Archaea and the Tree of Life • iBiology

00:00:01.11 I think archaea represent to some extent
00:00:05.01 a blind spot in our understanding
00:00:07.13 of natural diversity.
00:00:09.19 You hear a lot of people talk, in many different contexts,
00:00:13.00 about diversity,
00:00:14.15 and they’ll bring up viruses,
00:00:15.27 they’ll bring up eukaryotic cells,
00:00:17.18 and they’ll bring up bacteria.
00:00:19.05 But the archaea are often never even mentioned.
00:00:22.17 What I want people to acknowledge
00:00:24.11 when they hear about archaea
00:00:25.27 is that this is a completely distinct domain of life
00:00:28.06 that we should recognize for what it is,
00:00:30.06 rather than blend it in with some other domain.
00:00:34.18 Understanding the tree of life,
00:00:36.28 trying to figure out what the evolutionary relationships
00:00:39.01 of all life forms on our planet…
00:00:42.02 you know, it’s a point of curiosity.
00:00:43.12 We all want to know where we came from.
00:00:47.00 For the longest time,
00:00:48.07 we’ve kind of had this belief in biology
00:00:50.09 that there’s these two different and extremely distinct
00:00:54.23 forms of life on our planet.
00:00:56.06 One is everything that we can see,
00:00:58.09 you know, right?,
00:01:00.04 from the insects, to the trees,
00:01:01.21 human beings, other mammals,
00:01:03.21 fishes, and so on and so forth…
00:01:05.06 you know, the eukaryotes.
00:01:06.27 And then there’s everything that’s invisible,
00:01:08.26 and they were called the microorganisms or prokaryotes.
00:01:12.20 So, “prokaryote” was this all-encompassing term
00:01:15.01 that was used for unicellular microorganisms
00:01:17.24 that did not have organelles within the cells.
00:01:22.07 So, their chromosome essentially just floats around in their cytosol.
00:01:25.25 In contrast, the eukaryotes are organisms
00:01:28.09 that have kind of evolved these complex organelles,
00:01:30.24 one of which is the nucleus,
00:01:33.05 which encapsulates all of their chromosomal material.
00:01:36.11 And so, that distinction was what was used
00:01:38.28 to kind of make evolutionary relationships
00:01:41.09 between everything that does have a nucleus
00:01:43.16 and everything that doesn’t.
00:01:46.04 It turns out that it’s not as simple as that anymore.
00:01:52.05 In 1977, Carl Woese at the University of Illinois
00:01:55.18 wanted to use not just how organisms look
00:01:59.03 — their morphology —
00:02:01.03 as a way to understand how they relate to each other,
00:02:03.03 but looking at parts of their genetic material,
00:02:07.17 their DNA,
00:02:09.06 to make these evolutionary connections.
00:02:14.10 The evolution of new species
00:02:16.28 begin with mutations in DNA.
00:02:19.18 These mutations can change genes,
00:02:22.23 which in turn can change the physical traits of organisms.
00:02:27.27 Sometimes, when an organism passes
00:02:30.18 these genetic changes to their offspring,
00:02:32.17 it can cause a new species to emerge.
00:02:37.20 In the 1960s,
00:02:40.04 scientists began to wonder if they could
00:02:43.00 determine the evolutionary relationship
00:02:45.09 between different species
00:02:47.14 by comparing their DNA sequences.
00:02:51.12 The more similar the DNA sequences of two organisms,
00:02:54.16 the more closely related they must be.
00:02:58.28 Less shared DNA suggests
00:03:01.12 a more distant relationship.
00:03:07.11 To build a tree of life using this approach,
00:03:10.00 Carl Woese needed to find a gene
00:03:11.28 that he could compare across all life forms.
00:03:16.26 He chose one that is needed for cells
00:03:18.22 to perform one of their most essential functions:
00:03:21.26 making proteins.
00:03:24.26 By comparing the sequence of this gene
00:03:26.28 between different types of organisms,
00:03:29.24 he was able to infer the tree of life.
00:03:35.07 This particular molecule that he narrowed in on
00:03:37.23 is called the 16S ribosomal RNA.
00:03:41.29 By looking at just this one particular molecule
00:03:44.05 he was able to glean kind of the evolutionary relationships
00:03:47.13 of these organisms without even having to look at them.
00:03:51.10 So, the story goes that Woese was looking for
00:03:54.04 microbial samples to do 16S ribosomal RNA sequencing for.
00:03:59.04 He went up to one of his colleagues
00:04:01.14 and asked him for these weird methane-producing microorganisms
00:04:03.28 that his lab was studying.
00:04:06.04 This colleague was Ralph Wolfe,
00:04:08.20 who pioneered the study of these methane-producing microbes.
00:04:12.03 And Ralph then handed him a vial of these methane producers
00:04:15.06 and said, yeah, take these bacteria
00:04:17.21 if you want to look at their 16S ribosomal RNA.
00:04:20.15 And when Carl Woese and his students
00:04:22.05 took a look at those samples,
00:04:24.09 they found that they were nothing like
