基于 DNA 的全球环境调查在检测所有原生生物多样性方面的效果如何?以 Arcellinida 为例,说明其代表性存在偏差。

IF 4.3 2区 生物学 Q2 MICROBIOLOGY
Fernando Useros, Iván García-Cunchillos, Nicolas Henry, Cédric Berney, Enrique Lara
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引用次数: 0

摘要

针对微真核细胞的元条码方法深深改变了我们对原生生物环境多样性的看法。公共数据库 EukBank 包含来自全球 12,672 个样本的 18S v4 元条码。为了评估该数据库在多大程度上提供了对所有真核生物多样性的合理概述,我们以阿卡林虫(叶状睾丸变形虫)为案例进行了研究。我们假设:(1)这种方法可以发现意想不到的多样性,但(2)由于引物/测序偏差,某些类群的代表性不足。大多数 Arcellinida 序列出现在淡水和土壤中,但它们的丰度和多样性似乎代表性不足。此外,84% 的 ASV 属于 Phryganellina 亚目,这是一个物种稀少的支系,而记录最详尽的亚目(Glutinoconcha,600 个已描述的物种)仅有少量代表。我们探讨了造成这些偏差的一些可能原因。引物结合位点的错配似乎起了次要作用。目标区域过长可以解释部分偏差,但不是全部。肯定还有其他未知因素。总之,虽然基于核糖体基因的代谢条形码仍然是记录微生物真核生物支系的第一种好方法,但必须考虑基于其他基因或测序技术的替代方法,以无偏见地反映某些群体的多样性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation

How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation

How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation

Metabarcoding approaches targeting microeukaryotes have deeply changed our vision of protist environmental diversity. The public repository EukBank consists of 18S v4 metabarcodes from 12,672 samples worldwide. To estimate how far this database provides a reasonable overview of all eukaryotic diversity, we used Arcellinida (lobose testate amoebae) as a case study. We hypothesised that (1) this approach would allow the discovery of unexpected diversity, but also that (2) some groups would be underrepresented because of primer/sequencing biases. Most of the Arcellinida sequences appeared in freshwater and soil, but their abundance and diversity appeared underrepresented. Moreover, 84% of ASVs belonged to the suborder Phryganellina, a supposedly species-poor clade, whereas the best-documented suborder (Glutinoconcha, 600 described species) was only marginally represented. We explored some possible causes of these biases. Mismatches in the primer-binding site seem to play a minor role. Excessive length of the target region could explain some of these biases, but not all. There must be some other unknown factors involved. Altogether, while metabarcoding based on ribosomal genes remains a good first approach to document microbial eukaryotic clades, alternative approaches based on other genes or sequencing techniques must be considered for an unbiased picture of the diversity of some groups.

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来源期刊
Environmental microbiology
Environmental microbiology 环境科学-微生物学
CiteScore
9.90
自引率
3.90%
发文量
427
审稿时长
2.3 months
期刊介绍: Environmental Microbiology provides a high profile vehicle for publication of the most innovative, original and rigorous research in the field. The scope of the Journal encompasses the diversity of current research on microbial processes in the environment, microbial communities, interactions and evolution and includes, but is not limited to, the following: the structure, activities and communal behaviour of microbial communities microbial community genetics and evolutionary processes microbial symbioses, microbial interactions and interactions with plants, animals and abiotic factors microbes in the tree of life, microbial diversification and evolution population biology and clonal structure microbial metabolic and structural diversity microbial physiology, growth and survival microbes and surfaces, adhesion and biofouling responses to environmental signals and stress factors modelling and theory development pollution microbiology extremophiles and life in extreme and unusual little-explored habitats element cycles and biogeochemical processes, primary and secondary production microbes in a changing world, microbially-influenced global changes evolution and diversity of archaeal and bacterial viruses new technological developments in microbial ecology and evolution, in particular for the study of activities of microbial communities, non-culturable microorganisms and emerging pathogens
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