Ruegeria sp. (strain TM1040) (formerly Silicibacter sp.) belongs to the Roseobacter clade of the alpha-proteobacteria, which is among the most abundant and ecologically relevant marine bacterial groups. It was originally isolated as part of an investigation to understand the role of the bacteria in the physiology and toxigenesis of the dinoflagellate Pfiesteria piscicida. Ruegeria sp. (strain TM1040) is found within the phycosphere or physically attached to the surface of the dinoflagellate cell. Axenic cultures of P.piscicida grow poorly (and ultimately die) compared to cultures with associated bacterial assemblages. Although P.piscicida is a heterotrophic dinoflagellate, the Pfiesteria /TM1040 association is the only known "obligate" association between a dinoflagellate and a culturable bacterium. In addition, Ruegeria sp. (strain TM1040) metabolizes the dinoflagellate secondary metabolite dimethylsulfoniopropionate (DMSP) via demethylation to methylmercaptopropionic acid (MMPA). DMSP is the major source of organic sulfur in the world's oceans and plays a significant role in the global sulfur cycle. The genome of Ruegeria sp. (strain TM1040) is made up of one chromosome, one megaplasmid and one plasmid.