Genome-wide gene essentiality study for growth and survival in soil of the bacterium Pseudomonas veronii 1YdBTEX2

The genetic makeup that is important for growth and survival of potential bacterial inoculants for bioremediation in contaminated soils is poorly understood. Here we used massive transposon sequencing to identify and characterize genes in the monoaromatic-compound degrading bacterium Pseudomonas veronii 1YdBTEX2 of importance for its growth and survival. Two independent transposon libraries were constructed, which were inoculated into either liquid suspended culture, or two types of soil microcosms. Meta-populations of mutants were followed for up to 50 generations of growth, sampled at different generation-intervals and subjected to transposon insertion sequencing. Comparison between conditions and to an in silico referenced random insertion library served to identify genes with potential fitness defects or gain.