I think archaea represent, to some extent,
a blind spot in our understanding of natural diversity.
You hear a lot of people talk in many different contexts
about diversity and they’ll bring up viruses,
they’ll bring up eukaryotic cells,
and they’ll bring up bacteria.
But the archaea are often never even mentioned.
What I want people to acknowledge
when they hear about archaea is that this
is a completely distinct domain of life
that we should recognize for what it is
rather than blend it in with some other domain.
Understanding the Tree of Life,
trying to figure out the evolutionary relationships
of all life forms on our planet,
you know, it’s a point of curiosity.
We all wanna know where we came from.
For the longest time,
we’ve kind of had this belief in biology
that there’s these two different and extremely distinct
forms of life on our planet.
One is everything that we can see,
you know, right from the insects to the trees,
human beings, other mammals,
fishes, and so on and so forth.
You know, the eukaryotes.
And then, there’s everything that’s invisible,
and they were called the microorganisms, or prokaryotes.
So prokaryote was this all-encompassing term
that was used for unicellular microorganisms
that did not have organelles within the cells.
So their chromosome, essentially, just floats around
in their cytosol.
In contrast, the eukaryotes are organisms
that have kind of evolved these complex organelles,
one of which is the nucleus,
which encapsulates all of their chromosomal material.
And so that distinction was what was used to kind of
make evolutionary relationships between everything that
does have a nucleus and everything that doesn’t.
Turns out that it’s not as simple as that anymore.
In 1977, Carl Woese, at the University of Illinois,
wanted to use not just how organisms look,
their morphology, as a way to understand
how they’re related to each other,
but looking at parts of their genetic material, their DNA,
to make these evolutionary connections.
The evolution of new species begins with mutations in DNA.
These mutations can change genes,
which in turn can change the physical traits of organisms.
Sometimes, when an organism passes these genetic changes
to their offspring, it can cause a new species to emerge.
In the 1960’s, scientists began to wonder if they could
determine the evolutionary relationship between different
species by comparing their DNA sequences.
The more similar the DNA sequences of two organisms,
the more closely related they must be.
Less shared DNA suggests a more distant relationship.
To build a Tree of Life using this approach,
Carl Woese needed to find a gene
that he could compare across all life forms.
He chose one that is needed for cells to perform
one of their most essential functions, making proteins.
By comparing the sequence of this gene between different
types of organisms, he was able to infer the Tree of Life.
This particular molecule that he narrowed in on
is called the 16S ribosomal RNA.
By looking at just this one particular molecule
he was able to glean kind of the evolutionary relationships
of these organisms without even having to look at them.
So the story goes that
Woese was looking for microbial samples to do
16S ribosomal RNA sequencing for.
He went up to one of his colleagues,
and asked him for these
weird methane-producing microorganisms
that his lab was studying.
This colleague was Ralph Wolfe, who pioneered
the study of these methane-producing microbes.
And Ralph then handed him a vial of these methane producers
and said, "Yeah, take these bacteria
if you wanna look at their 16S ribosomal RNA."
And when Carl Woese and his students took
a look at those samples,
they found that they were nothing like
any of the others that they’d looked at
to the point that I think they had to repeat the study
at least two or three times to validate the fact
that the 16S ribosomal RNA was, in fact, that different.
And so, when you look at them under a microscope,
they might look similar.
But, if you look deeper into the cell,
into the DNA, you see that they’re actually
a very different group of organisms.
So he knew that he was on to something really, really big.
The microbes that we all thought
were just this one big pool of prokaryotes
were not that.
There were the bacteria
that are very well established and studied.
But then there were these archaea,
this, you know, enigmatic third domain of life.
Woese got so excited
that as soon as he made
that first three-domain Tree of Life,
he called up the New York Times
and it became the front page article the next day.
It was this interesting moment of serendipity.
You know, the reason why we discovered archaea
was this person, Carl Woese,
who had this pioneering technology,
but also, the fact that his lab
was situated next to that of someone
who was studying an archaea.
And then, it was those two things coming together
that gave rise to this paradigm-shifting
concept in biology.
So archaea, initially, when they were discovered
were found in extreme environments.
So, one of the first archaea that was sequenced,
was isolated from a hydrothermal vent
at the bottom of the ocean.
Now, we’ve essentially found archaea everywhere
in the environment around us, as well as within us.
So there’s archaea on our skin.
There’s archaea in our oral cavity.
We have archaea in our guts,
and every other place that you can think of,
there are archaea.
So often, they’re around us and we
can even see them sometimes.
We just don’t know them for who they are.
