The genomic sequence of Pseudomonas fluorescens Pf-5: Insights into biological control

The rhizosphere bacterium P. fluorescens Pf-5 suppresses seedling emergence diseases and produces a spectrum of antibiotics toxic to plant pathogenic fungi and Oomycetes. The complete 7.1 Mb genome of Pf-5 was sequenced recently by The Institute for Genomics Research. In addition to six known secondary metabolites produced by Pf-5, three novel secondary metabolite biosynthesis gene clusters were identified that may contribute to biological control. Various features were identified that contribute to the bacterium's capacity to colonize the rhizosphere, including broad catabolic and transport capabilities for utilizing root exudates and the presence of 28 outer membrane receptors for siderophore iron complexes produced by many different microorganisms. We found no evidence for a Type III secretion system or the biosynthesis of toxins found in phytopathogenic Pseudomonas spp. Analysis of the locations of over 1000 copies of repeat sequences in the Pf-5 genome suggests that six secondary metabolite gene clusters, seven phage regions and a mobile genomic island were acquired relatively recently by the bacterium.