Loki and behold: one microbial culture that brings us one leap closer to understanding the origins of eukaryotic cells

What were you doing 10 years ago? Can you remember? Were you, perhaps, trying to sort out the origins of eukaryotic life?

A pre-print (yet to be peer-reviewed) was released earlier this month by Imachi et al., describing a 12 year long effort to isolate what the authors refer to as a “Lokiarchaeota-related Asgard archaeon from deep marine sediments”. The results presented in this study have been widely covered in articles see here, here, here, or over here for just a few examples. So…what’s the big deal?

Science has long asked many big questions, including: What led to the first eukaryotic (that includes us, other animals, plants, and fungi) cells? Before we dive into the pre-print and how it relates to this question, let’s go back in time. *Cue Wayne’s World flashback music …doodooledoo…doodooledoo*

Humans like classifying things, and in 1735 Carolus Linnaeus published Systema Naturae, outlining a taxonomy of plant classification that eventually evolved to include basically everything (see Manktelow, History of Taxonomy for an informative but relatively brief overview). As you probably already know, we can thank good old Carolus for our current two-word method of scientific names. Since Linnaeus however, classifications have evolved, a landmark change came in 1977 when Carl Woese introduced a tree based on 16S rRNA genes outlining three domains of life that included: Archaea, Bacteria, and Eukarya (Woese and Fox, 1977).

Access to new sequencing technologies has changed how we understand relationships among organisms. Recently, the Lokiarchaeota (classified in the Asgard archaea superphylum) were discovered using metagenomic sequencing (Spang et al., 2015). The name was chosen since the original sample was from a site close to what is known as Loki’s Castle, an active hydrothermal vent. The Lokiarchaeota genome derived from binning sequences from the metagenome data, showed that this proposed organism had a lot of genes that were similar to what you might find in a eukaryote (oh hey, that’s us again). So maybe it’s not surprising that it was proposed that eukaryotes possibly originated from something closely related to the Asgard archaea. While very cool, genomes from metagenomes only get you so far, being able to study the physiology of a Asgard archaeon in culture would be key.

That is exactly what all the big fuss is about. In this pre-print, the authors spent 2,000 days (aka 48,000 hours or 2,880,000 minutes) using a bioreactor to enrich for organisms from anaerobic marine methane seep-sediments (say that three times fast). Ultimately, they were able to subculture a Lokiarchaeota, dubbed MK-D1. This strain had an estimated doubling time of 14 to 25 days….as a point of reference an average E. coli can double as quickly as 15-20 minutes (at least 1,344 times FASTER than MK-D1) .

“Based on cultivation and genomics, we propose an ‘Entangle-Engulf-Enslave (E3) model’ for eukaryogenesis through archaea-alphaproteobacteria symbiosis…” – Imachi et al., pre-print.

Interestingly, sub-culturing MK-D1 initially led to a “tri-culture”, basically 3 different things growing together. Some fancy scanning electron microscopy (SEM) and other visualization techniques allowed the researchers to see that this microbe liked to live in close physical association with the other strains in the culture. After many many transfers, and a total of 12 years, they ended up with a co-culture of just the precious MK-D1 and one other methane producing archaeon. The authors carefully and clearly detail the conditions used for growth and between the supplemental information and manuscript, relevant accession numbers and sequences are all available.

Having MK-D1 in culture means they can study how this organism grows to better characterize its physiology than just having sequence data in hand. Will we now be able to figure out if an Asgard-like archaeon engulfed a bacterial cell, eventually leading to the rise of eukaryotic cells? I’m not sure, but I do know that we are a giant leap closer to finding out.

With the culture of MK-D1, the authors were also able to sequence its genome, confirming that the Lokiarchaea have a lot of eukaryote-like genes. This was a hot topic of debate previously since constructing genomes from metagenomes is a bit like finding strands of yarn in a pile of hay and knitting them back into the sweater that the yarn originally came from.

The ability to sequence environmental samples has led to a ton of data. It has also shown us how many microbes are in the environment that we haven’t yet cultivated. Moving away from what might be regarded as traditional techniques to more specialized methods such as using bioreactors, is one way to expand on what might be grown in the lab. When working to understand the microbial cells that could unlock mysteries about the origin of eukaryotic life, it’s is clear that sequencing metagenomes is not enough. We need to continue to strive to find the conditions for the microbes that have not yet been cultivated.

“Endeavors in cultivation of other Asgard archaea and more deep-branching eukaryotes are essential to further unveil the road from archaea to eukaryotes.” – Imachi et al., pre-print.

About 10 years ago, in the midst of grad school, I was isolating actinobacteria from marine sediments, mildly annoyed about the 2 weeks that it took for a dense culture to grow in liquid media. I can’t imagine waiting 12 years to see the results of untold hours of work. It’s a mystery what innovations in cultivation might bring, but it’s amazing to think that we are getting closer to understanding the origins of eukaryotic life.

References

Imachi, H., Nobu, M.K., Nakahara, N., Morono, Y., Ogawara, M., Takaki, Y., Takano, Y., Uematsu, K., Ikuta, T., Ito, M. and Matsui, Y., 2019. Isolation of an archaeon at the prokaryote-eukaryote interface. bioRxiv, p.726976.

Spang, A., Saw, J.H., Jørgensen, S.L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A.E., van Eijk, R., Schleper, C., Guy, L. and Ettema, T.J., 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature521(7551), p.173.

Woese, C.R. and Fox, G.E., 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences74(11), pp.5088-5090.

About Kelle Freel

I'm currently a postdoc working at the Hawai'i Institute of Marine Biology with Dr. Mike Rappé. I'm interested in the biogeography and ecology of microbes, especially of the marine variety. After studying a unique genus of marine bacteria at Scripps Oceanography in grad school, I moved to France, where I worked with a group studying yeast population genomics. In my free time, I like to do outdoorsy stuff, travel, and cook.
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