Species-specific environmental DNA analysis of the index species in soil ecosystem, Allonychiurus kimi (Collembola: Onychiuridae)

Abstract

Collembola are abundant and have significant roles in the soil ecosystem. Therefore, the phenotypic endpoints of Collembola population or community have been used as an effective bioindicator for assessing soil quality. Since the identification and counting the collembolans in the soil is a laborious and costly procedure, environmental DNA (eDNA)-based biomonitoring was proposed as an analysis tool of collembolan species found in the soil. In this study, standard primer sets for the species-specific eDNA analysis using Allonychiurus kimi, a soil bioindicator species was selected. Then, the primers were tested for specificity and sensitivity from the soil samples. Two different eDNA samples were tested: (1) eDNA samples were extracted from the soil with A. kimi individuals (intra-organismal eDNA). (2) The samples from the soil without A. kimi individuals (extra-organismal eDNA). The two primers were confirmed in their sensitivity and specificity to the two types of eDNA samples selected. Ct-values from both intra- and extra-organismal eDNA showed the significant correlations to the number of inoculated A. kimi (adj. R2 = 0.7453–0.9489). These results suggest that in excretion, egg, and other exuviae had a significant effect on eDNA analysis from soil samples taken. Furthermore, our results suggest that environmental factors should be considered when analyzing eDNA collected from soil.