Activated Sludge and Biofilms: Molecular Techniques for Determining Community Composition

Loy, Alexander; Daims, Holger; Wagner, Michael

doi:10.1002/0471263397.env218

Cited by 13 publications

(35 citation statements)

References 130 publications

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“…It may have been possible to observe a larger number of the total microbiota by FISH with the use of additional probes specific for archaea and other organisms. However, as was previously observed in other studies, detection of all unknown organisms contained in the sample may be impossible by existing FISH methods due to the relatively high detection limit of approximately 10 3 -10 4 target cells per ml (Loy et al, 2002).…”

Section: Cirrhipathes Lutkenimentioning

confidence: 68%

The diversity of the bacterial communities associated with the azooxanthellate hexacoral Cirrhipathes lutkeni

Santiago-Vázquez

Brück

et al. 2007

The ISME Journal

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This study examined the symbiotic microbiota of the hexacoral Cirrhipathes lutkeni using traditional plate culture, fluorescence in situ hybridization (FISH) and 16S rDNA characterization. FISH counts for the whole coral (holobiont) showed a major presence of c-Proteobacteria (22%) and Actinobacteria (19%), followed by a-Proteobacteria (14%), Firmicutes (9%), Cytophaga-Flavobacterium (7%), b-Proteobacteria (6%) and Chloroflexi (2%). In contrast to the diversity observed by FISH, plate cultures were found to be selective for c-Proteobacteria (22 cultures) with the exception of an Actinobacterium. The methods employed in this study detected 76% of all microbes estimated by DAPI staining of C. lutkeni homogenates. The absence of zooxanthellae in this particular hexacoral was confirmed by PCR and spectrophotometry using fresh tissue isolated from the holobiont. This is the first study describing the microbial associations of shallow-water hexacorallia, which opens further insight into coral microbial ecology and may enhance the search for novel natural products in the near future.

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Section: Cirrhipathes Lutkenimentioning

confidence: 68%

The diversity of the bacterial communities associated with the azooxanthellate hexacoral Cirrhipathes lutkeni

Santiago-Vázquez

Brück

et al. 2007

The ISME Journal

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“…This apparent probing anomaly could be due to problems with either ALF1b or GAM42a. ALF1b is known to be highly unspecific for Alphaproteobacteria (Loy et al 2002) and GAM42a binding inconsistencies have previously been reported (Buchholz-Cleven et al 1997, Yeates et al 2003. Full length insert sequencing of the Alphaproteobacteria and Gammaproteobacteria 16S rDNA clones obtained in our library will facilitate the design of specific probes to determine the identity and abundance of coral-associated Alphaproteobacteria or Gammaproteobacteria, and to clarify their in situ spatial arrangements and global distribution.…”

Section: Microbial Analysismentioning

confidence: 72%

Dynamics of a temperature-related coral disease outbreak

Jones¹,

Bowyer²,

Høegh-Guldberg³

et al. 2004

Mar. Ecol. Prog. Ser.

127

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“…Two clones, each representing a single-sequence OTU, were identified as chimeras and excluded from further analyses. Based on sequence similarity (97% threshold), the remaining 16S rRNA clone sequences could be grouped in the same OTUs as suggested by RFLP analysis (Table 3) (23,30). The homologous coverage curve indicated that the 56 clones covered most of the expected richness in the pooled libraries B, C, and D if a sequence similarity threshold of up to 99% is applied (Fig.…”

Section: Resultsmentioning

confidence: 91%

Diversity of Bacteria Growing in Natural Mineral Water after Bottling

Loy

Beisker²,

Meier

2005

Appl Environ Microbiol

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Bacterial growth occurs in noncarbonated natural mineral waters a few days after filling and storage at room temperature, a phenomenon known for more than 40 years. Using the full-cycle rRNA approach, we monitored the development of the planktonic bacterial community in a noncarbonated natural mineral water after bottling. Seven 16S rRNA gene libraries, comprising 108 clones in total, were constructed from water samples taken at various days after bottling and from two different bottle sizes. Sequence analyses identified 11 operational taxonomic units (OTUs), all but one affiliated with the betaproteobacterial order Burkholderiales (6 OTUs) or the class Alphaproteobacteria (4 OTUs). Fluorescence in situ hybridization (FISH) was applied in combination with DAPI (4,6-diamidino-2-phenylindole) staining, viability staining, and microscopic counting to quantitatively monitor changes in bacterial community composition. A growth curve similar to that of a bacterium grown in a batch culture was recorded. In contrast to the current perception that Gammaproteobacteria are the most important bacterial components of natural mineral water in bottles, Betaproteobacteria dominated the growing bacterial community and accounted for 80 to 98% of all bacteria detected by FISH in the late-exponential and stationary-growth phases. Using previously published and newly designed genusspecific probes, members of the betaproteobacterial genera Hydrogenophaga, Aquabacterium, and Polaromonas were found to constitute a significant proportion of the bacterial flora (21 to 86% of all bacteria detected by FISH). For the first time, key genera responsible for bacterial growth in a natural mineral water were identified by applying molecular cultivation-independent techniques.

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Activated Sludge and Biofilms: Molecular Techniques for Determining Community Composition

Abstract: Methods for Microbial Diversity Analysis in Wastewater Treatment Plants (wwtps) General Microbial Diversity in Wastewater Treatment Plants Functional Groups of Microorganisms in Treatment Plants

Cited by 13 publications

References 130 publications

The diversity of the bacterial communities associated with the azooxanthellate hexacoral Cirrhipathes lutkeni

The diversity of the bacterial communities associated with the azooxanthellate hexacoral Cirrhipathes lutkeni

Dynamics of a temperature-related coral disease outbreak

Diversity of Bacteria Growing in Natural Mineral Water after Bottling

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