E. cells. coli used in the long-term evolution experiment (LTEE) on an agar plate. Credit: Jeffrey Barrick
On February 24, 1988, evolutionary biologist Richard Lenski filled 12 jars with sweetened growth medium and seeded each with Escherichia coli bacteria. For the past 34 years, Lenski, at Michigan State University in East Lansing, and colleagues have nurtured bacterial cultures, refreshing their growth media daily, and freezing samples for future studies every two months.
The long-term evolution experiment (LTEE) has become a cornerstone of evolutionary biology that researchers continue to use to obtain information. During its 75,000 generations of growth, bacteria have made great gains in their physical condition (the speed with which they grow relative to other bacteria) and some amazing traits have evolved.
Last month, Lenski and his lab attended LTEE for the last time. On the 12th E. coli The lines are now frozen in cryoprotective media and will soon be revived to begin a new life in the lab of Jeffrey Barrick, an evolutionary biologist at the University of Texas at Austin who first worked on the experiment in the 2000s as a postdoctoral fellow. Lenski’s laboratory.
The two talked Nature about the past, present, and future of one of the longest experiments in biology.
Jeffrey Barrick (left) will take over the direction of E.’s experiment. mentor Richard Lenski, who began the experiment in 1988. Credit: Laura Gerson / UT College of Natural Sciences, Sipa US / Alamy
What inspired you to start the experiment?
Richard Lenski: I like the big open questions. I wanted a very simple and long experiment to see how repeatable the evolution was. The original goal was 2000 generations. And I thought I deserved the nickname “the long-term evolution experiment.” I had no idea it would go as long as it happened, and I hope it lasts much longer.
Why did you keep it, and go and go?
Lenski: It’s actually a very easy experiment to maintain. The amount of work for a person on a normal day is perhaps half an hour. It’s 365 days a year, at least in principle, but the amount of work a day isn’t big.
And then, of course, the bacteria were doing very interesting things over time. New technologies emerged, such as the ability to sequence genomes economically. People like Jeff joined the lab and came up with new ideas and questions. And the bacteria kept doing interesting things. I realized that I should continue as long as humanly possible.
How many generations had passed when Jeff started working on the experiment?
Lenski: Did you join the lab around 2007? It was probably about 40,000 generations.
Jeffrey Barrick: Sounds good. He knew less about the history of the experiment, perhaps less than many of Rich’s postdoctoral and graduate students. But I was at one point in my career where I had been studying evolution at the molecular level, looking at all kinds of bacterial genomes. I wanted to study the evolution of whole organisms in the laboratory and be able to observe the evolution. It’s something that has fascinated me since I was a student.
Was it ever a challenge to keep experimenting?
Barrick: As Rich said, it’s pretty simple. There are some major snowstorms and other things that happen, and other infrastructure anomalies that can sometimes make it difficult, but you can always go back to the freezer, which is a very nice thing to experiment with and it does so much more. feasible than others. experiments. People have tried long-term experiments with mice and flies and other organisms where it is really difficult if something goes wrong.
Lenski: One of the advantages of the long-term experiment is that everything is so simple. We work with a chemically defined environment, we can freeze strains and revive them to touch wood, I think I should continue strongly in the new home.
What has the experiment taught us about the repeatability of evolution?
Lenski: My bias in the experiment was that all strains would come out in very different directions. He was thinking that the roles of chance and contingency in evolution would have been greater than they were. And over the years, we’ve actually seen amazing amounts of reproducibility. Thus, although a typical line has improved its relative aptitude compared to the ancestor by perhaps 70% or 80%, the variation in competitive aptitude between most lines is a bit more similar to one hundred. So they have all increased enormously, but very similar to each other.
But then over the years we’ve also seen some pretty surprising divergences between the lines. Thirty thousand generations in the experiment, one of the 12 lines developed the ability to consume citrate, rather than just glucose. And this drew a lot of attention, and even a certain, let’s say, hostility from some people who are skeptical about the power of evolution. And after 75,000 generations, it is still the only one of the 12 lines that has evolved this skill.
Are there any big questions about evolution that you hope to answer if you go further?
Barrick: For many bacteria that ended up in simple, constant environments, especially simple endosymbionts that live inside insect cells, their genomes gradually shrink over time. And I would say that one of the things that amazes me the most is that these E. coli they have been in a very constant environment, but their genomes have not shrunk much.
Lenski: I think part of the problem with genome contraction is that this is a slow process. Thirty years and 75,000 generations: it’s a drop in the evolutionary cube. So I guess if we could go back, in a million years or whatever, the bacteria would probably have extremely small genomes. This is a reason to continue.
The E. coli has now spread to about 75,000 generations. Credit: Brian Baer and Neerja Hajela via Wikimedia Commons (CC BY-SA 1.0)
Why did you decide to pass the torch to the LTEE?
Lenski: I won’t be there forever. I think it’s best to do these things now, plan them carefully and thoughtfully. So it just made sense. I am 65 years old and although I do not plan to retire at least in the next few years, the lab is getting smaller. And one of the important things about keeping your lines up in the long run is this daily pace. I think a lab that has half a dozen or more people is ideal for weekend and vacation coverage that benefits from the experiment.
So I asked Jeff, maybe in 2018 or 2019. I have a grant from the National Science Foundation to run the experiment, and Jeff is now a principal investigator of that. And when we wrote the most recent renewal, we outlined this plan for the move and what would be done right now.
Why did Jeff take it on?
Barrick: I’m a big supporter of open science. This is a great resource that I want to support, share and continue. It has become a kind of touchstone for many stories about bacterial evolution. And something that people can take in so many directions. I am excited to support the community.
Are you anxious to take responsibility for such a long experiment?
Barrick: As Rich said, it’s not very difficult to keep up with the experiment. What makes it difficult is to organize all the strains in the freezer, making sure you can send them to people and all the documentation related to this kind of thing.
I don’t want to have the experience where the experiment gets to my lab and then gets contaminated, and I put it on two or three years ago. I want to make sure I follow things very well. But there’s a lot of pressure, because it’s frozen, not only in Rich’s lab and mine, but also in labs in France and elsewhere. So this removes the pressure that could cause an irreparable problem. So I’m more excited to educate my classmates about the experiment.
Rich, what is your advice for Jeff?
Lenski: Keep calm and keep going. Frustrating things will happen. But the experiment is quite lenient. As long as my brain works, I will be very excited to see what new derivative experiments he and his collaborators generate, what new analyzes he and the community at large generate to make sense of what is happening with the long-term lines. Probably the most important thing Jeff will have to think about in 20 or 30 years is who will be next?
Barrick: Your job is not done, Richard. You are still the best scientific communicator and the person to bring the long-term evolution experiment to people and build that community. This is really the most intimidating thing anyone could replace right now. Doing the experiments is very easy.