Environmental Microbiology (2007) 9, 2260-2273

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Rodrigo Costa, Newton C.M. Gomes, Ellen Krögerrecklenfort, Katja Opelt, Gabriele Berg and Kornelia Smalla (2007)
Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses
Environmental Microbiology 9 (9), 2260-2273
Abstract: The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA 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 Pseudomonas in bulk and rhizosphere soils. Pseudomonas-specific gacA 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 Pseudomonas isolates antagonistic towards V. dahliae was shown to be genotypically conserved, to carry the phlD biosynthetic locus (involved in the biosynthesis of 2,4-diacetylphloroglucinol - 2,4-DAPG), and to correspond to a dominant and highly frequent Pseudomonas 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 Pseudomonas fluorescens phylogenetic lineage and showed closest relatedness to P. fluorescens strain F113 (97% gacA gene sequence identity in 492-bp sequences), a biocontrol agent and 2,4-DAPG producer. Partial gacA gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed Pseudomonas gacA gene clusters as revealed by phylogenetic analysis.
(The abstract is excluded from the Creative Commons licence and has been copied with permission by the publisher.)
Link to article at publishers website
Database assignments for author(s): Gabriele Berg

Research topic(s) for pests/diseases/weeds:
biocontrol - natural enemies
Research topic(s) for beneficials or antagonists:
molecular biology - genes

Pest and/or beneficial records:

Beneficial Pest/Disease/Weed Crop/Product Country Quarant.

Verticillium dahliae Rape/canola (Brassica napus)
Verticillium dahliae Strawberry (Fragaria)
Pseudomonas fluorescens (antagonist) Verticillium dahliae Strawberry (Fragaria)