Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Mark W. Silby, Ana M. Cerdeño-Tárraga, Georgios S. Vernikos, Stephen R. Giddens, Robert W. Jackson, Gail M. Preston, Xue-Xian Zhang, Christina D. Moon, Stefanie M. Gehrig, Scott A. C. Godfrey, Christopher G. Knight, Jacob G. Malone, Zena Robinson, Andrew J. Spiers, Simon Harris, Gregory L. Challis, Alice M Yaxley, David Harris, Kathy Seeger, Lee MurphySimon Rutter, Rob Squares, Michael A. Quail, Elizabeth Saunders, Konstantinos Mavromatis, Thomas S. Brettin, Stephen D. Bentley, Joanne Hothersall, Elton Stephens, Christopher M. Thomas, Julian Parkhill, Stuart B. Levy, Paul B. Rainey, Nicholas R. Thomson

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Abstract

Background: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plantinducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.
Original languageEnglish
Article numberR51
Number of pages16
JournalGenome Biology
Volume10
DOIs
Publication statusPublished - May 2009

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Silby, M. W., Cerdeño-Tárraga, A. M., Vernikos, G. S., Giddens, S. R., Jackson, R. W., Preston, G. M., Zhang, X-X., Moon, C. D., Gehrig, S. M., Godfrey, S. A. C., Knight, C. G., Malone, J. G., Robinson, Z., Spiers, A. J., Harris, S., Challis, G. L., Yaxley, A. M., Harris, D., Seeger, K., ... Thomson, N. R. (2009). Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology, 10, [R51]. https://doi.org/10.1186/gb-2009-10-5-r51