Monitoring Precursor 16S rRNAs of
            <i>Acinetobacter</i>
            spp. in Activated Sludge Wastewater Treatment Systems

Oerther, Daniel B.; Pernthaler, Jakob; Schramm, Andreas; Amann, Rudolf; Raskin, Lutgarde

doi:10.1128/aem.66.5.2154-2165.2000

Cited by 72 publications

(58 citation statements)

References 34 publications

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“…3 and 4). CARD-FISH on the rRNA precursor targeting the ITS region was previously performed (58,59), but in this study also introns in the rRNA precursors were hybridized. The successful and specific labeling of the different introns demonstrates their transcription into RNA, strongly indicating that the 16S rRNA genes retrieved by PCR were not pseudogenes.…”

Section: Discussionmentioning

confidence: 99%

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Salman

Amann

Shub³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The gene encoding the small subunit rRNA serves as a prominent tool for the phylogenetic analysis and classification of Bacteria and Archaea owing to its high degree of conservation and its fundamental function in living organisms. Here we show that the 16S rRNA genes of not-yet-cultivated large sulfur bacteria, among them the largest known bacterium Thiomargarita namibiensis , regularly contain numerous self-splicing introns of variable length. The 16S rRNA genes can thus be enlarged to up to 3.5 kb. Remarkably, introns have never been identified in bacterial 16S rRNA genes before, although they are the most frequently sequenced genes today. This may be caused in part by a bias during the PCR amplification step that discriminates against longer homologs, as we show experimentally. Such length heterogeneity of 16S rRNA genes has so far never been considered when constructing 16S rRNA-based clone libraries, even though an elongation of rRNA genes due to intervening sequences has been reported previously. The detection of elongated 16S rRNA genes has profound implications for common methods in molecular ecology and may cause systematic biases in several techniques. In this study, catalyzed reporter deposition–fluorescence in situ hybridization on both ribosomes and rRNA precursor molecules as well as in vitro splicing experiments were performed and confirmed self-splicing of the introns. Accordingly, the introns do not inhibit the formation of functional ribosomes.

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Section: Discussionmentioning

confidence: 99%

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Salman

Amann

Shub³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…We have also combined activity measurements with single-cell sorting (17) to remove specific cells of interest for further analysis, including denaturing gradient gel electrophoresis and 16S rRNA identification (unpublished data). This approach along with other direct methods (13,15), such as FISH with multiple (group-specific) rRNAtargeted oligonucleotide probes (1), may determine which bacteria are responsible for an efficient activated sludge reactor. This approach may help forge the much-needed link between identity and specific activity (2), finally removing the "black box" approach to bacterial analysis of wastewater.…”

Section: Discussionmentioning

confidence: 99%

Simultaneous Fluorescent Gram Staining and Activity Assessment of Activated Sludge Bacteria

Forster

Snape

Lappin‐Scott

et al. 2002

Appl Environ Microbiol

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“…Final washes were performed at temperatures 6.5°C below the experimentally determined T d for DNA-RNA hybridization (listed above). The decreased T w was necessary because DNA-DNA hybrids are less stable than DNA-RNA hybrids, and the experimentally determined difference in dissociation temperatures is approximately 6.5°C (33). Hybridization signals were captured using an Electronic Autoradiography Instant Imager (Packard Instruments, Meriden, Conn.).…”

Section: Methodsmentioning

confidence: 99%

Molecular Ecological Analysis of the Succession and Diversity of Sulfate-Reducing Bacteria in the Mouse Gastrointestinal Tract

Deplancke¹,

Hristova

Oakley³

et al. 2000

Appl Environ Microbiol

142

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Intestinal sulfate-reducing bacteria (SRB) growth and resultant hydrogen sulfide production may damage the gastrointestinal epithelium and thereby contribute to chronic intestinal disorders. However, the ecology and phylogenetic diversity of intestinal dissimilatory SRB populations are poorly understood, and endogenous or exogenous sources of available sulfate are not well defined. The succession of intestinal SRB was therefore compared in inbred C57BL/6J mice using a PCR-based metabolic molecular ecology (MME) approach that targets a conserved region of subunit A of the adenosine-5-phosphosulfate (APS) reductase gene. The APS reductase-based MME strategy revealed intestinal SRB in the stomach and small intestine of 1-, 4-, and 7-day-old mice and throughout the gastrointestinal tract of 14-, 21-, 30-, 60-, and 90-day-old mice. Phylogenetic analysis of APS reductase amplicons obtained from the stomach, middle small intestine, and cecum of neonatal mice revealed that Desulfotomaculum spp. may be a predominant SRB group in the neonatal mouse intestine. The toxic gas hydrogen sulfide (H 2 S) is generated from sulfate during anaerobic respiration by sulfate-reducing Archaea and Bacteria (21, 58). A possible link between H 2 S and chronic intestinal disorders has been evoked by data indicating increased numbers of intestinal sulfate-reducing bacteria (SRB) and rates of sulfidogenesis in inflammatory bowel disease (IBD) patients compared to healthy humans (12, 37). Hydrogen sulfide selectively impairs the oxidation of n-butyrate by colonic epithelial cells (42). Because membrane lipid biosynthesis, ion absorption, mucin synthesis, and detoxification processes in colonocytes depend on the oxidation of n-butyrate, diminished n-butyrate metabolism is likely to compromise the epithelial cell barrier (42). Sulfide-induced damage of the epithelial barrier function would promote translocation of bacterial and food antigens, resulting in local inflammatory responses to normally benign antigens, an outcome consistent with histopathological features of IBD (16, 61). Chronic exposure to H 2 S might also perturb normal cycles of epithelial renewal in the intestine, thereby predisposing to proliferative disorders such as colon cancer.Intestinal sulfate can be derived either from exogenous sources, namely sulfate in drinking water and dietary foodstuffs, or from endogenous sources such as sulfated mucins (sulfomucins), sulfate-conjugated bile, and chondroitin sulfate. Use of chemically bound, endogenous sulfate by SRB is facilitated through interactions with sulfatase-harboring bacteria (e.g., Bacteroides spp. [56]). Most goblet cells, a differentiated epithelial cell subtype that produces mucins, generate sulfomucins (22). The degree of sulfation, however, increases from proximal to distal segments of the intestine and is highest in those segments harboring dense bacterial populations, such as the cecum and colon (9,20).The ecology and taxonomy of intestinal SRB and their metabolic activities remain uncharacterized. Most studies of...

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Monitoring Precursor 16S rRNAs of Acinetobacter spp. in Activated Sludge Wastewater Treatment Systems

Cited by 72 publications

References 34 publications

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Simultaneous Fluorescent Gram Staining and Activity Assessment of Activated Sludge Bacteria

Molecular Ecological Analysis of the Succession and Diversity of Sulfate-Reducing Bacteria in the Mouse Gastrointestinal Tract

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