Abstract
BackgroundPseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported.ResultsComparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum. The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins.ConclusionsThe genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.
Highlights
Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere
The phylogenomics tree generated with such approach (Figure 1A) is mostly congruent with previous concatenated sequence trees obtained in different multilocus sequence analysis (MLSA) analyses [16,20,23]; and clearly highlighted the need to re-evaluate the taxonomic status of species belonging to the P. fluorescens group [18]
Fifty strains (Additional file 1) previously classified as P. fluorescens, P. brassicacearum, P. protegens, P. mandelii, P. chlororaphis, P. tolaasii, P. extremaustralis and Pseudomonas spp. formed a single cluster which branched significantly deeper than other clusters that represent defined species such as P. aeruginosa or P. syringae
Summary
Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. Pseudomonas fluorescens F113 is a PGPR strain isolated from the sugar-beet rhizosphere in Ireland [1] This strain was selected and studied because of its capacity to inhibit growth of a range of phytopathogenic bacteria, fungi, oomycetes and nematodes including Pectobacterium caratovorum [2], Fusarium oxysporum [3], Pythium ultimum [4] and Globodera spp. Several studies have sought to take advantage of this colonising ability by developing novel genetically modified derivatives with biotechnological traits, for example the capacity to degrade polychlorinated biphenyls and other environmental pollutants [11,15]
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