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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOLOGY AND MANAGEMENT OF SOILBORNE DISEASES OF HORTICULTURAL CROPS Title: Genomic diversity of Pseudomonas spp. isolated from aerial or root surfaces of plants

Authors
item Loper, Joyce
item Hassan, Karl -
item Davis, Edward
item Mavrodi, Dmitri -
item Lim, Chee Kent -
item Liam, Elbourne -

Submitted to: Pseudomonas
Publication Type: Abstract Only
Publication Acceptance Date: August 29, 2011
Publication Date: September 4, 2011
Citation: Loper, J.E., Hassan, K.H., Davis, E.W., Mavrodi, D., Lim, C., Liam, E. 2011. Genomic diversity of Pseudomonas spp. isolated from aerial or root surfaces of plants. Pseudomonas 2011. 13th International Conference abstract book. Pg. 10.

Technical Abstract: Among the diverse strains of Pseudomonas fluorescens and Pseudomonas chlororaphis inhabiting plant surfaces are those that protect plants from infection by pathogens. To explore the diversity of these bacteria, we derived genomic sequences of seven strains that suppress plant disease. Along with three previously-sequenced strains of P. fluorescens (Pf-5, Pf0-1 and SBW25), these bacteria share ca. 2800 core genes, with each strain having 300 to 900 genes not found in the other genomes. Phylogenetic analysis of the ten strains defined three distinct clades. Within each clade, the strains share 75 to 90% of their proteomes, with a smaller proportion, typically 60 to 70%, shared between strains in different clades. Bioinformatic analysis revealed genes with potential roles in the biology of each strain and its interactions on plant surfaces, including previously unrecognized genes for the production of toxins, antibiotics, and siderophores. Many orphan gene clusters containing non-ribosomal peptide synthetases or other genes characteristic of secondary metabolite biosynthesis are present and provide avenues for the future discovery of novel natural products. Orphan gene clusters expressed under the control of global regulators such as GacA have been identified in Pf-5, demonstrating the value of global-regulator-based genome mining to decipher the secondary metabolome of Pseudomonas spp. We are also employing microarrays to gain a holistic view of genome expression profiles of Pf-5 living on seed surfaces, where it interacts with seed-infecting fungi and Oomycetes to affect biocontrol. These approaches are providing new insights into the metabolic capacity of this bacterium, its activity on plant surfaces, and its interactions with plants, insects and other microorganisms.

Last Modified: 10/20/2014
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