Quantification of Microbial Communities in Forearc Sediment Basins off Sumatra

Abstract

Sediments in the Indian Ocean off the coast of the Indonesian island Sumatra were sampled at 25 stations in high resolution near the sediment surface and at three stations up to a maximum depth of 12 meter below seafloor (mbsf) for a quantitative microbial community analysis. Total cell counts were determined applying two different protocols including SYBR Green II as fluorescent staining dye. Total cell counts without detaching cells from sediment particles were 10 ⁹ cells/ mL sediments at the sediment surface with little variation between all stations. They decreased to 10 ⁸ cells/ mL at 0.2 to 0.4 mbsf and to 10 ⁷ cells/ mL below 6 mbsf. The total cell counts after detaching cells from sediment particles were up to one order of magnitude lower above 6 mbsf and showed similar values below. This difference for the two protocols can be explained by a loss of cells during the detachment procedure and/or counting of unspecific signals without detaching cells from sediment particles. Particular phylogenetic and physiological prokaryotic groups were quantified by quantitative, real-time PCR (Q-PCR) targeting 16S rRNA and functional genes. Archaea and Bacteria were found overall in similar 16S rRNA gene copy numbers in the range of the total cell counts at all sediment depths, thus, neither Archaea nor Bacteria could be considered as dominant. The eukaryotic 18S rRNA gene occurred in two orders of magnitude lower numbers than prokaryotic 16S rRNA genes. Fe(III)- and Mn(IV)-reducing bacteria (16S rRNA gene of Geobacteraceae) and sulfate-reducing bacteria (functional gene dsrA) were detected in variable (up to 10 ⁸ gene copies/ mL sediment) but in always significantly lower numbers than total Bacteria. The proportion of sulfate reducers on the prokaryotic community was between 0.2 and 19%. Calculated aereal sulfate reduction rates were overall low with values between 0.002 and 0.027 mmol m ^{− 2} a ^{− 1} , resulting in sulfate reduction rates per cell of 0.0007 and 0.81 fmol cell ^{− 1} a ^{− 1} , similar to published data for other deeply buried marine sediments. Methanogenesis did not seem to play a big role since methane was detected only below 6.5 mbsf, and the functional gene of methanogens and anaerobic methanotrophs mcrA could not be detected in any sample.

Keywords:

• marine sediments
• deep biosphere
• real-time PCR

We thank the shipboard party of RV SONNE for excellent support during expedition SO189–2, especially A. Lückge and M. Wiedicke-Hombach for leading the cruise. Many thanks to C. Haveland, G. Mengel-Jung, C. Rühlemann, S. Schlömer, C. Wöhrl and D. Zoch for sampling and technical support. We thank Anna Blazejak for comments that improved an earlier version of this manuscript. This work was funded by the BMBF research grant FKZ 03G0189A to BGR and by the DFG grants SCHI 535/5 and 535/6.

Axel Schippers and Gerrit Köweker contributed equally to this work.