Pervasive, persistent, problematic “prokaryote”

There are reasons to avoid using “prokaryote” in biology teaching.  So, why are so many biologists resistant to the idea?

Why not use “prokaryote”?  Norman Pace published a one-page piece in Nature, “Time for a change” that raised concern about use of “prokaryote” (in education), and the common biology textbook paradigm of splitting organisms up into prokaryotes vs. eukaryotes. Pace highlighted many of the differences between archaea and bacteria, discussed evolutionary relationships/history, and made a case for avoiding use of the term prokaryote with students.  (Check out the 2005 article by Jan Sapp discussing the history behind the prokaryote-eukaryote dichotomy, too.) Pace expanded on this with a lengthier educational piece in 2008.

Pace convinced many of us – I now  avoid using the term prokaryote, though I explain to students how it’s generally used (as they will encounter it), and I tell them why I prefer not to use the term. (I do the same thing when we explore the protists – or, as Tamara Kelly  and I like to call them, “Grab bag eukaryotes”.) Also see Mark O. Martin‘s blog post: Where Dictionary Definitions, Paradigm Shifts, and Microbiology Intersect: Use of the Term “Prokaryote”.  Biology textbooks are starting to include more information about archaea, but it’s not uncommon to find a “prokaryotic cell” or “prokaryotic flagellum”* figure, even in a current edition of a microbiology textbook.**  Prokaryote remains pervasive – biologists persist in using it.

Why are biologists resistant to avoiding the term “prokaryote”? My thoughts …

Prokaryotic attachment
My initial reaction to Pace’s article/suggestion was not enthusiastic. As a microbiologist, I had positive associations with the term “prokaryote” –  these amazing, fascinating, invisible organisms that I’ve devoted much of my life to. Many a microbiologist would likely feel like this was a “good” word … on an emotional level, at least! And now we’re not supposed to use it? It took me a little while to be convinced by the logic.

Biology is a huge field … and archaea are pretty new (to us)
How many biologists  (beyond archaeal microbiologists) actually know about the various differences between archaea and bacteria? Biology is a huge field, and it’s understandable that a specialist in a different area in biology may not encounter much of this information. I’m hoping that we’ll see further revisions in first year textbooks to address archaea specifically, discuss the most recent phylogenetic models, and highlight the differences between bacteria and archaea (as well as the similarities between archaea and eukaryotes). Up-to-date textbooks can help keep us informed as educators, and makes our jobs easier.

Specialists/experts & shared vocabulary
While it’s generally accepted that evolution is the unifying principle of biology (Dobzhansky 1973), if you’re not an evolutionary biologist, this may not be something that occupies your mind much of the time.  I’ve heard the claim that if you define and understand “prokaryote” to be “single-celled, no nucleus, has single RNA polymerase***, no ER, etc.”, it’s an acceptable term. Which is true, I guess, if you’re conversing with someone else who has the same understanding as you – i.e., if you’re talking to another expert. However, it’s worth considering that this could be misleading to non-experts,  reinforcing the (implicit, if not explicit) idea that prokaryotes are a monophyletic group.

Much of the time, people use prokaryote when they are only intending to refer to bacteria. It does take an effort to consider “Am I referring to both bacteria and archaea, or just bacteria?” when one is tempted to use “prokaryote”. For many biologists, using “prokaryote” is a habit, and it can be broken with a little work. (And isn’t it cool to actually find out whether something is true for both bacteria and archaea, or if it’s another difference between them? No? That’s just me? Okay.)

Ouch – the idea of being wrong
If one accepts that we shouldn’t be using the term “prokaryote” in our teaching, but has done so in the past, that isn’t a comfortable realization. Nobody likes to feel like that they’ve been doing something wrong. Yes, science is based on the premise that it’s okay to be wrong, and we should be trying to disprove our hypotheses and assumptions … but scientists are also people. I think it’s especially difficult when you are an expert in your area, and when you’ve chosen to spend your working life on expanding and sharing scientific knowledge. Nevertheless, I have a lot of faith in my colleagues as scientists, and their ability to evaluate information critically.

Speaking of which …

News: We’re all prokaryotes?
Very recently, a new report came out from Williams et al. (2013) , suggesting that eukaryotes arose from a partnership between bacteria and archaea, indicating Bacteria and Archaea are really the only two primary domains of life. I haven’t seen a lot of discussion around this, yet, but I’m hoping that it might get people thinking about what this means in terms of how we view the “tree of life”, and how we’ll approach this with our students.

A suggestion – Archaeal Giant Microbe(s)!
It’s time for an archaeal Giant Microbe to promote archaeal awareness! How about Haloquadratum walsbyi (square, flat, extreme halophiles)? Or thermophilic Nanoarchaeum equitans and its buddy (obligate symbiont) Ignicoccus hospitalis? (How can you not love something named “riding the fire sphere”!)

What do you think? What else can be done to help promote awareness of the issues surrounding use of “prokaryote” in biology education?

References & recommended reading:

Dobzhansky, T. 1973. Nothing in biology makes sense except in the light of evolution. American Biology Teacher, 35(3), 125-129.

Jarrell, K. F., & Albers, S. V. 2012. The archaellum: an old motility structure with a new name. Trends in Microbiology, 20(7), 307-312.

Martin, M.O. 2012.  Where Dictionary Definitions, Paradigm Shifts, and Microbiology Intersect: Use of the Term “Prokaryote.”

