“Started from the bottom” - The unexpected rise of Lokiarchaeota from the depth of the oceans to evolutionary significance.

Guest blogger Thomas Bonnin writes...

In a blog that often proposes analyses of our knowledge of large extinct animals, I invite the reader to explore something a little different.

Yes, I admit, I am a little jealous of people talking about dinosaurs and those other fantastic prehistoric animals. These charismatic critters capture the imagination, leave amazing looking fossil traces, feature in works of art and in movies, and all sorts of people say all sorts of nonsense about them. Due to the combined effect of the hard work of paleobiologists, and the vast media coverage they generate, people doubting the existence of Tyrannosaurus, despite the fact that the last of them roamed the Earth about 65 million years ago, are themselves an ‘endangered’ species. This, without a doubt, is nothing short of an amazing scientific achievement.

Granted, what I want to write to you about is, at face-value, a little less exciting. You cannot find plastic versions of it in 80s B movies (which is a shame). They don’t really make the headlines of ‘science vs. creationism’ debates. Worse, they are not even extinct!  Lokiarchaeota are contemporary archaea, and their cool name (derived from a Norse deity) is not the only interesting thing about them. This post narrates their unexpected journey from the depth of the ocean to evolutionary stardom. Expect a convoluted ride both into the depth of the oceans and to the origin of our cells: are you in?

  A giant Archaea monster would have been a lot cooler here.

A giant Archaea monster would have been a lot cooler here.

You may have never heard of archaea. This would be understandable as everything that is about a million times smaller than us is often dumped into the ‘microbe’ bag. Microbes are usually only conceived as ‘evil’ little things that should be fought before they invade your toenails. However, this is a mistake: first, and in case you don’t know, you are full of these microbes and a good portion of them contribute to your everyday survival. Second, there’s a least three distinct types of microbes: bacteria, archaea, and protists. Bacteria and archaea are prokaryotes, unicellular organisms without nucleus. Protists are unicellular eukaryotes, which are organisms made of cells with nucleus.

 Bacteria, Archaea, and Protists, in random order. The reader that guesses which one is which wins his/her weight in yeast extract.

Bacteria, Archaea, and Protists, in random order. The reader that guesses which one is which wins his/her weight in yeast extract.

All of the eukaryotes, including trees, dinosaurs and Spongiforma squarepantsii, possess within them a nucleus,  the ‘home of the DNA’, but also derive from an ancestor that possessed mitochondria, bean-shaped cellular structures responsible for energy production. For evolutionary biologists investigating the origin of eukaryotes, explaining how mitochondria appeared, and whether or not it preceded the origin of the nucleus, is currently considered to be the main mystery to be solved.

We know where mitochondria came from: they appeared about a billion years ago via endosymbiosis, a beautiful term for a process that started with the engulfment without digestion of one free-living cell by another. This rather impolite cellular interaction resulted in brand new organisms: an archaea-like 'host' cell with another 'little cell' within it, basically the invention of Kinder Surprise®. The little cell, secluded in the coziness of the host’s environment, didn't need the survival toolbox that protected it in the wild. Therefore, it made drastic cuts in superfluous components and specialized to a limited set of functions that contributed to the overall survival of the bigger cell it was now a part of. Cells with mitochondria were born: a major, if not the main, step on the way to eukaryotic cells was made. 

Part of the defense of this evolutionary narrative consists in a search for contemporary analogues of its main protagonists. The poor engulfed thing has been identified as a relative to present-day alphaproteobacteria, a form of bacteria. The identity of the sadistic host, however, is still an ongoing mystery. Some of our best evolutionary detectives have recently found clues that might be crucial in solving this billion-years-old case.

 Ever wondered why 'Cell' was given that name in Dragon Ball Z? This character gets more powerful by ingesting other organisms, just like in the evolution of eukaryotes.

Ever wondered why 'Cell' was given that name in Dragon Ball Z? This character gets more powerful by ingesting other organisms, just like in the evolution of eukaryotes.

It is becoming increasingly clear, for reasons on which I won’t expand, that the host of the interaction at the origin of mitochondria is a member of archaea. But this is not enough, we need to know what kind of archaea the host was. And this is where Lokiarchaeota comes in: it has recently (a) been identified and (b) defended as the closest contemporary organism we have to the host [1]. Exactly how this team of scientists came up with these two claims needs further exploration. 

