Moselio Schaechter

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« Biology By the Numbers | Main | Talmudic Question #52 »

August 17, 2009

A Call From Arms

by Elio


Toyotomi Hideyoshi (1536 –1598). Source.

Towards the end of the 16th century, the ruler of Japan, Toyotomi Hideyoshi, began a movement that led to the banning of firearms in that country. Not that these weapons hadn’t worked; on the contrary, at that time the Japanese made some of the best guns in the world. Many reasons have been put forward for this unique and drastic action, the most romantic being that the continued use of firearms would have undone the traditional role of the sword-wielding samurai. Now, microbes may not have such a convoluted social organization, but, when it comes to their making of antibiotics, there is something evocative of this remarkable chapter in history.

Antibiotics are now being thought about as benign compounds that, at least at low concentrations, have little to do with intraspecies warfare between organisms, and a great deal to do with the ways microbes communicate with one another. More and more examples are being reported of antibiotics that, at sub-inhibitory concentrations function, as community organizers, prodding bacteria into making protective biofilms. Indeed, antibiotic-induced biofilm formation has become the poster child for the argument that antibiotics serve mainly as signaling molecules between microbial cells. The evidence spans several bacterial species, including Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella enterica, and Bacillus subtilis. Surely, other species will be found to be listening and to respond in other ways besides biofilm formation. Already the literature is rich and diverse. For some particularly juicy articles click here, here, here, here, or here.

A key argument against antibiotics being mainly antibiotic is that their concentrations are too low even in soils that harbor producing species. However, such calculations represent the average concentration over large spaces. Within a volume of a few cubic micrometers—the effective world of many a microbe—the concentration of antibiotics may indeed be high enough to inhibit microbial neighbors. Hard to tell.

Did microbes invent these compounds and then "make a pact" not to use them for what their name implies—killing other living things? Or did these compounds function first as signaling molecules helping the "conversation" between and within microbial species? Highly appealing is the notion put forth by Julian Davies that antibiotics are "fossil molecules" that played a key role as effectors in the early evolution of life, molecules still made today and still serving to shape microbial communities.

These ideas are monumental. Yet, however stirring they are, they must fit within a holistic account. Questions remain. For instance, why is it that these compounds are, in fact, antibiotic at high concentrations? Their signaling functions (at lower concentrations) would have sufficed. One would guess that, by some sleight of organic chemical hands, signaling parts of the molecule could have been retained, and the antibiotic functions lost.

The lesson may well be that, as is true for all of science, scientific inferences are tentative and convictions conjectural. Sometimes, to our momentary consternation, cherished beliefs are turned on their head. But we must live with it. As Bertrand Russell said: I would never die for my beliefs because I might be wrong.


Hi Elio,

Thanks for the provocative post. I was going to reply, but had enough to say I figured I should make my argument in a proper blog post. You can find it here:

Thanks for the great blog.

Will Ratcliff

My argument actually applies to both signaling and competitive functions, because I'm not so sure that for signaling the amount would be small. It obviously depends on the signal being sent! For example, Quorum sensing signals are made in pretty large amounts, and the local concentration (in the squid light organ, for example) can get quite high. Also, we don't really know what the effective antibacterial concentrations of many of these compounds are in situ, so it's difficult to say whether the observed levels are consistent with that. Of course, I don't study this for a living, and Julian (and others) may have more informed input.

Elio replies:
Can't argue with that!

A provocative and interesting essay - I've been trying to think of a good way to comment on this, and am still struggling a bit, so if this comes out muddled, I apologize in advance :)

As I've said before in the comments here, it certainly seems to me that molecules with a strong antimicrobial activity ought to be presumed to have that activity for a purpose (which for bacteria in a competitive environment we can expect that purpose to relate to competition with other organisms). After all, making something like that is more costly than the equivalent type of molecule without said activity (because you have to resist its effects). Of course this logic only applies to bacterium derived antibacterials (or fungally derived antifungals, etc).

So if we are thinking about why bacteria and other soil denizens make antibiotics, it seems odd to try to ascribe a central purpose to them that is not antimicrobial, because any organism that made an antibiotic (and a resistance mechanism) principally as a communication tool would lose out to a competitor that made a similar communication molecule, but one that was non-toxic. However, making a molecule that serves both roles could be very useful, allowing you to communicate with your resistant sisters, while also causing harm to your sensitive competitors.

I think the point about heterogeneity of the soil is important as well, and although addressed, it seems to me that it needs to be addressed in the literature much more thoroughly. For example, a biofilm might produce a very high local concentration of antibiotic, clearing the nearby space for expansion. An additional consideration is pH and hydrophobicity, which may drastically alter the activity of the antibiotic in different places.

I basically agree with you about the overall complexity of the picture, however, I just would come at it from a slightly different angle. My slightly educated guess is that antibiotics do in fact play a significant role in the environment due to their killing or inhibitory effects, but that they also play a substantial signaling role, which is an "add-on" feature.

A gross oversimplification goes like this; BugA makes a secondary metabolite that kills bacteria by targeting their ribosomes, and a pump to keep it out of the cytoplasm of BugA. BugA becomes a dominant member of the soil flora, but subsequently resistance (pumps) become a part of the genomes of other members of the ecosystem. So the playing field has leveled out, but everyone is paying more to enter the system (because they all have to make the pump). BugA* enters the picture, with a twist. It makes a high-affinity antibiotic receptor, that allows it to control antibiotic and pump production based on the presence of the antibiotic. So it beats out BugA, because it saves on production costs. But now BugA* finds that antibiotic concentration is a useful signal for other things, such as biofilm formation, etc etc. Rinse and repeat a few billion times in a few trillion different places, and you've got the world we are all studying.

As a slight aside, here is another cite that adds even more complexity to the discussion. Pseudomonas (which makes a bewildering array of things) packages signals and antimicrobials into membrane vesicles, and delivers them to itself and its competitors.

Membrane vesicles traffic signals and facilitate group activities in a prokaryote.
Mashburn LM, Whiteley M.
Nature. 2005 Sep 15;437(7057):422-5.

Elio says:

I am curious to know what Julian may have to say, but for now, I wonder if your argument about energy expenditure doesn't refer to high concentrations of the antibiotic. For signaling purposes, the amount could be small, thus cheap to make.

What a thought provoking essay, Elio! Thomas Kuhn, in his "Structure of Scientific Revolutions," argues that "paradigm shifts" are very difficult in science, as anywhere else (I like to think in terms of "energy of activation").

So we look at antibiotics---heck, consider the name!---as purely negative utilitarian molecules. The truth, as always, is less simple. There have been a couple of billion years of "darwinnowing" of nature's toolbox, after all. We see antibiotics as, for example, interacting with the large ribosomal subunit, only thinking of negative effects. There is clearly a great deal more going on than simple inhibition, as your essay and the references suggest. Yes, I tend to anthropomorphize our microbial friends, but you must admit that they are clever and subtle in their approaches---at least from the investigator's point of view!

I suspect that we will need to change the name of "antibiotics" to something more accurate as investigators start looking at this concept with fresh eyes.

As for the negative effects of these molecules at high concentrations, isn't that true for any number of molecules? I can't wait to learn more about what microbiologists uncover about life at a very small scale indeed.

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