Meisel, R. P. 2010. Teaching tree-thinking to undergraduate biology students. Evolution: Education and Outreach, 3(4), 621-628.

Pace, N.R. 2006. Time for a change. Nature 441.7091: 289-289.

Pace, N. R. 2008. The molecular tree of life changes how we see, teach microbial diversity. Microbe: 3(1), 15.

Pace, N. R. 2009. Rebuttal: the modern concept of the procaryote. Journal of Bacteriology, 191(7), 2006-2007.

Pace, N. R. 2009. Problems with “procaryote”. Journal of Bacteriology  191(7), 2008-2010.

Sapp, J. (2005). The prokaryote-eukaryote dichotomy: meanings and mythology. Microbiology and Molecular Biology Reviews, 69(2), 292-305.

Whitman, W. B. 2009. The modern concept of the procaryote. Journal of Bacteriology.191(7), 2000-2005.

Williams, T. A., Foster, P. G., Cox, C. J., and Embley, T. M. 2013. An archaeal origin of eukaryotes supports only two primary domains of life. Nature, 504(7479), 231-236.

Whitman, W. B. 2009. Rebuttal: Problems with “Procaryote”. Journal of Bacteriology 191(7), 2011-2011.

* The bacterial flagellum is quite different from the archaeal one, resembling a type of bacterial pilus; Jarrell and Albers (2012) recommend using the term “archaellum”.

** Brock Biology of Microorganisms has long been one of the better books in terms of how archaea are presented,  IMHO, but of the microbiology textbooks I’ve looked at recently, I was noticeably impressed by the approach of the new “Microbiology” textbook by Wessner, Dupont and Charles (published by Wiley), for this reason (among others – I really like this book!).

*** Re: RNA polymerase … yes, bacteria and archaea each have a single RNA polymerase (at least, last time I checked – with archaea, I wouldn’t be surprised if someone discovered new weird archaea with more than one RNApol). However, the bacterial RNA polymerase is quite different from the archaeal one. The archaeal RNA polymerase is very similar to the eukaryotic RNA polymerase II (Werner, F., Eloranta, J. J., and Weinzierl, R. O. 2000. Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12. Nucleic Acids Research, 28(21): 4299-4305) (This isn’t that surprising, as many aspects of archaeal molecular biology have similarities to eukaryotic processes.) As biologists, do we care more that there are the same number of RNA polymerases? Or do we care about the homology of these enzymes between organisms? Or  is the fact that archaeal transcription appears to be hybrid between eukaryotic and bacterial mechanisms more important?

5 thoughts on “Pervasive, persistent, problematic “prokaryote”

  1. Tanya, I fully appreciate the reasons you state for not using the term “prokaryote” to represent bacteria, or to imply that they are a monophyletic group. I also emphasize to students that bacteria and archaea are as distinct from each other as eukaryotes from bacteria. I make efforts to clarify when something applies to bacteria, and when something applies to archaea. I teach from an evolutionary perspective, and discuss the idea (proposed long before Williams 2013) that eukaryotes evolved as a partnership of bacteria and archaea – that is one of my first week lessons in my intro class.
    Having said that, I still find “prokaryote” useful to denote bacteria and archaea collectively – they were both present before eukaryotes, and lack nuclei and other eukaryotic innovations. I’m puzzled why you and others advocate losing the term “prokaryote” while still using the term “microbe”, which is even less distinct, and a term I hardly ever use.

    1. Thanks for the comments/questions, Jung!

      I can’t speak for others, but I get the impression that students find it easier to understand that “microorganism” and “microbe” are not biologically/evolutionarily meaningful terms, as they include bacteria, archaea, protozoa, some algae, some fungi, etc. – very different organisms (genetically, physiologically) that happen to be extremely small. Of course, that’s my personal impression – would be nice to actually know! (Part of a misconception study?)

  2. Reblogged this on DownHouseSoftware and commented:
    It’s true that the term Prokaryote is going away. The problem is not that it is a bad word when contrasting Bacteria and Archae to Eukaryotes, but that it implies similarity between the two ‘Prokaryotic’ domains.
    I see the rationale, but I need to read up a bit on this before I start changing my lectures. Thanks to Nucleoid for pushing this topic.

  3. Tamara

    I wonder how often people actually use the term prokaryote to refer to both bacteria and archaea in class? My impression is that it’s used to refer to bacteria, so why not just call them that. As well many texts still talk about too many things as eukaryotic and prokaryotic such as transcription, structures such as the flagellum etc., when again they are referring to differences between eukaryotes and bacteria.

  4. Nice article. I think the main thing that can be done to promote awareness of this issue is to promote understanding of Archaea. As a microbiology student in my penultimate year of undergraduate study I have yet to see any teaching time dedicated to Archaea. Yes they are mentioned as being prokaryotes and a separate domain from eubacteria but really that is it. Clearly this is not an acceptable level of awareness if, as you say, there are enough differences between archaea and bacteria and even similarities between eukaryotes and archaea. I could understand it not coming up in a straight biology degree or other biological science disciplines but really a microbiology degree should address, what is essentially, a basic understanding of the groups that we are supposed to be being educated on.

    To some level I think the term prokaryote is still relevant considering its literal meaning is that of organisms without a membrane bound nucleus. Although further distinction to increase understanding is probably a better way to go.

    Thanks for the info!

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