00:04:26.14 any of the others that they’d looked at,
00:04:28.19 to the point that I think they had to repeat the study
00:04:31.04 at least two or three times to validate the fact
00:04:33.19 that the 16S ribosomal RNA was in fact that different.
00:04:37.04 And so, when you look at them under a microscope,
00:04:39.12 they might look similar.
00:04:41.02 But if you look deeper into the cell, into the DNA,
00:04:43.14 you see that they’re actually
00:04:44.27 a very different group of organisms.
00:04:47.07 So, he knew that… he knew that he was on
00:04:49.21 to something really, really big.
00:04:51.24 The microbes that we all thought were
00:04:54.03 just this one big pool of prokaryotes
00:04:55.22 were not that.
00:04:57.15 There were the bacteria
00:04:59.22 that are very well established and studied.
00:05:01.21 But then there were these archaea,
00:05:04.01 this, you know, enigmatic third domain of life.
00:05:08.00 Woese got so excited that as soon as he, like,
00:05:11.00 made that first three-domain tree of life,
00:05:12.28 he called up the New York Times,
00:05:15.04 and it became the front page article the next day.
00:05:19.28 It was this interesting moment of serendipity.
00:05:22.04 You know, the reason why we discovered archaea
00:05:24.18 was this person, Carl Woese,
00:05:26.13 who had this pioneering technology,
00:05:28.23 but also the fact that, you know,
00:05:30.26 his lab was situated next to that of someone
00:05:32.25 who was studying an archaea.
00:05:34.15 And then, it was those two things coming together
00:05:36.25 that, you know, gave rise to this…
00:05:38.25 this paradigm-shifting concept in biology.
00:05:43.11 So, archaea initially, when they were discovered,
00:05:46.02 were found in extreme environments.
00:05:48.25 So, one of the first archaea
00:05:50.28 that was sequenced
00:05:53.02 was isolated from a hydrothermal vent at the bottom of the ocean.
00:05:56.09 Now, we’ve essentially found archaea
00:05:59.12 everywhere in the environment around us,
00:06:01.09 as well as within us.
00:06:03.05 So, there’s archaea on our skin.
00:06:04.26 There’s archaea in our oral cavity.
00:06:07.07 We have archaea in our guts.
00:06:09.12 And every other place that you can think of,
00:06:11.01 there are archaea.
00:06:12.13 So, often, they’re around us,
00:06:14.02 and we can even see them sometimes.
00:06:15.16 We just don’t know them for who they are.
00:06:18.25 For instance, if you are flying into the San Francisco airport,
00:06:22.07 you’ll see these salt flats that have bright colors as you land.
00:06:26.20 And that’s just a visual cue to you saying,
00:06:29.18 here are archaea.
00:06:31.11 You know, you don’t have to go too far to find them;
00:06:33.11 they’re everywhere.
00:06:35.06 So, the methanogenic archaea that my lab studies…
00:06:37.21 they produce 80% of the methane
00:06:40.22 that’s being released to the atmosphere annually,
00:06:43.15 which has a significant impact on climate change.
00:06:46.17 They also have a very direct impact
00:06:48.22 on human health sometimes,
00:06:50.08 because these methanogens in our distal gut
00:06:53.27 can be up to 10% of the microbial population,
00:06:56.25 which is substantial.
00:06:59.03 So, the amount of calories that you get from your food,
00:07:02.02 and also how you digest your food…
00:07:04.02 what kinds of components come from it…
00:07:07.14 some of those factors also depend
00:07:09.29 on these archaea in your gut.
00:07:12.12 These archaea are actually a lot like us.
00:07:14.20 So, the way the cells replicate…
00:07:16.21 or the way one cell becomes two cells,
00:07:20.12 the way the cells make their proteins…
00:07:22.15 a lot of those things are very similar
00:07:24.29 to the way we do them,
00:07:26.13 compared to the bacteria that are also unicellular.
00:07:29.16 And that’s… and what that’s leading to
00:07:31.24 is this theory, now, that,
00:07:34.22 you know, the last common ancestor to all modern day eukaryotes
00:07:37.29 came from an archaeon.
00:07:41.13 There’s kind of been a revolution in the field of archaea
00:07:43.24 in the last five years.
00:07:47.04 So, people went and found these samples
00:07:49.08 in different marine sediments.
00:07:52.10 And when they sequenced the organisms that lived there,
00:07:55.14 they found this very evolutionarily distant group of archaea
00:08:00.25 called the Asgard archaea.
00:08:03.10 So, the Asgard essentially is a group.
00:08:05.10 Within the Asgard, you have the Lokis
00:08:08.07 and then a bunch of other archaea that are named after Norse gods.
00:08:11.15 These Asgard archaea…
00:08:13.29 they have proteins in their cell
00:08:16.06 that are called eukaryotic signature proteins or ESPs.
00:08:19.21 And the reason why I’m highlighting this
00:08:22.13 is because they’re typically proteins
00:08:25.13 that are only associated with eukaryotes.
