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Authors: Miyazaki, Ryo and Bertelli, Claire and Benaglio, Paola and Canton, Jonas and De Coi, Nicoló and Gharib, Walid H and Gjoksi, Bebeka and Goesmann, Alexander and Greub, Gilbert and Harshman, Keith and Linke, Burkhard and Mikulic, Josip and Mueller, Linda and Nicolas, Damien and Robinson-Rechavi, Marc and Rivolta, Carlo and Roggo, Clémence and Roy, Shantanu and Sentchilo, Vladimir and Siebenthal, Alexandra Von and Falquet, Laurent and van der Meer, Jan Roelof

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103?kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220?kb region and a prophage that drastically change the host metabolic capacity and survivability. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Journal: Environmental microbiology
DOI: 10.1111/1462-2920.12498
Year: 2015

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