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ARS Home Pacific West Area Corvallis, Oregon Horticultural Crops Research Unit Research Publications at this Location





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Title:   Author  item
                                            Loper, Joyceitem
                                            Davis, Edwarditem
                                            LIM, KENT - Macquarie Universityitem
                                            HASSAN, KARL - Macquarie Universityitem
                                            WILSON, NEIL - Macquarie Universityitem
                                            HARTNEY, SIERRA - Oregon State Universityitem
                                            Shaffer, Brendaitem
                                            STOCKWELL, VIRGINIA - Oregon State Universityitem
                                            Henkels, Marcellaitem
                                            SHEN, KEDY - Oregon State Universityitem
                                            Blumhagen, Rachelitem
                                            MAVRODI, DMITRI - Washington State Universityitem
                                            VAN MORTEL, JUDITH - Wageningen University And Research Centeritem
                                            SONG, CHUNXU - Wageningen University And Research Centeritem
                                            RADUNE, DIANA - J Craig Venter Instituteitem
                                            HOSTETLER, JESSICA - J Craig Venter Instituteitem
                                            Kluepfel, Danielitem
                                            Wechter, William

                                                         - *Pat*item
                                            ANDERSON, ANNE - Utah State Universityitem
                                            YOUNG, CHEOL KIM - Chonnam National Universityitem
                                            PIERSON, LELAND - Texas A&M Universityitem
                                            PIERSON, ELIZABETH - Texas A&M Universityitem
                                            LINDOW, STEVE - University Of Californiaitem
                                            RAAIJMAKERS, JOS - Wageningen University And Research Centeritem
                                            Weller, Daviditem
                                            Thomashow, Lindaitem
                                            ALLEN, ANDREW - J Craig Venter Instituteitem
                                            PAULSEN, IAN - Macquarie University
  Submitted to: International Symposium on Microbiology of Aerial Plant Surfaces
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 6/29/2010
                                    Publication  Date: 8/15/2010
                                    Citation: Loper, J.E., Davis, E.W., Lim, K., Hassan, K., Wilson, N., Hartney, S., Shaffer, B.T., Stockwell, V., Henkels, M.D., Shen, K., Blumhagen, R.Z., Mavrodi, D., Van Mortel, J., Song, C., Radune, D., Hostetler, J., Kluepfel, D.A., Wechter, W.P., Anderson, A., Young, C., Pierson, L., Pierson, E., Lindow, S., Raaijmakers, J., Weller, D.M., Thomashow, L.S., Allen, A., Paulsen, I. 2010. Genomic diversity of biocontrol strains of Pseudomonas spp. isolated from aerial or root surfaces of plants. International Symposium on Microbiology of Aerial Plant Surfaces Program Book. p.43.Interpretive Summary:
                                Technical Abstract: The striking ecological, metabolic, and biochemical diversity of Pseudomonas has intrigued microbiologists for many decades.  To explore the genomic diversity of biocontrol strains of Pseudomonas spp., we derived high quality draft sequences of seven strains known to suppress plant disease.  The strains were isolated from the phyllosphere of pear (P. fluorescens A506), the rhizosphere of wheat (three strains of P. fluorescens and two strains of P. chlororaphis), or the rhizosphere of peach (P. synxantha BG33R).  Genome size varies from ca. 5.9 MBases with 5500 ORFs (P. fluorescens A506) to 7.0 Megabases with 6400 ORFs (P. chlororaphis strain O-6).
Phylogenetic analysis of the seven strains and three previously-sequenced strains of P. fluorescens (Pf-5, Pf0-1 and SBW25) defined three distinct clades.  Within each clade, the genomes share 75 to 90% of their proteomes, whereas a smaller proportion of the proteome, typically 60 to 70%, is shared between strains in different clades.  Through comparative genomic analyses, we found that all seven strains share 2525 genes that represent a core genome, with each strain having approximately 600 to 1000 unique genes that are not found in the other genomes. Bioinformatic analysis revealed genes with potential roles in the biology of each strain and its multitrophic interactions on plant surfaces. Type III secretion systems with operonic structures that differ from those in SBW25 or P. syringae pv. syringae are present in five genomes, and one to three copies of clusters for type VI secretion systems are in each of the seven genomes.  All strains have putative insect toxin genes of either the Mcf or Tcc types.  In addition to the previously-described quorum sensing systems, many strains have one to four “luxR solos” similar to those responsive to exogenous signals in other bacteria.  Many orphan gene clusters are present in the genomes, and provide avenues for the future discovery of novel natural products.


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