This article is part of the Research Topic Deep Subsurface Microbiology

Original Research ARTICLE

Front. Microbiol., 22 December 2011 | doi: 10.3389/fmicb.2011.00253

Real-time PCR quantification and diversity analysis of the functional genes aprA and dsrA of sulfate-reducing prokaryotes in marine sediments of the Peru continental margin and the Black Sea

Anna Blazejak1† and Axel Schippers1,2*
  • 1 Geomicrobiology, Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
  • 2 Faculty of Natural Sciences, Leibniz Universität Hannover, Hannover, Germany

Sulfate-reducing prokaryotes (SRP) are ubiquitous and quantitatively important members in many ecosystems, especially in marine sediments. However their abundance and diversity in subsurface marine sediments is poorly understood. In this study, the abundance and diversity of the functional genes for the enzymes adenosine 5′-phosphosulfate reductase (aprA) and dissimilatory sulfite reductase (dsrA) of SRP in marine sediments of the Peru continental margin and the Black Sea were analyzed, including samples from the deep biosphere (ODP site 1227). For aprA quantification a Q-PCR assay was designed and evaluated. Depth profiles of the aprA and dsrA copy numbers were almost equal for all sites. Gene copy numbers decreased concomitantly with depth from around 108/g sediment close to the sediment surface to less than 105/g sediment at 5 mbsf. The 16S rRNA gene copy numbers of total bacteria were much higher than those of the functional genes at all sediment depths and used to calculate the proportion of SRP to the total Bacteria. The aprA and dsrA copy numbers comprised in average 0.5–1% of the 16S rRNA gene copy numbers of total bacteria in the sediments up to a depth of ca. 40 mbsf. In the zone without detectable sulfate in the pore water from about 40–121 mbsf (Peru margin ODP site 1227), only dsrA (but not aprA) was detected with copy numbers of less than 104/g sediment, comprising ca. 14% of the 16S rRNA gene copy numbers of total bacteria. In this zone, sulfate might be provided for SRP by anaerobic sulfide oxidation. Clone libraries of aprA showed that all isolated sequences originate from SRP showing a close relationship to aprA of characterized species or form a new cluster with only distant relation to aprA of isolated SRP. For dsrA a high diversity was detected, even up to 121 m sediment depth in the deep biosphere.

Keywords: deep biosphere, real-time PCR, subsurface, ODP, sulfate-reducing prokaryotes, aprA, dsrA

Citation: Blazejak A and Schippers A (2011) Real-Time PCR Quantification and Diversity Analysis of the Functional Genes aprA and dsrA of Sulfate-Reducing Prokaryotes in Marine Sediments of the Peru Continental Margin and the Black Sea. Front. Microbio. 2:253. doi: 10.3389/fmicb.2011.00253

Received: 11 August 2011; Accepted: 29 November 2011;
Published online: 22 December 2011.

Edited by:

Andreas Teske, University of North Carolina at Chapel Hill, USA

Reviewed by:

Julie A. Huber, Marine Biological Laboratory, USA
Kasthuri Venkateswaran, NASA-Jet Propulsion Laboratory, USA

Copyright: © 2011 Blazejak and Schippers. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.

*Correspondence: Axel Schippers, Geomicrobiology, Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany. e-mail: axel.schippers@bgr.de

Present address: Anna Blazejak, Max Planck Institute for Marine Microbiology, Bremen, Germany.

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