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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOLOGY AND MANAGEMENT OF SOILBORNE DISEASES OF HORTICULTURAL CROPS Title: Genomic Diversity of Biocontrol Strains of Pseudomonas spp. Isolated from Aerial or Root Surfaces of Plants

Authors
item Loper, Joyce
item Davis, Edward
item Lim, Kent -
item Hassan, Karl -
item Wilson, Neil -
item Hartney, Sierra -
item Shaffer, Brenda
item Stockwell, Virginia -
item Henkels, Marcella
item Shen, Kedy -
item Blumhagen, Rachel
item Mavrodi, Dmitri -
item Van Mortel, Judith -
item Song, Chunxu -
item Radune, Diana -
item Hostetler, Jessica -
item Kluepfel, Daniel
item Wechter, William
item Anderson, Anne -
item Young, Cheol Kim -
item Pierson, Leland -
item Pierson, Elizabeth -
item Lindow, Steve -
item Raaijmakers, Jos -
item Weller, David
item Thomashow, Linda
item Allen, Andrew -
item Paulsen, Ian -

Submitted to: International Symposium on Microbiology of Aerial Plant Surfaces
Publication Type: Abstract Only
Publication Acceptance Date: June 29, 2010
Publication Date: August 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.

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.

Last Modified: 11/27/2014
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