As a college biology major during the 1970s I was taught that cells in which the genetic material is separated from the cytoplasm by a nuclear membrane – such as those of animals, fungi, plants, and protists – are called eukaryotes. In contrast, the DNA of bacteria is not bounded by such a structure, and hence these microbes are called prokaryotes, a name that means ‘before the nucleus’. This concept was accepted by biologists until the late-1970s, when Carl Woese used ribosomal RNA sequences to deduce the relationships among living organisms. He found that microorganisms previously thought to be bacteria, because they have no nucleus, were no more related to bacteria than to eukaryotes. He proposed that living organisms should be classified into three lineages, now called bacteria, archaea, and eukarya. Nevertheless, the prokaryotic classification is still used by many biologists. The following letter from Elio Schaecter, sent to TWiV, explains why:
“Regarding your discussion of the term prokaryote in TWiV #93, I want to pipe in as a combatant in the P word wars. I am firmly in the camp of the users of the term. Although the term has carried a phylogenetic burden, meaning that it originally implied a close evolutionary relationship between the Bacteria and the Archaea, no one I know uses it in that sense now. Among biologists, the three domains model is widely accepted, in fact, not even discussed. It€™s true that there are leftover people who think that the prokaryote/eukaryote divide denotes a single evolutionary cleft, but that€™s simply because any concept of science takes time to filter out.
“I maintain that the term, used in a broad sense, is extraordinarily useful. In a college textbook I co-authored called Microbe, we used the P word some 300 times. How come? Had we not used it, we would have had to say Bacteria and Archaea that many times (and being parsimonious of verbiage, we eschewed that). This usage illustrates the reality that these two groups of microbes, though they likely diverged very early on in evolution, share a large number of common properties. Their sizes tend to overlap, their overall body plan is generally very similar, they often occupy the same habitats, they share many homologous genes. Presented with an EM thin section, you could not tell a typical bacterium from a typical archaeon. So, dissimilar as they may be in one sense, they are very similar in a number of important attributes. Saying prokaryotes is much like saying animals or plants, large groups that are extremely heterogeneous and that diverged a long time ago (although certainly not as far back as the prokaryotes and eukaryotes). I agree, there is danger in the P word being misunderstood out in the big wide world, but there is none within the family of biologists.
“Anyhow, the battle has been met and, yeah!, the victors are clearly the users of the word prokaryote. The term is found all over the place, notwithstanding the astonishing campaign waged against it. Just look at titles of recent articles in major journals.
“There is a more serious issue. Making phylogeny the overarching master of relatedness is readily justified if one thinks in these terms only. But isn€™t ecology just as important to understand biological behavior and relatedness? There is a tyranny to phylogeny, which demands that you view the world of living things in terms of where they came from, not what they are doing now.”
What does this nonmenclature issue have to do with virology? According to Patrick Forterre:
The discovery of unique viruses infecting archaea also corroborates the three domains concept from the virus perspective. Indeed, most viruses infecting archaea have nothing in common with those infecting bacteria, although they are still considered as bacteriophages by many virologists…David Prangishvili and myself have thus suggested to classify viruses into three categories, archaeoviruses, bacterioviruses and eukaryoviruses.
Woese, C. (1977). Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms Proceedings of the National Academy of Sciences, 74 (11), 5088-5090 DOI: 10.1073/pnas.74.11.5088
Prangishvili, D., Forterre, P., & Garrett, R. (2006). Viruses of the Archaea: a unifying view Nature Reviews Microbiology, 4 (11), 837-848 DOI: 10.1038/nrmicro1527