Scientists solve ancient puzzle: oxygen shaped the birth of complex life

Researchers at the University of Texas at Austin have found evidence that fundamentally changes our understanding of how complex life began on Earth. The discovery, published in the journal Nature, shows that the ancient microbes most closely related to all eukaryotes—including humans—were capable of using oxygen, suggesting that our earliest ancestors may have thrived in oxygen-rich environments billions of years ago.

The findings come from an ambitious DNA sequencing project that examined marine sediments collected from around the world. Scientists assembled over 400 new microbial genomes from a group called Asgard archaea, nearly doubling the known diversity of these microbes. Among these, 136 were from a particularly important lineage called Heimdallarchaeia, which is considered the closest living relative to the ancestor of all eukaryotes.

Background

For decades, scientists have puzzled over how complex life—cells with a nucleus and organelles—first emerged from simpler microbial ancestors. The leading theory holds that a major evolutionary leap occurred when an Asgard archaeon engulfed a type of bacterium called an alphaproteobacterium. Instead of being digested, the bacterium survived inside the archaeon and eventually evolved into the mitochondria, the energy-producing powerhouse found in all eukaryotic cells.

However, one aspect of this story never quite fit. Most Asgard archaea studied to date have been found living in oxygen-free environments deep in the ocean. This led scientists to believe that the merger creating complex life happened under low-oxygen conditions. Yet the geological record told a different story. Around 2.4 billion years ago, oxygen levels in Earth's atmosphere surged dramatically during an event called the Great Oxidation Event. Remarkably, the first clear fossils of eukaryotes appeared in the geological record not long after this shift.

The timing suggested oxygen played a role in the origin of complex life, but the microbial evidence seemed to contradict this. That contradiction is what the new research now resolves.

Key Details

"Most Asgards alive today have been found in environments without oxygen. 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." – Brett Baker, associate professor of marine science at the University of Texas at Austin

The research began with an enormous data collection effort. Scientists extracted DNA from marine sediments gathered during multiple ocean expeditions, processing approximately 15 terabytes of genetic information. From this massive dataset, they identified hundreds of new Asgard genomes and constructed a more detailed family tree of these microbes.

When researchers focused specifically on Heimdallarchaeia, they found something unexpected. These microbes carried genetic instructions for proteins involved in oxygen-based metabolism. They possessed genes for electron transport chains, haem biosynthesis, and mechanisms to detoxify reactive oxygen species—all hallmarks of organisms that use oxygen for energy production. The team even discovered novel types of respiratory hydrogenases that could potentially boost energy generation beyond what scientists previously thought possible for these microbes.

The protein evidence

To understand how these ancient proteins actually functioned, researchers used an artificial intelligence tool called AlphaFold2 to predict their three-dimensional shapes. Since protein function depends on structure, these predictions mattered. The analysis revealed that several proteins produced by Heimdallarchaeia closely resembled the oxygen-metabolizing proteins found in modern eukaryotes.

Geographically, the new genomes also painted a revealing picture. While most Asgard archaea live in oxygen-poor deep-sea environments, Heimdallarchaeia were found enriched in variably oxygenated coastal sediments and the water column—places where oxygen was actually present.

What This Means

The discovery suggests that our eukaryotic ancestor was not an organism struggling to survive in an oxygen-poor world. Instead, it was likely a microbe that had already adapted to use oxygen as a fuel source. When oxygen levels rose in Earth's atmosphere 2.4 billion years ago, these microbes possessed the metabolic machinery to exploit this new energy source.

Oxygen-based metabolism generates far more energy than the anaerobic pathways used by most bacteria. This energetic advantage would have been significant. A microbe with access to oxygen could produce more energy to grow, divide, and support more complex cellular machinery. For an Asgard archaeon already capable of using oxygen, the appearance of oxygen in the environment would have created a powerful incentive to develop closer relationships with other microbes—like the alphaproteobacterium that eventually became the mitochondria.

The findings align with what geologists and paleontologists have long suspected about Earth's history. The appearance of eukaryotic fossils in the geological record correlates with rising atmospheric oxygen. Now, the microbial evidence supports this connection.

The research also doubles the number of known enzymatic classes among Asgard archaea, revealing a previously hidden diversity of proteins and metabolic capabilities. This expanded catalog provides a more complete picture of how these ancient microbes lived and evolved.

Baker and his team plan to continue investigating Asgard archaea genomes to further understand their ecology and evolution. Each new genome discovered offers another piece of the puzzle in understanding how simple microbes eventually gave rise to the staggering complexity of modern life—from single-celled protists to plants, animals, and fungi.