A quantitative method for measuring the mass concentration of the filamentous bacterium Type 021N in activated sludge using fluorescence in situ hybridization

2003 ◽  
Vol 37 (2) ◽  
pp. 100-104 ◽  
Author(s):  
Y. Guan ◽  
F. Kurisu ◽  
H. Satoh ◽  
T. Mino
Keyword(s):  
In Situ Hybridization ◽  
Activated Sludge ◽  
Fluorescence In Situ Hybridization ◽  
Mass Concentration ◽  
Quantitative Method ◽  
Filamentous Bacterium

The in situ physiology of Nostocoida limicola II, a filamentous bacterial morphotype in bulking activated sludge, using fluorescence in situ hybridization and microautoradiography

2006 ◽  
Vol 54 (1) ◽  
pp. 47-53 ◽  
Author(s):  
E.M. Seviour ◽  
K. Eales ◽  
L. Izzard ◽  
M. Beer ◽  
E.L. Carr ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Activated Sludge ◽  
Fluorescence In Situ Hybridization ◽  
Filamentous Bacterium ◽  
Anaerobic Conditions ◽  
Pure Cultures

The in situ physiology of the actinobacterial bulking and foaming filamentous bacterium “Nostocoida limicola” II was studied by fluorescence in situ hybridization/microautoradiography. Substrate assimilation patterns of pure cultures of this bacterium were different to those seen in activated sludge biomass samples. There was no evidence to suggest that “N. limicola” II preferred hydrophobic substrates, but evidence was produced to support the view that it is metabolically active under anaerobic conditions in activated sludge.

scholarly journals Cytological Evidence for Association of the Ends of the Linear Chromosome in Streptomyces coelicolor

2001 ◽  
Vol 183 (17) ◽  
pp. 5180-5186 ◽  
Author(s):  
Melody C. Yang ◽  
Richard Losick
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Genetic Map ◽  
Streptomyces Coelicolor ◽  
Evidence Based ◽  
Filamentous Bacterium ◽  
Cytological Evidence ◽  
Circular Chromosome ◽  
Linear Chromosome

ABSTRACT The chromosome of the filamentous bacterium Streptomyces coelicolor is linear, but the genetic map is circular. We present cytological evidence based on the use of fluorescence in situ hybridization showing that the ends of the chromosome frequently colocalize, in agreement with the idea that the ends are held together, effectively forming a circular chromosome. These observations provide a possible explanation for how a linear bacterial chromosome can exhibit a circular genetic map.

scholarly journals Filamentous Bacterium Eikelboom Type 0092 in Activated Sludge Plants in Australia Is a Member of the Phylum Chloroflexi

2009 ◽  
Vol 75 (8) ◽  
pp. 2446-2452 ◽  
Author(s):  
Lachlan Speirs ◽  
Tadashi Nittami ◽  
Simon McIlroy ◽  
Sarah Schroeder ◽  
Robert J. Seviour
Keyword(s):  
In Situ Hybridization ◽  
Activated Sludge ◽  
Molecular Data ◽  
Phosphate Removal ◽  
Filamentous Bacterium ◽  
Eastern Australia ◽  
Intracellular Aggregates ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Molecular data show that the filamentous bacterium Eikelboom type 0092, frequently seen in Australian activated sludge plants, is a member of the phylum Chloroflexi. Fluorescence in situ hybridization (FISH) probes designed against cloned 16S rRNA sequences from a full-scale enhanced biological phosphate removal-activated sludge plant community, where this was a dominant filament morphotype, suggest that it can exist as two variants, differing in their trichome diameter. When applied to samples from several treatment plants in eastern Australia, each FISH probe targeted only the type 0092 filament morphotype against which it was designed. The patterns of FISH signals generated with both were consistent with the ribosomes not being evenly distributed but arranged as intracellular aggregates. The FISH survey data showed that these two variants appeared together in most but not all of the plants examined. None stained positively for intracellular presence of either poly-β-hydroxyalkanoates or polyphosphate.

scholarly journals Quantification of Target Molecules Needed To Detect Microorganisms by Fluorescence In Situ Hybridization (FISH) and Catalyzed Reporter Deposition-FISH

