Strains of Pseudomonas that produce antimicrobial metabolites and control soilborne plant disease... more Strains of Pseudomonas that produce antimicrobial metabolites and control soilborne plant diseases have often been isolated from soils defined as disease-suppressive, i.e., soils, in which specific plant pathogens are present, but plants show no or reduced disease symptoms. Moreover, it is assumed that pseudomonads producing antimicrobial compounds such as 2,4-diacetylphloroglucinol (DAPG) or phenazines (PHZ) contribute to the specific disease resistance of suppressive soils. However, pseudomonads producing antimicrobial metabolites are also present in soils that are conducive to disease. Currently, it is still unknown whether and to which extent the abundance of antimicrobials-producing pseudomonads is related to the general disease resistance of common agricultural soils. Moreover, virtually nothing is known about the conditions under which pseudomonads express antimicrobial genes in agricultural field soils. We present here results of the first side-by-side comparison of 10 repre...
We recently discovered large populations of phenazine-producing (Phz+) Pseudomonas strains and co... more We recently discovered large populations of phenazine-producing (Phz+) Pseudomonas strains and concentrations of the antibiotic phenazine-1-carboxylic acid (PCA) of up to 1.6 µg g-1 of root plus rhizosphere soil on roots of non-irrigated cereals grown over more than a million hectares of the Columbia Plateau of central Washington State. To test the hypothesis that these Phz+populations are enriched specifically under dryland conditions, we established adjacent irrigated and nonirrigated plots of wheat at the Washington State University Dryland Research Station at Lind, Washington in March of 2011. We monitored population densities and rhizosphere colonization frequencies of indigenous Phz+ bacteria, as well as rhizosphere concentrations of PCA, at two-week intervals until harvest four months later. With or without irrigation, Phz+ bacterial populations increased until mid-June, and then populations in the irrigated plots declined significantly as compared to those in the nonirrigate...
Fluorescent Pseudomonas isolated from the rhizosphere of diverse plants have been studied as bioc... more Fluorescent Pseudomonas isolated from the rhizosphere of diverse plants have been studied as biocontrol agents against soilborne pathogens worldwide. These bacteria are capable of exerting different mechanisms of plant growth promotion and protection, including the production of antibiotics such as phenazine (Phz) derivatives, 2,4-diacetylphloroglucinol (2,4-DAPG), pyrrolnitrin (Prn) and pyoluteorin (Plt). These four compounds are broadly active against several plant pathogens, including fungi, oomycetes, bacteria and nematodes. In addition to providing biocontrol activity, Phz-producing Pseudomonas outcompete indigenous microflora in the soil and their population density is regulated by a quorum sensing mechanism. 2,4-DAPG producers are responsible for the natural disease suppressiveness of some soils in the USA and Europe. Different genotypes were identified among 2,4-DAPG producing Pseudomonas showing the heterogeneity of this group. Some of these genotypes demonstrate specificit...
Rhizoctonia bare patch and root rot of wheat, caused by Rhizoctonia solani AG-8, develops as dist... more Rhizoctonia bare patch and root rot of wheat, caused by Rhizoctonia solani AG-8, develops as distinct patches of stunted plants, and limits the yield of direct-seeded (no-till) wheat in the Pacific Northwest USA. At a long-term cropping systems study near Ritzville, WA, a decline in Rhizoctonia patch was observed over an 11-year period. Bacterial communities from bulk and rhizosphere soil of plants from inside of patches, outside of patches, and recovered patches, were analyzed by pyrosequencing with primers designed to 16S rRNA. Taxa in the genera of Acidobacteria and Gemmatimonas were in higher frequency in the rhizosphere of healthy plants outside of patches, compared to diseased plants from inside of patches. Dyella and Acidobacteria Gp7 had higher frequencies in recovered patches. Chitinophaga, Pedobacter, Oxalobacteriaceae (Duganella and Massilia) and Chyseobacterium were higher in the rhizosphere of diseased plants from inside of patches. For selected taxa, trends were valida...
Genetic resistance to root diseases of plants is rare, and agriculture controls these diseases th... more Genetic resistance to root diseases of plants is rare, and agriculture controls these diseases through practices such as crop rotation and soil fumigation. However, plants have evolved a strategy of stimulating and supporting specific groups of antagonistic rhizosphere microorganisms as a defense against diseases caused by soilborne pathogens. Antibiotic production has a significant role in plant defense by many of these rhizobacteria. Information now is available about the genetics, biochemistry, and regulation of synthesis of some of the most commonly-produced antibiotics. Similarly, many genes that contribute to the ability of these bacteria to colonize roots have been identified. Studies of naturally suppressive soils have provided evidence of preferential interactions between plant hosts and protective populations, revealing the existence of functional diversity among otherwise almost indistinguishable strains. Here, we consider how this knowledge can be applied to aid in the selection of more effective biological control agents and the development of recombinant strains that may overcome impediments to inoculum preparation, formulation, and cost that currently limit commercial acceptance of highly promising candidate strains.
