Rosa Rubicondior: Abiogenesis News - Origin Of Complex (Eukaryote) Cells

Beginnings of symbiosis

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A Break in a Longstanding Mystery about Origin of Complex Life | College of Natural Sciences

Here are a couple of papers published today that deal with related aspects of the origins of complex (eukaryotic) cells — all living organisms apart from Bacteria, Archaea and viruses (the prokaryotes). There is little doubt in biology that eukaryotes evolved from symbiotic associations between prokaryotes, despite the regular creationist straw man claim that scientists are naïve enough — or somehow brainwashed by evil “Darwinists” — to believe that the first complex cell arose spontaneously in a single step so fantastically improbable that magical creation becomes an almost plausible alternative.

In reality, as these two papers demonstrate, the precise details of how these symbiotic associations arose remain matters of active research and debate. I will deal with the second paper in a separate blog post. This post concerns the paper by scientists from The University of Texas at Austin, published in *Nature*, which addresses the question of how the oxygen-dependent bacterium that became the mitochondrion came together with a presumed anaerobic (oxygen-intolerant) archaeon, given that the two would not be expected to occupy the same environment.

The team propose that this apparent problem may be resolved by evidence that some archaea of the Asgard group — which today live primarily in the deep sea and other oxygen-free environments — can use, or at least tolerate, oxygen.

The Asgard archaea most closely related to eukaryotic cells are found in shallow coastal sediments or floating in the marine column. Crucially, they possess metabolic pathways that use oxygen. It is therefore possible that their ancestors did as well, meaning they could have cohabited with the bacterial ancestors of mitochondria.

Asgard Archaea — Background Summary.

This false-color image shows a cell of thermophilic methanogenic archaea.
Image credit: University of California Museum of Paleontology.

Asgard archaea are a superphylum of Archaea regarded as the closest known prokaryotic relatives of eukaryotes. Their discovery over the past decade has substantially reshaped thinking about the origin of complex cells.

Discovery

The first members were identified in 2015 from metagenomic sequences recovered near a hydrothermal vent system in the Arctic Ocean. The initial lineage was named Lokiarchaeota, after Loki’s Castle hydrothermal vent. Subsequent related groups were named Thorarchaeota, Odinarchaeota, Heimdallarchaeota, and others — collectively dubbed “Asgard” archaea after figures from Norse mythology.

Why They Matter

Asgard archaea are significant because their genomes contain numerous genes previously thought to be unique to eukaryotes. These include genes encoding:

Actin-like cytoskeletal proteins
Small GTPases involved in membrane trafficking
Components associated with vesicle formation
Ubiquitin-related systems

These so-called eukaryotic signature proteins suggest that the archaeal host cell that partnered with the mitochondrial ancestor may already have possessed some degree of internal structural complexity.

Metabolism and Lifestyle

Most known Asgard archaea are anaerobic and have been found in:

Deep marine sediments
Hydrothermal vent systems
Anoxic muds and subsurface environments

They typically show metabolic versatility, including fermentation, hydrogen metabolism, and syntrophic interactions with bacteria. Some lineages appear capable of tolerating or even utilising low levels of oxygen, which is particularly relevant to hypotheses about how an archaeal host could have coexisted with the aerobic bacterial ancestor of mitochondria.

Cultivation

For several years, Asgard archaea were known only from environmental DNA. In 2019, researchers reported the first cultivated representative, “Candidatus Prometheoarchaeum syntrophicum”, a slow-growing organism that forms long branching protrusions. Its growth depends on syntrophic partnerships with bacteria — consistent with models proposing close metabolic cooperation at the origin of eukaryotes.

Evolutionary Significance

Current phylogenetic analyses place eukaryotes either within or as a sister group to Asgard archaea, supporting a “two-domain” tree of life (Bacteria and Archaea, with eukaryotes emerging from within Archaea) rather than the older three-domain model.

In most mainstream models:

An Asgard-like archaeon acted as the host cell.
It entered into syntrophy with an alphaproteobacterium.
That bacterium became the mitochondrion.
Subsequent gene transfer and cellular integration produced the first true eukaryotic cell.

Ongoing Questions

Despite rapid progress, major uncertainties remain:

Exactly which Asgard lineage is closest to eukaryotes?
Did the host archaeon already tolerate oxygen?
How were membrane systems and the nucleus established?*
What ecological setting fostered the initial symbiosis?

*My next blog post addresses this issue.

Details of the team’s work are given in a news item from the University of Texas at Austin, College of Natural Sciences:

A Break in a Longstanding Mystery about Origin of Complex Life
Breathe easy. It appears our microbial ancestors used oxygen, too.
The most widely accepted scientific explanation for the arrival of all complex life on Earth has had an unsolved mystery at its heart. According to the theory, all plants, animals and fungi, known collectively as eukaryotes, are thought to have evolved after two very different types of microbes came together. The problem was in figuring out how the two were in such close proximity in the first place, given that one of the microbes requires oxygen for survival and the other was known to live in spaces without oxygen.

Now scientists from The University of Texas at Austin, publishing in the journal Nature, appear to have solved the mystery. One of our microbial ancestors was part of a group called the Asgard archaea, which today live primarily in the deep sea and other oxygen-free spaces. But according to the new study, some Asgards use, or at least tolerate oxygen. The discovery lends more credence to the idea that complex life evolved as the theory predicted—and apparently in an oxygen-rich environment.
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.

Associate Professor Brett J. Baker, corresponding author.
Department of Marine Science
Marine Science Institute
University of Texas at Austin
Port Aransas, TX, USA.

An illustration of the process of two ancient microbes coming together to form a super organism that gave rise to all complex life on Earth An expanded catalog of Asgard genomes supports a new model of eukaryogenesis, or birth of complex life forms.
Credit: University of Texas at Austin.

