Phylogenetic structure of the prokaryotic domain: the primary kingdoms.

Ike’s comin’ right for us, so I don’t know when the my power and internet access will die, and if so how long it’ll be before it comes back. However, while I’m still connected I wanted to contribute something again to this month’s The Giant’s Shoulders blog carnival. Since it’s in three days and there’s a chance our power might be out when the deadline passes, I figured I’d better hurry. Because of the hurry there are no fancy graphics nor even too much explanatory text here, but I’ll do what I can. Fortunately, the basics of today’s post isn’t too complex.

Depending on how rigorous your biology education was, there are a variety of ways that you might tend to categorize the fundamental types of living things. You might vaguely recall something about “five kingdoms”, which as I recall were “Animals, Plants, Fungi, Protozoa [e.g. amoeba], and Bacteria”. You might just segregate everything into either “animal” or “plant”. If your memory of biology education is a bit stronger, you might remember that “bacteria” are a separate group from the true plants and animals. A step more precise and you may split living things into the two domains of “prokaryote” and “eukaryote”.

The “plant” and “animal” distinction is pretty classic – until comparatively recently, bacteria were assumed to be “plants”, just as fungi (“plants” that lacked chlorophyll) were. Non-photosynthetic bacteria were referred to as “schizomycetes” (literally “fission” [splitting in two] fungi, because they reproduce by splitting from one cell into two rather than forming spores), while bacteria with chlorophyll (cyanobacteria or “blue-green” algae, and possibly the “green sulfur bacteria”) were designated “schizophyta” (“fission plants”).

Within the last fifty years or so, though, it’s become obvious that bacteria were a different type of life from fungi, chlorophyll-containing plants, or animals. The latter critters have cells that in turn contain “organelles”, which are more or less very specialized “mini-cells” within themselves. The nucleus, for example, is a compartment within the cell where the cell’s DNA is kept and processed. Bacteria, it turned out, don’t have any of these organelles (in fact there’s good evidence that at least some if not all organelles used to be bacteria, but this post’s long enough already so I won’t go into that), and life was re-organized into the bacterial “prokaryotes” (“before nucleus”) and the “eukaryotes” (having a “true nucleus” – i.e. everything that isn’t bacteria).

Then, along comes Carl Woese, who spoils this nice simple dichotomy. In 1977, he published (along with G.E. Fox) the subject of today’s post:

Woese CR, Fox GE: “Phylogenetic structure of the prokaryotic domain: the primary kingdoms.”; Proc Natl Acad Sci U S A; 1977 November; 74(11):5088-5090

Scientists by that point had managed to identify a particular type of genetic sequence that every known living thing possessed: the “Small Subunit Ribosomal RNA”. Put simply enough to avoid turning this into a very long post, this is a small stretch of RNA that gets folded into part of the ribosome, which is the bit of protein-machinery that “reads” the code for a protein that has been transcribed from the cell’s DNA and hooks up the chain of amino acids appropriately to make the protein. This genetic sequence of this bit of RNA performs a fundamental function in all known living cells, and so it had to remain similar even between populations that haven’t had a common ancestor for potentially billions of years. At the same time, it still varies enough in places to be distinctive for each species.

Woese looked at the analysis of these sequences discovered something interesting about one particular kind of “bacteria”. The methanogens – which grow in places without oxygen and, as the name implies, produce methane – appeared to have sequences that are as much different from other types of bacteria as bacteria are different from eukaryotes. Evidently, these methanogenic “bacteria” were a group of their own. The paper also mentions a few other characteristics to support this notion, such as the fact that the cell wall material of the methanogens was different from all of the other bacteria. Woese’s paper further suggests that what was known at the time of the extreme halophilic (“salt-loving”) microbes suggested they might turn out to be in this same group. More recent phylogenetic studies show this to be the case.

From this paper we get the the modern fundamental three groups we still use today: Eukaryotes, Eubacteria [“True” bacteria], and the Archaea (or “Archaebacteria” as this paper names it). The name comes from the idea that the environment in which methanogens thrives resembles what has often been assumed to be the atmosphere of the very early Earth.
Phylogenetic tree showing how Bacteria, Archaea, and Eukaryotes are related

Yeah, I know, they wrote “Gram positives” instead of “Firmicutes” (and possibly Actinobacteria). Some people never learn… Incidentally, you might be interested to know that as the phylogenetic tree there suggests, despite the suggestion of “ancientness” from the name most studies seem to suggest that the archaea probably split from the eubacteria, not that the bacteria developed from the archaea. Or put more accurately, that the hypothetical “last common ancestor” of the eubacteria and archaea more closely resembled modern eubacteria than archaea. (Ike’s on its way to eat our power lines so forgive me for not digging up a proper citation for this, especially if my recollection of this turns out to be a little off – or completely wrong. While I’m at it, forgive me for not going through and editing this post for better clarity…)

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The Author is (currently) an autodidactic student of Industrial and Environmental microbiology, who is sick of people assuming all microbiology should be medical in nature, and who would really like to be allowed to go to graduate school one of these days now that he's finished his BS in Microbiology (with a bonus AS in Chemistry). He also enjoys exploring the Big Room (the one with the really high blue ceiling and big light that tracks from one side to the other every day) and looking at its contents from unusual mental angles.

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