Lopatina Anna, Medvedeva Sofia, Shmakov Sergey, Logacheva Maria D, Krylenkov Vjacheslav, Severinov Konstantin
Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia; Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Research Complex of "Nanobiotechnology", Saint-Petersburg State Polytechnical UniversitySaint-Petersburg, Russia.
Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and TechnologySkolkovo, Russia.
Front Microbiol. 2016 Mar 31;7:398. doi: 10.3389/fmicb.2016.00398. eCollection 2016.
The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.
通过对扩增的16S rRNA基因片段进行高通量测序和鸟枪法宏基因组测序，研究了东南极洲四个俄罗斯站点周围表层雪中存在的细菌多样性。结果显示，样本之间在纲和属水平上存在显著差异，表明南极雪中细菌存在站点间多样性。黄杆菌属是一个采样点的主要属，在其他站点也有检测到。通过宏基因组测序研究了样本中II-C型黄杆菌CRISPR间隔序列的多样性。发现了数千个独特的间隔序列，采样点之间的重叠率不到35%，这表明黄杆菌CRISPR间隔序列具有巨大的自然多样性，相应地，其CRISPR-Cas系统的适应性活性水平也很高。没有一个间隔序列与来自北半球的黄杆菌分离株的已知间隔序列匹配。此外，与本研究中获得的南极宏基因组序列匹配的间隔序列百分比，显著高于与来自大得多的公共环境宏基因组数据库的序列匹配的百分比。结果表明，尽管总体多样性水平非常高，但南极黄杆菌构成了一个独立的群体，受到的来自移动遗传元件的压力与世界其他地区不同。这些结果还确立了宏基因组CRISPR间隔序列含量分析作为研究细菌种群多样性的有力工具。
