Eubacterial 16S-rDNA amplicon profiling: a rapid technique for comparison and differentiation of heterotrophic plate count communities from drinking water

Farnleitner, Andreas H.; Zibuschka, F.; Burtscher, Martina M.; Lindner, Gerhard; Reischer, Georg H.; Mach, Robert L.

doi:10.1016/j.ijfoodmicro.2003.08.014

Cited by 22 publications

(19 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The short V3 region was selected because of the low tendency to form chimeric molecules using beat beating procedures but still enabling high population resolution capacity (Farnleitner et al, 2001;Farnleitner et al, 2004;Hoefel et al, 2005). In addition, a GC-rich sequence (5´-CGC CCG CCG CGC GCG GCG GGC GGG GCG GGG GCA CGG GGG G-3´) was attached to the 5´end of the forward primer for subsequent DGGE analysis (Muyzer et al, 1993;Rusin et al, 1997).…”

Section: Dna Extraction Pcr Amplification and Dgge Analysismentioning

confidence: 99%

“…Information about HPC population structure and taxon composition has mainly been recovered by pure culture-based procedures (e.g. Reasoner, 1990;Edberg et al, 1997;Farnleitner et al, 2004). Such an approach gives a high taxonomic resolution but often demands a practically unfeasible number of pure cultures to cover spatial and temporal distribution system variability (Edberg et al, 1997;Kalmbach et al, 1997;Norton and LeChevallier, 2000).…”

Section: Introductionmentioning

confidence: 99%

“…Molecular biological techniques offer new high-resolution and high-throughput tools to further investigate HPC populations and furthermore to compare them to the respective in situ bacterial communities (VivesRego et al, 2000;Dewettinck et al, 2001;Farnleitner et al, 2004;Hoefel et al, 2005;Martiny et al, 2005, Farnleitner et al 2005b. Preliminary investigations suggested that HPC population dynamics in a drinking water distribution system can be resolved by a polymerase chain reaction denaturing gradient gel electrophoresis (PCR DGGE) approach in respect of sampling location and sampling time.…”

mentioning

confidence: 99%

“…Preliminary investigations suggested that HPC population dynamics in a drinking water distribution system can be resolved by a polymerase chain reaction denaturing gradient gel electrophoresis (PCR DGGE) approach in respect of sampling location and sampling time. Moreover, 16S rRNA gene amplicon profiles recovered from HPC populations can easily be compared with corresponding profiles recovered from the in situ bacterial community (Farnleitner et al, 2004). However, it is of critical importance to consider the achievable methodical discrimination capacity and reproducibility of the PCR DGGE approach when higher numbers of samples are to be analysed (Farnleitner et al, 2004;Fromin et al, 2002).…”

mentioning

confidence: 99%

“…Moreover, 16S rRNA gene amplicon profiles recovered from HPC populations can easily be compared with corresponding profiles recovered from the in situ bacterial community (Farnleitner et al, 2004). However, it is of critical importance to consider the achievable methodical discrimination capacity and reproducibility of the PCR DGGE approach when higher numbers of samples are to be analysed (Farnleitner et al, 2004;Fromin et al, 2002). The aim of this study was the detailed investigation of the HPC vs. the in situ bacterial community structure in water samples recovered from different sampling points in a drinking water distribution system by the above-mentioned 16S rRNA gene PCR DGGE profiling approach.…”

mentioning

confidence: 99%

See 4 more Smart Citations

Heterotrophic plate count vs. <i>in situ</i> bacterial 16S rRNA gene amplicon profiles from drinking water reveal completely different communities with distinct spatial and temporal allocations in a distribution net

