Deep in Switzerland’s Lake Zug, a microorganism that has developed a strange way of “breathing” swims. A team of researchers discovered a novel association between a single-celled eukaryote (an organism with a clearly defined nucleus that contains its genome) and a bacterium that generates energy for its host. But instead of using oxygen to do it, it uses nitrate.
“This is very strange, [newly discovered] organism, ”said Jana Milucka, a biologist at the Max Planck Genome Center in Cologne and lead author of the resulting paper, published in Nature early March.
The team named the bacteria Candidatus Azoamicus ciliaticola, which means “friend of the nitrogen that lives inside a ciliate”. Its partner, the ciliate, is a microorganism that moves using cilia, small hair-like bumps outside its cell walls. The host organism is part of a group of ciliates called Plagiopylea.
Find a partnership
In 2016, the researcher traveled to Lake Zug in search of genetics. Milucka and his colleagues have been studying the body of water for almost a decade. It is completely stratified, with a layer of hydrogen peroxide on top and then a layer devoid of oxygen near the bottom. As such, organisms that thrive in the deep have had to evolve to survive without oxygen.
The team lowered a sample bottle about 190 meters and then sequenced the DNA of all organisms in the sample. They found a bacterial genome that contained a complete metabolic pathway for nitrate respiration. But the genome was small and lacked enough genes to imply that it belonged to an organism that would need to carry another to survive. The genome was similar in size to the genomes of symbiotic microorganisms that reside in the bodies of insects and have many genetic similarities.
But insects cannot survive in the deepest parts of lakes, so that does not explain the presence of this genome. If the bacteria lived in another organism, the obvious question was “which one?” Researchers began probing the water and found a possible candidate: the ciliate in question. Shortly before the COVID-19 border closures and lockdowns in February 2020, the team returned to the lake for the last time to collect a sample for testing, confirming their findings.
Milucka said that, inside the eukaryotic body, the bacterium acts in a similar way to mitochondria in other cells, except instead of using oxygen, it uses nitrate to generate ATP for its host.
The symbiosis between a eukaryote and a bacterium is common. But the association described by Milucka and her team is different in some ways. First, the bacterium has evolved together with its host long enough that it can no longer live apart; this is not totally unknown, but it is rare. It is also rare for a bacterium to provide ATP directly to its host. Finally, there is no evidence for an association between eukaryotes and bacteria that is based on nitrate respiration and in which the ability to use oxygen has been completely lost.
“There really isn’t a similar example among the endosymbionts we know of today,” Milucka said.
Power to move
Eukaryotes move on their cilia. This allows them to hunt other eukaryotes and bacteria, but increases their energy needs in an oxygen-free ecosystem, making nitrate respiration an ideal adaptation. “It moves. In fact, it’s super fast,” Milucka said. “It’s like a rocket.”
The team suspects that the bacteria had the ability to use oxygen somewhere in its past, but could have lost it by adapting to life in an environment without oxygen. Alternatively, you could simply have accidentally lost the gene. “We really don’t know if it was on purpose or by chance that he lost the gene,” he said.
In any case, the team used DNA analysis and comparisons to similar gene sequences to estimate that the association between the two microorganisms began between 200 and 300 million years ago, and has deepened ever since. But this raises questions in the case of Candidatus Azoamicus ciliaticola and its host, because Lake Zug only formed about 10,000 years ago, during the last interglacial period.
Considering how long ago the association between the microorganisms formed, it’s unlikely it started in the lake, Milucka said. The team checked for genes similar to those in bacteria and found that the closest sequences also existed in layered lakes such as Lake Zug. Therefore, it is possible that the adaptation originally came from similar lakes, although the ocean is another option. “There seems to be a pattern where at least the closest relative sequences are found in very similar habitats,” he said.
The findings have implications far beyond the oddity of all of this. Endosymbiosis is the main explanation for how cells originally got their mitochondria. Billions of years ago1,450 million according to some sourcesSingle-celled life forms devoured bacteria, which, in turn, began to provide them with energy. Eventually the bacteria became part of the cells.
This association between the organisms of Lake Zug is comparatively quite new. According to Milucka, this discovery could offer insight into how mitochondria formed in the past, as it could somehow resemble an early time in the process.
This research is one of the first examples of an endosymbiont bacterium in the process of becoming an organelle that generates energy for its host, said Michael Gray, professor emeritus in the Department of Biochemistry and Molecular Biology at Dalhousie University in Nova Scotia. According to Gray, who has written extensively on endosymbiosis, it has historically been quite difficult to understand how mitochondria formed, simply because it happened a long time ago. As such, Candidatus Azoamicus ciliaticola and his ciliate offers a relatively modern example of how it could have happened.
Furthermore, understanding the process of endosymbiosis is critical to understanding the origins of complex life. “It’s an example of an accidental discovery that has really opened our eyes a little bit more to what biology is capable of,” he said.
Nature, 2021. DOI: 10.1038 / s41586-021-03297-6 (About DOIs).
Doug Johnson (@DougcJohnson) is a Canadian freelance reporter. His works have appeared in National Geographic, Undark, and Hakai Magazine, among others.