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

Image of a spiky oval with yellow and blue shapes inside.
Enlarge / The bacteria (yellow) live inside a larger eukaryotic cell.

Deep in Switzerland’s Lake Zug swims a microorganism that has evolved a strange way to “breathe.” A team of researchers discovered a novel partnership between a single-celled eukaryote—an organism with a clearly defined nucleus holding its genome—and a bacteria that generates energy for its host. But instead of using oxygen to do so, it uses nitrate.

“This is a very weird, [newly discovered] organism,” said Jana Milucka, a biologist at the Max Planck Genome Center in Cologne and senior author on the resulting paper, published in Nature in early March.

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

Finding a partnership

In 2016, the researcher journeyed out into Lake Zug in search of genetics. Milucka and her peers have been studying the body of water for nearly a decade. It is completely stratified, with a layer of oxygenated water on top, and then a layer devoid of oxygen near the bottom. As such, the organisms that thrive in the depths have had to evolve to get by without oxygen.

The team lowered a sample bottle down to around 190 meters, 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 enough genes to imply that it belonged to an organism that would need to piggyback on another to survive. The genome was similar in size to the genomes of symbiotic microorganisms that reside in the bodies of insects and bore many genetic similarities.

But insects can’t survive in the deepest parts of lakes, so that didn’t explain the presence of this genome. If the bacteria was living in another organism, the obvious question was, ‘which one?’ The researchers began probing the water and found a likely candidate: the ciliate in question. Slightly before COVID-19 lockdowns and border closures in February of 2020, the team went back to the lake one last time to collect a sample for testing, which confirmed their findings.

Milucka said that, within the body of the eukaryote, the bacteria acts similarly to mitochondria in other cells—except instead of using oxygen, it uses nitrate to generate ATP for its host. 

Symbiosis between a eukaryote and a bacteria are commonplace. But the partnership described by Milucka and her team is distinct in a few ways. First, the bacteria has evolved alongside its host long enough that it can no longer live apart—this is not totally unheard of, but it is rare. It’s also rare for a bacteria to provide ATP directly to its host. Finally, there is no evidence of a eukaryote-bacteria partnership that relies on nitrate respiration and in which the ability to use oxygen has completely been lost.

“There is not really a similar example among the endosymbionts that we know today,” Milucka said.

Power to move

The eukaryotes jet around on their cilia. This lets them hunt other eukaryotes and bacteria but increases their energy needs in an ecosystem without oxygen, making nitrate respiration an ideal adaptation. “It moves. It’s actually super quick,” Milucka said. “It’s like a rocket.”

The team suspects that the bacteria had the ability to use oxygen somewhere in its past, but it could have lost it as it adapted to life in an oxygen-free environment. Alternatively, it 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 it lost the gene,” she said.

In any case, the team used DNA analysis and comparisons to 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 since. But this raises questions in the case of Candidatus Azoamicus ciliaticola and its host, because Lake Zug only formed around 10,000 years ago, during the last interglacial period. 

Considering how long ago the partnership between the microorganisms formed, it’s unlikely that it began in the lake, Milucka said. The team checked to see if genes similar to the bacteria’s existed and found that the closest sequences also existed in stratified lakes like Lake Zug. So, it’s possible the adaptation originally hails from similar lakes, though the ocean is another option. “There seems to be a pattern that at least the closest relative sequences are found in very similar habitats,” she said.

The findings have implications well beyond the sheet oddity of it all. Endosymbiosis is the leading explanation for how cells originally got their mitochondria. Billions of years ago—1.45 billion by some sources—single-celled life forms gobbled up bacteria that, in turn, began to provide them with energy. Eventually, the bacteria became part of the cells.

This partnership between the organisms in Lake Zug is, comparatively, quite new. According to Milucka, this discovery could offer a glimpse into how mitochondria formed in the past, as, in some ways, it could resemble an early moment in the process.

This research is one of the first examples of an endosymbiont bacteria in the process of becoming an organelle that generates energy for its host, said Michael Gray, professor emeritus at the Department of Biochemistry and Molecular biology at Dalhousie University in Nova Scotia. According to Gray, who has written extensively about 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 its ciliate offer a relatively modern-day example of how it may have happened.

Further, understanding the process of endosymbiosis is fundamental to understanding the origins of complex life. “It’s an example of an accidental discovery that has really opened our eyes a little more widely 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.