Three strains of Pseudomonas putida, one non-fluorescent and two fluorescent, were investigated in a series of complementary experiments to characterise their inhibitory effects on peas under different environmental conditions. Firstly, a gnotobiotic growth pouch system was developed to observe the deleterious effects of the strains on pea root development. A negative impact of the strains was observed on the development of the root morphology using these pouches which was accompanied with a subsequent reduction in root biomass. By using this method it was concluded that the deleterious effect of one of the strains was dependent on the inoculum density. Secondly, two complementary studies in non-sterile growth systems where pea seeds/seedlings were inoculated with the bacteria, showed deleterious effects on plant biomass by two of the strains. Thirdly, by using a sterile plant growth system allowing microscopic observations on root hair development, all strains were found to be able to induce root hair deformations on pea seedlings. The results showed that the mode of action for the deleterious effect differ between the strains. Based on our findings, we would like to emphasise the necessity to include a palette of different sterile and non-sterile growth systems to be able to identify characteristics of importance for deleterious rhizosphere bacteria.