REVIEW ARTICLE Comparative genomics and functional analysis of niche-speci¢c adaptation in Pseudomonas putida Xiao Wu1,2,Sebastien´ Monchy1, Safiyh Taghavi1, Wei Zhu2, Juan Ramos3 & Daniel van der Lelie1 1Biology Department, Brookhaven National Laboratory, Upton, NY, USA; 2Department of Applied Mathematics & Statistics, State University of New York, Stony Brook, NY, USA; and 3EEZ-CSIC, Granada, Spain Correspondence: Daniel van der Lelie, Abstract Biology Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA. Pseudomonas putida is a gram-negative rod-shaped gammaproteobacterium that is Tel.: 11 631 344 5349; fax: 11 631 344 found throughout various environments. Members of the species P. putida show a 3407; e-mail:
[email protected] diverse spectrum of metabolic activities, which is indicative of their adaptation to various niches, which includes the ability to live in soils and sediments contami- Received 27 February 2010; revised 7 July 2010; nated with high concentrations of heavy metals and organic contaminants. accepted 19 July 2010. Pseudomonas putida strains are also found as plant growth-promoting rhizospheric Final version published online 26 August 2010. and endophytic bacteria. The genome sequences of several P. putida species have become available and provide a unique tool to study the specific niche adaptation DOI:10.1111/j.1574-6976.2010.00249.x of the various P. putida strains. In this review, we compare the genomes of four P. putida strains: the rhizospheric strain KT2440, the endophytic strain W619, the Editor: Bernardo Gonzalez´ aromatic hydrocarbon-degrading strain F1 and the manganese-oxidizing strain Keywords GB-1. Comparative genomics provided a powerful tool to gain new insights into Pseudomonas putida; comparative genomics; the adaptation of P.