Molecular identification of soil eukaryotes and focused approaches targeting protist and faunal groups using high-throughput metabarcoding

While until recently the application of high-throughput sequencing approaches has mostly been restricted to bacteria and fungi, these methods have now also become available to less often studied (eukaryotic) groups, such as fauna and protists. Such approaches allow routine diversity screening for large numbers of samples via DNA metabarcoding. Given the enormous taxonomic diversity within the eukaryote tree of life, metabarcoding approaches targeting a single specific DNA region do not allow to discriminate members of all eukaryote clades at high taxonomic resolution. Here, we report on protocols that enable studying the diversity of soil eukaryotes and, at high taxonomic resolution, of individual faunal and protist groups therein using a tiered approach: first, the use of a general eukaryotic primer set targeting a wide range of eukaryotes provides a rough impression on the entire diversity of protists and faunal groups. Second, more focused approaches enable deciphering subsets of soil eukaryotes in higher taxonomic detail. We provide primers and protocols for two examples: soil microarthropods and cercozoan protists.