Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE

Abstract

The bacterial candidate division JS1 dominates a number of 16S rRNA gene libraries from deep subseafloor sediments, yet its distribution in shallow, subsurface sediments has still to be fully documented. Sediment cores (down to 5.5 m) from Wadden Sea tidal flats (Neuharlingersieler Nacken and Gröninger Plate) were screened for JS1 16S rRNA genes using targeted PCR-denaturing gradient gel electrophoresis (DGGE), which also detects some other important Bacteria. Bacterial subpopulations at both sites were dominated by Gammaproteobacteria in the upper sediment layers (down to 2 m) and in deeper layers by members of the Chloroflexi. The deeper layers of Neuharlingersieler Nacken consisted of grey mud with low sulphate (0.1-10 mM), elevated total organic carbon (TOC) ( approximately 1-2%) and JS1 sequences were abundant. In contrast, the deeper sandy layers of Gröninger Plate, despite also having reduced sulphate concentrations, had lower TOC (<0.6%) with few detectable JS1 sequences. Results indicated that JS1 prefers muddy, shallow, subsurface sediments with reduced sulphate, whereas Chloroflexi may out-compete JS1 in shallow, sandy, subsurface sediments. Bacterial population changes at both sites ( approximately 2 m) were confirmed by cluster analysis of DGGE profiles, which correlated with increased recalcitrance of the organic matter. This study extends the biogeographical range of JS1. The presence of JS1 and Chloroflexi in Wadden Sea sediments demonstrates that subsurface tidal flats contain similar prokaryotic populations to those found in the deeper subseafloor biosphere.

Bacterial diversity in sediments of core MD05-2902 from the Xisha Trough, the South China Sea

“…TOC represents total organic carbon, TON total organic nitrogen, N15 δ 15 N, and C13 δ 13 C. Numbers represent the sampling depth. (Blazejak and Schippers, 2010;Fry et al, 2008;Inagaki et al, 2006;Orcutt et al, 2011;Webster et al, 2004;Webster et al, 2007). JS1 often co-occurs with Chloroflexi in anoxic sediment zones (Briggs et al, 2012;Orcutt et al, 2011), which was also observed in this study.…”

“…An alternative holds the idea that this phylum is not restricted to hydrate-containing sediments, but adapts to surviving in sediments with reasonable concentration of TOC Webster et al, 2007). Some JS1-associated bacteria, may involve in the biochemical processes of benzene mineralization, anaerobic methane oxidation, and removal of hydrocarbon (Alain et al, 2006;Dhillon et al, 2003;Phelps et al, 1998;Teske et al, 2002;Webster et al, 2007).…”

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

“…Geochemical pore water profiles in marine sediments show distinct redox zones (27), suggesting that each of these zones are shaped by organisms with specific metabolic traits. In agreement with this notion, several studies have demonstrated down-core stratification of microbial community composition (28)(29)(30)(31). Furthermore, a few specific microbial groups, such as anaerobic methane oxidizers (ANME) (32,33) and anaerobic ammonium oxidizers (anammox) (34) have been associated consistently with specific redox zones.…”

Microbial diversity in Frenulata (Siboglinidae, Polychaeta) species from mud volcanoes in the Gulf of Cadiz (NE Atlantic)

“…DGGE profiles were analysed as described by Fry et al (2006) and agglomerative cluster analysis was carried out using the software COMMUNITY ANALYSIS PACKAGE version 3.1 (Pisces Conservation Ltd). Dendrograms were constructed by average linkage and average distance method (Webster et al 2007). …”