Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots

The rhizosphere of Trifolium repens and Lolium perenne was divided into three fractions: the bulk soil; the soil adhering to the roots; and the washed roots (rhizoplane and endorhizosphere). After isolation and purification of DNA from these fractions, 16S rDNA was amplified by PCR and cloned to obtain a collection of 16S rRNA genes representative of the bacterial communities of these three fractions. The cloned 16S rRNA genes ware then partially sequenced and analysed by a molecular phylogenetic approach. Our data show a high diversity in the bulk soil, which is dominated by clones related to Gram-positive, Cytophaga-Flexibacter-Bacteroides, Proteobacteria, and Holophaga-Acidobacterium groups. The ubiquity of members of the Holophaga-Acidobacterium group, which is composed of sequences of yet,uncultivated microorganisms, is confirmed. The plant roots have a selective effect towards the gamma Proteobacteria, to the detriment of the Gram-positive and the Holophaga-Acidobacterium bacteria, leading to a dominance of Pseudomonas. This work shows by a culture independent approach that the phylogenetic diversity decreases in the proximity of plant roots. (C) 1999 Elsevier Science B.V. All rights reserved.