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.

[1]  B. Jørgensen,et al.  Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerrak, Denmark). , 2007, Environmental microbiology.

[2]  B. Engelen,et al.  Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea. , 2007, FEMS microbiology ecology.

[3]  A. Boetius,et al.  Microbial methane turnover at mud volcanoes of the Gulf of Cadiz , 2006 .

[4]  J. Santamarina,et al.  Mechanical limits to microbial activity in deep sediments , 2006 .

[5]  J. Prosser,et al.  Analysis of DGGE pro¢les to explore the relationship between prokaryotic community composition and biogeochemical processes in deep subsea£oor sediments from the Peru Margin , 2006 .

[6]  J. Fry,et al.  Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. , 2006, FEMS microbiology ecology.

[7]  R. Evershed,et al.  A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries. , 2006, Environmental microbiology.

[8]  A. Teske.  Microbial Communities of Deep Marine Subsurface Sediments: Molecular and Cultivation Surveys , 2006 .

[9]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[10]  B. Flemming,et al.  Late Holocene stratigraphic evolution of a back-barrier tidal basin in the East Frisian Wadden Sea, southern North Sea: transgressive deposition and its preservation potential , 2006 .

[11]  B. Engelen,et al.  Deep biosphere-related bacteria within the subsurface of tidal flat sediments. , 2006, Environmental microbiology.

[12]  B. Engelen,et al.  Specific Bacterial, Archaeal, and Eukaryotic Communities in Tidal-Flat Sediments along a Vertical Profile of Several Meters , 2006, Applied and Environmental Microbiology.

[13]  T. Treude,et al.  Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania. , 2006, Environmental microbiology.

[14]  B. Jørgensen,et al.  Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[16]  Heribert Cypionka,et al.  Microbial Diversity in Coastal Subsurface Sediments: a Cultivation Approach Using Various Electron Acceptors and Substrate Gradients , 2005, Applied and Environmental Microbiology.

[17]  Andrew J. Weightman,et al.  Deep sub-seafloor prokaryotes stimulated at interfaces over geological time , 2005, Nature.

[18]  R. Amann,et al.  Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. , 2005, Environmental microbiology.

[19]  M. Simon,et al.  Composition of free-living, aggregate-associated and sediment surface-associated bacterial communities in the German Wadden Sea , 2005 .

[20]  J. Handelsman,et al.  Status of the Microbial Census , 2004, Microbiology and Molecular Biology Reviews.

[21]  J. Fry,et al.  Widespread Occurrence of a Novel Division of Bacteria Identified by 16S rRNA Gene Sequences Originally Found in Deep Marine Sediments , 2004, Applied and Environmental Microbiology.

[22]  J. Fry,et al.  Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. , 2004, Environmental microbiology.

[23]  J. Chun,et al.  Remarkable Bacterial Diversity in the Tidal Flat Sediment as Revealed by 16S rDNA Analysis , 2004 .

[24]  K. Stetter,et al.  Thiobacillus prosperus sp. nov., represents a new group of halotolerant metal-mobilizing bacteria isolated from a marine geothermal field , 1989, Archives of Microbiology.

[25]  G. Muyzer,et al.  Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology , 2004, Antonie van Leeuwenhoek.

[26]  K. Nealson,et al.  Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk , 2003, Applied and Environmental Microbiology.

[27]  D. Cowan,et al.  Review and re-analysis of domain-specific 16S primers. , 2003, Journal of microbiological methods.

[28]  Gordon Webster,et al.  Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale. , 2003, Journal of microbiological methods.

[29]  Jo Handelsman,et al.  Biotechnological prospects from metagenomics. , 2003, Current opinion in biotechnology.

[30]  D. Stahl,et al.  Molecular Characterization of Sulfate-Reducing Bacteria in the Guaymas Basin , 2003, Applied and Environmental Microbiology.

[31]  Y. Fujita,et al.  Microbial Communities from Methane Hydrate-Bearing Deep Marine Sediments in a Forearc Basin , 2002, Applied and Environmental Microbiology.

[32]  H. Cypionka,et al.  Microbial communities in a Wadden Sea sediment core: clues from analyses of intact glyceride lipids, and released fatty acids , 2002 .

[33]  H. Cypionka,et al.  Ongoing Modification of Mediterranean Pleistocene Sapropels Mediated by Prokaryotes , 2002, Science.

[34]  M. Sogin,et al.  Microbial Diversity of Hydrothermal Sediments in the Guaymas Basin: Evidence for Anaerobic Methanotrophic Communities , 2002, Applied and Environmental Microbiology.

[35]  T. Martin Embley,et al.  Grassland Management Regimens Reduce Small-Scale Heterogeneity and Species Diversity of β-Proteobacterial Ammonia Oxidizer Populations , 2002, Applied and Environmental Microbiology.

[36]  J. Volkman,et al.  Sources and diagenesis of organic matter in tidal flat sediments from the German Wadden Sea , 2000 .

[37]  R. Parkes,et al.  Recent studies on bacterial populations and processes in subseafloor sediments: A review , 2000 .

[38]  K. Horikoshi,et al.  Microbial Diversity in Sediments Collected from the Deepest Cold-Seep Area, the Japan Trench , 1999, Marine Biotechnology.

[39]  L. Young,et al.  Molecular characterization of a sulfate-reducing consortium which mineralizes benzene , 1998 .

[40]  Philip Hugenholtz,et al.  Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity , 1998, Journal of bacteriology.

[41]  Niels B. Ramsing,et al.  Sulfate-Reducing Bacteria and Their Activities in Cyanobacterial Mats of Solar Lake (Sinai, Egypt) , 1998, Applied and Environmental Microbiology.

[42]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[43]  J. Fry,et al.  Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis , 1994 .

[44]  A. Uitterlinden,et al.  Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA , 1993, Applied and environmental microbiology.

[45]  H. Noller,et al.  Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. , 1981, Journal of molecular biology.