Phylogenetic and ecological diversity of apusomonads, a lineage of deep-branching eukaryotes

Apusomonads are a mysterious group of heterotrophic gliding biflagellates branching deeply in the eukaryotic tree of life as sister group to opisthokonts (including animals, fungi, and a variety of unicellular protists). Despite their evolutionary interest, their diversity and ecology remain largely unknown, with very few described species and environmental sequences in databases. Most environmental 18S rRNA gene-based studies generally fail to identify apusomonad sequences, which might be due to primer bias, low abundance, and/or to the fact that their biotopes remain poorly explored. We have carried out an extensive search of 18S rRNA genes using an apusomonad-specific primer in a wide variety of ecosystems. Our study significantly broadens the diversity of apusomonads showing that, despite being mostly rare protists, they often dwell in freshwater and marine benthic environments, generally associated with low-oxygen concentrations. Apusomonads have been identified in environments across a wide salinity range. Some operational taxonomic units (OTUs), occurring in both marine and freshwater ecosystems, seem truly euryhaline, indicating that members of this deep-branching lineage easily cross such ecological barriers.