Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

Ian T. Paulsen*, Caroline M. Press, Jacques Ravel, Donald Y. Kobayashi, Garry S. A. Myers, Dmitri V. Mavrodi, Robert T. DeBoy, Rekha Seshadri, Qinghu Ren, Ramana Madupu, Robert J. Dodson, A. Scott Durkin, Lauren M. Brinkac, Sean C. Daugherty, Stephen A. Sullivan, Mary J. Rosovitz, Michelle L. Gwinn, Liwei Zhou, Davd J. Schneider, Samuel W. CartinhourWilliam C. Nelson, Janice Weidman, Kisha Watkins, Kevin Tran, Hoda Khouri, Elizabeth A. Pierson, Leland S. Pierson, Linda S. Thomashow, Joyce E. Loper

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

514 Citations (Scopus)


Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.

Original languageEnglish
Pages (from-to)873-878
Number of pages6
JournalNature Biotechnology
Issue number7
Publication statusPublished - 2005
Externally publishedYes

Bibliographical note

A corrigendum for this article exists and can be found in Nature Biotechnology, vol. 24, no. 4, p. 466. DOI: 10.1038/nbt0406-466b


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