Most eukaryotes generate energy through breathing oxygen. This happens in mitochondria, specialized organelles likely acquired by the ancestor of eukaryotes when it engulfed a free-living prokaryote. Over time, this prokaryote became an obligate endosymbiont, meaning that neither the prokaryote nor its eukaryotic host could survive without the other. Then with more time it became an organelle, by keeping only the genes needed for oxygen respiration and losing genes for independent living.

But not all eukaryotes breathe oxygen. In a paper published in Nature, researchers investigating a lake in Switzerland found many eukaryotic ciliates (single-celled eukaryotic organisms covered with tiny hairs they use to move) which swam away from oxygen, indicating that they used something else for energy. 

When the researchers stained the ciliates with a DNA-binding dye, they found multiple pockets of DNA within each ciliate outside of its nucleus. Using a different fluorescent dye, they found that these pockets contained only bacterial DNA. The researchers extracted and sequenced the DNA, and obtained a small circular genome not belonging to any known bacterium. They named this novel organism ‘Candidatus Azoamicus ciliaticola’.

Why was this bacterium inside these ciliates? The researchers compared its genome to other bacteria to answer this question. Like many other endosymbionts, the bacterium's genome was very small and lacked the genes needed for independent living. In particular, this genome contained a high proportion of genes for energy production, similar to mitochondrial genomes. However, it lacked genes for oxygen respiration. It instead possessed the genes needed for nitrate respiration. These clues led the researchers to conclude that ‘Candidatus Azoamicus ciliaticola’ was an obligate endosymbiont that enabled its ciliate host to breathe nitrate — not oxygen — for energy. This adaptation allows the ciliate to live in waters low in oxygen but high in nitrate.

While many free-living prokaryotes can respire nitrate, this is the first instance of this metabolism in a prokaryotic endosymbiont. Perhaps other eukaryotes out there have acquired new metabolisms with the help of endosymbionts. These interkingdom partnerships may allow eukaryotes to colonize environments formerly assumed to be the domain of only bacteria and archaea.