Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (1) in silico PCRs using all standard sequences in the EMBL public database as templates, (2) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway, and (3) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (~ 16 000–50 000 yr BP) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a paleoecological tool.

宏条形码（metabarcoding）技术依托环境样本中提取的、通常已发生降解的总DNA开展生物群落分析，理论上可用于检测生态系统中的所有生物类群。此类分析依赖于一类被称为宏条形码（metabarcodes）的特异性标记序列，这类标记需在分类学分辨率、靶类群扩增偏倚控制以及序列长度三方面实现优化。本研究借助生物信息学工具，针对真菌、苔藓植物、线蚓类、甲虫类与鸟类这五大类生物开发了专用宏条形码。本研究通过以下三种方式系统评估了这些宏条形码对靶类群的扩增能力：（1）以欧洲分子生物学实验室（EMBL）公共数据库中的全部标准序列作为模板开展电子PCR（in silico PCR）；（2）以挪威北部瓦朗厄尔地区一处样地的表层土壤DNA提取物为模板开展体外PCR（in vitro PCR）；（3）以西伯利亚两处采样点——杜万尼亚尔（Duvanny Yar）与梅因河（Main River）——的晚更新世（距今约16000~50000年BP）永久冻土沉积物DNA提取物为模板开展体外PCR。将电子PCR结果与体外PCR结果进行比对后发现，电子PCR方法可可靠评估标记序列的适用性。所有靶类群均在环境DNA样本中被检出，但不同类群间以及现代与古代样本间的检出水平存在显著差异。晚更新世样本中，真菌DNA的扩增成功率最高；苔藓植物、甲虫类与鸟类的序列虽也可被检出，但检出率显著更低。宏条形码技术在现代样本的生物多样性筛查以及古生态学研究中均具备可观的应用潜力。