Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene‐based analyses

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.

Spatio-temporal dynamics of bacterial communities associated with two plant species differing in organic acid secretion: A one-year microcosm study on lupin and wheat

“…This is in line with previous reports that demonstrated the influence of plant species on global communities (Westover et al, 1997;Marschner et al, 2004Marschner et al, , 2005Phillips et al, 2006) as well as on specific phylogenetic or functional groups of rhizosphere bacteria (Costa et al, 2006(Costa et al, , 2007Patra et al, 2006). Surprisingly, there was no effect of plant species in rhizosphere soil communities, in contrast to what was observed by Jossi et al (2006), where the effect of plant species was also clearly visible in the soil communities.…”

Most of the Dominant Members of Amphibian Skin Bacterial Communities Can Be Readily Cultured

“…In addition, B. dendrobatidis zoospores exhibit chemotaxis away from several of these compounds (79). Therefore, dominant bacteria that produce secondary metabolites with antifungal properties may also play important roles in host defense, as demonstrated previously in a plant rhizosphere microbial community (80). Specifically, Costa et al (80) demonstrated that the most dominant members exhibited antagonistic properties against a plant fungal pathogen.…”

Rhizosphere Communities of Genetically Modified Zeaxanthin-Accumulating Potato Plants and Their Parent Cultivar Differ Less than Those of Different Potato Cultivars

“…To test the hypothesis that the effect of genetic modification of the GM lines on rhizosphere communities was less pronounced than the effect of genotype differences among cultivars, the similarities of the DGGE fingerprints of all plant genotypes to that of 'Baltica' were compared. Analysis of the median similarities of all bacterial fingerprints for samples obtained from both Roggenstein (in 2005 and2007) and Oberviehhausen (in 2006) revealed that the GM lines were, on average, more similar to the parent 'Baltica' than all other cultivars were (Fig. 1A).…”