Genotypic and Phenotypic Diversity of phlD -Containing Pseudomonas Strains Isolated from the Rhizosphere of Wheat

Abstract

Production of 2,4-diacetylphloroglucinol (2,4-DAPG) in the rhizosphere by strains of fluorescent Pseudomonas spp. results in the suppression of root diseases caused by certain fungal plant pathogens. In this study, fluorescent Pseudomonas strains containing phlD, which is directly involved in the biosynthesis of 2,4-DAPG, were isolated from the rhizosphere of wheat grown in soils from wheat-growing regions of the United States and The Netherlands. To assess the genotypic and phenotypic diversity present in this collection, 138 isolates were compared to 4 previously described 2,4-DAPG producers. Thirteen distinct genotypes, one of which represented over 30% of the isolates, were differentiated by whole-cell BOX-PCR. Representatives of this group were isolated from eight different soils taken from four different geographic locations. ERIC-PCR gave similar results overall, differentiating 15 distinct genotypes among all of the isolates. In most cases, a single genotype predominated among isolates obtained from each soil. Thirty isolates, representing all of the distinct genotypes and geographic locations, were further characterized. Restriction analysis of amplified 16S rRNA gene sequences revealed only three distinct phylogenetic groups, one of which accounted for 87% of the isolates. Phenotypic analyses based on carbon source utilization profiles revealed that all of the strains utilized 49 substrates and were unable to grow on 12 others. Individually, strains could utilize about two-thirds of the 95 substrates present in Biolog SF-N plates. Multivariate analyses of utilization profiles revealed phenotypic groupings consistent with those defined by the genotypic analyses.

Biocontrol agents applied individually and in combination for suppression of soilborne diseases of cucumber

“…The related strains B. cepacia BC-1, B. ambifaria BC-F, and B. cepacia BC-2 strongly inhibited, slightly inhibited, and had no effect, respectively, on populations of T. virens GL21 in cucumber rhizosphere. There is considerable genotypic diversity among certain related biocontrol agents and these microbes have been shown to vary with regard to antibiotic production and other phenotypes (Keel et al, 1996;Sharifi-Tehrani et al, 1998;McSpadden-Gardener et al, 2000;Raaijmakers and Weller, 2001). It is possible that differences such as these are responsible for differences in compatibility among closely related strains seen here.…”

Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt

“…decline soils (Raaijmakers et al, 1997;Raaijmakers and Weller, 1998;McSpadden-Gardener et al, 2000;Weller et al, 2002;Souza et al, 2003a) and for soils suppressive to black root rot of tobacco (Wang et al, 2001;Ramette et al, 2003Ramette et al, , 2006Frapolli et al, 2007). This strategy encompasses a comparative analysis of the densities, diversity and activity of antibiotic-producing pseudomonads in two soils chosen for their opposite level of suppressiveness to Fusarium wilt: one being suppressive (Châteaur-enard) and the other being conducive (Carquefou).…”

“…Also the antibiotic 2,4-diacetylphloroglucinol (DAPG) has substantial activity against pathogenic F. oxysporum (Schouten et al, 2004), and populations of DAPG-producing pseudomonads were highly enriched in a soil naturally suppressive to Fusarium wilt of peas (Landa et al, 2002). Following similar molecular-based approaches used to unravel the role of antibiosis in take-all decline soils (Raaijmakers et al, 1997;Raaijmakers and Weller, 1998;McSpadden-Gardener et al, 2000;Weller et al, 2002;Souza et al, 2003a) and in soils suppressive to black root rot of tobacco (Wang et al, 2001;Ramette et al, 2003Ramette et al, , 2006Frapolli et al, 2007), the objectives of this study were to determine the frequency, diversity and biocontrol activity of DAPG (phlD þ )-and phenazine (phzC þ )-producing pseudomonads in the Fusarium-wilt suppressive soil from Châteaurenard (France) in comparison with the conducive soil of Carquefou (France). The results showed that densities of phlD þ populations were not significantly different between the two soils but that their genotypic diversity differed significantly.…”

Exploiting Genotypic Diversity of 2,4-Diacetylphloroglucinol-Producing Pseudomonas spp.: Characterization of Superior Root-Colonizing P. fluorescens Strain Q8r1-96

“…Root-associated fluorescent Pseudomonas spp., which produce the antibiotic DAPG, are highly enriched in various TAD soils (37) and are key components of the natural biological control that operates in these soils (38,39). Identification and analysis of the genotypic diversity of DAPG producers from wheatgrowing regions in the United States and The Netherlands have been conducted recently using a combination of phenotypic and PCR-based molecular techniques (31). A significant amount of diversity occurs within this group of fluorescent pseudomonads isolated from wheat rhizosphere.…”