Dubuffet Aurore, Chauvet Marina, Moné Anne, Debroas Didier, Lepère Cécile
CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, F-63000, France.
Environ Microbiol. 2021 Aug;23(8):4344-4359. doi: 10.1111/1462-2920.15618. Epub 2021 Jun 10.
Microsporidia are obligate intracellular eukaryotic parasites known to parasitize many species of the animal kingdom as well as some protists. However, their diversity is underestimated, in part as a consequence of the failure of 'universal' primers to detect them in metabarcoding studies. Besides, due to the inconsistency between taxonomy and phylogenetic data, available databases may assign incorrectly sequences obtained with high-throughput sequencing. In this work, we developed a comprehensive reference database which positions microsporidian SSU rRNA gene sequences within a coherent ranked phylogenetic framework. We used this phylogenetic framework to study the microsporidian diversity in lacustrine ecosystems, focusing on < 150 μm planktonic size fractions. Our analysis shows a high diversity of Microsporidia, with the identification of 1531 OTUs distributed within seven clades, of which 76% were affiliated to clade IV2 and 20% to clade I (nomenclature presented hereby). About a quarter of the obtained sequences shared less than 85% identity to the closest known species, which might represent undescribed genera or families infecting small hosts. Variations in the abundance of Microsporidia were recorded between the two lakes sampled and across the sampling period, which might be explained by spatio-temporal variations of their potential hosts such as microeukaryotes and metazooplankton.
微孢子虫是专性细胞内真核寄生虫，已知寄生于动物界的许多物种以及一些原生生物。然而，它们的多样性被低估了，部分原因是在宏条形码研究中“通用”引物未能检测到它们。此外，由于分类学和系统发育数据之间的不一致，现有的数据库可能会错误地分配通过高通量测序获得的序列。在这项工作中，我们开发了一个综合参考数据库，将微孢子虫的小亚基核糖体RNA（SSU rRNA）基因序列置于一个连贯的、有等级的系统发育框架内。我们利用这个系统发育框架来研究湖泊生态系统中的微孢子虫多样性，重点关注浮游生物大小小于150微米的部分。我们的分析显示微孢子虫具有高度多样性，鉴定出1531个操作分类单元（OTU），分布在七个进化枝中，其中76%隶属于进化枝IV2，20%隶属于进化枝I（此处给出命名法）。约四分之一的获得序列与最接近的已知物种的同一性低于85%，这可能代表感染小型宿主的未描述属或科。在所采样的两个湖泊之间以及整个采样期间，记录到了微孢子虫丰度的变化，这可能是由其潜在宿主（如微型真核生物和后生浮游动物）的时空变化所解释的。