2008 ◽  
Vol 74 (16) ◽  
pp. 5068-5077 ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
L. Safak Yilmaz ◽  
Daniel R. Noguera ◽  
Holger Daims ◽  
Michael Wagner
Keyword(s):  
In Situ Hybridization ◽  
16S Rrna ◽  
Activated Sludge ◽  
Fluorescence In Situ Hybridization ◽  
Oligonucleotide Probes ◽  
Pure Cultures ◽  
Technical Modifications ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

ABSTRACT Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a method that is widely used to detect and quantify microorganisms in environmental samples and medical specimens by fluorescence microscopy. Difficulties with FISH arise if the rRNA content of the probe target organisms is low, causing dim fluorescence signals that are not detectable against the background fluorescence. This limitation is ameliorated by technical modifications such as catalyzed reporter deposition (CARD)-FISH, but the minimal numbers of rRNA copies needed to obtain a visible signal of a microbial cell after FISH or CARD-FISH have not been determined previously. In this study, a novel competitive FISH approach was developed and used to determine, based on a thermodynamic model of probe competition, the numbers of 16S rRNA copies per cell required to detect bacteria by FISH and CARD-FISH with oligonucleotide probes in mixed pure cultures and in activated sludge. The detection limits of conventional FISH with Cy3-labeled probe EUB338-I were found to be 370 ± 45 16S rRNA molecules per cell for Escherichia coli hybridized on glass microscope slides and 1,400 ± 170 16S rRNA copies per E. coli cell in activated sludge. For CARD-FISH the values ranged from 8.9 ± 1.5 to 14 ± 2 and from 36 ± 6 to 54 ± 7 16S rRNA molecules per cell, respectively, indicating that the sensitivity of CARD-FISH was 26- to 41-fold higher than that of conventional FISH. These results suggest that optimized FISH protocols using oligonucleotide probes could be suitable for more recent applications of FISH (for example, to detect mRNA in situ in microbial cells).

scholarly journals Abundance and Phylogenetic Affiliation of Iron Reducers in Activated Sludge as Assessed by Fluorescence In Situ Hybridization and Microautoradiography

2002 ◽  
Vol 68 (9) ◽  
pp. 4629-4636 ◽  
Author(s):  
Jeppe Lund Nielsen ◽  
Stefan Juretschko ◽  
Michael Wagner ◽  
Per Halkjær Nielsen
Keyword(s):  
In Situ Hybridization ◽  
Activated Sludge ◽  
Fluorescence In Situ Hybridization ◽  
Most Probable Number ◽  
Probable Number ◽  
Iron Reducing Bacteria ◽  
Reducing Conditions ◽  
Phylogenetic Affiliation ◽  
Reducing Bacteria

ABSTRACT Microautoradiography (MAR) was used to enumerate acetate-consuming bacteria under Fe(III)-reducing conditions in activated sludge. This population is believed to consist of dissimilatory iron-reducing bacteria, because the applied incubation conditions and the use of specific inhibitors excluded consumption of radiolabeled acetate by other physiological groups such as sulfate reducers. By use of this approach, dissimilatory iron reducers were found in a concentration of 1.1 × 108 cells per ml, corresponding to approximately 3% of the total cell count as determined by DAPI (4′,6′-diamino-2-phenylindoledihydrochloride-dilactate) staining. The MAR enumeration method was compared to the traditional most-probable-number (MPN) method (FeOOH-MPN) and a modified MPN method, which contains Ferrozine directly within the MPN dilutions to determine the production of small amounts of ferrous iron (Ferrozine-MPN). The Ferrozine-MPN method yielded values 6 to 10 times higher than those obtained by the FeOOH-MPN method. Nevertheless, the MAR approach yielded counts that were 100 to 1,000 times higher than those obtained by the Ferrozine-MPN method. Specific in situ Fe(III) reduction rates per cell (enumerated by the MAR method) were calculated and found to be comparable to the respective rates for pure cultures of dissimilatory iron-reducing bacteria, suggesting that the new MAR method is most reliable. A combination of MAR and fluorescence in situ hybridization was used for phylogenetic characterization of the putative iron-reducing bacteria. All activated-sludge cells able to consume acetate under iron-reducing conditions were targeted by the bacterial oligonucleotide probe EUB338. Around 20% were identified as gamma Proteobacteria, and 10% were assigned to the delta subclass of Proteobacteria.

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