It is remarkable to think that ‘Lokis’ (the cute nickname for Lokiarchaeota) can harbour such evolutionary significance despite having neither been seen nor isolated. Why do we even think they exist?

Lokis are the fruit of metagenomics. Metagenomics is a technique that collects and studies the genetic material of a given environment. It involves collecting a sample from one of these environments (it could be pretty much anything, from human hair to university keyboards) and indiscriminately sequencing the DNA of the organisms that are found there. Because the sample contains a large amount of DNA, from a variety of organisms, what comes out of your sequencing machine is, so to speak, a large unattributed chunk of genome: the metagenome.

Metagenomics can have a long reach: even into the depths of the ocean. ‘Loki’s Castle’, is the home of 5 hydrothermal vents—underwater analogues of gysers or hot springs. In the cold depths of the ocean, they have a direct line to the sulphurous heat underneath the Earth’s crust and create tiny oases of life: the only life on earth which does not in some way depend on the sun’s light. The castle lies 3283m deep in the mid-Atlantic ocean, about 600km away from the Norwegian coastline (and nearly 2,000km away from the nearest UK Tory constituency – an overall good place to be). This combination of depth and geological activity provides a tricky to access, but incredibly interesting and biodiverse niche: a perfect place for metagenomics.

 Introducing  'Dumbo'  at Loki's Castle

Introducing 'Dumbo' at Loki's Castle

Lokiarchaeota were reconstructed from the LCGC14 metagenome obtained from sediments sampled 15km away from Loki’s Castle. As I said above, this metagenome is composed of bits of genomes from a wide variety of organisms. How do you get from the metagenome of many organisms, to genomes of specific species, to descriptions of the organisms that lived in your sample? The epistemic challenge here is similar to the one facing palaeontologists when, instead of having well-separated fossil bones, they have to deal with a barely differentiated mass of collated ancient bones. They would have to extract individual bones from it, sometimes attributing them to yet unknown species, and from these attributions reconstruct extinct organisms that contributed to the mass of bones. All these things are tricky jigsaws.

 Good luck with that.

Good luck with that.

Jigsaw puzzles are much easier when you have some information about what the complete puzzle is supposed to look like. Reconstituting unknown genomes from metagenomes requires a similar process. The metagenome from Loki’s castle was cut into shorter pieces of DNA, called ‘reads’. It is crucial to note that while metagenomes contain contributions from a variety of different organisms, they also contain multiple copies of the genome of similar organisms. This, for the sake of specific genome reconstruction, is great news. This means that, from your metagenome, multiple genomes from the same species are cut at different points, generating reads that partially overlap each other. This overlap allows scientists to associate reads together as belonging to the same genome, and to progressively generate larger fragments of DNA.

If you’re lucky, this process of reconstitution can associate a sufficient number of fragments of DNA to constitute full genomes. This was the case here, as the analysis from Loki’s Castle LCGC14 metagenome unveiled a ‘92% complete, 1.4 fold-redundant composite genome’: Lokiarchaeota was born. That is, although we’ve never seen Lokis, we’ve detected their presence in the jumbled jigsaw that is the LCGC14 metagenome of Loki’s Castle.

How has Lokiarchaeota emerged as prime nominee for the ‘best analogue of the host at the origin of mitochondria' prize? To know how this genome positions itself within the diversity of archaea, and how it relates to the eukaryotes, evolutionary biologists perform phylogenetic analyses. This set of techniques compares Loki’s reconstructed genome with a wide variety of others in order to find out its closest evolutionary relatives. To everyone’s surprise, it turned out that Loki’s genome was the closest thing we have to a eukaryotic genome, establishing them as a serious candidate for the long sought-after host archaea at the origin of eukaryotes. This genealogy has recently been reinforced by the reconstitution, through the use of metagenomics in a variety of places on the planet, of other genomes closely related to Lokis and to eukaryotes. Keeping with the Nordic theme, scientists now speak of these as forming the Asgard archaea [2].

