Žure Marina, Fernandez-Guerra Antonio, Munn Colin B, Harder Jens
Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
Oxford e-Research Centre, University of Oxford, Oxford, UK.
ISME J. 2017 Feb;11(2):478-489. doi: 10.1038/ismej.2016.123. Epub 2016 Nov 1.
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.
海洋红皮菌属的成员是附着生活的细菌，基于培养的红皮菌菌株的研究表明，三个密切相关的物种——波罗的海红皮菌、“欧洲红皮菌”和“冰岛红皮菌”在欧洲的地理分布有限。为了验证这一假设，我们开发了一种巢式PCR，用于检测从欧洲各地潮间带沉积物中提取的单个基因拷贝的部分乙酰辅酶A合成酶（acsA）。此外，我们在一系列温度、盐度和光照条件下进行了生长实验。使用基本局部比对搜索工具（BLAST）和最小熵分解（MED）相结合的方法来分析序列，旨在探索这些物种和亚种的地理分布。MED主要用于16S rRNA基因的分析，在此我们提出了一种分析蛋白质编码基因的方案，该方案考虑了密码子的简并性以及功能多样性可能被高估的情况。高分辨率分析揭示了不同地理区域种内群落结构的差异。然而，我们发现所有三个物种都存在于所有采样区域，并且与生长实验结果一致，我们证明红皮菌属物种在欧洲没有有限的地理分布。
