The Battle of Microbial Asgard and the Rise of Complex Life

How Asgardian microbes are challenging our understanding of life

Section of the Ash Yggdrasil by Friedrich Wilhelm Heine (1886) (Wikimedia Commons)

One, two, three domains of life

You, eukaryote.

No, I’m not insulting you. You are a eukaryote. So am I, and so are all the plants and animals you know. ‘Eukaryote’ refers to all organisms that have cells with a nucleus¹ — a tiny compartment that contains the DNA. Organisms that don’t have cells with a nucleus, like bacteria, are called prokaryotes.

In 1938, French biologist Édouard Chatton proposed that this split between pro- and eukaryotes was life’s most basic division. This became the two-empire system of life. Every organism was either a pro- or eukaryote. An organism belongs to a species; species belong to genera, and so on, all the way up to one of the two empires at the top of the classification pyramid: prokaryote or eukaryote.

Life, however, rarely yields to simple dichotomies.

In 1977, biologists Carl Woese and George Fox came up with a proposal that would change the face of biology, even though it was dismissed and ignored for a long time (which the shy and introverted Woese took hard). They didn’t quit building their case, though.

What if there were three instead of two domains?

Woese was a physicist by training, but he wandered into microbiology because he wanted to unravel the origin of the genetic code. To do so, he focused on ribosomes, molecules made out of RNA (DNA’s evolutionarily older cousin) that help our cells transcribe and translate DNA into proteins. More specifically, ribosomes are the assemblers in our cells that string amino acids together into a functional protein.

But when Woese looked at the ribosomal RNA of bacteria, he saw something odd. The ribosomes of some bacteria, especially bacteria that live in extreme conditions like hot springs, were different². Substantially different. Different enough even to warrant putting those bacteria in a different ‘empire’.

Today, we call those empires domains, and there are three. Bacteria, eukaryotes, and, thanks to Woese, archaea. The archaea that were described first came from extreme environments such as hot springs, salt flats, and deep-sea hydrothermal vents, but by now we know that they’re everywhere: soil, water, and even our guts.

The three domain tree of life (Wikimedia Commons, Chiswick Chap). LUCA is short for Last Universal Common Ancestor — the organism at the root of all earthly life.

Those archaea also contain a bunch of ancient Norse gods.

Meet the real Loki

There is a group of archaea that is, and I’m serious, Asgardian — related to ancient Norse gods. These archaea, after all, were discovered in Loki’s Castle.

In 2008, scientists discovered boiling hot water in the cold seas between Greenland and Norway. The source of this water is a cluster of hydrothermal vents, called black smokers. These cracks in the ocean floor squirt mineral-rich hot water from inside the earth’s crust. Given its location, this cluster of hydrothermal vents was named Loki’s Castle and it’s the home of peculiar archaea: the Lokiarchaeota, which includes the Thor-, Odin- and Heimdallarchaeota. The whole pantheon showed up.

A vent chimney of Loki’s Castle (Centre for Geobiology/U. of Bergen, Wikimedia Commons)

What makes the Loki microbes so odd is that they’re a lot like us. Until a few years ago, the dwellers of Loki’s Castle were shrouded in mystery and boiling black water full of minerals. Archaea in general are very hard to keep in the lab.

That changed in 2022, when researchers cultivated Candidatus Lokiarchaeum ossiferum, which can thrive without oxygen at a low temperature — for archaea (20°C). On top of that, it divides every 7–14 days and reaches cell densities of up to 5 million cells per milliliter. In other words, we could finally take a look at that shapeshifting trickster Loki.

The true face of Loki. (From Imachi, Nobu, et al. 2020. Isolation of an archaeon at the prokaryote–eukaryote interface. Nature. 577(7791): 519–525). The white arrows indicate ‘membrane vesicles’, or small bags of molecules with various functions excreted by these critters.

The researchers were particularly interested in ESPs, or eukaryotic signature proteins.

Wait, eukaryotic? I thought archaea were not eukaryotes? Exactly. But it seems that they share a lot more with us than we thought. ESPs likely play a role in the formation of a cytoskeleton, which is a network of fibers that act as a structural support for cells and their components.

Our cultivated Loki has a genome with a lot of ESP-coding genes.

The coccoid (spherical) cells of Loki sprout protrusions with frequent constrictions. Both Loki’s cell ‘body’ and ‘arms’ are made of twisted double-stranded filaments that are similar in structure to F-actin, a protein that is important in the cytoskeleton of… eukaryotes.

The researchers suggest that

…a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.

Translation: the first step toward eukaryotes, including (maybe) our distant ancestors, may have been taken in Asgard.

And now the Asgardians are coming for us.

The battle of Asgard

While the three-domain picture (bacteria, archaea, and eukaryotes) remains the default assumption, the foundations of life’s empires are rumbling. Are the Asgard microbes too much like us?

Some scientists argue for the resurrection of the old two-domain view. Not by reuniting the archaea with the bacteria, but by seeing us, eukaryotes, as an offshoot of archaea. Are we all Loki’s children? Or maybe the children of one of Loki’s frenemies, the guardian god Heimdall?

A 2020 study that looked at >3000 gene families (related genes) in archaea and eukaryotes, not only found that the most fitting evolutionary tree had two domains, but also identifies,

… the Heimdallarchaeota as the current best candidate for the closest archaeal relatives of the eukaryotic nuclear lineage.

One year later, a study that included genomes from newly discovered Asgardians suggests,

… either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota–Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea.

Then, in 2023, yet another study finds,

… that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia.

Even if we don’t quite know which Norse god we are descendants of³, the general hypothesis that eukaryotes come from somewhere deep in the Asgardian family tree is known as the ‘eocyte hypothesis’. Simplified, the battle between the established three-domain model (A), and the two-domain model (B) looks like this:

(From MacLeod et al. 2019. Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes. AIMS Microbiol. 5(1): 48–61.)

For now, the three-domain model remains the standard, but the Asgardians are chipping away at it.

And Loki always has a trick up his sleeves (or cell protrusions).

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(If you’re a fellow newsletter writer and think your readers might appreciate my mental fieldwork, you can recommend Subtle Sparks…)

1. We have a few exceptions in our bodies. Red blood cells don’t have a nucleus, while skeletal muscle cells and some bone cells have many.

2. More specifically, the gene sequences that code for 16S ribosomal RNA, a subunit of the ribosome.

3. My first name, Gunnar, has old Norwegian roots, so how can I not root for the Asgardians? (I’m pretty sure that if I trace my family tree back far enough, I’ll meet Loki…)