Bukin Yu S, Kravtsova L S, Peretolchina T E, Fedotov A P, Tupikin A E, Kabilov M R, Sherbakov D Yu, Mincheva E V
Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
Vavilovskii Zhurnal Genet Selektsii. 2022 Feb;26(1):86-95. doi: 10.18699/VJGB-22-12.
Here we report new data describing the biodiversity of phytobenthic communities based on DNA-metabarcoding using the 18S rDNA marker and the Illumina MiSeq system. The study was initiated due to the blooming of f ilamentous algae (mainly of the genus Spirogyra) and cyanobacteria in the coastal zone of Lake Baikal under climate change and anthropogenic impact. The composition and taxonomic diversity of algae and other organisms associated with them on different sites of Lake Baikal (near Bolshoi Ushkaniy Island, in Listvennichny Bay) and in the Kaya (within the city of Irkutsk, located in the same drainage basin as Lake Baikal) were determined using DNAmetabarcoding. About 15 thousand reads of the 18S rRNA marker were obtained by applying NGS (next-generation sequencing). The species of algae dominating in the number of reads, as well as the diff icult-to-identify taxa (Stramenopiles, Alveolata, Euglenozoa, Chromista, Rhizaria, Amoebozoa, etc.), which play an important role in the functioning and formation of the structure of algal communities, were revealed. The Shannon index of the communities studied ranges from 1.56 to 2.72. The advantages and weaknesses of using DNA-metabarcoding based on the 18S rRNA gene fragment for studying the structure of algal communities are shown. The advantage of this method is the possibility to more fully determine the diversity of eukaryotes taxa, which are diff icult to identify by morphology, without involving a large number of specialists, while the disadvantage of the method is the distortion that may occur during the PCR. Here, ways of solving this problem are proposed. The results of the study show that the analysis of the minor component of the eukaryotic community in samples (organisms with low biomass) consisting of a mixture of multicellular and unicellular organisms requires a read-depths of at least 100,000 sequences per sample. In general, the DNA-metabarcoding method is recommended for studying the structure of algal communities and eukaryotes associated with them.
在此，我们报告了基于使用18S rDNA标记和Illumina MiSeq系统的DNA代谢条形码技术所获得的有关底栖植物群落生物多样性的新数据。该研究起因于气候变化和人为影响下贝加尔湖沿岸丝状藻类（主要是水绵属）和蓝细菌的大量繁殖。利用DNA代谢条形码技术确定了贝加尔湖不同地点（大乌什卡尼岛附近、利斯韦尔尼奇内湾）以及位于与贝加尔湖同一流域的伊尔库茨克市内的卡亚的藻类及其相关其他生物的组成和分类多样性。通过应用新一代测序（NGS）获得了约1.5万个18S rRNA标记的读数。揭示了读数数量上占主导的藻类物种，以及在藻类群落结构的形成和功能中发挥重要作用的难以鉴定的分类群（不等鞭毛类、囊泡虫类、眼虫类、色素界、根足虫类、变形虫类等）。所研究群落的香农指数范围为1.56至2.72。展示了基于18S rRNA基因片段的DNA代谢条形码技术在研究藻类群落结构方面的优缺点。该方法的优点是能够更全面地确定难以通过形态学鉴定的真核生物分类群的多样性，且无需大量专家参与，而该方法的缺点是在聚合酶链式反应（PCR）过程中可能会出现偏差。在此，提出了解决该问题的方法。研究结果表明，对由多细胞和单细胞生物混合组成的样本中的真核生物群落的次要成分（生物量低的生物体）进行分析，每个样本至少需要100,000个序列的测序深度。总体而言，推荐使用DNA代谢条形码技术来研究藻类群落及其相关真核生物的结构。
