Evolution in the Lab

29 June 2008

Interview with

Professor Richard Lenski, Michigan State University

Professor Richard Lenski works at Michigan State University and in his lab he's grown over 40,000 generations of E. coli for over twenty years.  He persuaded the bacteria to evolve totally new characteristics and giving scientists new insights into how organisms adapt and change over time.

E. coli bacteriaRichard - I've always been interested in the tension between evolution being a random process at the level of mutations.  Yet natural selection provides a force that moves populations to become ever more adapted.  This experiment with E. coli has been designed to look at how reproducible evolution really would be if we could repeat it.  I created 12 lines of E. coli, all started from the same ancestral cell.  We've been propagating them in my lab for about 20 years now and the bacteria have gone though 40,000 generations and we're watching how they change and evolve.

Ben - What are the advantages of using bacteria like E. coli to observe evolution in the lab?

Richard - One of the advantages of bacteria is that they have such short generations.  Also they have very large population sizes so in a little flask in the corner of the lab we can have millions of cells.  What's really cool to me is that we can freeze the bacteria away.  That allows us to directly compare ancestral and evolved organisms.  Actually comparing the living organisms is not just fossils.  It's the real-live bacteria.  Imagine if we could bring Neanderthal back to life.  We might try to play a game of football with the Neanderthals and we could see how the organisms in their performance, not just in their fossil morphology, but in their real performance have changed over time.

Ben - What sort of evolutionary changes have you seen since your very first cell line?

Richard - One of the most important changes is that the evolved bacteria are demonstrably much more fit in this environment.  They actually grow twice as fast as the ancestors.  When you compete them the evolved bacteria kick butt.  The evolved cells are much larger.  We're looking at how they've changed in many other properties.  In particular in the last few years we've been looking at how they've changed in the genotype.  We're actually sequencing the DNA and finding the mutations that are responsible for their adaptation.

Ben - Recently you reported on a slightly more dramatic change that happened in that they seem to have been able to use a different source of food.  What had happened here?

E coli evolving in the labRichard - In this medium that we've been feeding them every day for the last 20 years they've been growing on glucose as the only source of energy that they can use that's in that environment.  Throughout this entire experiment we've had another carbon source that's been present in the medium.  It's called citrate.  One of the features that's been recognised of E. coli cells is that they're not able to use citrate as an energy source.  It can't get inside the cell.

Ben - So this is one of the defining features that makes them an E. coli bacterium rather than something else.

Richard - It is, pretty much. There are little grey areas around the edge that are rather technical but certainly the general property of E. coli, one of the defining characteristics by virtually all assays.  For 20 years they've been eating their glucose and not recognising there's an open niche, another resource in their environment.  One of the twelve populations suddenly woke up, as it were, in an evolutionary sense and said, "Hmm.  There's something else to eat.  There's a desert tray around the corner after we finish our glucose."  That population evolved this new capacity to use this new carbon source as an energy source.  What we've done has been to try to ask, "Could any of the populations have evolved that new trait at any point in the experiment?"  We've been trying to ask if the genetic context changed so that this new phenotype became possible by virtue of the more-or-less inconsequential differences that it accumulated in one population versus the other 11 populations.  We took advantage of the fact that we have all these time points frozen away in our freezer.  With an extraordinarily dedicated graduate student, Zachary Blount, he essentially went back to the freezer and started the evolution experiments over from different time points along the way to the evolution of this interesting new trait.  What he found was that only after a certain point in time did he ever find mutants that were able to use citrate as a carbon source.  A sort of accident of the genetic changes in one line versus the other lines had opened up this door that there was another possible way of making a living in this extremely simple laboratory environment.

Ben - So you need a series of smaller, seemingly irrelevant mutations in order to have this big mutation that lets you change your food source?

Richard - Yes.  It's very clearly established that there were many mutations in these lines and that some subset of them that occurred in this population set up the potential to then get additional mutations that gave this very interesting new trait or phenotype.  In this simple little experiment that we've been doing in my lab this one population of the twelve that we've been studying took a different road, got on a different evolutionary path and that influenced its subsequent potential.

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