A new form of symbiosis has been discovered

Researchers from Bremen, together with their colleagues from the Max Planck Genome Center in Cologne and the Swiss aquatic research institute Eawag, have discovered a unique bacterium that lives inside a unicellular eukaryote and gives energy for him. Unlike mitochondria, the so-called endosymbiont receives energy from nitrate release, not oxygen. “Such a partnership is completely new,” said Jana Milucka, lead author of the Nature. “Symbiosis based on relief and the transfer of energy to this day is unique”.

In general, among eukaryotes, symbioses are quite common. Eocaryotic hosts often live in combination with other organisms, such as bacteria. Some bacteria live inside the host cells or tissue, and perform certain services, such as protection or nutrition. As a reward, the guest provides shelter and a suitable living setting for the symbiont. Endosymbiosis can even go so far that the bacterium loses its ability to survive on its own outside the host.

This was also true of the symbiosis discovered by Bremen scientists in Lake Zug in Switzerland. “Our discovery opens up the possibility that simple unidirectional eukaryotes, such as activators, can host endosymbionts that provide energy to augment or even replace the functions of their mitochondria,” he said. Jon Graf, first author of the study. “This protector has survived without oxygen by working in conjunction with a nitrate-releasing endosymbiont.” The endosymbiont name ‘Candidatus Azoamicus ciliaticola’ appears this; a ‘nitrogen friend’ who lives within a ciliate.

Close partnership grows closer

To date, eukaryotes in oxygen-free environments have been accepted to survive through fermentation, as mitochondria need oxygen to generate energy. The fermentation process is well documented and has been observed in many anaerobic ciliates. However, microorganisms cannot extract as much energy from fermentation, and they usually do not grow and divide as fast as their aerobic counterparts.

“Our kiliate has found a solution for this,” Graf said. “It has captured a bacterium with the ability to breathe nitrate and introduce it into its cell. We estimate that the fusion occurred at least 200 to 300 million years ago.” Since then, evolution has deepened this close partnership.

Evolutionary death

Evolution of mitochondria has proceeded in the same manner. “All mitochondria have a common origin,” explains Jana Milucka. It is believed that over a billion years ago when an ancestral archaeon captured a bacterium, these two began a very important symbiosis: this event marked the origin the eukaryotic cell.Over time, the bacterium became more and more integrated into the cell, gradually reducing the genome.Once needed properties were no longer lost and only those that were beneficial were lost. Eventually, mitochondria developed, as we know them today, a tiny genome as well as a cell, and they exist as organelles called eukaryotes. , for example, they are present in almost every cell and give them energy – and so do we.

“Our endosymbiont is capable of performing many mitochondrial functions, even if it does not share a common evolutionary origin with mitochondria,” Milucka says. “It’s embarrassing to think that the symbiont could follow the same path as mitochondria, and eventually become an organelle.”

Meet opportunity

It is truly remarkable that this symbiosis has not been known for so long. Mitochondria work so well with oxygen – why shouldn’t there be such for nitrate? One possible answer is that no one was aware of this ability so no one was looking for it. Studying endosymbioses is challenging, as most symbolic microorganisms cannot be grown in the laboratory. However, recent advances in metagenomic studies have allowed us to gain a better insight into the complex interactions between hosts and symbionts. When analyzing a metagenome, scientists look at each species in a sample. This approach is often used for environmental samples because the genes in a sample cannot be automatically assigned to the organisms present. This means that scientists typically look for specific gene sequences that are relevant to their research question. Metagenomes often involve millions of different gene sequences and it is quite common that very few of them are studied in detail.

Initially, the Bremen scientists were also looking for something else. The Research Group’s Greenhouse Gases at the Max-Planck-Institute for Marine Microbiology study microorganisms involved in methane metabolism. For this, they have been exploring the deep waters of Lake Zug. The lake is very stratified, meaning there is no direct water exchange. The deep waters of Lake Zug are therefore unrelated to surface water and are relatively isolated. That is why they contain no oxygen but are rich in methane and nitrogen fertilizers, such as nitrate. While looking for methane-munching bacteria with genes for nitrogen conversion, Graf came across a surprisingly small gene sequence encoding the entire metabolic pathway for nitrate release. “This discovery surprised us all and I started comparing the DNA with similar gene sequences in a database,” Graf said. But the same DNA belonged to those of symbionts that live in aphids and other insects. “This didn’t make sense. How would insects get into those deep waters? And why ?,” Graf recalls. The scientists of the research group began measuring games and bets.

He is not alone in the dark lake

Ultimately, there was one idea going: The genome must have an endosymbiont that is not yet known. To test this theory, members of the research team made several trips to Lake Zug in Switzerland. With the help of local collaboration partner Eawag they collected samples to look specifically for the organism that contains this particular endosymbiont. In the laboratory, the scientists would fish different eukaryotes out of the piped water samples. Finally, using a gene signal, it was possible to see the endosymbiont and identify its protist host.

A final visit a year ago was supposed to give a final confirmation. The middle of winter was hard work. The stormy weather, dense fog and pressure of time made the first news of Coronavirus as well as locking which could make the study in the big lake even more difficult. Nevertheless, the scientists managed to recover several samples from the deep water and take them to Bremen. These samples gave them conclusive proof of their theory. “It’s good to know they’re down there together,” said Jana Milucka. “These ciliates usually eat bacteria. But this one allowed them to live and be in partnership with.”

Lots of new questions

This discovery raises many interesting new questions. Are there similar symbioses that have existed much longer and where the endosymbiont has already crossed the border into an organelle? If there is such a symbiosis for nitrate relief, is it also there for other fertilizers? How did this symbiosis, which has existed from 200 to 300 million years ago, end up in a post-glacial lake in the Alps that was only created 10,000 years ago? Moreover: “Now that we know what we are looking for, we have discovered the gene sequences of the endosymbiont worldwide,” says Milucka. In France, as well as in Taiwan, or in East African lakes that are somewhat older than Lake Zug. Is the origin of this symbiosis in any of them? Or did it start in the ocean? These are the questions the research group wants to investigate next.

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