Baker and his team research Asgard archaea genomes, uncovering new lineages, expanding enzymatic diversity and exploring their metabolic pathways. The team’s latest finding agrees with the picture geologists and paleontologists have reconstructed of Earth’s history. Until about 1.7 billion years ago, Earth’s atmosphere had very little oxygen. Then, oxygen levels spiked dramatically, like levels seen today. Within a few hundred thousand years after this Great Oxidation Event, the first known microfossils of eukaryotes appeared, suggesting that the presence of oxygen might have been important for the origin 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. Oxygen appeared in the environment, and Asgards adapted to that. They found an energetic advantage to using oxygen, and then they evolved into eukaryotes.

Associate Professor Brett J. Baker.

Scientists believe eukaryotes arose when an Asgard archaeon developed a symbiotic relationship with an alphaproteobacterium. Eventually, they become one organism with the latter evolving to become an energy-producing organelle within eukaryotes called the mitochondria. In the new paper, the scientists vastly expand the number of Asgard archaea genomes and point to specific types of Asgard archaea, such as Heimdallarchaeia, which are closely related to eukaryotes but less common today.

These Asgard archaea are often missed by low-coverage sequencing. 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.

Dr. Kathryn E. Appler, first-author
Department of Marine Science
Marine Science Institute
University of Texas at Austin
Port Aransas, TX, USA.

An expanded family tree of Asgard archaea. The concentric rings (in-out) highlight the predicted genome size (Mb), metabolic guilds, sampling locations, and black stars for the genomes added by this study.

Credit: University of Texas at Austin.

This research stems from Appler’s Ph.D. work at The University of Texas Marine Science Institute, which started by extracting DNA from marine sediments in 2019. The UT group and its collaborators assembled more than 13,000 new microbial genomes. This massive effort compiled data from several marine expeditions and involved wrangling about 15 terabytes of environmental DNA. From this dataset, they obtained hundreds of new Asgard genomes, nearly doubling the group’s known genomic diversity. Using genetic similarities and differences of these microbes, they constructed a new expanded Asgard archaea tree of life. These new genomes also revealed previously unknown groups of proteins, doubling the number of known enzymatic classes.

Next, they looked at Heimdallarchaeia and compared proteins they produce to eukaryotic proteins involved in energy and oxygen metabolism. Using an artificial intelligence model called AlphaFold2, they predicted how these proteins fold into three-dimensional shapes. The shapes, or structures, of proteins dictate how they function. The results showed that several proteins produced by Heimdallarchaeia closely resemble those used by eukaryotes for oxygen-based, energy-efficient metabolism.

Other authors of the study include previous 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). Additionally, James Lingford and Chris Greening at Monash University in Australia and Kassiani Panagiotou and Thijs Ettema at Wageningen University in the Netherlands participated in the research.

Publication:
Appler, K.E., Lingford, J.P., Gong, X. et al.
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor.
Nature (2026). https://doi.org/10.1038/s41586-026-10128-z

Abstract
Asgard archaea were pivotal in the origin of complex cellular life¹. Heimdallarchaeia (a class within the phylum Asgardarchaeota) are inferred to be the closest relatives of eukaryotes. Limited sampling of these archaea constrains our understanding of their ecology and evolution^2,3, including their role in eukaryogenesis. Here we use massive DNA sequencing of marine sediments to obtain 404 Asgardarchaeota metagenome-assembled genomes, including 136 new Heimdallarchaeia and several novel lineages. Analyses of their global distribution revealed they are widespread in marine environments, and many are enriched in variably oxygenated coastal sediments. Detailed metabolic reconstructions and structural predictions suggest that Heimdallarchaeia form metabolic guilds that are distinct from other Asgardarchaeota. These archaea encode hallmark proteins of an aerobic lifestyle, including electron transport chain complex (IV), haem biosynthesis and reactive oxygen species detoxification. Heimdallarchaeia also encode novel clades of respiratory membrane-bound hydrogenases with additional Complex I-like subunits, which potentially increase proton-motive force generation and ATP synthesis. Thus, we propose an updated Heimdallarchaeia-centric model of eukaryogenesis in which hydrogen production and aerobic respiration may have been present in the Asgard-eukaryotic ancestor. This expanded catalogue of Asgard archaeal genomic diversity suggests that bioenergetic factors influenced eukaryogenesis and constitutes a valuable resource for investigations into the origins and evolution of cellular complexity.

Appler, K.E., Lingford, J.P., Gong, X. et al.
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor.
Nature (2026). https://doi.org/10.1038/s41586-026-10128-z

© 2026 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

If creationist caricatures of evolutionary theory were accurate, discoveries like this would not keep happening. We would not see careful, incremental refinements of a well-supported framework; we would instead see the framework collapsing under the weight of its own contradictions. Instead, what we observe is the opposite: detailed molecular evidence that narrows the plausible ecological and metabolic conditions under which the first eukaryotic cells arose.

The origin of complex life was not a single improbable leap, but a sequence of interactions between already-evolved organisms, shaped by natural selection and constrained by biochemistry. The growing evidence from Asgard archaea strengthens the case that the host cell which gave rise to eukaryotes was not a simple, featureless prokaryote, but an organism already equipped with some of the molecular toolkit that would later characterise complex cells.

Far from invoking magic, this research continues to replace gaps with mechanisms. And, as always, the deeper we look into the history of life, the clearer it becomes that complexity is the product of cumulative evolutionary processes operating over immense stretches of geological time — not the result of a sudden act of supernatural manufacture.

My next post will deal with a question raised in this one - the origin of the eukaryote cell nucleus.

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