Molecular profiling of soil animal diversity in natural ecosystems: Incongruence of molecular and morphological results

A major problem facing ecologists is obtaining a complete picture of the highly complex soil community. While DNA-based methods are routinely used to assess prokaryote community structure and diversity in soil, approaches for measuring the total faunal community are not yet available. This is due to difficulties such as designing primers specific to a range of soil animals while excluding other eukaryotes. Instead, scientists use laborious and specialized taxonomic methods for extracting and identifying soil fauna. We examined this problem using DNA sequencing to profile soil animal diversity across two Alaskan ecosystems and compare the results with morphological analyses. Of 5267 sequences, representing 549 operational taxonomic units (OTU), only 18 OTUs were common to both sites. Representatives included 8 phyla, dominated by arthropods and nematodes. This is the most comprehensive molecular analysis of soil fauna to date, and provides a tool to rapidly assess a missing component of soil biodiversity.