Abstract: Ammonia-oxidizing microorganisms (AOB and AOA) and nitrite oxidizing bacteria (NOB) are the most important organisms responsible for ammonia and nitrite oxidation in agricultural ecosystems and growing media. Ammonia and nitrite oxidation are critical steps in the soil nitrogen cycle and can be affected by the application of mineral fertilizers or organic fertilizers. The functionality of the microbial community has a major impact on the nutrient turnover and will finally influence plant performance. The microbial community associated with the growing medium and its functionality will also be influenced by the rhizosphere and the bulk soil. In our study, we used a tomato plant with a high root exudation capacity in order to stimulate microbial activity. We studied plant performance in rhizotrons (a phentotyping system for imaging roots), including an optical method (planar optodes) for non-invasive, quantitative and high-resolution imaging of pH dynamics in the rhizosphere and adjacent medium. The horticultural growing medium was supplemented with organic-derived nitrogen or ammonium derived from struvite. The possible differences in the root structure between treatments is compared with the total root length. Destructive growing medium sampling and high throughput sequencing analysis of the bacterial abundance of the communities present in the rhizosphere and the bulk soil is used to study the growing medium-associated microbial community structure and functionality, and this will be related to pH changes in the rhizosphere and the bulk soil. Our hypothesis is that the growing medium-associated microbial community structure changes depending on the nitrogen form provided and we expect a higher abundance of bacteria in the treatment with organic fertilizer and a higher abundance of AOB and NOB in the rhizosphere in comparison to the bulk soil.