Environmental DNA of insects and springtails from caves reveals complex processes of eDNA transfer in soils

Subterranean environments host a substantial amount of biodiversity, however assessing the distribution of species living underground is still extremely challenging. Environmental DNA (eDNA) metabarcoding is a powerful tool to estimate biodiversity in poorly known environments, and has excellent performance for soil organisms. Here we tested 1) whether eDNA metabarcoding from cave soils allows to successfully detect springtails (Hexapoda: Collembola) and insects (Hexapoda: Insecta); 2) whether eDNA mostly represents autochthonous (cave-dwelling) organisms, or it also incorporates information from species living in surface environments; 3) if eDNA detection probability changes across taxa with different ecology. eDNA metabarcoding analyses detected a large number of molecular operational taxonomic units (MOTUs) of both insects and springtails. For springtails, detection probability was high, with a substantial proportion of hypogean species, suggesting that eDNA provides good information on the distribution of these organisms in caves. Conversely, for insects most of MOTUs represented taxa living outside caves, and the majority of eDNA reads were from MOTUs living in freshwater environments (Ephemeroptera, Plecoptera and Trichoptera). The eDNA of freshwater insects was particularly abundant in deep sectors of caves, far from the entrance. Furthermore, average detection probability of insects was significantly lower than the one of springtails. This suggests that cave soils act as "conveyer belts of biodiversity information", possibly because percolating water lead to the accumulation of eDNA of organisms living in nearby areas. Cave soils hold a complex mix of autochthonous and allochthonous DNA. eDNA provides unprecedented information on the understudied subterranean cave organisms; analyses of detection probability and occupancy can help teasing apart local eDNA from the eDNA representing spatially-integrated biodiversity for whole landscape.
We present the complete dataset used for this analysis.For both insects (marker Ins01) and springails (Coll01) we present the table reporting the filtered sequences, with the number of reads obtained for each MOTU in each PCR replicate of each sample. The table also includes the taxonomic and ecological classification of each MOTU.
The dataset is a excel file including 2 data sheets and one legend sheet