Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters

Abstract

The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as "tidal-flat cluster 1." Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.

FIG. 1.

Simplified lithological profiles of the three sediment cores. The widths of the bars indicate grain sizes. The arrows show characteristic layers that were used for correlating the cores. Sediment cores were collected in June 2002 (core A), October 2003 (core B), and February 2004 (core C).

FIG. 2.

Geochemical profiles along the sediment cores. A) Sulfate; B) methane; C) ammonium; D) chloride; E) TOC; F) DOC. Core A, black circles; core B, dark gray circles; core C, light gray circles; core D, open circles. The zone between 100 and 200 cm shows low sulfate values, high methane and ammonium values, and a higher ratio of DOC to TOC.

FIG. 3.

Cluster analysis of DGGE band patterns from cores A to C obtained by the separation of specific PCR amplicons from Bacteria, Archaea, and Eukarya. The dendrograms were calculated by Pearson correlation and the unweighted-pair group method with arithmetic averages. The geochemically defined sediment horizons are indicated by different colors: white for the surface layer, light gray for the sulfate-free and methane-rich layers, and dark gray for the deeper layers including the deep sulfate maximum. Samples that affiliated to a different cluster are marked in boldface.