Nattural Selection in a microbial culture?

[raid517]

Hi, I have been given the following paper by my course tutor to review: http://www.ncbi.nlm.nih.gov/pubmed/19377097 Having read it I have become slightly puzzled by it. http://www.jbc.org/content/284/27/18377.full

 

What I couldn't work out is why when the researchers had created such a unique condition wasn't an evolutionary and adaptive explanation given in the paper rather than just assume that this 'zinc concentrating' mechanism was common and innate to all strains of E. Coli. After all the condition they created would be so rare in nature that there would almost never be a reason for it to exist? So why should it be considered useful to regard it as common? Was it not more likely that the researchers had simply created a super strain of E. coli through induced selection within their apparatus that had a much increased affinity for zinc than most other strains?

 

Why is it useful to do this? Why not include a discussion of the adaptive pressures set up by the experiment?

Edited April 28, 2012 by raid517

[CharonY]

Evolutionary effects are not going to play a significant role in the presented time scales, unless they only require very small changes. The goal of this paper is to figure out molecular mechanisms that cope with extreme conditions. If you apply mild ones, many effects can mask the mechanisms you are hunting for. Extreme and well-defined cultivation can better elucidate adaptations, although you are correct that in some cases effects may occur that do not occur in nature.

Yet, one should keep in mind that growing under replete conditions as found in the lab, is actually much more unrealistic than hunger conditions. In nature, hunger is more likely that normal state as each bug is competing ferociously with others for limited resources.

 

Note that there is nothing like an adaptive pressure as your post implies (i.e. if faced starvation the chance of occurrence of a super zinc acquirer does not increase, only the spread of mutations that may result in it, which is on a different time scale). There is a certain selective pressure, but the base assumption is that the cells are already adept at acquire low level of zinc. Whether that is true for E. coli or not is rather a physiological discussion rather than an evolutionary one.

 

If we assume mutation, the most likely one to actually affect the physiological state is within the regulatory mechanisms and it may be true that some mutants have spread that actually express higher level than the WT under the same condition. But then this study is aimed at finding targets using semi-quantitative approaches, and is not a quantitative inspection of the regulatory network.

[raid517]

So even though the strain of E. Coli was able to gather 5x more zinc from the apparatus than the researchers added to the experiment, despite going to extraordinary lengths to prevent this, there is no possibility that a mutation may have occurred and spread that could have produced this vastly increased affinity for zinc? In other words, although the conditions of this experiment were so unusual and so extreme and a condition was created that wild strains of E. Coli are hardly ever likely to encounter, it's safe to consider this full "zinc concentrating" mechanism as innate to this organism and to most other E. Coli strains?

 

The thing that really struck me was the ability of this strain of E. Coli, to gather 5x more zinc from the apparatus than the researchers put in. Why should an innate ability to do this exist when the conditions of the experiment were so unique and unusual and would be unlikely to ever be encountered?

 

I get it that this research was useful, in that it sought to uncover elements of the zinc regulatory pathway. This can certainly be achieved in experiments of this kind. Perhaps it is just a case of the question of an adaptation occurring is not significant in this context?

 

Over what time scale (if at all) would one expect to see selection and mutation occurring under these conditions?

 

I get that the conditions of this experiment were in many ways ideal for E. Coli growth and that there may have been less selective pressure than would normally be experienced under wild conditions (where there is a great deal of interspecific competition for resources as you said) and given that in this case the only limiting factor was less zinc than this organism may normally have had access to, that any potential for mutations may have spread more slowly.

 

But are you saying that there would have been insufficient time within this experiment for such a mutation to have spread throughout this microbial community?

 

I have often wondered why in microbial studies, many of which used an identical experimental set up and extreme resource depleted (or resource abundant) conditions, or in some cases where a less favourable food source was substituted for (for example) a glucose solution, such as a different type of sugar, microbiologists don't often take the potential for selection and mutation to occur in these conditions into account. Is this simply a matter of the time scales involved, and that the time scales are too short for selection to have any meaningful effect?

 

I have seen many other examples using an identical set up to this again with some other resource depleted/abundant medium, in which selection and adaptation of E. Coli under these conditions was considered. So is it really just a matter of what question you are asking and over what time scale?

 

Is it possible that any part (although certainly not all!) of the effect noted may have been the result of a selective mutation within this strain?

 

Also you appear to draw a distinction between "adaptive pressure" and "selective pressure". But why should these be considered different?

 

Finally I don't really understand your last comment? Is this just another way of saying that it depends on what question you are asking?

Edited May 3, 2012 by raid517

[CharonY]

I think you misread the paper. Zinc deficient strains had five times less zinc as compared during growth during replete conditions. That being said, it is expected that normal cells accumulate nutrients, how else are they going to survive?

What they measured in the end is that they found more total zing than they added, which is indicative that there was contamination after all.

 

Finally, they were mostly interested in finding elements of zinc transport as e.g. ZinT. I.e. genes regulated in a zinc dependent way. To figure out whether a mutation exists that e.g. upregulates ZinT higher than WT would require a different set of experiments.

[raid517]

Mmm, I was pretty sure she said she got 5x more zinc out of the experiment than she put in, due to contamination from her apparatus. I went to a seminar she gave and I was pretty sure that's what she said.

 

But this probably says nothing about mutation. It probably just means that this organism is very good at what it does.

 

This is a quote from the powerpoint presentation she gave.

 

"Cells grown in low Zn “find” extra Zn – almost 5× more than was originally added to the culture. Where is this from?"

 

She then goes on to explain that she thinks (in fact she can be pretty sure) that this is due to contamination from her experiment.

 

The 5x less number you quoted is also accurate, since studies have shown that zinc deficient E. coli strains can grow unaffected with up to 5x less zinc than zinc replete strains.

 

If I misread the experiment, then so did my PhD Biology course tutor, as he made a similar assumption. I asked him and he told me to ask her what in the end probably was a very stupid question. I guess we both look pretty dumb at the moment, lol.

 

What's the difference between "adaptation" and "natural selection"? As I said previously you appear to draw firm distinctions between "adaptive pressure" and "selective pressure", but you didn't explain this?

 

Also what is the difference between a quantitative and semi-quantitative analysis? Can you please give an example and explain this a little too?

Edited May 3, 2012 by raid517