Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2006
Publication Date: 2/1/2007
Citation: Loper, J.E., Kobayashi, D., Paulsen, I. The genomic sequence of Pseudomonas fluorescens Pf-5: insights into biological control. Phytopathology. 97(2):233-238. Interpretive Summary: This article provides new analysis of the genomic sequence of the biological control agent Pseudomonas fluorescens Pf-5. The analysis focuses on genes that contribute to the suppression of plant diseases by this biological control agent, including genes specifying the production of anti-fungal compounds that are toxic to plant pathogens. It also discusses properties of the biological control agent that are evident from the genomic sequence, but were not recognized previously. These include the capacity to grow on diverse substrates, to utilize iron from many different sources, and to compete with other microorganisms present in the soil. Knowledge of the genomic sequence of Pf-5 will be invaluable to scientists studying this and related bacteria and is already being used to advance knowledge of biological control for the benefit of agriculture.
Technical Abstract: The complete sequence of the 7.07 Mb genome of the biological control agent Pseudomonas fluorescens Pf-5 is now available, providing a new opportunity to advance knowledge of biological control through genomics. P. fluorescens Pf-5 is a rhizosphere bacterium that suppresses seedling emergence diseases and produces a spectrum of antibiotics toxic to plant pathogenic fungi and Oomycetes. In addition to six known secondary metabolites produced by Pf-5, three novel secondary metabolite biosynthesis gene clusters identified in the genome could also contribute to biological control. The genomic sequence provides numerous clues as to mechanisms used by the bacterium to survive in the spermosphere and rhizosphere. These features include broad catabolic and transport capabilities for utilizing seed and root exudates, an expanded collection of efflux systems for defense against environmental stress and microbial competition, and the presence of 45 outer membrane receptors that should allow for the uptake of a wide array of siderophores produced by soil microrganisms. As expected for a bacterium with a large genome that lives in a rapidly changing environment, Pf-5 has an extensive collection of regulatory genes, only some of which have been characterized for their roles in regulation of secondary metabolite production or biological control. Consistent with its commensal lifestyle, Pf-5 appears to lack a number of virulence factors found in plant pathogens.