Diversity of Rhodopirellula and related planctomycetes in a North Sea coastal sediment employing carB as molecular marker

Abstract

Rhodopirellula is an abundant marine member of the bacterial phylum Planctomycetes. Cultivation studies revealed the presence of several closely related Rhodopirellula species in European coastal sediments. Because the 16S rRNA gene does not provide the desired taxonomic resolution to differentiate Rhodopirellula species, we performed a comparison of the genomes of nine Rhodopirellula strains and six related planctomycetes and identified carB, coding for the large subunit of carbamoylphosphate synthetase, as a suitable molecular marker. In this study, we investigated the diversity of Rhodopirellula in coastal intertidal surface sediments of Sylt island, North Sea, using the 16S rRNA and carB genes as molecular markers. The carB clone and pyrosequencing libraries revealed the presence of 12 species of Rhodopirellula and of 66 species in closely related undescribed genera, a diversity that was not detected with a 16S rRNA gene library. This study demonstrates that the carB gene is a powerful molecular marker for detecting Rhodopirellula species in the environment and may be used for the taxonomic evaluation of new strains.