Single-celled eukaryotes (protists) often harbor bacterial or archaeal symbionts inside their cells. However, the functional role of these endosymbionts is in most cases unknown. Diplonemids (Excavata: Euglenozoa: Diplonemida) are heterotrophic protists found in marine and freshwater environments. Only a handful of diplonemids species from seven genera were described so far, yet planktonic diplonemids likely contain thousands of species and were found to be among the most abundant marine protists. Although they clearly play an important role in marine ecosystems, their lifestyle and interactions with other species are extremely poorly understood.
Here, we attempt to fill this gap by characterizing bacterial symbionts of diplonemids by genome sequencing, transcriptomics, and microscopy. We describe two lineages of bacterial symbionts that closely interact with mitochondria of diplonemids. These symbionts were acquired independently and cluster within Holosporales and Rickettsiales (Alphaproteobacteria).
Surprisingly, they have the smallest genomes (616-632 kbp) reported from protist symbionts to date. Their genome reduction converged on extremely similar gene content and very limited metabolic potential. The most striking features found in both of these endosymbionts include type VI secretion systems, toxin-antitoxin systems, and numerous secreted proteins. Due to their very limited metabolic potential, nutritional symbiosis seems to be highly unlikely and we hypothesize that their functional role is either parasitism or defensive symbiosis.