Biogeography of Rhodopirellula in European coastal sediments

Abstract

Rhodopirellula is a marine representative of the globally distributed and environmentally important bacterial phylum Planctomycetes. In cultivation studies, 70 strains had been isolated from European coastal seas and sediments and several of those strains shared a sequence identity over 99.5% of the 16S rRNA gene. A multilocus sequence analysis (MLSA) in combination with DNA-DNA hybridization experiments had arranged those strains into 13 operational taxonomic units (OTUs), suggesting a high diversity and a limited habitat size for Rhodopirellula species in European seas and sediments. The classification of microorganisms using only differences in 16S rRNA gene sequences is limited due to the high degree of conservation of this gene. Closely related species with nearly identical 16S rRNA gene sequences often show ecologically meaningful genetic and physiological differences. Thus, other genes have to be investigated to characterize biogeographic structures in environmental studies at the species level. To investigate the diversity and biogeography of Rhodopirellula in the environment, without cultivation and beyond the resolution of the commonly used 16S rRNA gene, we performed a comparison of the genomes of Rhodopirellula strains and related planctomycetes and identified the carB gene, coding for the large subunit of carbamoylphosphate synthetase, and the acsA gene, coding for acetyl CoA synthetase, as suitable molecular markers. The carB primers were designed to detect all known and potentially new Rhodopirellula species. The detection of 12 species of Rhodopirellula in a single sample from Sylt island in the North Sea demonstrated 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. R. baltica, 'R. europaea' and 'R. islandica' were present in Sylt sediments. The biogeography of these three species in intertidal sediments around Europe was investigated targeting the acsA partial gene sequence with specific primers. Growth experiments in different temperature, salinity and light conditions showed that the three Rhodopirellula species have different optimal growth conditions, however, they all grew in all the conditions tested. The acsA study, in agreement with the growth experiments, revealed the presence of all three species in all regions sampled and provided evidence that the Rhodopirellula species are ubiquitously present as a seed bank in European and Philippines samples.