Deep in Switzerland’s Lake Zug swims a microorganism that has developed a strange way of ‘breathing’. A team of researchers has discovered a new partnership between a unicellular 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, it uses nitrate.
‘It’s very strange, [newly discovered] organism, ”said Jana Milucka, a biologist at the Max Planck Genome Center in Cologne and senior author of the resulting article, published in Nature in early March.
The team named the bacteria Candidatus Azoamicus ciliaticola, which means “nitrogen friend living in a silicate.” Its counterpart, the ciliate, is a microorganism that moves around by using cilia, small hair-like protrusions outside their cell walls. The host organism is part of a group of ciliates called Plagiopylea.
Find a partnership
In 2016, the researcher traveled to the Zugmeer in search of genetics. Milucka and her friends have been studying water mass for almost a decade. It is completely stratified, with a layer of oxygen-containing water on top, and then a layer containing oxygen near the bottom. As such, the organisms that thrive in depth had to evolve to get by without oxygen.
The team dropped a sample bottle after about 190 meters and then traced the DNA of all the organisms in the sample. They found a bacterial genome that contained a complete metabolic pathway for nitrate respiration. But the genome was small and did not have enough genes to indicate that it belonged to an organism that needed another bulge to survive. The genome was similar to the genome of symbiotic microorganisms found in the bodies of insects and has many genetic similarities.
But insects cannot survive in the deepest parts of lakes, and this does not explain the presence of this genome. If the bacteria lived in another organism, the obvious question was ‘which one?’ The researchers began investigating the water and found a possible candidate: the ciliate in question. Shortly before COVID-19 closures and the closure of the border in February 2020, the team returned to the lake for the last time to collect a sample for testing, confirming their findings.
Milucka said the bacteria inside the eukaryotic body act similarly to mitochondria in other cells – in addition to using oxygen, it uses nitrate to generate ATP for its host.
Symbiosis between a eukaryote and a bacterium is common. But the partnership that Milucka and her team describe is clear in a few ways. First, the bacteria have evolved long enough next to the host so that they can no longer live separately – this is not entirely unheard of, but it is rare. It is also rare for a bacterium to supply ATP directly to its host. Finally, there is no evidence of a eukaryotic bacterial partnership that relies on nitrate respiration and in which the ability to use oxygen is completely lost.
“There’s not really a similar example among the endosymbionts we know today,” Milucka said.
Power to move
The eukaryotes radiate on their cilia. It 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’s moving. It’s actually super fast, ‘said Milucka. “It’s like a rocket.”
The team suspects the bacteria had the ability to use oxygen somewhere in the past, but it could have lost it because it adapted in an oxygen-free environment. Alternatively, it could have accidentally lost the genes. “We do not really know if it was intentional or if it was just a coincidence that he lost the gene,” she said.
In any case, the team used DNA analysis and comparisons with similar gene sequences to estimate that the partnership between the two microorganisms began between 200 and 300 million years ago, and it has grown deeper ever since. But this raises questions in the case of Candidatus Azoamicus ciliaticola and its host, because Lake Zug formed only about 10,000 years ago during the last interglacial period.
Given how long the partnership between the microorganisms has lasted, it is unlikely to have started in the lake, Milucka said. The team looked for similarities to the bacteria, and found that the nearest ranges also exist in layered lakes such as the Zugmeer. It is therefore possible that the adaptation originally came from similar lakes, although the ocean is another option. “There seems to be a pattern that at least the closest relative ranges occur in very similar habitats,” she said.
The findings have implications that are far more than the strangeness of everything. Endosymbiosis is the main explanation for how cells originally got their mitochondria. Billions of years ago—1.45 billion by some sources—Local life forms devour bacteria that in turn begin to supply energy. Eventually, the bacteria became part of the cells.
This partnership between the organisms in the Zugmeer is relatively new. According to Milucka, this discovery may provide a glimpse into how mitochondria were formed in the past, as they may in some ways appear at an early stage in the process.
This study 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, emeritus professor at the Department of Biochemistry and Molecular Biology at Dalhousie University in Nova Scotia , said. According to Gray, who has written extensively on endosymbiosis, it has historically been quite difficult to gain insight into how mitochondria formed simply because it happened so long ago. As such, Candidatus Azoamicus ciliaticola and his ciliate provides a relatively modern example of how this may have happened.
Furthermore, understanding the process of endosymbiosis is fundamental to understanding the origin of complex life. “This is an example of an accidental discovery that opened our eyes a little wider 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 appear in National Geographic, Undark and Hakai Magazine, among others.