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.元条形码（Metabarcoding）技术利用环境样品中的总DNA（通常为降解DNA）分析生物群落，理论上可用于检测生态系统中的任意一类生物。此类分析依赖于特定标记序列，本文中将其称为元条形码（metabarcodes），这类标记需针对分类学分辨率、目标类群扩增的最小偏倚以及较短的序列长度进行优化。借助生物信息学工具，我们针对真菌（fungi）、苔藓植物（bryophytes）、颤蚓类（enchytraeids）、甲虫（beetles）和鸟类（birds）这几类生物开发了元条形码序列。我们通过以下三种方式系统评估了这些元条形码对目标类群的扩增能力：（1）以欧洲分子生物学实验室（EMBL）公共数据库中的所有标准序列作为模板，开展计算机模拟PCR（in silico PCR）；（2）以挪威北部瓦朗厄尔（Varanger）地区某位点的表层土壤样品DNA提取物进行体外PCR扩增；（3）以两处西伯利亚位点——杜万尼亚尔（Duvanny Yar）和主河（Main River）——的晚更新世时期（距今约16000–50000 yr BP）永久冻土沉积物样品的DNA提取物开展体外PCR扩增。将计算机模拟PCR的结果与体外实验结果对比后发现，计算机模拟方法可可靠地评估标记序列的适用性。所有目标类群均在环境DNA中被检出，但不同类群间以及现代与古代样品间的检出水平存在显著差异。晚更新世样品中，真菌DNA的扩增成功率最高，苔藓植物、甲虫和鸟类的序列虽也可被检出，但检出率要低得多。元条形码技术在现代样品的生物多样性筛查以及作为古生态学研究工具方面均具有巨大应用潜力。