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Applied and Environmental Microbiology, December 2004, p. 6998-7009, Vol. 70, No. 12
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.12.6998-7009.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Microarray and Functional Gene Analyses of Sulfate-Reducing Prokaryotes in Low-Sulfate, Acidic Fens Reveal Cooccurrence of Recognized Genera and Novel Lineages

Alexander Loy,1 Kirsten Küsel,2 Angelika Lehner,3 Harold L. Drake,2 and Michael Wagner1*

Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Vienna, Austria,1 Department of Ecological Microbiology, University of Bayreuth, Bayreuth,2 Department of Microbiology, Technical University of Munich, Freising, Germany3

Received 9 March 2004/ Accepted 27 July 2004

Low-sulfate, acidic (approximately pH 4) fens in the Lehstenbach catchment in the Fichtelgebirge mountains in Germany are unusual habitats for sulfate-reducing prokaryotes (SRPs) that have been postulated to facilitate the retention of sulfur and protons in these ecosystems. Despite the low in situ availability of sulfate (concentration in the soil solution, 20 to 200 µM) and the acidic conditions (soil and soil solution pHs, approximately 4 and 5, respectively), the upper peat layers of the soils from two fens (Schlöppnerbrunnen I and II) of this catchment displayed significant sulfate-reducing capacities. 16S rRNA gene-based oligonucleotide microarray analyses revealed stable diversity patterns for recognized SRPs in the upper 30 cm of both fens. Members of the family "Syntrophobacteraceae" were detected in both fens, while signals specific for the genus Desulfomonile were observed only in soils from Schlöppnerbrunnen I. These results were confirmed and extended by comparative analyses of environmentally retrieved 16S rRNA and dissimilatory (bi)sulfite reductase (dsrAB) gene sequences; dsrAB sequences from Desulfobacca-like SRPs, which were not identified by microarray analysis, were obtained from both fens. Hypotheses concerning the ecophysiological role of these three SRP groups in the fens were formulated based on the known physiological properties of their cultured relatives. In addition to these recognized SRP lineages, six novel dsrAB types that were phylogenetically unrelated to all known SRPs were detected in the fens. These dsrAB sequences had no features indicative of pseudogenes and likely represent novel, deeply branching, sulfate- or sulfite-reducing prokaryotes that are specialized colonists of low-sulfate habitats.

* Corresponding author. Mailing address: Abteilung Mikrobielle Ökologie, Institut für Ökologie und Naturschutz, Universität Wien, Althanstr. 14, A-1090 Vienna, Austria. Phone: 43 1 4277 54390. Fax: 43 1 4277 54389. E-mail: wagner{at}microbial-ecology.net.

Applied and Environmental Microbiology, December 2004, p. 6998-7009, Vol. 70, No. 12
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.12.6998-7009.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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