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的总DNA（通常为降解态DNA）解析生物群落组成，理论上可覆盖生态系统内的所有生物类群。此类分析依赖于特定标记序列——本文将其称为宏条形码标记（metabarcodes），其需在分类学分辨率、目标类群扩增偏差控制及序列长度三方面进行优化。本研究借助生物信息学工具，针对真菌、苔藓植物、线蚓类、甲虫及鸟类这几类生物开发了专属宏条形码标记。我们通过三类实验系统评估了上述宏条形码标记的目标类群扩增效能：其一，以欧洲分子生物学实验室（EMBL）公共数据库内的全部标准序列为模板，开展计算机模拟PCR（in silico PCR）；其二，以挪威北部瓦朗厄尔地区某采样点的表层土壤DNA提取物为模板，开展体外PCR；其三，以两处西伯利亚采样点（杜万尼雅尔与主河）的晚更新世时期（距今约16000~50000年）永久冻土沉积物的DNA提取物为模板，开展体外PCR。将计算机模拟PCR结果与体外PCR结果进行比对后发现，计算机模拟方法可可靠评估标记序列的适用性。所有目标类群均在环境DNA样本中被成功检出，但不同类群间以及现代与古样本间的检出水平存在显著差异。晚更新世样本中，真菌DNA的检出成功率最高；苔藓植物、甲虫及鸟类的序列虽也可被成功获取，但检出率显著偏低。宏条形码技术在现代样本的生物多样性筛查中具备极大应用潜力，同时亦可作为古生态学研究的有效工具。