**5. Conclusions**

The endosymbiotic green algae of *Paramecium bursaria* can be clearly identified at the species level using the diagnostic PCR approach. This approach is also applicable for other mixotrophic ciliates if species-specific primers were designed. For the design of these primers, it is necessary to know which green algal endosymbionts occur in the green algal–ciliate association. This can be provided by isolation of the endosymbionts using the three-step method described above. Axenic cultures of isolated endosymbionts allow further genomic studies, such as the sequencing of whole genomes and plastomes.

**Author Contributions:** Conceptualization, T.P. and T.D.; methodology, C.S., T.B. and T.P.; software, T.P.; validation, T.P., T.D. and B.S.; formal analysis, T.P.; investigation, C.S., T.B. and T.P.; resources, T.P.; data curation, T.P., T.D. and B.S.; writing—original draft preparation, C.S., T.D., B.S. and T.P.; writing—review and editing, T.D., B.S. and T.P.; visualization, T.P. and T.D.; supervision, T.P.; project administration, B.S. and T.P.; funding acquisition, B.S. and T.P. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by the Austrian Science Fund (FWF): gran<sup>t</sup> number P28333-B25.

**Conflicts of Interest:** The authors declare no conflict of interest.
