The Nature and Application of Biocontrol Microbes III: Pseudomonas spp. The Genomic Sequence of Pseudomonas fluorescens Pf-5: Insights Into Biological Control

Loper, J. E., Kobayashi, D. Y., and Paulsen, I. T. 2007. The genomic sequence of Pseudomonas fluorescens Pf-5: Insights into biological control. Phytopathology 97:233-238. 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 iron from a wide array of siderophores produced by soil microorganisms. 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 and pathogenicity factors found in plant pathogens. Recently, the genomic sequence of the biological control agent Pseudomonas fluorescens Pf-5 was completed (47). The genomic sequence of Pf-5 is the first published for a biological control agent for plant disease. In this symposium paper, we briefly review the literature describing Pf-5, describe aspects of the genomic sequence that are particularly relevant to the capacity of Pf-5 to suppress plant disease, and provide our perspectives on how the genomic sequence data are advancing knowledge of biological control. Plant disease suppression by P. fluorescens Pf-5. Pf-5 was isolated from the cotton rhizosphere and first described for its capacity to suppress seedling diseases of cotton caused by Rhizoctonia solani (17) and Pythium ultimum (18). R. solani and Pythium ultimum are widespread pathogens with broad host ranges that constrain food and fiber production worldwide (34). The pathogens are the major causes of seed rot and seedling death of cotton and many other crop plants. Since Pf-5 was first described, it has been shown to suppress these pathogens on a variety of plant hosts including cucumber, pea, and maize (26; M. D. Henkels and J. E. Loper, unpublished data). Furthermore, Pf-5 suppresses a number of other soilborne or residue-borne fungal pathogens. For example, when inoculated onto wheat straw residue, Pf-5 suppresses ascocarp formation by the tan spot pathogen of wheat, Pyrenophora tritici-repentis, thereby decreasing inoculum available for infection of the subsequent wheat crop (49). On turfgrass, Pf-5 suppresses dollar spot caused by Sclerotinia homoeocarpa and leaf spot caused by Drechslera poae, which are destructive and widespread diseases affecting golf courses, home lawns, and amenity turf areas (56). Pf-5 also suppresses Fusarium crown and root rot of tomato, caused by Fusarium oxysporum f. sp. radicis-lycopersici (61), and seed piece decay of potato caused by the bacterial pathogen Erwinia carotovora (70). Because of the wide variety of diseases it suppresses, Pf-5 is well recognized by biological control researchers around the world, and commonly is included as a reference strain in studies of biocontrol agents (21,25,38,61,70). Secondary metabolite production by Pf-5. Pf-5 produces at least seven secondary metabolites, including pyrrolnitrin (17), pyoluteorin (18), 2,4-diacetylphloroglucinol (44), hydrogen cyanide (26), the siderophores pyochelin (or related compounds) and pyoverdine, and a lipopeptide (H. Gross, J. E. Loper, and W. Gerwick, unpublished data). In addition, two putative metabolites are assumed to exist due to the presence of biosynthetic gene clusters in the Pf-5 genome (47). Five of these secondary metabolites are known to be produced by P. fluorescens strain CHA0, a rhizosphere bacterium isolated in Switzerland whose biological control characteristics, mechanisms of disease suppression, and regulatory networks controlling secondary metabolite production have been extensively characterized (14). Some other biological control strains produce a subset of metabolites produced by Pf-5, and their broad spectrum antibiotic activities have been reviewed elsewhere (52). Regulation of secondary metabolite production. Production of secondary metabolites by strains CHA0 or Pf-5 is controlled by complex regulatory networks that respond to environmental and density-dependent signals and are coupled to the physiological status of the bacterium. Loci that regulate the production of antiCorresponding author: J. E. Loper; E-mail address: [email protected] DOI: 10.1094 / PHYTO-97-2-0233 This article is in the public domain and not copyrightable. It may be freely reprinted with customary crediting of the source. The American Phytopathological