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.

蚯蚓在生态系统运转中发挥着关键作用，其物种多样性可作为生态系统健康状况的指示指标。迄今为止，学界多通过手捡法、土样淘洗法或芥末溶液驱提法等传统方式开展蚯蚓多样性调查，但这类方法耗时较长且往往难以推广应用。本研究证实，将DNA宏条形码（DNA metabarcoding）与下一代测序（next generation sequencing）相结合，可实现土壤样本中蚯蚓物种的高效鉴定。本研究的实验第一步，是针对法国阿尔卑斯山区发现的14种蚯蚓，构建线粒体DNA（mtDNA）16S基因的参考数据库。基于该参考数据库，本研究设计了两对全新引物，靶向长度约30bp和70bp的高信息含量短DNA序列，可实现精准的物种鉴定。最后，本研究对两个采样地点的土壤样本中的细胞外DNA（extracellular DNA）进行了分析：每个采样点设置2个样地，每个样地采集8份样本。上述两段短宏条形码序列区域共鉴定出8种蚯蚓。基于DNA检测方法得到的蚯蚓群落，在两个采样地点间呈现出显著的群落分化特征，且与手捡法调查得到的结果相一致。通过土壤细胞外DNA即可对成百上千个采样点的蚯蚓群落进行评估，这一方法无疑将推动针对这类生物的后续生态学研究。此外，本研究还证实，利用相同的DNA提取物，环境DNA（environmental DNA）可作为评估其他土壤栖息动物类群多样性的有效工具。