To understand better what Lokiarchaeota are like, we need to know more about their shape, diet, like, dislikes, and the rest of their little quirks. To do that, the 5,301 proteins encoded in the composite genome have been put under serious scrutiny. You are probably aware that proteins are not merely things to be ingested in large quantities in order to be ‘beach body ready’. Rather, they are cellular components that carry out most of the activities within living organisms. This way, finding out which proteins are encoded in a genome can already give you a lot of information about how the respective organism may work. Such analyses resulted in the identification in Lokis and other members of Asgard of a striking variety of ‘eukaryote-specific proteins’ (ESPs) which are, as the name suggests, proteins usually exclusive to eukaryotic cells.

Some of the ESPs found in Lokis are involved, in eukaryotes, in processes regulating cell and membrane shape. This was interpreted as suggesting that Lokiarchaeota were capable of doing things with their membrane, which only eukaryotes generally do (and prokaryotes can't). Among these, it was suggested that they are capable of engulfing things via the process of phagocytosis.

Assuming that Lokiarchaeota can perform phagocytosis puts the evolutionary story together in a spectacular way. If accepted, it provides us with a long-sought-after contemporary version of the archaeal host which, a long time ago, recklessly engulfed an archaebacteria and changed the face of the world forever. It would both make perfect sense of the evolutionary proximity of the Lokiarchaeota genome from eukaryotes and provide strong evidence for the evolutionary scenario postulated for the origin of eukaryotes.

 A beautiful depiction of the endosymbiotic origin of mitochondria from Nick Lane's  'Power, Sex, Suicide' .

A beautiful depiction of the endosymbiotic origin of mitochondria from Nick Lane's 'Power, Sex, Suicide'.

Let’s take a step back from the story I've just told: scientists have journeyed to a volcanic vent in the depths of the ocean and done some random DNA trawling. From this they obtained a big pile of DNA which they then cut up in small pieces, and glued back together to form a genome from a new group of organisms hitherto completely unknown. They have then worked out, merely from the reconstructed genome, the genealogical relationship of this new group of organisms and devised a profile of how these organisms must be like. This whole process did not only add a new entry to the Pokedex of contemporary life, it also had the baffling consequence of helping scientists to infer all the way back to the origin of mitochondria. This is not the script for Inception 2; this is evolutionary biology at its very best. This sort of case is the equivalent of St-Emilion wine for philosophers of historical sciences.

Hold on Jean-Pierre, why does the case of Loki possess fantastique potential for philosophical investigation? Ha! I'm glad you asked! This case is extraordinaire for at least three reasons. First, this is currently unfolding science. The claims described here are currently being formulated, refined and defended. It is thererfore possible for philosophers to observe, and discuss with, protagonists in the heat of the moment, allowing us to capture the dazzling richness of 'science in action'. Some of this richness disappears as discussions cool off and memories get progressively erased (or worse, distorted). Second, historical sciences are often characterized as inferring from observable contemporary traces to past, forever unobservable, events and processes. The spicy plot twist, in this case, comes from the additional inference from contemporary traces to probably inaccessible contemporary organisms, which in turn feeds into our knowledge of the past. Third, familiar contemporary animals can usually provide interesting analogues to help understanding the behaviour of dinosaurs and other extinct animals. However, excursions in the world of unicellular organisms, because of their tremendously smaller size, is like stepping in a completely different universe. It adds extra difficulty to the task of understanding how they work and where they come from, and makes a philosophical study of how we acquire knowledge about both contemporary and extinct 'microbes' all the more worthwhile.

[1] A. Spang et al., “Complex archaea that bridge the gap between prokaryotes and eukaryotes”, Nature, 521, pp. 173-179, 2015.

[2] K. Zaremba-Niedzwiedzka et al., "Asgard archaea illuminate the origin of eukaryotic cellular complexity”, Nature, 541, pp. 353-358, 2017.

Many thanks to Adrian for his invitation and always helpful feedback and to Jonathan Lombard for careful scrutiny of an earlier version. Thanks to both of them for (not) laughing at my (bad) jokes.

Bio

Thomas Bonnin is a third year PhD student at the University of Exeter, in the southwest of England. As a philosopher of science, his work focuses on understanding the production of scientific knowledge about the history of life, with a particular interest on unicellular evolution from the origin of life to the origin of eukaryotes.