Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques

@article{Amann2008SinglecellII,
  title={Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques},
  author={Rudolf I. Amann and Bernhard M. Fuchs},
  journal={Nature Reviews Microbiology},
  year={2008},
  volume={6},
  pages={339-348}
}
  • R. Amann, B. Fuchs
  • Published 1 May 2008
  • Biology, Medicine
  • Nature Reviews Microbiology
The ribosomal-RNA (rRNA) approach to microbial evolution and ecology has become an integral part of environmental microbiology. Based on the patchy conservation of rRNA, oligonucleotide probes can be designed with specificities that range from the species level to the level of phyla or even domains. When these probes are labelled with fluorescent dyes or the enzyme horseradish peroxidase, they can be used to identify single microbial cells directly by fluorescence in situ hybridization. In this… Expand
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References

SHOWING 1-10 OF 104 REFERENCES
Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes.
TLDR
The past year has seen significant methodological improvements in fluorescence in situ hybridisation, as well as in the combination of this method with other techniques for inferring functional traits of microorganisms within their environment. Expand
Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells.
TLDR
Quantitative microfluorimetry shows that the amount of an rRNA-specific probe that binds to Escherichia coli varies with the ribosome content and therefore reflects growth rate. Expand
An in situ hybridization protocol for detection and identification of planktonic bacteria
Summary The fraction of planktonic bacteria in oligo- and mesotrophic lakes that can be classified by in situ hybridization has been significantly increased with an optimized protocol. By the use ofExpand
Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations
TLDR
Fluorescent oligonucleotide hybridization probes were used to label bacterial cells for analysis by flow cytometry and the intensity of fluorescence was increased additively by the combined use of two or three fluorescent probes complementary to different regions of the same 16S rRNA. Expand
Recognition of individual genes in a single bacterial cell by fluorescence in situ hybridization – RING‐FISH
TLDR
An improved FISH technique is presented, which goes beyond the detection of high copy intracellular nucleic acids such as rRNA and allows for the first time the in situ detection of individual genes or gene fragments on plasmids and chromosomal DNA in a single cell. Expand
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
TLDR
Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts. Expand
Bacterioplankton Compositions of Lakes and Oceans: a First Comparison Based on Fluorescence In Situ Hybridization
TLDR
FISH with rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of bacterioplankton communities in several freshwater and marine samples, finding that Beta subclass proteobacteria constituted a dominant fraction in freshwater systems and members of the Cytophaga-Flavobacterium cluster were the most abundant group detected in the marine systems. Expand
Combined Microautoradiography–16S rRNA Probe Technique for Determination of Radioisotope Uptake by Specific Microbial Cell Types In Situ
TLDR
A novel method for studying the function of specific microbial groups in situ with group-specific fluorescent 16S rRNA probes and simultaneously determines 3H-substrate uptake by each of the subgroups present via microautoradiography (MAR). Expand
Combined Microautoradiography–16S rRNA Probe Technique for Determination of Radioisotope Uptake by Specific Microbial Cell Types In Situ
TLDR
A novel method for studying the function of specific microbial groups in situ, substrate-tracking autoradiographic fluorescent in situ hybridization (STARFISH), which should aid in the “dissection” of microbial communities by type and function. Expand
Identifying members of the domain Archaea with rRNA-targeted oligonucleotide probes
TLDR
Two 16S rRNA-targeted oligonucleotide probes were designed for the archaeal kingdoms Euryachaeota and Crenarchaeota to facilitate rapid in situ monitoring of the populations present in hydrothermal systems and support cultivation attempts. Expand
...
1
2
3
4
5
...