For instance, if you are flying
into the San Francisco Airport,
you’ll see these salt flats that have bright colors
as you land.
And that’s just a visual cue to you saying
here are archaea.
You know, you don’t have to go too far to find them.
They’re everywhere.
So the methanogenic archaea that my lab studies,
they produce 80% of the methane that's being released
to the atmosphere annually
which has a significant impact on climate change.
They also have a very direct impact on human health sometimes
because these methanogens in our distal gut
can be up to 10% of the microbial population,
which is substantial.
So the amount of calories that you get from your food
and also, how you digest your food,
what kinds of components come from it,
some of those factors also depend
on these archaea in your gut.
These archaea are actually a lot like us.
So the way the cells replicate,
or the way one cell becomes two cells,
the way the cells make their proteins,
a lot of those things are very similar
to the way we do that compared to the bacteria
that are also unicellular.
And what that’s leading to is this theory now
that the last common ancestor
to all modern-day eukaryotes came from an archaeon.
There’s kind of been a revolution
in the field of archaea in the last five years.
So people went and found these samples
in different marine sediments
And when they sequenced the organisms
that live there, they found these very
evolutionarily-distant group of archaea
called the Asgard archaea.
So the Asgard essentially is a group.
Within the Asgard you have the Lokis,
and then a bunch of other archaea
that are named after Norse gods.
These Asgard archaea
they have proteins in their cell
that are called eukaryotic signature proteins, or ESPs.
And the reason why I’m highlighting this is because
they’re typically proteins that are
only associated with eukaryotes.
These ESPs have not been found
in other archaea or in bacteria.
But now we’re seeing the presence of these proteins
in archaea as well.
So these organisms, when you put them back
on the Tree of Life to figure out where they are,
they’ve essentially changed the topology
or the way the tree looks now.
Previously, there were three domains,
and there was a shared ancestor between the archaea
and all of modern-day eukaryotes.
There was a last common ancestor that we shared,
and then the archaea split off
and the eukaryotes split off.
But now what we’re seeing
is that there is an archaeal ancestor
that gave rise to the eukaryots.
What this seems to indicate
is that these eukaryotes are branching from within the archaea
and are closely related to these distant groups
that we’ve recently found.
So that essentially makes archaea
even more closely related to us now
than we’d initially believed.
And that’s kind of changing that view
of the three-domain Tree of Life back
to maybe a two-domain Tree of Life,
but the two domains are different.
The two domains are both actually unicellular organisms,
and the eukaryotes are branching from one group
of these unicellular organisms.
So now that we’re think about the Tree of Life slightly differently,
one question that arises as a result is how did
that unicellular archaeal ancestor give rise
to this complex eukaryotic cell?
Now, one key evolutionary step that happened
along the way to becoming a eukaryote
was the fact that these cells
had to acquire the mitochondria.
What one hypothesis out there is
is that an archaeal cell engulfed a bacterial cell,
a free-living bacterial cell, and eventually,
that particular bacterial cell, living inside
the archaeon, went on to become
the mitochondria as we know it today.
So these Loki archaea encode
these eukaryotic signature proteins
And, when we look a little closer
into what these proteins do,
they also provide us a hint as to how
the complex eukaryotic cell may have arisen.
A lot of these proteins encode
for interesting cytoskeletal features,
so features that make up the body of the cell.
They produce these appendages outside the cell,
and these appendages look like they could be used to engulf
another organism that would eventually become
the mitochondria for the eukaryotic cell.
There are also proteins
that confer the cell the ability to engulf other cells
through endocytosis.
All of these proteins have functions
that we can use to kind of make sense
of how that engulfment
of a mitochondria may have occurred.
It almost seems like these Asgard archaea
are primed for some of the functions
that we ascribe to have happened
for the first eukaryotic cell to have arisen.
It’s an interesting time to be an archael biologist because
we’re kind of in this, you know,
major transition in thinking about archaea
from an evolutionary standpoint.
Right now, we’re in this phase
that we’re gathering a lot of information,
and that information is kind of letting us
build new hypotheses about the tree of life.
As more information is revealed to us,
we will kind of keep refining the tree of life.
It is extremely likely that in the future
we will find something else,
and that might make us wanna revisit the tree of life again.
They’re such an understudied group of organisms
that I don’t think there’s one right question to ask.
I think there’s so many things that we can look at.
We know what’s unique about eukaryotes,
and similarly with the bacteria.
But very little is known about
what it means to be an archaea,
what is kind of unique and distinctive about them.
We have a few things that we know, but we don't really know
their deep, dark secrets, so to say.
It's a good time to go learn more about that.