Environmental Microbiology, September 2007, Vol.9(9), pp.2260-2273
The community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen ) were assessed. The use of a new PCR‐DGGE system, designed to target ‐specific gene fragments in environmental DNA, circumvented common biases of 16S rRNA gene‐based DGGE analyses and proved to be a reliable tool to unravel the diversity of uncultured in bulk and rhizosphere soils. ‐specific fingerprints of total‐community (TC) rhizosphere DNA were surprisingly diverse, plant‐specific and differed markedly from those of the corresponding bulk soils. By combining multiple culture‐dependent and independent surveys, a group of isolates antagonistic towards was shown to be genotypically conserved, to carry the biosynthetic locus (involved in the biosynthesis of 2,4‐diacetylphloroglucinol – 2,4‐DAPG), and to correspond to a dominant and highly frequent population in the rhizosphere of field‐grown strawberries planted at three sites in Germany which have different land use histories. This population belongs to the phylogenetic lineage and showed closest relatedness to strain F113 (97% gene sequence identity in 492‐bp sequences), a biocontrol agent and 2,4‐DAPG producer. Partial gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed gene clusters as revealed by phylogenetic analysis.
Ecosystem ; Anti-Infective Agents -- Metabolism ; Bacterial Proteins -- Genetics ; Plant Roots -- Microbiology ; Pseudomonas -- Genetics;