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Title: Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5

item MAVRODI, DMITRI - Washington State University
item Loper, Joyce
item PAULSEN, IAN - Macquarie University
item Thomashow, Linda

Submitted to: BMC Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/20/2008
Publication Date: 1/13/2009
Citation: Mavrodi, D.V., Loper, J.E., Paulsen, I.T., Thomashow, L.S. 2009. Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5. BMC Microbiology, 9: ART No. 8.

Interpretive Summary: Root diseases caused by soilborne pathogens are major yield-limiting factors in the production of food, fiber and ornamental crops. Trends in agriculture toward greater sustainability and less dependence on synthetic fungicides have created a need for more ecologically sound methods of disease control. Biological control, which exploits the natural antagonistic activity of certain root-colonizing bacteria against fungal pathogens, is one such approach. In this study, the DNA sequence of one well-known biocontrol agent, strain Pf-5, was examined for features that could provide insight into its ability to compete and survive in the microbiologically complex and dynamic rhizosphere environment. The study revealed that the genome of strain Pf-5 contains at least eight large DNA segments that have have evolved following introduction via genetic exchange with related plant-associated bacteria. These segments resemble those found in related bacteria, but they also carry genes that could affect the survival of the strain in nature. The results of the study indicate that strain Pf-5 has exchanged genetic information with other plant-associated bacteria, both beneficial and pathogenic, throughout its evolution, that no genes associated with pathogenicity have been retained, and that some of the genes acquired through genetic exchange may be advantageous to survival in the rhizosphere habitat.

Technical Abstract: Background: Pseudomonas fluorescens Pf-5 is a plant-associated bacterium that inhabits the rhizosphere of a wide variety of plant species and and produces secondary metabolites suppressive of fungal and oomycete plant pathogens. The Pf-5 genome is rich in features consistent with its commensal lifestyle, and its sequence has revealed attributes associated with the strain's ability to compete and survive in the dynamic and microbiologically complex rhizosphere habitat. In this study, we analyzed mobile genetic elements of the Pf-5 genome in an effort to identify determinants that might contribute to Pf-5's ability to adapt to changing environmental conditions and/or colonize new ecological niches. Results: Sequence analyses revealed that the genome of Pf-5 is devoid of transposons and IS elements and that mobile genetic elements (MGEs) are represented by prophages and genomic islands that collectively span over 260 kb. The prophages include an F-pyocin-like prophage 01, a chimeric prophage 03, a lambdoid prophage 06, and decaying prophages 02, 04 and 05 with reduced size and/or complexity. The genomic islands are represented by a 115-kb integrative conjugative element (ICE) PFGI-1, which shares plasmid replication, recombination, and conjugative transfer genes with those from ICEs found in other Pseudomonas spp., and PFGI-2, which resembles a portion of pathogenicity islands in the genomes of the plant pathogens Pseudomonas syringae and P. viridiflava. Almost all of the MGEs in the Pf-5 genome are associated with phage-like integrase genes and are integrated into tRNA genes. Conclusion: Comparative analyses reveal that MGEs found in Pf-5 are subject to extensive recombination and have evolved in part via exchange of genetic material with other Pseudomonas spp. having commensal or pathogenic relationships with plants and animals. Although prophages and genomic islands from Pf-5 exhibit similarity to MGEs found in other Pseudomonas spp., they also carry a number of putative niche-specific genes that could affect the survival of P. fluorescens Pf-5 in natural habitats. Most notable are a similar to 35-kb segment of "cargo" genes in genomic island PFGI-1 and bacteriocin genes associated with prophages 1 and 4.