Certain strains of the rhizosphere bacterium Pseudomonas fluorescens contain the phenazine biosyn... more Certain strains of the rhizosphere bacterium Pseudomonas fluorescens contain the phenazine biosynthesis operon (phzABCDEFG) and produce redox-active phenazine antibiotics that suppress a wide variety of soilborne plant pathogens. In 2007 and 2008, we isolated 412 phenazine-producing (Phz(+)) fluorescent Pseudomonas strains from roots of dryland wheat and barley grown in the low-precipitation region (<350 mm annual precipitation) of central Washington State. Based on results of BOX-PCR genomic fingerprinting analysis, these isolates, as well as the model biocontrol Phz(+) strain P. fluorescens 2-79, were assigned to 31 distinct genotypes separated into four clusters. All of the isolates exhibited high 16S rDNA sequence similarity to members of the P. fluorescens species complex including Pseudomonas orientalis, Pseudomonas gessardii, Pseudomonas libanensis, and Pseudomonas synxantha. Further recA-based sequence analyses revealed that the majority of new Phz(+) isolates (386 of 413) form a clade distinctly separated from P. fluorescens 2-79. Analysis of phzF alleles, however, revealed that the majority of those isolates (280 of 386) carried phenazine biosynthesis genes similar to those of P. fluorescens 2-79. phzF-based analyses also revealed that phenazine genes were under purifying selection and showed evidence of intracluster recombination. Phenotypic analyses using Biolog substrate utilization and observations of phenazine-1-carboxylic acid production showed considerable variability amongst members of all four clusters. Biodiversity indices indicated significant differences in diversity and evenness between the sampled sites. In summary, this study revealed a genotypically and phenotypically diverse group of phenazine producers with a population structure not seen before in indigenous rhizosphere-inhabiting Phz(+) Pseudomonas spp.
Strains of Pseudomonas that produce antimicrobial metabolites and control soilborne plant disease... more Strains of Pseudomonas that produce antimicrobial metabolites and control soilborne plant diseases have often been isolated from soils defined as disease-suppressive, i.e., soils, in which specific plant pathogens are present, but plants show no or reduced disease symptoms. Moreover, it is assumed that pseudomonads producing antimicrobial compounds such as 2,4-diacetylphloroglucinol (DAPG) or phenazines (PHZ) contribute to the specific disease resistance of suppressive soils. However, pseudomonads producing antimicrobial metabolites are also present in soils that are conducive to disease. Currently, it is still unknown whether and to which extent the abundance of antimicrobials-producing pseudomonads is related to the general disease resistance of common agricultural soils. Moreover, virtually nothing is known about the conditions under which pseudomonads express antimicrobial genes in agricultural field soils. We present here results of the first side-by-side comparison of 10 repre...
We recently discovered large populations of phenazine-producing (Phz+) Pseudomonas strains and co... more We recently discovered large populations of phenazine-producing (Phz+) Pseudomonas strains and concentrations of the antibiotic phenazine-1-carboxylic acid (PCA) of up to 1.6 µg g-1 of root plus rhizosphere soil on roots of non-irrigated cereals grown over more than a million hectares of the Columbia Plateau of central Washington State. To test the hypothesis that these Phz+populations are enriched specifically under dryland conditions, we established adjacent irrigated and nonirrigated plots of wheat at the Washington State University Dryland Research Station at Lind, Washington in March of 2011. We monitored population densities and rhizosphere colonization frequencies of indigenous Phz+ bacteria, as well as rhizosphere concentrations of PCA, at two-week intervals until harvest four months later. With or without irrigation, Phz+ bacterial populations increased until mid-June, and then populations in the irrigated plots declined significantly as compared to those in the nonirrigate...