Burtscher¹,

Zibuschka²,

Mach³

et al. 2009

WSA

View full text Add to dashboard Cite

Heterotrophic plate count using ISO 6222 agar (HPC) vs. in situ bacterial (DF) community structure from corresponding samples of a drinking water distribution system were investigated by 16S rRNA gene-based polymerase chain reaction denaturing gradient gel electrophoresis (PCR DGGE) profiling. The investigation regime covered 10 different sampling locations and 2 points in time (t1, t2). In order to ensure accurate and reproducible 16S rRNA gene profile analysis, rigorous methodical evaluation and standardisation procedures were undertaken (DGGE optimisation, replication of PCR, multiplelane standardisation, representative sampling volume determination, application of multiple similarity coefficients). The reproducibility level of the profile analysis was determined to be ≥ 90% similarity. Two completely different communities were revealed from HPC vs. DF as indicated by DGGE analysis and sequencing. HPC populations could be identified as ubiquitously occurring cultivable copiotrophic microbes, whilst most DF sequences could be allocated to sequences from microorganisms found in oligotrophic aquatic environments. Spatial-and temporal-based 16S rRNA gene amplicon profile analysis from recovered communities further revealed contrasting results. As proven by Jackknife simulations, DF profiles remarkably corresponded to sampling time, whereas HPC profiles revealed spatial associations within the distribution system. Recovered data demonstrate that cultivation based HPC vs. direct cell-based investigations can result in completely different results if used for monitoring purposes in distribution systems.

show abstract

Section: Dna Extraction Pcr Amplification and Dgge Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Heterotrophic plate count vs. <i>in situ</i> bacterial 16S rRNA gene amplicon profiles from drinking water reveal completely different communities with distinct spatial and temporal allocations in a distribution net

Burtscher¹,

Zibuschka²,

Mach³

et al. 2009

WSA

View full text Add to dashboard Cite

show abstract

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management

et al. 2018

Self Cite

View full text Add to dashboard Cite

Over the past 15 years, pioneering interdisciplinary research has been performed on the microbiology of hydrogeologically well‐defined alpine karst springs located in the Northern Calcareous Alps (NCA) of Austria. This article gives an overview on these activities and links them to other relevant research. Results from the NCA springs and comparable sites revealed that spring water harbors abundant natural microbial communities even in aquifers with high water residence times and the absence of immediate surface influence. Apparently, hydrogeology has a strong impact on the concentration and size of the observed microbes, and total cell counts (TCC) were suggested as a useful means for spring type classification. Measurement of microbial activities at the NCA springs revealed extremely low microbial growth rates in the base flow component of the studied spring waters and indicated the importance of biofilm‐associated microbial activities in sediments and on rock surfaces. Based on genetic analysis, the autochthonous microbial endokarst community (AMEC) versus transient microbial endokarst community (TMEC) concept was proposed for the NCA springs, and further details within this overview article are given to prompt its future evaluation. In this regard, it is well known that during high‐discharge situations, surface‐associated microbes and nutrients such as from soil habitats or human settlements—potentially containing fecal‐associated pathogens as the most critical water‐quality hazard—may be rapidly flushed into vulnerable karst aquifers. In this context, a framework for the comprehensive analysis of microbial pollution has been proposed for the NCA springs to support the sustainable management of drinking water safety in accordance with recent World Health Organization guidelines. Near‐real‐time online water quality monitoring, microbial source tracking (MST) and MST‐guided quantitative microbial‐risk assessment (QMRA) are examples of the proposed analytical tools. In this context, this overview article also provides a short introduction to recently emerging methodologies in microbiological diagnostics to support reading for the practitioner. Finally, the article highlights future research and development needs.This article is categorized under: Engineering Water > Water, Health, and SanitationScience of Water > Water ExtremesWater and Life > Nature of Freshwater Ecosystems

show abstract

Library-Independent Bacterial Source Tracking Methods

Wuertz

Wang²,

Reischer³

et al. 2011

Microbial Source Tracking: Methods, Applications, and Case Studies

View full text Add to dashboard Cite

Eubacterial 16S-rDNA amplicon profiling: a rapid technique for comparison and differentiation of heterotrophic plate count communities from drinking water

Cited by 22 publications

References 24 publications

Heterotrophic plate count vs. <i>in situ</i> bacterial 16S rRNA gene amplicon profiles from drinking water reveal completely different communities with distinct spatial and temporal allocations in a distribution net

Heterotrophic plate count vs. <i>in situ</i> bacterial 16S rRNA gene amplicon profiles from drinking water reveal completely different communities with distinct spatial and temporal allocations in a distribution net

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management

Library-Independent Bacterial Source Tracking Methods

Contact Info

Product

Resources

About