Data from: Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil fauna

Protists, the most diverse soil eukaryotes, are largely considered to be free-living bacterivores, but vast numbers of taxa are known to parasitize plants or animals. High-throughput sequencing (HTS) approaches now consecutively replace cultivation-based approaches in studying soil protists, but insights into common biases associated to this method are limited to aquatic taxa and samples. We applied 454 HTS on known mock communities containing common soil protists to evaluate whether HTS quantitatively reveals true relative abundances of soil protists. We added DNA extracted from members of various major groups of soil fauna to investigate whether the expected protist community structure is altered by the co-amplfication of additional, fauna-associated, protist taxa. Indeed, protist communities identified by HTS strongly differed from what was expected. Among sequences of added taxa, ciliates were highly overrepresented, while those of most amoebae and flagellates were underrepresented or totally absent. We further detected a wide range of non-added protist taxa that affected the protist community structure and were likely introduced along faunal DNA. Among those were 20 potential parasitic taxa. Therewith, we here provide the first HTS data in support of classical observational studies that showed that soil fauna hosts protist parasites. Our results underpin the biases introduced by HTS that prevent reliable quantitative estimations of free-living protist communities. Profound differences in amplification success between protist taxa and an inevitable co-extraction of protist taxa parasitizing soil fauna obscure the true diversity of free-living soil protist communities.