Scientists widely agree that complex life emerged after two very different microbes formed a close partnership. That merger eventually gave rise to plants, animals, and fungi, collectively known as eukaryotes. Yet one key question has lingered for years. How did these two organisms meet if one required oxygen to survive while the other was believed to thrive only in oxygen-free environments?
Researchers at The University of Texas at Austin now report evidence that may resolve that puzzle. Writing in the journal Nature, the team focused on a group of microbes called Asgard archaea, which are considered close relatives of the ancestors of complex life. Although most known Asgards live in deep-sea or other oxygen-poor environments, the new study shows that some members of this group can tolerate or even use oxygen. The discovery strengthens the long-standing theory that complex life evolved as predicted, likely in an environment where oxygen was present.
“Most Asgards alive today have been found in environments without oxygen,” explained Brett Baker an associate professor of marine science and integrative biology at UT. “But it turns out that the ones most closely related to eukaryotes live in places with oxygen, such as shallow coastal sediments and floating in the water column, and they have a lot of metabolic pathways that use oxygen. That suggests that our eukaryotic ancestor likely had these processes, too.”
The Great Oxidation Event and Early Eukaryotes
Baker’s team studies the genomes of Asgard archaea to identify new branches of the group and better understand how these microbes generate energy. Their latest findings align with what geologists and paleontologists have reconstructed about Earth’s early atmosphere.
More than 1.7 billion years ago, oxygen levels in the atmosphere were extremely low. Then oxygen concentrations rose sharply during what scientists call the Great Oxidation Event, eventually approaching levels similar to those today. Within a few hundred thousand years of this dramatic increase, the earliest known microfossils of eukaryotes appear in the fossil record. This close timing suggests that oxygen may have played a crucial role in the emergence of complex life.
“The fact that some of the Asgards, which are our ancestors, were able to use oxygen fits in with this very well,” Baker said. “Oxygen appeared in the environment, and Asgards adapted to that. They found an energetic advantage to using oxygen, and then they evolved into eukaryotes.”
Symbiosis and the Birth of Mitochondria
The prevailing model holds that eukaryotes arose when an Asgard archaeon formed a symbiotic relationship with an alphaproteobacterium. Over time, the two organisms became integrated into a single cell. The alphaproteobacterium eventually evolved into the mitochondria, the structure inside eukaryotic cells that produces energy.
In this study, researchers significantly expanded the known genetic diversity of Asgard archaea. They identified specific groups, including Heimdallarchaeia, that are especially closely related to eukaryotes but are relatively uncommon today.
“These Asgard archaea are often missed by low-coverage sequencing,” said co-author Kathryn Appler, a postdoctoral researcher at the Institut Pasteur in Paris, France. “The massive sequencing effort and layering of sequence and structural methods enabled us to see patterns that were not visible prior to this genomic expansion.”
Massive Genome Sequencing Effort
The work began with Appler’s Ph.D. research at The University of Texas Marine Science Institute in 2019, when she extracted DNA from marine sediments. The UT team and collaborators ultimately assembled more than 13,000 new microbial genomes. The project combined samples from multiple marine expeditions and required analyzing roughly 15 terabytes of environmental DNA.
From this extensive dataset, the researchers recovered hundreds of new Asgard genomes, nearly doubling the known genomic diversity of the group. By comparing genetic similarities and differences, they built an expanded Asgard archaea tree of life. The newly identified genomes also revealed previously unknown protein groups, doubling the number of recognized enzymatic classes within these microbes.
AI Analysis of Oxygen Metabolism Proteins
The team then examined Heimdallarchaeia more closely, comparing their proteins to those found in eukaryotes that are involved in energy production and oxygen metabolism. To do this, they used an artificial intelligence system called AlphaFold2 to predict the three-dimensional shapes of the proteins. Because a protein’s structure determines how it functions, this analysis provided important clues.
The results showed that several Heimdallarchaeia proteins closely resemble those used by eukaryotic cells for oxygen-based, energy-efficient metabolism. This structural similarity offers additional support for the idea that the ancestors of complex life were already adapted to using oxygen.
Other contributors to the study included former UT researchers Xianzhe Gong (currently at Shandong University in China), Pedro Leão (now at Radboud University in the Netherlands), Marguerite Langwig (now at the University of Wisconsin-Madison) and Valerie De Anda (currently at the University of Vienna). James Lingford and Chris Greening at Monash University in Australia, along with Kassiani Panagiotou and Thijs Ettema at Wageningen University in the Netherlands, also participated in the research.
Funding was provided in part by the Gordon and Betty Moore and Simons Foundations, the National Natural Science Foundation of China and the National Health and Medical Research Council of Australia.
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