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Environ Microbiol Rep. 2010 Apr;2(2):281-8. doi: 10.1111/j.1758-2229.2009.00117.x. Epub 2010 Jan 5.

Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil.

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1
INRA, UMR1136 INRA-Nancy Université'Interactions Arbres-Microorganismes', IFR 110, Centre INRA de Nancy, 54280 Champenoux, France.

Abstract

Several reports have highlighted that forest soil samples are more phylum-rich than agricultural soil samples. However, little is known about the structure and richness of the bacterial communities in forest soil. Using high-throughput next generation 454 pyrosequencing, we deeply investigated the diversity of bacterial communities colonizing the oak rhizosphere niche and the surrounding soil. From three spatially independent soil samples, we obtained over 300 000 partial 16S rRNA gene sequences. The most abundant bacterial groups were the Acidobacteria, Proteobacteria and unclassified bacteria. Multifactorial analysis of the relative proportions of the different phyla revealed a net differentiation of the bacterial communities present in the rhizosphere and soil environments, suggesting an oak rhizosphere effect. Significantly more β-, γ- and unclassified Proteobacteria inhabited the rhizosphere when compared with the surrounding soil. Conversely, significantly more unclassified bacteria were detected in the bulk soil than in the rhizosphere, demonstrating that the soil remains a challenging reservoir of complexity. This work increases our understanding of the niche effect on bacterial diversity and on the rare phylogenetic groups inhabiting the soil.

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