00:08:27.14 These ESPs have not been found in other archaea
00:08:29.14 or in bacteria.
00:08:30.24 But now, we’re seeing the presence of these proteins
00:08:33.15 in archaea as well.
00:08:35.00 So, these organisms…
00:08:36.24 when you put them back on the tree of life
00:08:38.22 to figure out where they are,
00:08:40.12 they’ve essentially changed the topology
00:08:42.19 or the way the tree looks now.
00:08:44.28 Previously, there were three domains,
00:08:46.19 and there was a shared ancestor
00:08:48.13 between the archaea and all of modern day eukaryotes.
00:08:52.08 There was a last common ancestor that we shared,
00:08:55.19 and then the archaea split off and the eukaryotes split off.
00:08:57.29 But now, what we’re seeing is that
00:09:01.15 there is an archaeal ancestor
00:09:03.09 that gave rise to the eukaryotes.
00:09:05.02 What this seems to indicate is that these eukaryotes
00:09:07.25 are branching from within the archaea
00:09:09.16 and are closely related to these distant groups
00:09:12.12 that we’ve recently found.
00:09:15.08 So, that essentially makes archaea
00:09:17.18 even more closely related to us, now,
00:09:19.29 than we’d initially believed.
00:09:21.24 And that’s kind of changing
00:09:23.24 that view of the three-domain tree of life
00:09:26.10 back to maybe a two-domain tree of life —
00:09:28.26 but the two domains are different.
00:09:30.10 The two domains are both actually unicellular organisms,
00:09:32.15 and the eukaryotes are branching from one group
00:09:35.26 of these unicellular organisms.
00:09:39.29 So, now that you’re thinking about the tree of life
00:09:43.09 slightly differently,
00:09:45.00 one question that arises as a result is,
00:09:47.05 how did that unicellular archaeal ancestor
00:09:49.10 give rise to this complex eukaryotic cell?
00:09:52.18 Now, one key evolutionary step
00:09:55.09 that happened along the way
00:09:57.16 to becoming a eukaryote
00:09:59.09 was the fact that these cells had to acquire
00:10:01.22 the mitochondrion.
00:10:03.22 What one hypothesis out there is
00:10:07.11 is that an archaeal cell engulfed a bacterial cell,
00:10:09.17 a free-living bacterial cell,
00:10:11.15 and eventually that particular bacterial cell
00:10:14.00 living inside the archaeon
00:10:16.08 went on to become the mitochondria as we know it today.
00:10:19.19 So, these Loki archaea
00:10:23.25 encode these eukaryotic signature proteins.
00:10:25.23 And when we look a little closer into what these…
00:10:28.09 what these proteins do,
00:10:30.08 they also provide us a hint as to how
00:10:33.10 the complex eukaryotic cell may have arisen.
00:10:36.07 A lot of these proteins encode for
00:10:38.19 interesting cytoskeletal features,
00:10:40.23 the features that make up the body of the cell.
00:10:46.13 They produce these appendages outside the cell,
00:10:49.09 and these appendages look like they could be used to engulf
00:10:52.18 another organism
00:10:54.28 that would eventually become the mitochondria
00:10:56.23 for the eukaryotic cell.
00:10:58.24 There are also proteins that confer the cell
00:11:02.12 the ability to engulf other cells through endocytosis.
00:11:05.07 All of these proteins have functions
00:11:07.10 that we can use to kind of make sense
00:11:10.03 of how that engulfment of a mitochondria
00:11:12.27 may have occurred.
00:11:14.18 It almost seems like these Asgard archaea
00:11:16.18 are primed for some of the functions
00:11:19.10 that we ascribe to have happened
00:11:21.03 for the first eukaryotic cell to have arisen.
00:11:26.09 It’s an interesting time to be an archaeal biologist
00:11:28.27 because we’re kind of in this… this…
00:11:31.27 you know, major transition in thinking about archaea
00:11:34.15 from an evolutionary standpoint.
00:11:36.29 Right now, we’re in this phase that we’re gathering a lot of information,
00:11:40.27 and that information is kind of letting us
00:11:43.11 build new hypotheses about the tree of life.
00:11:45.29 As more information is revealed to us,
00:11:47.25 we’ll kind of keep refining the tree of life.
00:11:50.02 It is extremely likely that in the future
00:11:51.27 we’ll find something else,
00:11:53.26 and that might make us want to revisit the tree of life again.
00:11:56.23 They’re such an understudied group of organisms
00:11:59.01 that I don’t think there’s one right question to ask.
00:12:02.00 I think there’s so many things that we can look at.
00:12:05.19 We know what’s unique about eukaryotes,
00:12:08.06 and similarly with the bacteria.
00:12:09.29 But very little is known about what it means to be an archaea.
00:12:12.12 What is kind of unique and distinctive about them?
00:12:15.06 We have a few things that we know,
00:12:17.15 but we don’t really know their deep, dark secrets, so to say.
00:12:20.04 It’s a good time to go learn more about that.

