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.

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 FluorescenceIn SituHybridization (FISH) and Peptide Nucleic Acid Probe-Based FISH for Diagnosis of Q Fever Endocarditis and Vascular Infections

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Elsa Prudent ◽  
Hubert Lepidi ◽  
Emmanouil Angelakis ◽  
Didier Raoult
Keyword(s):  
Peptide Nucleic Acid ◽  
Q Fever ◽  
Immunohistochemical Analysis ◽  
Content Type ◽  
Peptide Nucleic Acid Probe ◽  
Vascular Infections ◽  
Pna Fish ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACTEndocarditis and vascular infections are common manifestations of persistent localized infection due toCoxiella burnetii, and recently, fluorescencein situhybridization (FISH) was proposed as an alternative tool for their diagnosis. In this study, we evaluated the efficiency of FISH in a series of valve and vascular samples infected byC. burnetii. We tested 23C. burnetii-positive valves and thrombus samples obtained from patients with Q fever endocarditis. Seven aneurysms and thrombus specimens were retrieved from patients with Q fever vascular infections. Samples were analyzed by culture, immunochemistry, and FISH with oligonucleotide and PNA probes targetingC. burnetii-specific 16S rRNA sequences. The immunohistochemical analysis was positive for five (17%) samples with significantly more copies ofC. burnetiiDNA than the negative ones (P= 0.02). FISH was positive for 13 (43%) samples and presented 43% and 40% sensitivity compared to that for quantitative PCR (qPCR) and culture, respectively. PNA FISH detectedC. burnetiiin 18 (60%) samples and presented 60% and 55% sensitivity compared to that for qPCR and culture, respectively. Immunohistochemistry had 38% and 28% sensitivity compared to that for FISH and PNA FISH, respectively. Samples found positive by both immunohistochemistry and PNA FISH contained significantly more copies ofC. burnetiiDNA than the negative ones (P= 0.03). Finally, PNA FISH was more sensitive than FISH (60% versus 43%, respectively) for the detection ofC. burnetii. We provide evidence that PNA FISH and FISH are important assays for the diagnosis ofC. burnetiiendocarditis and vascular infections.

Combining fluorescent in situ hybridization (fish) with cultivation and mathematical modeling to study population structure and function of ammonia-oxidizing bacteria in activated sludge

1998 ◽  
Vol 37 (4-5) ◽  
pp. 441-449 ◽  
Author(s):  
Michael Wagner ◽  
Daniel R. Noguera ◽  
Stefan Juretschko ◽  
Gabriele Rath ◽  
Hans-Peter Koops ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
In Situ Hybridization ◽  
Activated Sludge ◽  
Heterotrophic Bacteria ◽  
Sewage Treatment Plant ◽  
Laser Scanning Microscopy ◽  
Industrial Plant ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers

16S rRNA-targeted oligonucleotide probes for phylogenetically defined groups of autotrophic ammonia-oxidizing bacteria were used for analyzing the natural diversity of nitrifiers in an industrial sewage treatment plant receiving sewage with high ammonia concentrations. In this facility discontinuous aeration is used to allow for complete nitrification and denitrification. In situ hybridization revealed a yet undescribed diversity of ammonia oxidizers occurring in the plant. Surprisingly, the majority of the ammonia oxidizers were detected with probe combinations which indicate a close affiliation of these cells with Nitrosococcus mobilis. In addition, low numbers of ammonia-oxidizers related to the Nitrosomonas europaea - Nitrosomonas eutropha cluster were present. Interestingly, we also observed hybridization patterns which suggested the occurrence of a novel population of ammonia oxidizers. Confocal laser scanning microscopy revealed that all specifically stained ammonia oxidizers were clustered in microcolonies formed by rod-shaped bacteria. Combination of FISH and mathematical modeling was used to investigate diffusion limitation of ammonia and O2 within these aggregates. Model simulations suggest that mass transfer limitations inside the clusters are not as significant as the substrate limitations due to the activity of surrounding heterotrophic bacteria. To learn more about the ammonia-oxidizers of the industrial plant, we enriched and isolated ammonia-oxidizing bacteria from the activated sludge by combining classical cultivation techniques and FISH. Monitoring the isolates with the nested probe set allowed us to specifically identify those ammonia oxidizers which were found in situ to be numerically dominant. The phylogenetic relationship of these isolates determined by comparative 16S rDNA sequence analysis confirmed the affiliation suggested by FISH.

