ArticleApplied and environmental microbiology2001
Application of the 5' fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments.
Article in Applied and environmental microbiology, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
32 citing papers in PubMed, 187 citations in OpenAlex.
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- Effect of Contact Area and Shape of Anode Current Collectors on Bacterial Community Structure in Microbial Fuel Cells.Molecules (Basel, Switzerland) · 2022Article
- Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments.Microbes and environments · 2017Article
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- Re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degraders.FEMS microbiology ecology · 2015Article
- Comparison of droplet digital PCR and quantitative real-time PCR inBiotechnology reports (Amsterdam, Netherlands) · 2014Article
- Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents.The ISME journal · 2013Article
- Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities.AMB Express · 2012Article
- Ecophysiology of Fe-cycling bacteria in acidic sediments.Applied and environmental microbiology · 2010Article
- Bacterial capture by peptide-mimetic oligoacyllysine surfaces.Applied and environmental microbiology · 2010Article
- Accurate quantification of microorganisms in PCR-inhibiting environmental DNA extracts by a novel internal amplification control approach using Biotrove OpenArrays.Applied and environmental microbiology · 2009Article
- Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies.PloS one · 2009Article
- Changes in microbial community composition and geochemistry during uranium and technetium bioimmobilization.Applied and environmental microbiology · 2007Article
- Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments.Applied and environmental microbiology · 2007Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study, we report on the development of quantitative PCR and reverse transcriptase PCR assays for the 16S rRNA of Geobacter spp. and identify key issues related to fluorogenic reporter systems for nucleic acid analyses of sediments. The lower detection limit of each assay was 5 to 50 fg of genomic DNA or < or =2 pg of 16S rRNA. TaqMan PCR spectral traces from uncontaminated, amended aquifer sediments were significantly lower (P < 0.0002) than traces for the external standard curve. We also observed a similar, significant decrease in mean quencher emissions for undiluted extracts relative to those for diluted extracts (P < 0.0001). If PCR enumerations were based solely upon the undiluted sample eluant, the TaqMan assay generated an inaccurate result even though the threshold cycle (C(t)) measurements were precise and reproducible in the sediment extracts. Assay accuracy was significantly improved by employing a system of replicate dilutions and replicate analyses for both DNA and rRNA quantitation. Our results clearly demonstrate that fluorescence quenching and autofluorescence can significantly affect TaqMan PCR enumeration accuracy, with subsequent implications for the design and implementation of TaqMan PCR to sediments and related environmental samples.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.