This Talk

Speaker: Dipti Nayak

Audience:

General Public
Educators of H. School / Intro Undergrad
Student
Educators

Recorded: December 2019

Talk Overview

Before 1977, all life on Earth was classified into two groups: single-celled microorganisms and complex cellular life such as fungi, plants, and animals. A seminal discovery in 1977 rewrote the tree of life and introduced a whole new domain of organisms known as the archaea – mysterious microbes that are genetically distinct from bacteria. Fast forward to the 21st century, and again new discoveries about archaea are leading scientists to reshape the tree of life and rewrite the evolutionary history of complex organisms. Dr. Dipti Nayak introduces the fascinating organisms known as archaea and explains how they are helping scientists answer the question Where do we come from?.

Speaker Bio

Dipti Nayak

Dipti Nayak

Dipti Nayak received her PhD in Organismic and Evolutionary Biology from Harvard University in 2014. She performed postdoctoral research at the University of Illinois, where she studied the physiology and evolution of methanogenic archaea. The Nayak lab at UC Berkeley employs genetic, genomic, and biochemical tools to study the physiology, metabolism, evolution, and cell biology… Continue Reading

Credits

Elliot Kirschner (Wonder Collaborative): Executive Producer
Shannon Behrman (iBiology): Executive Producer
Brittany Anderton (iBiology): Producer
Eric Kornblum (iBiology): Editor, Videographer
Derek Reich (ZooPrax Productions): Videographer
Adam Bolt (The Edit Center): Editor
Gb Kim (Explorer’s Guide to Biology): Illustrations
Chris George: Design and Graphics
Maggie Hubbard: Design and Graphics

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