Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.
Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Mol Ecol Resour. 2020 May;20(3). doi: 10.1111/1755-0998.13147. Epub 2020 Mar 11.
Surveying microbial diversity and function is accomplished by combining complementary molecular tools. Among them, metagenomics is a PCR free approach that contains all genetic information from microbial assemblages and is today performed at a relatively large scale and reasonable cost, mostly based on very short reads. Here, we investigated the potential of metagenomics to provide taxonomic reports of marine microbial eukaryotes. We prepared a curated database with reference sequences of the V4 region of 18S rDNA clustered at 97% similarity and used this database to extract and classify metagenomic reads. More than half of them were unambiguously affiliated to a unique reference whilst the rest could be assigned to a given taxonomic group. The overall diversity reported by metagenomics was similar to that obtained by amplicon sequencing of the V4 and V9 regions of the 18S rRNA gene, although either one or both of these amplicon surveys performed poorly for groups like Excavata, Amoebozoa, Fungi and Haptophyta. We then studied the diversity of picoeukaryotes and nanoeukaryotes using 91 metagenomes from surface down to bathypelagic layers in different oceans, unveiling a clear taxonomic separation between size fractions and depth layers. Finally, we retrieved long rDNA sequences from assembled metagenomes that improved phylogenetic reconstructions of particular groups. Overall, this study shows metagenomics as an excellent resource for taxonomic exploration of marine microbial eukaryotes.
调查微生物多样性和功能是通过结合互补的分子工具来完成的。其中，宏基因组学是一种无 PCR 方法，包含微生物组合的所有遗传信息，并且如今可以在相对较大的规模和合理的成本下进行，主要基于非常短的读取。在这里，我们研究了宏基因组学提供海洋微生物真核生物分类报告的潜力。我们准备了一个经过精心策划的数据库，其中包含 V4 区 18S rDNA 的参考序列，这些序列在 97%的相似性处聚类，并使用该数据库提取和分类宏基因组读取。其中超过一半的序列可以明确地与唯一的参考序列相关联，而其余的序列可以分配给特定的分类群。尽管 18S rRNA 基因的 V4 和 V9 区的扩增子测序或两者都不能很好地用于原生动物门、变形虫门、真菌门和甲藻门等群体，但宏基因组学报告的总体多样性与通过这些扩增子调查获得的多样性相似。然后，我们使用来自不同海洋的从表层到深海层的 91 个宏基因组研究了微微真核生物和纳米真核生物的多样性，揭示了大小分数和深度层之间的明显分类分离。最后，我们从组装的宏基因组中检索了长 rDNA 序列，这些序列改进了特定群体的系统发育重建。总体而言，这项研究表明宏基因组学是海洋微生物真核生物分类探索的极好资源。
