title: Genome Analysis of Pseudomonas fluorescens PCL1751: A Rhizobacterium that Controls Root Diseases and Alleviates Salt Stress for Its Plant Host.
abstract: Pseudomonas fluorescens PCL1751 is a rod-shaped Gram-negative bacterium isolated from the rhizosphere of a greenhouse-grown tomato plant in Uzbekistan. It controls several plant root diseases caused by Fusarium fungi through the mechanism of competition for nutrients and niches (CNN). This mechanism does not rely on the production of antibiotics, so it avoids the concerns of resistance development and is environmentally safe. Additionally, this bacterium promotes plant growth by alleviating salt stress for its plant host. To investigate the genetic mechanisms that may explain these observations, we determined the complete genome sequence of this bacterium, examined its gene content, and performed comparative genomics analysis with other Pseudomonas strains. The genome of P. fluorescens PCL1751 consisted of one circular chromosome that is 6,143,950 base-pairs (bp) in size; no plasmid was found. The annotation included 19 rRNA, 70 tRNA, and 5,534 protein-coding genes. The gene content analysis identified a large number of genes involved in chemotaxis and motility, colonization of the rhizosphere, siderophore biosynthesis, and osmoprotectant production. In contrast, the pathways involved in the biosynthesis of phytohormones or antibiotics were not found. Comparison with other Pseudomonas genomes revealed extensive variations in their genome size and gene content. The presence and absence of secretion system genes were highly variable. As expected, the synteny conservation among strains decreased as a function of phylogenetic divergence. The integration of prophages appeared to be an important driver for genome rearrangements. The whole-genome gene content analysis of this plant growth-promoting rhizobacterium (PGPR) provided some genetic explanations to its phenotypic characteristics. The extensive and versatile substrate utilization pathways, together with the presence of many genes involved in competitive root colonization, provided further support for the finding that this strain achieves biological control of pathogens through effective competition for nutrients and niches.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Shu-Ting
authors.initials: ST
authors.lastname: Cho
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Hsing-Hua
authors.initials: HH
authors.lastname: Chang
authors.affiliation: Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder str. 84, Müncheberg, Germany.
authors.forename: Dilfuza
authors.initials: D
authors.lastname: Egamberdieva
authors.affiliation: Koppert Biological Systems, Veilingweg 14, 2651 BE Berkel en Rodenrijs, the Netherlands.
authors.forename: Faina
authors.initials: F
authors.lastname: Kamilova
authors.affiliation: Institute of Biology, Sylvius Laboratory, Leiden University, Leiden, the Netherlands.
authors.forename: Ben
authors.initials: B
authors.lastname: Lugtenberg
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan; Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.
authors.forename: Chih-Horng
authors.initials: CH
authors.lastname: Kuo
mesh_terms: D001422:Bacterial Adhesion / Q000235:genetics; D002244:Carbon / Q000378:metabolism; D002633:Chemotaxis / Q000235:genetics; D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000235:genetics*; D018551:Solanum lycopersicum / Q000382:microbiology; D008969:Molecular Sequence Data; D010935:Plant Diseases / Q000382:microbiology; D018517:Plant Roots / Q000382:microbiology*; D011551:Pseudomonas fluorescens / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D058441:Rhizosphere; D012492:Salts / Q000494:pharmacology*; D012988:Soil Microbiology; D013312:Stress, Physiological / Q000187:drug effects* / Q000235:genetics
chemical_list: D012492:Salts; D002244:Carbon