Unlocking Eukaryotic Origins: Oxygen-Tolerant Archaea Rewrite the Story of Complex Life
Scientists have long understood that the emergence of complex life – eukaryotes, encompassing plants, animals, and fungi – stemmed from a symbiotic partnership between two ancient microbes. However, a persistent puzzle has clouded this narrative: how could these progenitors unite when one was thought to require oxygen for survival, while the other thrived in its absence? New research from The University of Texas at Austin offers compelling evidence that may resolve this longstanding question, suggesting the ancestral archaeon was, in fact, capable of utilizing oxygen.
The findings, published in the journal Nature, center on Asgard archaea, a group considered the closest known relatives to the ancestors of eukaryotes. While many Asgards inhabit oxygen-deprived environments like the deep sea, the UT Austin team discovered that certain members of this group not only tolerate oxygen but actively employ it in their metabolic processes. This discovery bolsters the theory that the evolution of complex life occurred in an oxygenated environment, a scenario previously challenged by the presumed oxygen-intolerance of one of the key players.
“Most Asgards alive today have been found in environments without oxygen,” explains Brett Baker, an associate professor of marine science and integrative biology at UT Austin. “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 the Rise of Eukaryotes
The research aligns with established geological and paleontological understanding of Earth’s early atmosphere. Over 1.7 billion years ago, atmospheric oxygen levels were minimal. Then, during a period known as the Great Oxidation Event (GOE), beginning approximately 2.460–2.426 billion years ago, oxygen concentrations rose dramatically, eventually reaching levels comparable to those of today. Remarkably, the earliest microfossils of eukaryotes appear in the fossil record within a few hundred thousand years of this oxygen surge. This close temporal correlation strongly suggests a link between oxygen availability and 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.” The GOE, initially termed the “Oxygen Catastrophe” due to its detrimental effects on many existing anaerobic lifeforms, now appears to have been a pivotal catalyst for the evolution of more complex, energy-efficient life.
Symbiosis and the Birth of Mitochondria
The prevailing model for eukaryotic origins posits a symbiotic relationship between an Asgard archaeon and an alphaproteobacterium. Over time, these two organisms integrated into a single cell, with the alphaproteobacterium eventually evolving into the mitochondria – the energy-producing organelles found in all eukaryotic cells. The new findings regarding oxygen tolerance in certain Asgard lineages strengthen this model by demonstrating that the ancestral archaeon could have thrived in an oxygen-rich environment, facilitating the establishment of this crucial symbiotic partnership.
The UT Austin team’s work involved a significant expansion of the known genetic diversity of Asgard archaea. They specifically identified the Heimdallarchaeia group as being particularly closely related to eukaryotes, yet relatively uncommon in current microbial ecosystems. “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.”
A Massive Genomic Sequencing Undertaking
The research was fueled by a substantial genomic sequencing effort, beginning with DNA extracted from marine sediments in 2019. The team ultimately assembled over 13,000 new microbial genomes, combining samples from multiple marine expeditions and analyzing approximately 15 terabytes of environmental DNA. This resulted in nearly doubling the known genomic diversity of the Asgard archaea group.
By comparing genetic similarities and differences, the researchers constructed an expanded Asgard archaea tree of life. The newly identified genomes also revealed previously unknown protein groups, effectively doubling the number of recognized enzymatic classes within these microbes.
AI-Powered Protein Analysis Reveals Oxygen Metabolism
To further investigate the oxygen-utilizing capabilities of Heimdallarchaeia, the researchers employed artificial intelligence. They used AlphaFold2, an AI system capable of predicting the three-dimensional structures of proteins, to analyze proteins involved in energy production and oxygen metabolism. A protein’s structure dictates its function, making this analysis a powerful tool for understanding metabolic pathways.
The results revealed that several Heimdallarchaeia proteins closely resemble those used by eukaryotic cells for oxygen-based, energy-efficient metabolism. This structural similarity provides further evidence supporting the idea that the ancestors of complex life were already adapted to utilizing oxygen. This suggests that the metabolic machinery for aerobic respiration was present in the Asgard-eukaryotic ancestor, potentially influencing the evolution of the symbiotic relationship that led to the first eukaryotes.
The study involved contributions from researchers at multiple institutions, including Shandong University in China, Radboud University in the Netherlands, the University of Wisconsin-Madison, the University of Vienna, Monash University in Australia, and Wageningen University in the Netherlands. Funding was provided 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.
