Detection of filamentous and nitrifying bacteria in activated sludge with 16S rRNA probes

Waarde, J.J. van der; Geurkink, Bert; Henssen, Maurice J. C.; Heijnen, Guido

doi:10.2166/wst.1998.0699

Cited by 5 publications

(2 citation statements)

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“…16S rRNA are available, namely 21N and TNI (Wagner et al, 1994), and G1B, G2M, G3M and G123T (Kanagawa et al, 2000). However, probe 21N, designed to detect members of Type 021N, has been shown to hybridise only with a limited number of strains (Nielsen et al, 1998;Pernelle et al, 1998;van der Waarde et al, 1998;Kanagawa et al, 2000); other probes have been effectively used for the in situ detection of different Thiothrix groups for instance probes G1B, G2M and G3M detect subgroups of Eikelboom Type 021N, and probe TNI is specific for the T. nivea group. However, probes have not been developed for species such as T. fructosivorans or "T. ramosa", representatives of these taxa form an independent phylogenetic clade within the Thiothrix 16S rDNA tree (Howarth et al, 1999;Kanagawa et al, 2000).…”

Section: Introductionmentioning

confidence: 99%

Application of oligonucleotide probes for the detection of Thiothrix spp. in activated sludge plants treating paper and board mill wastes

Kim

Goodfellow

Kelly

et al. 2002

Water Science and Technology

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Filamentous bacteria belonging to the genus Thiothrix were detected in activated sludge samples using the fluorescent in situ hybridisation (FISH) technique. A 16S rRNA-targeted oligonucleotide probe was developed for the detection of members of the T. fructosivorans group, and the performance of probe TNI for the detection of Thiothrix nivea group was enhanced by using an unlabeled competitor. A set of 5 probes covering all phylogenetic groups of Thiothrix were used to examine samples taken from selected activated sludge plants treating paper and board mill wastes. Members of the T. eikelboomii group formed the predominant filamentous bacterial population in plants experiencing poor sludge settleability, whereas members of the T. nivea group were commonly found but not dominantly in the remaining plants. Members of the T. fructosivorans group were not detected at any significant level in any of the samples. The distribution of the main Thiothrix types remained unchanged throughout the investigation period. It was evident that mixed populations of Thiothrix spp. were present in all activated sludge samples investigated, the observed differences were in the relative abundance of the various groups. These findings were supported by the results obtained using conventional microscopy.

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Section: Introductionmentioning

confidence: 99%

Application of oligonucleotide probes for the detection of Thiothrix spp. in activated sludge plants treating paper and board mill wastes

Kim

Goodfellow

Kelly

et al. 2002

Water Science and Technology

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“…Accurately quantifying the abundance of microorganisms is important in monitoring the proper functioning of a wastewater treatment plant that relies on the activated sludge system. For instance, the problem of sludge bulking in wastewater plant has a strong correlation to the high abundance of filamentous bacteria (De Los Reyes et al, 1998;Van Der Waarde et al, 1998). Using quantitative FISH to track the early stages of filamentous bacteria growth can help to circumvent the problem of sludge bulking.…”

Section: Fluorescence In Situ Hybridisation (Fish)mentioning

confidence: 99%

Novel method of probe design for characterising unclassified microbial taxa in wastewater

Tan¹

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for their tremendous help with the flow cytometry work. The flow cytometry work would not have gone smoothly without their invaluable expertise and advice. Prof Federico Lauro had proposed the use of FISH-FACS tool for the enrichment of the unclassified bacteria and I appreciate his input. The sequencing team in SCELSE has helped with the sequencing aspect of my thesis. Special thanks go to Dr Daniela Moses whom I have consulted on the type of sequencing platform to use and Mr Alexander Putra who has efficiently handled my samples for sequencing.Mr Larry Liew was instrumental in obtaining sludge samples from Ulu Pandan Water Reclamation Plant, and I will like to thank him for his time and effort.Dr Xie Chao was the author of the RiboTagger software and he suggested the design of FISH probes from RiboTags. Mr Wesley Goi rendered advice in the updating of the SILVA database in the RiboTagger software. Dr Xiang Hui Liu was instrumental in attempting genomic binning using other software that was not covered in this thesis. Recovery of draft genomes from enriched samples was influenced through discussions with Dr Rohan Williams.My sincerest appreciation goes towards Dr Muhammud Hafiz, Dr Martin Tay, Dr Rasmus Kirkegaard and Miss Krithika Arumugam for their kind patience in imparting basic bioinformatics knowledge to me. The thesis would not have been a success without the acquisition of these essential skills.

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Quantification of an Eikelboom type 021N bulking event with fluorescence in situ hybridization and real-time PCR

Vervaeren

Wilde²,

Matthys

et al. 2005

Appl Microbiol Biotechnol

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Primers targeting 16S rRNA genes were designed to detect and quantify Eikelboom type 021N organisms by real-time PCR. Eikelboom type 021N filamentous bulking was induced in a laboratory-scale sequencing batch reactor and the evolution of Eikelboom type 021N 16S rRNA and 16S rRNA genes was monitored. A significant correlation was found between the sludge volume index and the amount of these filamentous organisms present in the sludge (r (2)=94.6%, n=10, P<0.01), as measured by real-time PCR. The amount of Eikelboom type 021N 16S rRNA genes increased by a factor of 21 during the experiment, while the 16S rRNA increased by a factor of 33. Moreover, Eikelboom type 021N 16S rRNA increased with increased feeding frequency. It was observed that the RNA:DNA ratio peaked before the sludge volume index increased. In parallel, a fluorescence in situ hybridization study indicated a factor of four increase in the length of Eikelboom type 021N filaments, due to a factor of two increase in both length and number of Eikelboom type 021N filaments. Further, an increase in the fraction of filaments extending outside the activated sludge flocs was observed (19-55%). Monitoring of 16S rRNA genes and 16S rRNA of Eikelboom type 021N was shown to be valuable in evaluating activated sludge settling characteristics; and measuring RNA:DNA ratios may be used as an early warning tool for sludge bulking.

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Detection of filamentous and nitrifying bacteria in activated sludge with 16S rRNA probes

Cited by 5 publications

References 0 publications

Application of oligonucleotide probes for the detection of Thiothrix spp. in activated sludge plants treating paper and board mill wastes

Application of oligonucleotide probes for the detection of Thiothrix spp. in activated sludge plants treating paper and board mill wastes

Novel method of probe design for characterising unclassified microbial taxa in wastewater

Quantification of an Eikelboom type 021N bulking event with fluorescence in situ hybridization and real-time PCR

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