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Abstract Radiolarians are marine protists with a global distribution. Epipelagic radiolarians host photosynthetic endosymbionts, but the identity and specificity of this relationship appears to vary between radiolarian subgroups. While the class Acantharea and the order Collodaria both possess stable and relatively specific relationships with the haptophyte Phaeocystis and the dinoflagellate Brandtodinium nutricula, respectively, the orders Nassellaria and Spumellaria (which comprise the solitary Polycystinea) might have greater flexibility in terms of the identity of their photosymbionts. However, little molecular data has been generated to identify the phytoplankton with which polycystines can associate. Here, we performed short-read 16S and 18S rRNA gene sequencing with universal primers on single polycystine cells collected from the Sargasso Sea to determine common members of the polycystine holobiont. While previous work on polycystine photosymbioses suggested that they almost always exclusively associate with B. nutricula, we determined that polycystines instead associated with a wide diversity of phytoplankton, and the diversity of the polycystine holobiont is distinct from the diversity of environmental samples. Finally, we found that a substantial proportion of the reads associated with cell samples were of opisthokont origin (mostly copepods), revealing other possible interactions between an uncultivable and difficult-to-study protist with its environment. 

Abstract The early evolution of eukaryotes and their adaptations to low-oxygen environments are fascinating open questions in biology. Genome-scale data from novel eukaryotes, and particularly from free-living lineages, are the key to answering these questions. The Parabasalia are a major group of anaerobic eukaryotes that form the most speciose lineage of Metamonada. The most well-studied are parasitic parabasalids, including Trichomonas vaginalis and Tritrichomonas foetus, but very little genome-scale data are available for free-living members of the group. Here, we sequenced the transcriptome of Pseudotrichomonas keilini, a free-living parabasalian. Comparative genomic analysis indicated that P. keilini possesses a metabolism and gene complement that are in many respects similar to its parasitic relative T. vaginalis and that in the time since their most recent common ancestor, it is the T. vaginalis lineage that has experienced more genomic change, likely due to the transition to a parasitic lifestyle. Features shared between P. keilini and T. vaginalis include a hydrogenosome (anaerobic mitochondrial homolog) that we predict to function much as in T. vaginalis and a complete glycolytic pathway that is likely to represent one of the primary means by which P. keilini obtains ATP. Phylogenomic analysis indicates that P. keilini branches within a clade of endobiotic parabasalids, consistent with the hypothesis that different parabasalid lineages evolved toward parasitic or free-living lifestyles from an endobiotic, anaerobic, or microaerophilic common ancestor.