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Literature DB >> 11097934

Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition.

R I Griffiths¹, A S Whiteley, A G O'Donnell, M J Bailey.

Abstract

A rapid protocol for the extraction of total nucleic acids from environmental samples is described. The method facilitates concomitant assessment of microbial 16S rRNA diversity by PCR and reverse transcription-PCR amplification from a single extraction. Denaturing gradient gel electrophoresis microbial community analysis differentiated the active component (rRNA derived) from the total bacterial diversity (ribosomal DNA derived) down the horizons of an established grassland soil.

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Year: 2000 PMID： 11097934 PMCID： PMC92488 DOI： 10.1128/AEM.66.12.5488-5491.2000

Source DB: PubMed Journal: Appl Environ Microbiol ISSN： 0099-2240 Impact factor: 4.792

12 in total

1. Quantification of bias related to the extraction of DNA directly from soils.

Authors: A Frostegård; S Courtois; V Ramisse; S Clerc; D Bernillon; F Le Gall; P Jeannin; X Nesme; P Simonet
Journal: Appl Environ Microbiol Date: 1999-12 Impact factor: 4.792

2. Bacterial community structure and physiological state within an industrial phenol bioremediation system.

Authors: A S Whiteley; M J Bailey
Journal: Appl Environ Microbiol Date: 2000-06 Impact factor: 4.792

3. Stable-isotope probing as a tool in microbial ecology.

Authors: S Radajewski; P Ineson; N R Parekh; J C Murrell
Journal: Nature Date: 2000-02-10 Impact factor: 49.962

4. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures.

Authors: A E McCaig; L A Glover; J I Prosser
Journal: Appl Environ Microbiol Date: 1999-04 Impact factor: 4.792

5. Direct extraction and purification of rRNA for ecological studies.

Authors: M A Moran; V L Torsvik; T Torsvik; R E Hodson
Journal: Appl Environ Microbiol Date: 1993-03 Impact factor: 4.792

6. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands).

Authors: A Felske; A Wolterink; R Van Lis; A D Akkermans
Journal: Appl Environ Microbiol Date: 1998-03 Impact factor: 4.792

7. Microbial Evolution, Diversity, and Ecology: A Decade of Ribosomal RNA Analysis of Uncultivated Microorganisms

Authors:
Journal: Microb Ecol Date: 1998-01 Impact factor: 4.552

8. Creating a ribonuclease-free environment.

Authors: D D Blumberg
Journal: Methods Enzymol Date: 1987 Impact factor: 1.600

9. Direct ribosome isolation from soil to extract bacterial rRNA for community analysis.

Authors: A Felske; B Engelen; U Nübel; H Backhaus
Journal: Appl Environ Microbiol Date: 1996-11 Impact factor: 4.792

10. Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid RNA extraction procedure and RT-PCR.

Authors: Ian P Miskin; Paul Farrimond; Ian M Head
Journal: Microbiology Date: 1999-08 Impact factor: 2.777

345 in total

1. Community structure of ammonia-oxidizing bacteria within anoxic marine sediments.

Authors: Thomas E Freitag; James I Prosser
Journal: Appl Environ Microbiol Date: 2003-03 Impact factor: 4.792

2. Effect of sulfadiazine on abundance and diversity of denitrifying bacteria by determining nirK and nirS genes in two arable soils.

Authors: Kristina Kleineidam; Shilpi Sharma; Anja Kotzerke; Holger Heuer; Sören Thiele-Bruhn; Kornelia Smalla; Berndt-Michael Wilke; Michael Schloter
Journal: Microb Ecol Date: 2010-06-08 Impact factor: 4.552

3. Effect of sulfadiazine-contaminated pig manure on the abundances of genes and transcripts involved in nitrogen transformation in the root-rhizosphere complexes of maize and clover.

Authors: Julien Ollivier; Kristina Kleineidam; Rüdiger Reichel; Sören Thiele-Bruhn; Anja Kotzerke; Reimo Kindler; Berndt-Michael Wilke; Michael Schloter
Journal: Appl Environ Microbiol Date: 2010-10-22 Impact factor: 4.792

4. Spatial analysis of archaeal community structure in grassland soil.

Authors: Graeme W Nicol; L Anne Glover; James I Prosser
Journal: Appl Environ Microbiol Date: 2003-12 Impact factor: 4.792

5. Physiological and community responses of established grassland bacterial populations to water stress.

Authors: Robert I Griffiths; Andrew S Whiteley; Anthony G O'Donnell; Mark J Bailey
Journal: Appl Environ Microbiol Date: 2003-12 Impact factor: 4.792

6. Molecular analysis of a bacterial chitinolytic community in an upland pasture.

Authors: A C Metcalfe; M Krsek; G W Gooday; J I Prosser; E M H Wellington
Journal: Appl Environ Microbiol Date: 2002-10 Impact factor: 4.792

7. Differences between betaproteobacterial ammonia-oxidizing communities in marine sediments and those in overlying water.

Authors: Thomas E Freitag; James I Prosser
Journal: Appl Environ Microbiol Date: 2004-06 Impact factor: 4.792

8. Impact of soil drying-rewetting stress on microbial communities and activities and on degradation of two crop protection products.

Authors: Manuel Pesaro; Gilles Nicollier; Josef Zeyer; Franco Widmer
Journal: Appl Environ Microbiol Date: 2004-05 Impact factor: 4.792

9. The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil.

Authors: B S Griffiths; H L Kuan; K Ritz; L A Glover; A E McCaig; C Fenwick
Journal: Microb Ecol Date: 2004-01 Impact factor: 4.552

10. 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales".

Authors: Alexander Loy; Claudia Schulz; Sebastian Lücker; Andreas Schöpfer-Wendels; Kilian Stoecker; Christian Baranyi; Angelika Lehner; Michael Wagner
Journal: Appl Environ Microbiol Date: 2005-03 Impact factor: 4.792