Soil eukaryote communities (per sample) differed most at the taxonomic rank approximating to order level.

The primary outcome was the relative abundance of bacteria at the phylum, family, and genus taxonomic ranks.

This has challenged many of the definitions of taxonomic groups, especially higher taxonomic ranks such as eukaryotic kingdoms.

Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level.