Are We All Actually Archaea?

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In 1977, American biologist Carl Woese announced that he’d stumbled on a new form of life.

He’d been developing a new  method for reconstructing  evolutionary relationships between organisms, one based on comparing specific genetic sequences rather than on comparing physical traits.

One day, while analyzing  sequences from methane-producing  bacteria, he discovered something remarkable.

While the microbes seemed like typical bacteria, their genetic sequences were wildly different.

Different enough, in fact, that he realized they must actually be part of an early branch of life that had diverged billions of years in the past and had remained hidden all this time.

Eventually, in 1990, Woese redrew the tree of life.

He proposed that prokaryotes - single-celled organisms without a nucleus - should be split into two separate domains: Bacteria, and the  new domain Archaea, which  literally means ‘the old ones’.

Along with our domain, Eukarya, this left  us with the three-domain system  that we’ve been using ever since.

Everything that's alive falls into one of these three groups.

If you’re from planet Earth, you’re either a eukaryote, a bacterium, or an archaeon.

The unexpected discovery of an entirely new  domain of life was pretty huge and surprising  - even if they do just look like bacteria.

But, in recent years, it’s been their connection to us that's turned out to be particularly   full of surprises - ones that may mean we have to redraw the tree of life yet again.

Despite being an entire domain of life, archaea  have often been a bit of a blind spot  for both scientists and non-scientists.

For a long time following their initial discovery, they were only known to thrive in very particular   and often extreme environmental conditions  that are hard to replicate in a lab.

Think low-oxygen deep-sea sediment, or boiling and acidic hydrothermal vents.

Plus, microbes in general  tend to be underappreciated  - especially considering their diversity,  abundance, and importance in the history of life.

Most folks only think about microbes when  they're doing something to or for them  – like, causing disease or making beer.

So archaea have been a blind spot within a blind spot.

But by examining the ones we can culture, and  probing the molecules of the ones we can’t,   we've managed to figure out some  pretty interesting things about them.

Like bacteria, they’re single-celled and don’t have a nucleus or other organelles.

And they reproduce asexually through a process  called binary fission, in which a  cell divides into two daughter cells.

Also like bacteria, they usually have protective  cell walls and propeller-like  structures for getting around.

Though, in both cases, these features are  built very differently from  those found in bacteria.

As are their cell membranes, which have a  unique molecular composition  compared to the other domains.

And we now know that archaea aren’t just confined to extreme habitats.

They seem to be pretty widespread in a range of terrestrial and aquatic environments.

Once we knew what to look for, they started turning up everywhere - even living in and on   our bodies, though none are known to cause diseases.

Tens of thousands of species have been identified to date.

And genetic analyses of these species cluster them into a complex family tree that’s   regularly added to, rearranged,  and argued over by researchers.

But they’re all definitely part  of the ancient domain Archaea,   billions of years removed from  both bacteria and eukaryotes.

But perhaps not equally removed from both.

See, despite looking like bacteria, they’re  actually more closely related to us  eukaryotes -- yeah, organisms with large,   complex cells that have nuclei, like  animals, plants, fungi, and protists.

And a few shared traits from this ancient common ancestry are still visible.

For example, some of the enzymes they use to process, read and replicate their genetic code   are very similar to ones found in eukaryotes  and very different from those in bacteria.

So in Woese’s three-domain system - the  currently accepted tree of life - they’re  considered a sister group of ours.

Archaea and eukaryotes shared a common ancestor with each other more recently than they do   with bacteria, so they’re each other’s closest relatives at the domain level.

Which means that archaea are more closely  related to people, dinosaurs, mushrooms,  and bananas than they are to any bacteria.

But as our understanding of archaea has grown, an even more radical idea has emerged… What if eukaryotes don't just share an ancient common ancestor with archaea?

What if we actually evolved within archaea,  and should really just be considered a part of their domain?

Now, a big moment in the origin of eukaryotes was endosymbiosis.

A mysterious ancestral cell engulfed a bacterium and formed a symbiotic relationship with it.

This became the energy-producing mitochondria  that helped fuel the rise of complex  eukaryotes, a feature we all still have today.

Could that ancestral engulfing cell have been an archaeon?

Did eukaryotes emerge from a fusion of an archaeon and a bacterium?

Are we actually just a branch of the Archaea family tree?

If we could determine which branch we trace  our ancestry to, that might help  answer all of those questions.

But for that, we would need to find a specific  group of living archaea that eukaryotes  were particularly related to.

And in 2015, a group of researchers announced they’d found exactly that.

They’d been sampling marine sediment near a field of underwater hydrothermal vents   called Loki’s Castle, about halfway  between Greenland and Norway.

And they were able to isolate and sequence enough DNA from the sample to reconstruct a   92% complete genome of an archaeon from  a new group they called Lokiarchaeota.

Lokiarcheota were a part of a distinct group  within the Domain Archaea, and many other  members have since been discovered around   the world, including Odinarcheota,  Thorarcheota, and Heimdallarchaeota.

In keeping with the Norse mythology theme, this group has been named the Asgard Archaea.

When researchers compare the genomes of those Asgard archaea to other archaea,   as well as to eukaryotes, their results generally  suggest that they’re our closest  living archaeal relatives.

Some analyses even conclude that eukaryotes arose specifically within the Asgard group!

And their genomes include the instructions  for a bunch of proteins that were previously  considered exclusive to eukaryotes.

The discovery of these ‘eukaryote-like’  Asgardians was another major clue  in the origins of eukaryotes.

Their existence supports the archaeal origin  hypothesis for eukaryotes by bridging  the gap between the two groups.

And some researchers suggest that we might  even trace our ancestry to their particular  branch of the Archaea family tree.

Now the debate is far from settled, and we’re  finding more and more clues as our  understanding of archaea continues to grow.

But if it does turn out that we descend from an ancient Asgard or Asgard-related archaea   that engulfed a bacterium, gained the  mitochondria, and gave rise to all eukaryotes,   that would mean that Carl Woese was  both right and also…kinda wrong.

Yes - he was correct in separating archaea  from bacteria, but maybe his three-domain system  was wrong to separate them from eukaryotes.

Perhaps the tree of life only has two domains after all.

Hey, hello, it's Blake, hi!

If  you enjoyed this episode about   some of the tiniest lifeforms on our  planet, there’s a lot more where that   came from on another show produced by  our team: Journey To The Microcosmos.

Join hosts Hank Green and Deboki Chakravarti  as they dive into the tiny,  unseen world that surrounds us.

Check it out over at youtube.com/Microcosmos!

Wanna know more about the mysterious origin of complex life?

Then check out our episode, “How Two Microbes Changed History”.

And may the blessings of Asgard be showered upon this month’s Eontologists!

Jacksy Weiss, Colton, Melanie Lam Carnevale,  Chase Archambault, Annie & Eric  Higgins, John Davison Ng, and Jake Hart.

Become an Eonite at patreon.com/eons and you  can get fun perks like  submitting a joke for us to read.

Here’s one from The Burgins.

What do you call a velociraptor that can play the piano?

Talon-ted!

And as always thanks for joining me in the Adam Lowe studio.

Subscribe at youtube.com/eons for more ancient adventures.

Eu-car-ya, Eu-care-ya,  Eu-care-yotes, Eu-care-yah... ar-KEE-ah!