Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE.
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.
Webster
Gordon
G
Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK. websterg@cardiff.ac.uk
Yarram
Laura
L
Freese
Elke
E
Köster
Jürgen
J
Sass
Henrik
H
Parkes
R John
RJ
Weightman
Andrew J
AJ
D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D044822:Biodiversity; D002244:Carbon / Q000032:analysis; D016000:Cluster Analysis; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel; D019015:Geologic Sediments / Q000737:chemistry / Q000382:microbiology*; D005858:Germany; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D009930:Organic Chemicals / Q000032:analysis; D012336:RNA, Ribosomal, 16S / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013431:Sulfates / Q000032:analysis
D004269:DNA, Bacterial; D009930:Organic Chemicals; D012336:RNA, Ribosomal, 16S; D013431:Sulfates; D002244:Carbon