To assess the effect of the higher than ambient light doses received by bacteria in the optical trapping experiments, we investigated both the effect on the mortality of the bacteria and the ability of the bacteria to colonise potato roots. In a trapping experiment, it is not possible to follow the fate of a single cell to study the impact of the light dose received. Therefore, we designed two slightly different microscopic systems to expose entire bacterial colonies to light doses that are equivalent or larger than those received during a trapping experiment. The two systems were designed for precise targeting of bacterial colonies on a petri dish with either the low power infrared laser used for trapping, or a high-power pulse laser with known ability to damage biological cells. Once targeted, the region receiving the laser light can either be studied for viability using dead-cell staining or they can be sampled for root colonisation experiments.