Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany.
Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Mol Ecol Resour. 2018 Mar;18(2):306-318. doi: 10.1111/1755-0998.12725. Epub 2017 Nov 4.
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
单细胞真核生物（原生动物）作为微生物的主要捕食者，在土壤食物网中起着关键作用。然而，由于原生动物的多源性，无法为该类群建立单一的通用条形码，许多原生动物群落的结构仍然没有得到解决。原质团粘菌（粘菌门或黏菌纲）通过形成子实体在原生动物中脱颖而出，这使得它们具有形态物种概念。通过对大量形态物种进行 Sanger 测序，本研究提供了迄今为止最大的暗孢粘菌类数据库，并评估了部分 18S SSU 基因标记用于物种注释。我们确定并讨论了在环境 PCR 研究（ePCR）中使用 99.1%的种内序列相似性阈值来区分物种（OTU 聚类），并估计了潜在的物种多样性，比描述的形态物种多 99%。当将确定的阈值应用于 ePCR 数据集（包括来自 NGS 和克隆的序列）时，我们发现了 64 个 OTU，其中 21.9%与数据库有直接匹配（>99.1%相似度），其余的平均与最佳匹配的相似度为 90.2±0.8%，因此被认为代表了暗孢粘菌类未被发现的多样性。
