title: Geographic distribution at subspecies resolution level: closely related Rhodopirellula species in European coastal sediments.
abstract: Members of the marine genus Rhodopirellula are attached living bacteria and studies based on cultured Rhodopirellula strains suggested that three closely related species R. baltica, 'R. europaea' and 'R. islandica' have a limited geographic distribution in Europe. To address this hypothesis, we developed a nested PCR for a single gene copy detection of a partial acetyl CoA synthetase (acsA) from intertidal sediments collected all around Europe. Furthermore, we performed growth experiments in a range of temperature, salinity and light conditions. A combination of Basic Local Alignment Search Tool (BLAST) and Minimum Entropy Decomposition (MED) was used to analyze the sequences with the aim to explore the geographical distribution of the species and subspecies. MED has been mainly used for the analysis of the 16S rRNA gene and here we propose a protocol for the analysis of protein-coding genes taking into account the degeneracy of the codons and a possible overestimation of functional diversity. The high-resolution analysis revealed differences in the intraspecies community structure in different geographic regions. However, we found all three species present in all regions sampled and in agreement with growth experiments we demonstrated that Rhodopirellula species do not have a limited geographic distribution in Europe.
authors: Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
authors: Marina
authors: M
authors: Žure
authors: Oxford e-Research Centre, University of Oxford, Oxford, UK.|Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
authors: Antonio
authors: A
authors: Fernandez-Guerra
authors: School of Marine Sciences and Engineering, University of Plymouth, Plymouth, UK.
authors: Colin B
authors: CB
authors: Munn
authors: Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
authors: Jens
authors: J
authors: Harder
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005060:Europe; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D005843:Geography; D019015:Geologic Sediments / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D061328:Planctomycetales / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal