Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
Mark W. Silby,Ana Cerdeño-Tárraga,Georgios S. Vernikos,Stephen R. Giddens,Robert W. Jackson,Robert W. Jackson,Gail M. Preston,Xue-Xian Zhang,Christina D. Moon,Christina D. Moon,Stefanie M. Gehrig,Scott A. C. Godfrey,Scott A. C. Godfrey,Christopher Knight,Christopher Knight,Jacob G. Malone,Jacob G. Malone,Zena Robinson,Andrew J. Spiers,Andrew J. Spiers,Simon R. Harris,Gregory L. Challis,Alice M. Yaxley,David Harris,Kathy Seeger,Lee Murphy,Simon Rutter,Rob Squares,Michael A. Quail,Elizabeth Saunders,Konstantinos Mavromatis,Thomas Brettin,Stephen D. Bentley,Joanne Hothersall,Elton R. Stephens,Christopher M. Thomas,Julian Parkhill,Stuart B. Levy,Paul B. Rainey,Nicholas R. Thomson +39 more
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TLDR
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.Abstract:
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. 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. 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.read more
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Pseudomonas genomes: diverse and adaptable
Mark W. Silby,Mark W. Silby,Craig Winstanley,Scott A. C. Godfrey,Stuart B. Levy,Robert W. Jackson +5 more
TL;DR: Genome sequences of Pseudomonas spp.
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Experimental evolution of bet hedging
TL;DR: The de novo evolution of bet hedging in experimental bacterial populations is reported, suggesting that risk-spreading strategies may have been among the earliest evolutionary solutions to life in fluctuating environments.
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Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates
Nicholas Oteino,Richard D. Lally,Samuel Kiwanuka,Andrew T. Lloyd,David Ryan,Kieran J. Germaine,David N. Dowling +6 more
TL;DR: The results showed that many of the endophytic strains produced GA and have moderate to high phosphate solubilization capacities, and when inoculated into P. sativum L. plants grown in soil under soluble phosphate limiting conditions, theendophytes that produced medium-high levels of GA displayed beneficial plant growth promotion effects.
Journal ArticleDOI
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions
Joyce E. Loper,Joyce E. Loper,Karl A. Hassan,Dmitri V. Mavrodi,Edward W. Davis,Chee Kent Lim,Brenda T. Shaffer,Liam D. H. Elbourne,Virginia O. Stockwell,Sierra L. Hartney,Katy Breakwell,Marcella D. Henkels,Sasha G. Tetu,Lorena I. Rangel,Teresa A. Kidarsa,Neil L. Wilson,Judith E. van de Mortel,Chunxu Song,Rachel Z Blumhagen,Diana Radune,Jessica B. Hostetler,Lauren M. Brinkac,A. Scott Durkin,Daniel A. Kluepfel,W. Patrick Wechter,Anne J. Anderson,Young Cheol Kim,Leland S. Pierson,Elizabeth A. Pierson,Steven E. Lindow,Donald Y. Kobayashi,Jos M. Raaijmakers,David M. Weller,Linda S. Thomashow,Andrew E. Allen,Ian T. Paulsen +35 more
TL;DR: A comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences found genes for traits that were not known previously in the strains, highlighting the enormous heterogeneity of the P. fluorescenceens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.
Journal ArticleDOI
Genomics of secondary metabolite production by Pseudomonas spp.
Harald Gross,Joyce E. Loper +1 more
TL;DR: An overview of the astonishing metabolic capacity of the Pseudomonads is provided, the knowledge of secondary metabolite biosynthesis in this group of organisms is summarized, and the biological significance of these compounds to the diverse life styles exhibited by PseUDomonas spp.
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