Deep biosphere‐related bacteria within the subsurface of tidal flat sediments

Abstract

Biogeochemical and microbiological processes in the upper sediment layers of tidal flats were analysed in many investigations, while deeper zones remained largely unexplored. Therefore, denaturant gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments along the depth profile of up to 5.5 m-long sediment cores was performed in comparison with lithological and geochemical parameters. The investigation revealed that different compartments of the sediment columns were characterized by specific microbial communities. These compartments were analysed by sequencing of 113 DGGE bands. The upper layers down to 160-200 cm were dominated by gamma- and delta-Proteobacteria representing more than 60% of the total number of phylotypes. Underneath, a striking shift in community composition was observed, as the Proteobacteria were replaced by Chloroflexi with more than 60% of all sequences. As sulfate was still available as an electron acceptor in these layers, the abundance of Chloroflexi might be promoted by the electron donor or the quality of the carbon source. The dominance of this group, previously known as green non-sulfur bacteria, indicates the presence of a typical deep-biosphere microbial community in relatively young subsurface sediments. Thus, tidal flats might offer a convenient possibility to study and understand certain aspects of the deep biosphere in general.

Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches

“…Although it has been known that burrowing organisms affect sediment biogeochemistry, the interactions are often complex and detailed investigations on the effect of geochemical microzonations on microbial diversity are scarce (Kostka et al, 2002;Lucas et al, 2003;Matsui et al, 2004;Papaspyrou et al, 2006). This is not surprising because studies on microbial diversity in marine sediments have also only just begun (Mu mann et al, 2005;Wilms et al, 2006;Wu et al, 2008). The impact of bioturbation is speciesspecific and activity dependent (for example, Contour lines represent increments of 45 mM cm À3 wet sediment (ferric iron), 100 mM cm À3 wet sediment (ferrous iron), 5 mM (nitrate) and 10 mM (ammonium), respectively.…”

“…Few studies on microbial diversity have been performed in benthic systems (Llobet-Brossa et al, 1998;Köpke et al, 2005;Có rdova-Kreylos et al, 2006;Wilms et al, 2006;Liang et al, 2007) and studies on the effect of bioturbation on microbial community structure remain extremely scarce (Plante and Wilde, 2004;Papaspyrou et al, 2005Papaspyrou et al, , 2006. Environmental parameters vary quickly, especially in coastal sediments.…”

Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria

“…It was detected in all three cores to depths of ca. 2 m, indicating its presence not only in oxic but also in anoxic environments, as the sandy sediments in the Wadden Sea become readily anoxic below the surface (Wilms et al, 2006). Analysis of the abundance of the MMC in cores from the Grö ninger Plate and the Neuharlingersieler Nacken by quantitative PCR revealed that this cluster constituted 2.8 and 2.0% at the sediment surface, and 4.2 and 1.6% of bacterial 16S rRNA genes in the undermost horizons where the MMC was detected (ca.…”

Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes

“…They are characterized by high primary production rates and an intense heterotrophic activity (Wilms et al, 2006a). The high microbial activity leads to oxygen depletion within the first few millimeters of the sediment, below anoxic conditions are prevailing.…”