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Pseudomonas putida KT2440 is a biosafety strain, which has retained its capability to survive and function in the environment. Its broad metabolic capability to degrade a broad spectrum of aromatic compounds and still grow at temperatures as low as 5°C makes it a good candidate as a model organism to study genome wide responses to changing growth conditions which mimic environmental changes in natural habitats. In this study a functional genomics approach was used to examine the stress response of P. putida KT2440 wild type and five cold sensitive Tn5 mutants (with plasposons inserted in cbrA, cbrB, pcnB, vacB and bipA) to cold shock by decreasing the temperature from 30°C to 10°C. For this, transcriptome data derived from three different transcriptome platforms (Illumina cDNA sequencing, Affymetrix microarrays and Progenika microarrays), as well as metabolome and proteome data were combined. The wild type and a pcaI:Tn5 mutant were furthermore exposed to high concentrations of sodium benzoate (45 mM).