All together now: Limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences

The soil environment contains a large, but historically underexplored, reservoir of biodiversity. Sequencing prokaryotic marker genes has become commonplace for the discovery and characterization bacteria archaea. Increasingly, this approach is also applied to eukaryotic characterize diversity distribution eukaryotes. However, understanding properties limitations sequences essential correctly analysing, interpreting, synthesizing resulting data. Here, we illustrate several biases from sequencing data that affect measurements biodiversity arise variation in morphology, taxonomy phylogeny between organisms, as well sampling designs. We recommend analytical approaches overcome these limitations, outline how benchmarking standardization protocols may improve comparability