Strange microbe “breathes” nitrates using a mitochondria-like symbiont

At the bottom of Lake Zug, Switzerland, swims a microorganism that has developed a strange way of “breathing”. A team of researchers has discovered a new partnership between a single-celled eukaryote – an organism with a clearly defined nucleus containing its genome – and a bacterium that generates energy for its host. But instead of using oxygen to do this, it uses nitrate.

“It’s a very strange, [newly discovered] organism, ”said Jana Milucka, biologist at the Max Planck Genome Center in Cologne and lead author of the resulting article, published in Nature early March.

The team named the bacteria Candidatus Azoamicus ciliaticola, meaning “friend of nitrogen that lives inside a ciliate”. Its partner, the ciliate, is a microorganism that moves with the help of cilia, tiny hair-like protrusions on the outside of their cell walls. The host organism is part of a group of ciliates called Plagiopylea.

Find a partnership

In 2016, the researcher visited Lake Zug to research genetics. Milucka and his peers have been studying the body of water for nearly a decade. It’s completely layered, with a layer of hydrogen peroxide on top, then an oxygen-free layer near the bottom. As such, organisms that thrive in the depths have had to evolve to get by without oxygen.

The team lowered a sample bottle to about 190 meters and then sequenced 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 lacked genes to suggest that it belonged to an organism that would need to be grafted onto another to survive. The genome was similar in size to the genomes of symbiotic microorganisms that reside in the bodies of insects and carried many genetic similarities.

But insects cannot survive in the deeper parts of lakes, which therefore does not explain the presence of this genome. If the bacteria lived in another organism, the obvious question was: “which one?” Researchers began to probe the water and found a likely candidate: the ciliate in question. Shortly before the COVID-19 lockdown and border closure in February 2020, the team returned to the lake one last time to collect a sample to test, which confirmed their findings.

Milucka said that in the body of the eukaryote, the bacteria act in the same way as mitochondria in other cells – except that instead of using oxygen, it uses nitrate to generate l ‘ATP for its host.

Symbiosis between a eukaryote and a bacterium is common. But the partnership described by Milucka and his team is distinct in several ways. First, the bacteria evolved alongside its host long enough that it could no longer live apart – it’s not entirely unheard of, but it’s rare. It is also rare for a bacterium to supply ATP directly to its host. Finally, there is no evidence of a eukaryotic-bacteria partnership that relies on nitrate respiration and in which the ability to use oxygen has been completely lost.

“There isn’t really a similar example among the endosymbionts that we know of today,” Milucka said.

The power to move

Eukaryotes spring up on their eyelashes. 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’s moving. It’s actually super fast,” Milucka said. “It’s like a rocket.”

The team suspect that the bacteria had the ability to use oxygen somewhere in their past, but they could have lost it by adjusting to life in an oxygen-free environment. Alternatively, he could have simply lost the gene by accident. “We don’t really know if it was on purpose or if it was just by chance that he lost the gene,” she said.

In all cases, the team used DNA analysis and comparisons with similar genetic sequences to estimate that the partnership between the two microorganisms began between 200 and 300 million years ago, and it s ‘has been in depth 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 the length of the partnership between the microorganisms, it is unlikely that it started in the lake, Milucka said. The team checked whether genes similar to the bacteria existed and found that the closest sequences also existed in layered lakes like Lake Zug. It is therefore possible that adaptation originally came from similar lakes, although the ocean is another option. “There seems to be a trend that at least the closest relative sequences are found in very similar habitats,” she said.

The findings have implications far beyond the uniqueness of the leaf of it all. Endosymbiosis is the main explanation for how cells originally got their mitochondria. Billions of years ago –1.45 billion according to some sources– single-celled life forms engulfed bacteria which, in turn, began to provide them with energy. Eventually the bacteria became part of the cells.

This partnership between the organizations of Lake Zug is comparatively quite recent. According to Milucka, this finding could offer some insight into how mitochondria formed in the past, because in some ways it might sound like an early point in the process.

This research is one of the first examples of an endosymbiont bacteria developing into 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 always been quite difficult to understand how mitochondria formed, simply because it happened so long ago. As such, Candidatus Azoamicus ciliaticola and its ciliates offer a relatively modern example of how this could have happened.

In addition, understanding the process of endosymbiosis is fundamental to understanding the origins of complex life. “This is an example of an accidental discovery that has really 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 journalist. His works have appeared in National Geographic, Undark, and Hakai Magazine, among others.