Marine eukaryotes provide a unique habitat for surface colonization by marine microorganisms where competition between these communities is likely to influences microbial diversity. Seaweed-associated bacteria are known to produce a range of antibiotics in defense against competition and to protect the host from further colonization. For example, Phaeobacter inhibins, a member of the abundant marine Roseobacter clade is known to be an effective colonizer of biotic and abiotic marine surfaces. The competitive success of P.inhibins is thought to be, in part, due to the production of the antibiotic tropodithietic acid(TDA), however few studies have investigated the role of this metabolite in an ecological setting. Here we used the common marine diatom Thalassiosira rotula as a model to investigate the role of TDA production on the ability of P. inhibins to colonize eukaryotic host surfaces and its influence on the structure of the natural community of the host. Batch cultures of the axenic T.rotula were incubated with natural seawater collected from the North Sea and inoculated with either GFP-tagged P.inhibins WT or a TDA-deficient mutant(WP75) and subsequent surface colonization on T.rotula was monitored using epifluorescence-microscopy over a period of 8 days. P.inhibins WT colonized the surface of T. rotula better than WP75 and was able to out-compete other bacteria. DGGE of PCR-amplified-16S-rRNA gene fragments revealed pronounced differences in bacterial community composition between the attached and the free-living bacteria. DGGE analysis revealed that for both attached and free-living bacterial communities of the algae cultures exposed to WP75 resembled the original attached bacterial community from the North Sea. The microbial composition of both attached and free-living bacteria of algal cultures exposed to P.inhibins WT and WP75 will be further analyzed using a deep sequencing approach (454-pyrosequencing). Our results indicate that TDA production by P.inhibins WT was important in colonizing the surface of the diatom T.rotula and competing with other bacteria to structure the natural community in a way that will benefit the host.