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.
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Acknowledgements
We would like to thank all sample contributors from EMBC (http://www.embcplus.org), MARES (http://www.mares-eu.org), Plymouth University and Max Planck-Institute, Bremen. We thank Maryia Khomich and Christina Probian for technical assistance. This work was supported by the Max Planck Society and MARES (Erasmus Mundus Joint Doctorate programme coordinated by Ghent University, FPA 2011-0016). AFG was supported by the Micro B3 project, which is funded from the European Union's Seventh Framework Programme (FP7; Joint Call OCEAN.2011-2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under grant agreement no. 287589.
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Žure, M., Fernandez-Guerra, A., Munn, C. et al. Geographic distribution at subspecies resolution level: closely related Rhodopirellula species in European coastal sediments. ISME J 11, 478–489 (2017). https://doi.org/10.1038/ismej.2016.123
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DOI: https://doi.org/10.1038/ismej.2016.123
