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Sampling DNA from the rhizosphere of Brassica napus to investigate rhizobacterial community structure

Lookup NU author(s): Dr Andrew Macrae, Dr David Rimmer, Professor Anthony O'Donnell

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Abstract

We have compared, using DNA analysis, the classical 'pull and shake' method for sampling rhizosphere soil with a model rhizosphere system in which the soil was sampled at increasing distances (0.5 mm) from the root mat of Brassica napus. These studies showed that more DNA was extracted from the soil slices closest to the roots. Whilst the gradient in DNA recovered cannot be attributed solely to differences in microbial biomass, it clearly illustrates the lack of spatial resolution characteristic of the 'pull and shake' method of sampling from the rhizosphere. The DNA-rich fraction (rhizosphere soil) was compared with bulk soil DNA by PCR using actinomycete 16S rDNA primers and 16S rDNA sequencing. Phylogenetic analyses of 16S rDNA sequences showed that these primers were not specific for actinomycetes but also amplified Gram positive low G+C bacterial sequences. Comparative 16S rDNA analysis of these sequences showed an enrichment for Gram positive low G+C bacteria in the rhizosphere of Brassica napus.

Publication metadata

Author(s): Macrae A, Lucon CMM, Rimmer DL, O'Donnell AG

Publication type: Article

Publication status: Published

Journal: Plant and Soil

Year: 2001

Volume: 233

Issue: 2

Pages: 223-230

Print publication date: 01/01/2001

ISSN (print): 0032-079X

ISSN (electronic): 1573-5036

Publisher: Springer Netherlands

URL: http://dx.doi.org/10.1023/A:1010397304969

DOI: 10.1023/A:1010397304969

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