Complex interactions between microalgae and bacteria, such as mutualism, parasitism and competition, shape the structure and functioning of photosynthetic microbial mats. Using experimental co-cultures, we aimed at obtaining a better understanding of the interactions and exchanges that underlie the association between the marine benthic diatom Seminavis robusta (SR) and bacteria that were recruited from two very different bacterial inocula, one from the brackish lagoon Veerse Meer (The Netherlands), the natural habitat of SR, and a second from a forest soil sample, an alien environment to SR.