Open Access Highly Accessed Research article

Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction

Miguel Redondo-Nieto1, Matthieu Barret23, John Morrissey3, Kieran Germaine4, Francisco Martínez-Granero1, Emma Barahona1, Ana Navazo1, María Sánchez-Contreras1, Jennifer A Moynihan23, Candela Muriel1, David Dowling4, Fergal O’Gara23, Marta Martín1 and Rafael Rivilla1*

Author Affiliations

1 Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin, 2, Madrid, 28049, Spain

2 BIOMERIT Research Centre, Microbiology Department, University College Cork, Cork, Ireland

3 Microbiology Department, Food Science Building, University College Cork, Cork, Ireland

4 Institute of Technology, Carlow, Ireland

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BMC Genomics 2013, 14:54  doi:10.1186/1471-2164-14-54

Published: 25 January 2013



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. The F113 genome sequence and annotation has been recently reported.


Comparative 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.


The 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.