Archaea and the Tree of Life
Transcript of Part 1: Archaea and the Tree of Life
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.