Discovering a new “unprecedented” form of coexistence

Discovering a new “unprecedented” form of coexistence

The energy-saving bacterial endocytosis enables its single-celled host eukaryotes to respire nitrates, indicating that single-celled eukaryotes may acquire endosymbiosis to supplement or replace the functions of mitochondrial organelles.

Bremen researchers, along with colleagues from the Max Planck Genome Center in Cologne and the Eawag Aquatic Research Institute from Switzerland, have discovered a unique bacterium that lives inside single-celled eukaryotes and powers them. Unlike mitochondria, this so-called symbiosis derives energy from breathing nitrates, not oxygen. “This partnership is completely new,” says Jana Meluka, senior author at Temperate nature paper. “The coexistence of breathing and transfer of energy is unprecedented so far.”

In general, among eukaryotes, symbiosis is fairly common. Eukaryotic hosts often coexist with other organisms, such as bacteria. Some bacteria live inside the host cells or tissues, and perform certain services, such as defense or nutrition. In return, the host provides adequate shelter and living conditions for cohabitants. Inbound symbiosis can go so far as the bacteria lose their ability to survive on their own outside their host.

This was also the case with the coexistence that Bremen scientists discovered in Lake Zug in Switzerland. “Our discovery opens up the possibility that simple single-celled eukaryotes, such as protists, could host an energy-saving endocytosis to supplement or even replace their mitochondrial functions,” says John Graff, first author of the study. “This protozoan was able to survive without oxygen by cooperating with an endosymbiosis that is able to breathe with nitrates.” The endosymbiosis name “Candidatus Azoamicus ciliaticola” reflects this; The “nitrogen friend” that dwells inside the cilia.

Candida Azoamicus ciliaticola

The figure is composite from a scanning electron microscope image (SEM, gray) and fluorescence images. Visible is the endosymbiosis of “Candidatus Azoamicus ciliaticola” (visualized by FISH in yellow) and bacterial prey in food vacuoles as well as large cell nuclei (stained by DAPI, in blue). The exoskeleton of weak fluorescent cilia as well as cilia can be seen. Credit: Max Planck Institute for Marine Microbiology, S.

An intimate partnership is getting closer than ever

So far, eukaryotes in oxygen-free environments have been assumed to survive through fermentation, because mitochondria require oxygen to generate energy. The fermentation process is well documented and has been observed in several anaerobic companies. However, microorganisms cannot extract the same amount of energy from fermentation, and they usually do not grow and divide as quickly as their aerobic counterparts.

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“Our affiliate found a solution,” says Graff. “We have swallowed a bacterium that has the ability to breathe nitrates and incorporate it into their cells. We estimate that the absorption took place at least 200 to 300 million years ago.” Since then, the development has deepened this intimate partnership.

Time shift evolution

Mitochondria evolution continued in a similar manner. “All mitochondria have a common origin,” Jana Meluka explains. It is thought that more than a billion years ago when the ancestors of Arcturus swept into a bacterium, these two began a very important symbiosis: This event marked the origin of the eukaryotic cell. Over time, the bacteria became more integrated into the cell, which gradually reduced their genome. The property is no longer required to be lost and only the property that has benefited the host is preserved. Ultimately, mitochondria as we know them today evolved. They have their small genome as well as a cell membrane, and they are found as organelles in eukaryotes. In the human body, for example, they are present in nearly every cell and provide them – and thus us – with energy.

“Our endosymbiosis is capable of performing many mitochondrial functions, although it does not share a common evolutionary ancestry with mitochondria,” says Meluka. “It is tempting to speculate that a symbiont may follow the same pathway as the mitochondria, and eventually become an organelle.”

Encounter by chance

It is really surprising that this symbiosis has remained unknown for so long. Mitochondria work well with oxygen – so why is there no nitrate equivalent? One possible answer is that no one was aware of this possibility and so no one was looking for it. The study of endosymbiosis is challenging, as most symbiotic microorganisms cannot be grown in the laboratory. However, recent developments in metagenomic analyzes have allowed us to gain a better insight into the complex interactions between hosts and symbionts. When analyzing metagenomes, scientists look at all of the genes in the sample. This approach is often used for environmental samples as the genes in the sample cannot be automatically assigned to the organisms present. This means that scientists usually look for specific genetic sequences that are relevant to their research question. Metagenomes often contain millions of different genetic sequences and it is perfectly normal for a small fraction of them to be analyzed in detail.

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Originally, Bremen scientists were also looking for something else. The Greenhouse Gas Research Group at the Max Planck Institute for Marine Microbiology is investigating the microorganisms involved in methane metabolism. For this, they were studying the deep water layers of Lake Zug. The lake is highly stratified, which means that there is no vertical exchange of water. Thus, the deep water layers of Lake Zug do not come into contact with the surface waters and are largely isolated. This is why it does not contain oxygen but is rich in methane and nitrogen compounds, such as nitrates. While searching for methane-chewing bacteria with nitrogen-converting genes, Graf came across a stunningly small genetic sequence encoding the entire metabolic pathway for nitrate respiration. “We were all stunned with this result and I started a comparison DNA With similar gene sequences in a database, “says Graff. But the only identical DNA belongs to symbionts that live in aphids and other insects.” That didn’t make sense. How will insects get into these deep waters? Why? “Graf recalls. The research group scientists began guessing games and betting.

He is not alone in the dark lake

In the end, one thought prevailed: the genome must belong to an anonymous endosymbiosis. To verify this theory, members of the research team made several expeditions to Lake Zug in Switzerland. With the help of local collaboration partner Eawag, they collected samples to specifically search for the organism that contained this unique internal symbiosis. In the laboratory, scientists extracted many eukaryotes from water samples using a pipette. Finally, by using the gene marker, it was possible to visualize an endosymbiosis and identify its primary host.

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A final flight one year before was supposed to achieve final certainty. It was a difficult task in the middle of winter. Stormy weather, dense fog and time pressure due to the first news of the Coronavirus, as well as the possible lockdown have made searching the large lake even more difficult. Nevertheless, the scientists managed to extract several samples from the deep waters and bring them to Bremen. These samples provided them with the final confirmation of their theory. “It’s nice to know that they’re out there together,” says Jana Milucka. Usually, these giants eat bacteria. But this left him alive and shared with him. “

Many new questions

This discovery raises many new and exciting questions. Are there similar symbionts that have been around for the longest time and where the endosymbiosis has actually crossed into an organelle? If this symbiosis exists for nitrate respiration, is it also present for other compounds? How did this symbiosis, which existed 200-300 million years ago, end in a post-glacial lake in the Alps that formed only 10,000 years ago? Moreover: “Now that we know what we’re looking for, we have found endogenous genetic sequences for symbiosis all over the world,” says Meluka. In France, as well as in Taiwan, or in the lakes of East Africa that are in part much older than Lake Zug. Is the origin of this coexistence in one of them? Or did it start in the ocean? These are the questions that the research group wants to investigate next.

Reference: 3 March 2022, Temperate nature.
DOI: 10.1038 / s41586-021-03297-6

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