 71 5475. E-mail: wagner{at}microbial-ecology.de.

Applied and Environmental Microbiology, October 2002, p. 5064-5081, Vol. 68, No. 10
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.10.5064-5081.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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