The Roseobacter clade represents one of the most important bacterial groups in marine environments. While some of its members are heterotrophs, many Roseobacter clade members contain bacterial photosynthetic reaction centers. We investigated the phylogeny of pufL and pufM genes encoding the L and M subunits of reaction centers using available genomic data and our own cultured species. Interestingly, phylogeny of pufL and pufM genes largely deviated from 16S rRNA-based phylogeny. The sequences split into two clearly distinct clades. While most of the studied species contained pufL and pufM sequences related to those found in Roseobacter litoralis, some of the marine species contained sequences related to the freshwater Rhodobacter species. In addition, genomic data documents that Roseobacter-type centers contain cytochrome c subunits (pufC gene product), whereas Rhodobacter-type centers incorporate PufX proteins. This indicates that the two forms of the reaction centers are not only distinct phylogenetically, but also structurally. The large deviation of pufL and pufM phylogeny from 16S phylogeny indicates multiple horizontal transfers of the puf operon among members of the order Rhodobacterales.
