The overall goal of my current research program is to unravel the diversity, dynamics and functions of microorganisms associated with plants. Several PhD and Postdoc projects aim to elucidate the genomic, genetic and metabolic potential of specific bacterial and fungal species living on or in plant tissues. The functions of the plant microbiome we study in detail are: 1) microbial protection of plants against biotic stress (pests, diseases, parasitic weeds); 2) microbial modulation of root architecture and plant development, and 3) microbial modulation of plant secondary metabolism. The ongoing projects involve model plants species, natural plant species and also crops important for agriculture/horticulture and the bio-based economy. Over the past years, we also initiated new lines of research to investigate microbiomes in aquatic environments. More specifically, we study the diversity of microorganisms associated with fish that suffer from emerging diseases. Understanding the influence of environmental conditions on the dynamics, assembly and activities of microbiomes will help to design strategies to limit the proliferation and spread of these (re-)emerging pathogens in natural and man-made ecosystems. Next to these fundamental scientific aspects, my program also contributes to the discovery of new antimicrobial compounds and the development of new disease control strategies to reduce pesticide use or to control diseases for which no other effective control measures exist.