One of the things that scientists do naturally, I think, is try to organize their observations. And something that's been done since much longer than we knew about bacteria is the classification of organisms based on relatedness. So people would look at, for example, a chimpanzee and a human and realize that they had a lot of similarities.
Whereas if you look at a tree and a bush, they look more similar to each other. And a fish and a shark would look more similar to each other as well. So we refer to this classification of organisms as taxonomy.
And we care about using taxonomy to both identify organisms and then name them in a logical way. And the goal is to create a phylogenetic system. And when you look at phylogenetic systems based on phenotypic, the way things look, their characteristics, you automatically group organisms based on their evolutionary relatedness as a result. Because organisms that look very similar, that have many similar features, almost always are closely related evolutionarily, meaning that they evolved around the same time when you look at the tree of life.
When I was in high school, we learned about the five king and actually in college too we learned about the five kingdoms plants fungi animals protists and the prokaryotes and this was the idea really predominated this this organization of the life on earth this predominated until around 1990. and in 1990 a gentleman named carl woos proposed a new three domain system based on molecular clocks um there was a article by a gentleman named Norman Pace who's a microbiologist at the University of Colorado in Boulder and he says that woos is to biology what Einstein is to physics so in case you don't think this is a monumental rethinking of science it really was so he proposed this in 1990 and what he did is he said let's not look at how things are on the outside let's look at their the genetic information So in order to do this, we had to be able to sequence DNA and RNA, and that technology wasn't available until the 1990s. But what he discovered was that when you look at ribosomal RNA sequences, so these are sequences of RNA, which are encoded in our DNA, in our genetic information, that are part of the protein synthesis machinery in the cell. So these are really...
important. And the idea here is that in both eukaryotes and prokaryotes, that these RNA structures are so critical that they evolve very, very slowly. And you can look at them as like a molecular clock.
The closer eukaryotic and prokaryotic RNA is in two different organisms, then the more similar those RNA molecules are, the more closely these organisms are in terms of their evolutionary... relationships. And so this actually allowed him to measure evolutionary history using these molecular clocks.
And when he did this he really made a monumental discovery. This is a picture of ribosomal RNA if you're interested. This is the molecule that Carl was used to sequence. And again it's just a really critical component of protein synthesis and because of that it changes very very slowly over time.
All right, so back to Carl Wuz's discovery. When he, instead of organizing organisms into five kingdoms, when he organized them based on the similarity between their ribosomal RNA, he found that they nicely grouped into three major categories. And so all of the eukaryotes are shown in this category, which means that we are in the same group as protists and animals and plants and fungi.
So this is all one group. He found that there was another group called bacteria, and so all of the bacteria are in this group. And then he found a third, which he called these domains, he found a third domain called archaea.
And he determined that the, it turns out that archaea is a completely new category that we'd always lumped with the prokaryotes, because it's also prokaryotic. But he found that it's actually closer to eukaryotes than bacteria were. terms of their evolutionary history. Now this is one of the original drawings of the three domain theory but this is a more modern one and I love this one because it As a microbiologist, we know I really like bacteria. And what this shows is actually, this is the same drawing, but you see that archaea are this small group here, and eukaryotes are this small group here.
And then look at this massively diverse group of bacteria up here. So what this doesn't show you here is the fact that actually eukaryotes are a much less diverse group. I know you think you're really different than a plant.
But when we look at you genetically, you're actually much less diverse than many of the bacteria that exist on planet Earth. So we now use a three domain system, and this is how we organize all of the life on Earth now, is in this three domain system. This is a picture of the Wu's tree, just showing how the last universal common ancestor may have resulted in the origination of bacteria. as one domain. And then there were other common ancestors that then differentiated into the eukarya and then the archaea that we see here.
Archaea, I'll say very little about them, but we refer to them as extremophiles. They tend to live in really extreme environments. You have archaea in your gut. Those are some of the methanogens that produce gas, for example. This is actually a picture that came out of an article that was in the New York Times and they were talking about the fact that there are actually, when we look at extreme environments like the hot springs in Yellowstone or the very coldest parts of the earth, we almost always find bacteria.
But in this article they were pointing out the fact that there are some places that are so extreme that bacteria can't live, not even the archaea. We won't spend a lot of time on archaea in this class, but just realize that they are a third domain and that we tend to associate them with very extreme environmental conditions. So they live where nothing else can, although you can create environments where even they are unable to survive. All right, what about the classification of bacteria?
We have always classified bacteria based on phenotypic traits. just like we classified plants and animals and fungi based on phenotypic traits. And it turns out that when you measure the accuracy of classification based on phenotype, based on how things look for plants and fungi and animals, we get a lot right by just looking at them in terms of their structure. But when you do this with bacteria, it's a disaster.
And that's because bacteria can, they're so tiny, it's very hard to see them and really get a lot of information from how they look. Their phenotypes, they're simple, so they don't have a lot of differentiating structures. We've used their shape.
So are they round? Are they rod shaped? We've looked at how they stain. When we apply stains to them and look at them under the microscope, we've looked at the conditions they need to grow and the waste products they produce.
We've sort of... attempted to use those to classify them. And it hasn't worked out very well. So nowadays, when we classify microorganisms, we use genetic analysis, we use the tools of DNA sequencing.
And again, thinking back on Carl Wuz's use of ribosomal RNA, that allows us to get a much more accurate classification of bacteria into groups in terms of their evolutionary relatedness and in terms of their function as well. All right, in our last segment for this lecture, we're going to talk about how microbes are named.