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

Mark W Silby1* email, Ana M Cerdeño-Tárraga2* email, Georgios S Vernikos2* email, Stephen R Giddens3 email, Robert W Jackson3,4 email, Gail M Preston3 email, Xue-Xian Zhang5 email, Christina D Moon3,12 email, Stefanie M Gehrig3 email, Scott AC Godfrey3,13 email, Christopher G Knight3,14 email, Jacob G Malone3,15 email, Zena Robinson3 email, Andrew J Spiers3,16 email, Simon Harris2 email, Gregory L Challis6 email, Alice M Yaxley7 email, David Harris2 email, Kathy Seeger2 email, Lee Murphy2 email, Simon Rutter2 email, Rob Squares2 email, Michael A Quail2 email, Elizabeth Saunders8 email, Konstantinos Mavromatis9 email, Thomas S Brettin8 email, Stephen D Bentley2 email, Joanne Hothersall10 email, Elton Stephens10 email, Christopher M Thomas10 email, Julian Parkhill2 email, Stuart B Levy1 email, Paul B Rainey5,11 email and Nicholas R Thomson2 email

1  Centre for Adaptation Genetics and Drug Resistance and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA

2  Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

3  Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK

4  School of Biological Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, UK

5  New Zealand Institute for Advanced Study, Massey University, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand

6  Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK

7  Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK

8  DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

9  Genome Biology Program, Department of Energy's Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

10  Department of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK

11  Allan Wilson Centre for Molecular Ecology and Evolution, Massey University Auckland, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand

12  Current address: AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand

13  Current address: School of Life Sciences, University of the West of England, Bristol, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK

14  Current address: Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, UK

15  Current address: Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland

16  Current address: SIMBIOS Centre, Level 5, Kydd Building, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK

author email corresponding author email* Contributed equally

Genome Biology 2009, 10:R51doi:10.1186/gb-2009-10-5-r51

Published: 11 May 2009

Subject areas: Evolution, Microbiology and parasitology, Plant biology

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 plant-inducible 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.

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