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Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE.
FEMS Microbiol Ecol. 2007 Oct; 62(1):78-89.FM

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.

Authors+Show Affiliations

Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK. websterg@cardiff.ac.ukNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17692095

Citation

Webster, Gordon, et al. "Distribution of Candidate Division JS1 and Other Bacteria in Tidal Sediments of the German Wadden Sea Using Targeted 16S rRNA Gene PCR-DGGE." FEMS Microbiology Ecology, vol. 62, no. 1, 2007, pp. 78-89.
Webster G, Yarram L, Freese E, et al. Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE. FEMS Microbiol Ecol. 2007;62(1):78-89.
Webster, G., Yarram, L., Freese, E., Köster, J., Sass, H., Parkes, R. J., & Weightman, A. J. (2007). Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE. FEMS Microbiology Ecology, 62(1), 78-89.
Webster G, et al. Distribution of Candidate Division JS1 and Other Bacteria in Tidal Sediments of the German Wadden Sea Using Targeted 16S rRNA Gene PCR-DGGE. FEMS Microbiol Ecol. 2007;62(1):78-89. PubMed PMID: 17692095.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE. AU - Webster,Gordon, AU - Yarram,Laura, AU - Freese,Elke, AU - Köster,Jürgen, AU - Sass,Henrik, AU - Parkes,R John, AU - Weightman,Andrew J, Y1 - 2007/08/10/ PY - 2007/8/19/pubmed PY - 2007/11/14/medline PY - 2007/8/19/entrez SP - 78 EP - 89 JF - FEMS microbiology ecology JO - FEMS Microbiol Ecol VL - 62 IS - 1 N2 - 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. SN - 0168-6496 UR - https://www.unboundmedicine.com/medline/citation/17692095/Distribution_of_candidate_division_JS1_and_other_Bacteria_in_tidal_sediments_of_the_German_Wadden_Sea_using_targeted_16S_rRNA_gene_PCR_DGGE_ L2 - https://academic.oup.com/femsec/article-lookup/doi/10.1111/j.1574-6941.2007.00372.x DB - PRIME DP - Unbound Medicine ER -