Data from: Tracking earthworm communities from soil DNA

Earthworms are known for their important role within the functioning of an ecosystem, and their diversity can be used as an indicator of ecosystem health. To date, earthworm diversity has been investigated through conventional extraction methods such as handsorting, soil washing or the application of a mustard solution. Such techniques are time-consuming and often difficult to apply. We showed that combining DNA metabarcoding and next generation sequencing facilitates the identification of earthworm species from soil samples. The first step of our experiments was to create a reference database of mitochondrial DNA (mtDNA) 16S gene for 14 earthworm species found in the French Alps. Using this database, we designed two new primer pairs targeting very short and informative DNA sequences (about 30 bp and 70 bp) that allow unambiguous species identification. Finally, we analyzed extracellular DNA taken from soil samples in two localities (two plots per locality, eight samples per plot). The two short metabarcode regions led to the identification of a total of eight earthworm species. The earthworm communities identified by the DNA-based approach appeared to be well-differentiated between the two localities, and are consistent with results derived from inventories collected using the handsorting method. The possibility of assessing earthworm communities from hundreds or even thousands of localities through the use of extracellular soil DNA will undoubtedly stimulate further ecological research on these organisms. Using the same DNA extracts, our study also illustrates the potential of environmental DNA as a tool to assess the diversity of other soil-dwelling animal taxa.蚯蚓在生态系统功能运转中发挥着核心作用，其多样性可作为生态系统健康状况的指示指标。迄今为止，针对蚯蚓多样性的调查多采用手拣法、土壤洗脱法或芥末溶液浸提等传统提取手段，但此类方法往往耗时费力且应用局限性较强。本研究证实，将DNA元条形码（DNA metabarcoding）与下一代测序技术相结合，可实现土壤样本中蚯蚓物种的高效鉴定。本实验的首要步骤是为法国阿尔卑斯山区分布的14种蚯蚓构建线粒体DNA（mtDNA）16S基因参考数据库。依托该数据库，我们设计了两对全新引物，可靶向扩增长度约30bp与70bp的信息性短DNA序列，实现物种的精准无歧义鉴定。最后，我们对两个采样区域的土壤样本胞外DNA（extracellular DNA）进行了分析，每个区域设置2个样地，每个样地采集8份样本。本次研究通过两段短元条形码序列，共鉴定出8种蚯蚓。基于DNA技术解析得到的蚯蚓群落在两个采样区域间呈现显著分化，且与手拣法野外调查所得结果高度吻合。借助土壤胞外DNA即可完成成百上千个采样区域的蚯蚓群落评估，这无疑将极大推动该类群的相关生态学研究。此外，本研究还通过同一套DNA提取物证实，环境DNA（environmental DNA）可作为评估其他土壤栖居动物类群多样性的有效工具。