looking through the magnifying glass

Does size really matter? or what “save the whales” doesn’t tell you about the microcosm

Red blood cells on an agar plate are used to d...

Red blood cells on an agar plate are used to diagnose infection. The plate on the left shows a positive staphylococcus infection. The plate on the right shows a positive streptococcus infection and with the halo effect shows specifically a beta-hemolytic group A. (Photo credit: Wikipedia)

Yesterday I, once more, found myself trying to explain my work. Usually that ends up being some kind of rather nerdy conversation, typically including something like “it’s actually more interesting then it sounds” or “you know I really don’t want to bore you with that”. The usual thing you could say. And as always with that symptomatic self induced doubts all scientists have about their work. Which is good. If we wouldn’t have doubts on what we are doing we couldn’t assess errors in our hypothesises if we encounter them. Although it’s not quite the optimal thing when it comes to PR-work, given that this attitude is usually not likewise shared among shareholders.

However this time, their was a slight twist in my trials of explanation. That was the backround of the person sitting opposite to me. She had a little more of a medical view on microbiology while I’m clearly more into the whole (switching to a Tim Minchin voice) Environment thing.

So what was that little problem I came across? – It was the main question we environmental microbiologists always ask, and around which our whole lives circle.  – Who is there, and what do they do? – and quite regularly we already fail at answering the first question.

In medical microbiology it’s usually a little bit different. At least many more of the bugs you encounter there can be cultivated, isolated, sequenced and tested for all those little things one wants to test them. And much more important, by this means they are clearly defined as Vibrio something, Yersinia somethin, Neisseria something and so on. 

In environmental microbiology, though we apply the same idea of a species, we usually have no idea how to cultivate them, sometimes it’s not even possible, and thus have to rely on different techniques to get our informations. However, it’s not as easy as doing a gram- staining, incubating some blood agar and doing some tests and then ultimately pin pointing it down to that one species of bacteria (I don’t want to minimalize the work my colleages are doing with this little exaggeration, so please, no offence ment)

But what is a bacterial species? (And if by chance I haven’t lost you by now, good thing, now we’re getting to the melting point of it, so get excited.) Conservatively spoken, a bacterial species is defined by a threshold of 97% sequence identity within the 16Sr DNA gene, with 90% defining the genus level. Lets put that in numbers, just for the fun of it. That means that if within the 1500 nucleotides of the 16Sr DNA gene 1455 are identical it is still the same species. And we are only talking of one single, rather conserved gene here and still we allow for 45 differing positions and still call it one species. Lets extrapolate this a little. I think it is commonly known, that humans and chimpanzee differ by roughly 1% within their whole genome.  And that, once again, really struck my mind. If we would apply that idea in general, then I guess it would be totally valid to assume that on planet earth there would be around one genus of monkeys, with maybe two or three species. (I don’t really have the numbers here, so be forgiving) And that would just continue on and on like that, and all that diversity we so desperatly try to sustain would vanish in a haze of name calling and phenotyping. And it wouldn’t stop there. With diversity decreasing so drastically we would really have to reconsider things. I could only imagine the WWF for example, being forced to reduce so drastically, that it would have to give up both it’s double-U’s and would be left there with a big capital F!

Now that would be horrible, because no one would be left or care to save the pandas, the polar bears, the cute little seals and beware, the whales. But really, no one gives a s… about bacteria, they dissappear on a daily basis, and luckily quite a lot appear about the same rate. Especially so, since we cannot really distinguish whether we are dealing with just a phenotype or two different species, based on our crude assumption of species concept.

And furthermore, we do not even have the slightest idea of how many species we are actually talking of here, there use for human society completely set aside.

Yet, I do not have a solution for all of this, but I’m deeply admiring the problem.Oh and here’s something to read a little further if you still care to, after my little rant.

http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej20133a.html

So enjoy, and don’t forget, bacteria (and archaea) want to be protect just as the fish in the ocean, and the polar bears.

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One response

  1. Ulrike Jeske

    Phasinating brother. Honestly, allthough I barely understood half of what you wrote (I work in an IT company), I think this is a very interesting point you are making. Sounds like a comfortable double standard we are living. But then again, it’s what we are quite good at.
    Yet, you got me convinced: save the bacs!

    April 17, 2013 at 5:13 am

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