Deep in Lake Zug in Switzerland is a micro-organism that has developed a strange way of ‘breathing’. A team of researchers discovered a new partnership between a single-celled eukaryote – an organism with a clearly defined nucleus that holds its genome – and a bacteria that generates energy for its host. But instead of using oxygen, it uses nitrate.
“This is a very strange one, [newly discovered] organism, ”said Jana Milucka, biologist at the Max Planck Genome Center in Cologne and senior author of the resulting paper, published in Nature beginning of March.
The team named the bacteria Candidatus Azoamicus ciliaticola, meaning “nitrogen friend living in a ciliate.” Its partner, the ciliate, is a microorganism that moves with the help of cilia, small 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 traveled to Lake Zug in search of genetics. Milucka and her peers have been studying the body of water for nearly a decade. It is completely layered, with a layer of oxygenated water on top and then a layer with no oxygen near the bottom. As such, the organisms that thrive in the depths have had to evolve to survive without oxygen.
The team lowered a sample bottle to about 190 meters and the DNA of all organisms in the sample was sequenced. They found a bacterial genome that contained a complete metabolic pathway for nitrate respiration. But the genome was small and lacked enough genes to suggest that it belonged to one organism that would have to hitch a ride on another to survive. The genome was similar in size to the genomes of symbiotic microorganisms residing in the bodies of insects and showed many genetic similarities.
But insects cannot survive in the deepest parts of lakes, so that didn’t explain the presence of this genome. If the bacteria lived in another organism, the obvious question was “which one?” The researchers began to examine the water and found a likely candidate: the ciliate in question. Slightly before COVID-19 lockdowns and border closures in February 2020, the team went back to the lake one last time to collect a sample for testing, confirming their findings.
Milucka said the bacterium in the eukaryote’s body works in the same way as mitochondria in other cells – except instead of using oxygen, it uses nitrate to generate ATP for its host.
Symbiosis between a eukaryote and a bacterium is common. But the partnership described by Milucka and her team stands out in a number of ways. First, the bacterium has evolved alongside its host long enough that it can no longer live alone – this is not entirely unheard of, but it is rare. It is also rare for a bacterium to deliver 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 has been completely lost.
“There isn’t really a similar example among the endosymbiontes we know today,” said Milucka.
Power to move
The eukaryotes shoot around on their cilia. This allows them to hunt other eukaryotes and bacteria, but increases their energy requirements in an ecosystem without oxygen, making nitrate respiration an ideal adaptation. “It’s moving. It’s actually super fast,” said Milucka. “It’s like a missile.”
The team suspects that the bacteria had the ability to use oxygen at some point in the past, but it could have lost it because it adapted to living in an oxygen-free environment. Alternatively, it could have simply accidentally lost the gene. “We don’t really know if it was on purpose or if it was accidental that it 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 has since grown deeper. But this raises questions in the case of Candidatus Azoamicus ciliaticola and its host, because Lake Zug was not formed until about 10,000 years ago, during the last interglacial period.
Considering how long ago the partnership between the microorganisms started, it is unlikely to have started in the lake, Milucka said. The team checked for genes similar to the bacteria and found that the closest sequences also existed in stratified lakes such as Lake Zug. So it’s possible that the adaptation was originally from similar lakes, although 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 that go far beyond the idiosyncrasy of all this. Endosymbiosis is the main explanation for how cells originally got their mitochondria. Billions of years ago-1.45 billion by some sources– single-celled life forms stored bacteria which in turn began to supply their energy. Eventually the bacteria became part of the cells.
This collaboration between the organisms in the Zugersee is relatively new. According to Milucka, this discovery could provide a glimpse of how mitochondria formed in the past, as in some ways it could seem like an early point 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, understanding how mitochondria formed historically was quite difficult simply because it happened so long ago. As such, Candidatus Azoamicus ciliaticola and its ciliate provide a relatively modern example of how it may have happened.
Furthermore, understanding the process of endosymbiosis is fundamental to understanding the origins of complex life. “It’s an example of an accidental discovery that really opened our eyes a little wider to what biology is capable of,” he said.
Nature, 2021. DOI: 10.1038 / s41586-021-03297-6 (over DOIs).
Doug Johnson (@BuienRadarNL) is a Canadian freelance reporter. His works have appeared in National Geographic, Undark and Hakai Magazine, among others.