Fluorescent Pseudomonas isolated from the rhizosphere of diverse plants have been studied as bioc... more Fluorescent Pseudomonas isolated from the rhizosphere of diverse plants have been studied as biocontrol agents against soilborne pathogens worldwide. These bacteria are capable of exerting different mechanisms of plant growth promotion and protection, including the production of antibiotics such as phenazine (Phz) derivatives, 2,4-diacetylphloroglucinol (2,4-DAPG), pyrrolnitrin (Prn) and pyoluteorin (Plt). These four compounds are broadly active against several plant pathogens, including fungi, oomycetes, bacteria and nematodes. In addition to providing biocontrol activity, Phz-producing Pseudomonas outcompete indigenous microflora in the soil and their population density is regulated by a quorum sensing mechanism. 2,4-DAPG producers are responsible for the natural disease suppressiveness of some soils in the USA and Europe. Different genotypes were identified among 2,4-DAPG producing Pseudomonas showing the heterogeneity of this group. Some of these genotypes demonstrate specificit...
Rhizoctonia bare patch and root rot of wheat, caused by Rhizoctonia solani AG-8, develops as dist... more Rhizoctonia bare patch and root rot of wheat, caused by Rhizoctonia solani AG-8, develops as distinct patches of stunted plants, and limits the yield of direct-seeded (no-till) wheat in the Pacific Northwest USA. At a long-term cropping systems study near Ritzville, WA, a decline in Rhizoctonia patch was observed over an 11-year period. Bacterial communities from bulk and rhizosphere soil of plants from inside of patches, outside of patches, and recovered patches, were analyzed by pyrosequencing with primers designed to 16S rRNA. Taxa in the genera of Acidobacteria and Gemmatimonas were in higher frequency in the rhizosphere of healthy plants outside of patches, compared to diseased plants from inside of patches. Dyella and Acidobacteria Gp7 had higher frequencies in recovered patches. Chitinophaga, Pedobacter, Oxalobacteriaceae (Duganella and Massilia) and Chyseobacterium were higher in the rhizosphere of diseased plants from inside of patches. For selected taxa, trends were valida...
Genetic resistance to root diseases of plants is rare, and agriculture controls these diseases th... more Genetic resistance to root diseases of plants is rare, and agriculture controls these diseases through practices such as crop rotation and soil fumigation. However, plants have evolved a strategy of stimulating and supporting specific groups of antagonistic rhizosphere microorganisms as a defense against diseases caused by soilborne pathogens. Antibiotic production has a significant role in plant defense by many of these rhizobacteria. Information now is available about the genetics, biochemistry, and regulation of synthesis of some of the most commonly-produced antibiotics. Similarly, many genes that contribute to the ability of these bacteria to colonize roots have been identified. Studies of naturally suppressive soils have provided evidence of preferential interactions between plant hosts and protective populations, revealing the existence of functional diversity among otherwise almost indistinguishable strains. Here, we consider how this knowledge can be applied to aid in the selection of more effective biological control agents and the development of recombinant strains that may overcome impediments to inoculum preparation, formulation, and cost that currently limit commercial acceptance of highly promising candidate strains.
Certain strains of the rhizosphere bacterium Pseudomonas fluorescens contain the phenazine biosyn... more Certain strains of the rhizosphere bacterium Pseudomonas fluorescens contain the phenazine biosynthesis operon (phzABCDEFG) and produce redox-active phenazine antibiotics that suppress a wide variety of soilborne plant pathogens. In 2007 and 2008, we isolated 412 phenazine-producing (Phz(+)) fluorescent Pseudomonas strains from roots of dryland wheat and barley grown in the low-precipitation region (<350 mm annual precipitation) of central Washington State. Based on results of BOX-PCR genomic fingerprinting analysis, these isolates, as well as the model biocontrol Phz(+) strain P. fluorescens 2-79, were assigned to 31 distinct genotypes separated into four clusters. All of the isolates exhibited high 16S rDNA sequence similarity to members of the P. fluorescens species complex including Pseudomonas orientalis, Pseudomonas gessardii, Pseudomonas libanensis, and Pseudomonas synxantha. Further recA-based sequence analyses revealed that the majority of new Phz(+) isolates (386 of 413) form a clade distinctly separated from P. fluorescens 2-79. Analysis of phzF alleles, however, revealed that the majority of those isolates (280 of 386) carried phenazine biosynthesis genes similar to those of P. fluorescens 2-79. phzF-based analyses also revealed that phenazine genes were under purifying selection and showed evidence of intracluster recombination. Phenotypic analyses using Biolog substrate utilization and observations of phenazine-1-carboxylic acid production showed considerable variability amongst members of all four clusters. Biodiversity indices indicated significant differences in diversity and evenness between the sampled sites. In summary, this study revealed a genotypically and phenotypically diverse group of phenazine producers with a population structure not seen before in indigenous rhizosphere-inhabiting Phz(+) Pseudomonas spp.
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