Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5

Authors: MAVRODI, DMITRI - WASHINGTON STATE UNIV.; Loper, Joyce; PAULSEN, IAN - MACQUARIE UNIVERSITY; Thomashow, Linda

Submitted to: BMC Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/6/2009
Publication Date: 1/13/2009
Citation: Mavrodi, D.V., Loper, J.E., Paulsen, I.T., Thomashow, L.S. 2009. Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5. BMC Microbiology. 9:8.

Interpretive Summary: Pseudomonas fluorescens Pf-5 is a plant-associated bacterium that colonizes the roots of a wide variety of plant species and produces compounds that suppress fungal pathogens. In this study, we analyzed mobile genetic elements, which are regions of the genome that commonly contain genes acquired by transfer from other bacteria, in an effort to identify determinants that might contribute to Pf-5’s ability to compete and survive in the dynamic and microbiologically complex environment on roots. Of eight elements identified, six resemble sequences found in bacterial viruses. One contains sequences typically present in bacterial plasmids, and another resembles a portion of a gene cluster found in certain foliar pathogens of plants. Comparative DNA sequence analyses showed that the mobile elements in Pf-5 have undergone extensive and complicated DNA rearrangements and have evolved partly through exchange of genetic material with other Pseudomonas spp., including nonpathogens and pathogens of plants and animals. Although the mobile elements from Pf-5 are similar to those found in other Pseudomonas spp., they nevertheless carry a number of putative niche-specific genes that could affect the survival of P. fluorescens Pf-5 in natural habitats.

Technical Abstract: Pseudomonas fluorescens Pf-5 is a plant-associated bacterium that inhabits the rhizosphere of a wide variety of plant species and produces secondary metabolites suppressive of fungal and oomycete plant pathogens. The Pf-5 genome is rich in features consistent with its commensal lifestyle, but has revealed fewer attributes associated with the strain’s ability to compete and survive in the dynamic and microbiologically complex rhizosphere habitat. In this study, we analyzed mobile genetic elements of the Pf-5 genome in an effort to identify determinants that might contribute to Pf-5’s ability to adapt to changing environmental conditions and/or colonize new ecological niches. Sequence analyses revealed that the genome of Pf-5 is devoid of transposons and IS elements and that mobile genetic elements (MGEs) are represented by prophages and genomic islands that collectively span over 260 kb. The prophages include an F-pyocin-like prophage 01, a chimeric prophage 03, a lambdoid prophage 06, and decaying prophages 02, 04 and 05 with reduced size and/or complexity. The genomic islands are represented by a 115-kb conjugative genomic island (CGI) PFGI-1, which shares plasmid replication, recombination, and conjugative transfer genes with those from CGIs found in other Pseudomonas spp., and PFGI-2, which resembles part of tripartite type III secretion pathogenicity islands from the plant pathogens Pseudomonas syringae and P. viridiflava. Almost all of the MGEs in the Pf-5 genome are associated with phage-like integrase genes and are integrated into tRNA genes. Comparative analyses reveal that MGEs found in Pf-5 are subject to extensive and complicated recombination and have evolved in part via exchange of genetic material between commensal Pseudomonas spp. and pseudomonads pathogenic to plants and animals. Although prophages and genomic islands from Pf-5 exhibit similarity to MGEs found in other Pseudomonas spp., they nevertherless carry a number of putative niche-specific genes that could affect the survival of P. fluorescens Pf-5 in natural habitats. Most notable are a ~35-kb segment of “cargo” genes in genomic island PFGI-1 and bacteriocin genes associated with prophages 1 and 4.