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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research Unit » Research » Publications at this Location » Publication #260293
Title: Genomic Diversity of Biocontrol Strains of Pseudomonas spp. Isolated from Aerial or Root Surfaces of Plants

Author
item Loper, Joyce
item Davis, Edward
item LIM, KENT - Macquarie University
item HASSAN, KARL - Macquarie University
item WILSON, NEIL - Macquarie University
item HARTNEY, SIERRA - Oregon State University
item Shaffer, Brenda
item STOCKWELL, VIRGINIA - Oregon State University
item Henkels, Marcella
item SHEN, KEDY - Oregon State University
item Blumhagen, Rachel
item MAVRODI, DMITRI - Washington State University
item VAN MORTEL, JUDITH - Wageningen University And Research Center
item SONG, CHUNXU - Wageningen University And Research Center
item RADUNE, DIANA - J Craig Venter Institute
item HOSTETLER, JESSICA - J Craig Venter Institute
item Kluepfel, Daniel
item Wechter, William - Pat
item ANDERSON, ANNE - Utah State University
item YOUNG, CHEOL KIM - Chonnam National University
item PIERSON, LELAND - Texas A&M University
item PIERSON, ELIZABETH - Texas A&M University
item LINDOW, STEVE - University Of California
item RAAIJMAKERS, JOS - Wageningen University And Research Center
item Weller, David
item Thomashow, Linda
item ALLEN, ANDREW - J Craig Venter Institute
item 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.