Literature DB >> 9451814

Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis.

F von Wintzingerode1, U B Göbel, E Stackebrandt.   

Abstract

After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs for ecological studies it seems necessary to summarize reported pitfalls of this approach which will most likely lead to an erroneous description on the microbial diversity of a given habitat. The following article will cover specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis.

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Year:  1997        PMID: 9451814     DOI: 10.1111/j.1574-6976.1997.tb00351.x

Source DB:  PubMed          Journal:  FEMS Microbiol Rev        ISSN: 0168-6445            Impact factor:   16.408


  469 in total

1.  Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms.

Authors:  M Derakshani; T Lukow; W Liesack
Journal:  Appl Environ Microbiol       Date:  2001-02       Impact factor: 4.792

2.  rrndb: the Ribosomal RNA Operon Copy Number Database.

Authors:  J A Klappenbach; P R Saxman; J R Cole; T M Schmidt
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

3.  Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA.

Authors:  B M Duineveld; G A Kowalchuk; A Keijzer; J D van Elsas; J A van Veen
Journal:  Appl Environ Microbiol       Date:  2001-01       Impact factor: 4.792

4.  Development and application of a most-probable-number-pcr assay to quantify flagellate populations in soil samples.

Authors:  L Fredslund; F Ekelund; C S Jacobsen; K Johnsen
Journal:  Appl Environ Microbiol       Date:  2001-04       Impact factor: 4.792

5.  Spatial heterogeneity of bacterial populations along an environmental gradient at a shallow submarine hydrothermal vent near Milos Island (Greece).

Authors:  S M Sievert; T Brinkhoff; G Muyzer; W Ziebis; J Kuever
Journal:  Appl Environ Microbiol       Date:  1999-09       Impact factor: 4.792

6.  Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities.

Authors:  M M Fisher; E W Triplett
Journal:  Appl Environ Microbiol       Date:  1999-10       Impact factor: 4.792

7.  Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input.

Authors:  J C Cho; S J Kim
Journal:  Appl Environ Microbiol       Date:  2000-03       Impact factor: 4.792

8.  In situ analysis of sulfate-reducing bacteria related to Desulfocapsa thiozymogenes in the chemocline of meromictic Lake Cadagno (Switzerland).

Authors:  M Tonolla; A Demarta; S Peduzzi; D Hahn; R Peduzzi
Journal:  Appl Environ Microbiol       Date:  2000-02       Impact factor: 4.792

9.  Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis.

Authors:  E O Casamayor; H Schäfer; L Bañeras; C Pedrós-Alió; G Muyzer
Journal:  Appl Environ Microbiol       Date:  2000-02       Impact factor: 4.792

10.  Peptide nucleic acid-mediated PCR clamping as a useful supplement in the determination of microbial diversity.

Authors:  F von Wintzingerode; O Landt; A Ehrlich; U B Göbel
Journal:  Appl Environ Microbiol       Date:  2000-02       Impact factor: 4.792

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