This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re‐introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under‐sampled areas and from environmental genomic information.

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

Dinophytes are widely distributed in marine‐ and fresh‐waters, but have yet to be conclusively documented in terrestrial environments. Here, we evaluated the presence of these protists from an environmental DNA metabarcoding dataset of Neotropical rainforest soils. Using a phylogenetic placement approach with a reference alignment and tree, we showed that the numerous sequencing reads that were phylogenetically placed as dinophytes did not correlate with taxonomic assignment, environmental preference, nutritional mode, or dormancy. All the dinophytes in the soils are rather windblown dispersal units of aquatic species and are not biologically active residents of terrestrial environments.

The soil food web is often described as having three main energy channels: root, bacterial and fungal. Here we provide quantitative data using a sensitive stable isotope ratio mass spectrometry procedure with microcosms on species interactions in the fungal pathway. We measured ¹⁵N and ¹³C enrichment in microarthropods through grazing rare isotope enriched fungal mycelia. Experimental treatments were various combinations of 1, 2, 3, 4 microarthropods species. We used three fungivores (the collembolan Lepidocyrtus curvicollis, the Astigmata Tyrophagus putrescentiae, the Oribatida Oribatula tibialis), and the Mesostigmata predator Hypoaspis acquilifer. We collected individuals of each species separately, as well as their feces, and molt where available. All three fungivorous microarthropods consumed significantly more than their own body weight per day. The three fungivores differed in their consumption of the mycelium as it was not equally palatable to each. The Mesostigmata predator Hypoaspis also differed in its microarthropod prey preference. In multiple species combinations microarthropod behavioral interactions modified consumption and predation rates. Our selection of mites of different sizes, with varied preference for the mycelium, combined with differing predation rates on each mite, demonstrate that even three trophic level interactions with only five interacting species are not predictably simple. The interpretation of the stable isotope results and consumed-excreted weights indicate that: (a) behavior and microscopic observations should not be ignored in competition-predation interactions, and (b) functional guilds can take advantage of more diverse food opportunities. The reality of mixed diets complicates functional guild assignments that are reflected in ¹⁵N and ¹³C isotope levels at natural abundances in the environment. Microcosm experiments with this sensitive technique can help decipher the interpretation of rare isotope natural abundance values, as well as providing measured consumption, growth, and excretion rate values for modeling soil food web interactions.

Collembola display a variety of feeding habits, and prey on many types of food at different trophic levels in the soil. In most cases, their feeding selections are widely varied. In the interest of the food preferences of E. proxima, we attempted to confirm how the Collembola utilize food when feeding on carrion (unusual sources). Four different soil animals (with different stable isotope values and increasing trophic levels) were used to examine whether collembolans can use dead insects as a food resource in specific manners, depending on food preference. Our results demonstrated that the food preference of a collembolan changed significantly after feeding on insects with different feeding habits for 60 days. We found that stable isotope values (δ¹³C) of Entomobrya proxima approached those of the food sources. A large proportion of the diet (more than 50%) should directly consist of insect body parts, with the remainder consisting of indirectly used, mixed microorganisms naturally growing on animal food, such as fungi (Rhizopus sp., Alternaria sp., Penicillium sp., and Aspergillus sp.) and bacteria (Bacillus sp1. and Bacillus sp2.). Based on this research, the food preference of collembolans is more focused on carcasses (dead insect bodies) than microorganisms during the animal-food decomposition process.