scholarly journals Investigation of an Acetate-Fed Denitrifying Microbial Community by Stable Isotope Probing, Full-Cycle rRNA Analysis, and Fluorescent In Situ Hybridization-Microautoradiography

2005 ◽  
Vol 71 (12) ◽  
pp. 8683-8691 ◽  
Author(s):  
Maneesha P. Ginige ◽  
Jürg Keller ◽  
Linda L. Blackall
Keyword(s):  
In Situ Hybridization ◽  
Stable Isotope ◽  
Activated Sludge ◽  
Fluorescent In Situ Hybridization ◽  
Batch Reactor ◽  
External Source ◽  
Stable Isotope Probing ◽  
Rrna Gene ◽  
The Impact

ABSTRACT The acetate-utilizing microbial consortium in a full-scale activated sludge process was investigated without prior enrichment using stable isotope probing (SIP). [13C]acetate was used in SIP to label the DNA of the denitrifiers. The [13C]DNA fraction that was extracted was subjected to a full-cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the 13C library were closely related to the bacterial families Comamonadaceae and Rhodocyclaceae in the class Betaproteobacteria. Seven oligonucleotide probes for use in fluorescent in situ hybridization (FISH) were designed to specifically target these clones. Application of these probes to the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated for 16 days revealed that there was a significant positive correlation between the CFDSBR denitrification rate and the relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH-microautoradiography demonstrated that the DEN581 and DEN124 probe-targeted cells that dominated the CFDSBR were capable of taking up [14C]acetate under anoxic conditions. Initially, DEN444 and DEN1454 probe-targeted bacteria also dominated the CFDSBR biomass, but eventually DEN581 and DEN124 probe-targeted bacteria were the dominant bacterial groups. All probe-targeted bacteria assessed in this study were denitrifiers capable of utilizing acetate as a source of carbon. The rapid increase in the number of organisms positively correlated with the immediate increase in denitrification rates observed by plant operators when acetate is used as an external source of carbon to enhance denitrification. We suggest that the impact of bacteria on activated sludge subjected to intermittent acetate supplementation should be assessed prior to the widespread use of acetate in the wastewater industry to enhance denitrification.

Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in biofilms from wastewater treatment plants: diversity and in situ physiology

2000 ◽  
Vol 41 (4-5) ◽  
pp. 85-90 ◽  
Author(s):  
H. Daims ◽  
P.H. Nielsen ◽  
J.L. Nielsen ◽  
S. Juretschko ◽  
M. Wagner
Keyword(s):  
Wastewater Treatment ◽  
In Situ Hybridization ◽  
16S Rrna ◽  
Fluorescent In Situ Hybridization ◽  
Wastewater Treatment Plants ◽  
Combined Application ◽  
Fundamental Understanding ◽  
Unculturable Bacteria ◽  
Rrna Sequences

The frequency and distribution of putatively nitrite-oxidizing, Nitrospira- like bacteria in nitrifying biofilms from two reactors receiving wastewater with different ammonia and salt concentrations were observed by fluorescent in situ hybridization. For this purpose, new 16S rRNA-directed oligonucleotide probes targeting the bacterial phylum Nitrospira and the three main lineages within this phylum were developed and evaluated. The diversity of Nitrospira-like bacteria in the reactors was additionally investigated by retrieval and comparative analysis of full 16S rRNA sequences from the biofilms. We found that, despite of the differences in the influent composition, Nitrospira-like bacteria form dominant populations in both reactors. In addition, first insights into the physiology of these still unculturable bacteria were obtained by the incubation of active biofilm samples with radioactively labeled substrates followed by the combined application of fluorescent in situ hybridization and microautoradiography. The results are discussed in consideration of the frequently observed dominance of Nitrospira-like bacteria in nitrifying bioreactors. Consequently, high priority should be assigned to future studies on the ecology and physiology of these organisms in order to increase our fundamental understanding of nitrogen cycling and to enable knowledge-driven future improvements of nitrifying wastewater treatment plants.

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.

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