Abstract
Pseudomonas putida is a gram-negative rod-shaped gammaproteobacterium that is found throughout various environments. Members of the species P. putida show a diverse spectrum of metabolic activities, which is indicative of their adaptation to various niches, which includes the ability to live in soils and sediments contaminated with high concentrations of heavy metals and organic contaminants. Pseudomonas putida strains are also found as plant growth-promoting rhizospheric 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 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 aromatic hydrocarbon-degrading strain F1 and the manganese-oxidizing strain GB-1. Comparative genomics provided a powerful tool to gain new insights into the adaptation of P. putida to specific lifestyles and environmental niches, and clearly demonstrated that horizontal gene transfer played a key role in this adaptation process, as many of the niche-specific functions were found to be encoded on clearly defined genomic islands.
Highlights
The group of the pseudomonads comprises a heterogeneous set of microorganisms that can be isolated from many different niches (Clarke, 1982)
This review focuses on the diversity and adaptation of four P. putida strains (KT2440, W619, F1 and GB-1) in terms of their respective environments from a genome point of view, and provides further insights into their potential applications for the bioremediation of contaminated environments or as plant growth-promoting bacteria
Different from 105 predicted genomic islands of KT2440 as described by Weinel et al (2002), a number that was based on the compositional bias of the GC, di- and tetranucleotides of the chromosome itself, the 61 putative genomic islands in KT2440 that we identified in our analysis were predicted based on the lack of synteny against the genomes of the other three P. putida strains, GC bias and the existence of mobile genetic elements
Summary
The group of the pseudomonads comprises a heterogeneous set of microorganisms that can be isolated from many different niches (Clarke, 1982). These putative genomic islands have conferred the P. putida species with many accessory capabilities, including heavy metal resistance, aromatic compound degradation and stress responses, all Journal compilation c 2010 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. No claim to original US government works of which are highly relevant for the specific niche adaption of P. putida.
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