MICROBIOLOGY AN EVOLVING SCIENCE, THIRD EDTION Joan L. Slonczewski, Kenyon College • John W. Foster, University of South Alabama PAPERBACK WITH EBOOK REGISTRATION CODE • ISBN 978-0-393-12367-8 • PAPERBACK • OCTOBER 2013 FIND US ON FACEBOOK: FOLLOW US ON TWITTER: YUCK FACTOR: NortonScience NortonScience YuckFactor.Tumblr.com AN INTERVIEW WITH: Richard Lenski Evolution in the Lab Richard Lenski, an evolutionary biologist, has taught for over 20 years as the John Hannah Distinguished Professor at Michigan State University. Since 1988, Lenski and his students have been tracking phenotypic and genetic changes in 12 initially identical populations of bacteria. Their report of E. coli bacteria evolving a new trait in the laboratory earned headlines from the New York Times and other media around the world. Lenski cofounded BEACON, the National Science Foundation’s Center for the Study of Evolution in Action. COURTESY OF RICHARD LENSKI COURTESY Richard Lenski, Hannah Distinguished Professor, Michigan State University. How did you decide to make a career for the bacteria to adapt to a particular generations. So many interesting things in microbial evolution? environment. have happened that I’ve kept it going all I got interested in biology as an under- I set up 12 populations, all started from these years. In fact, I hope the experiment grad at Oberlin College, and I was espe- the same E. coli strain, and each one in an will continue even after I’m gone. cially fascinated by ecology because there identical flask containing a medium where This project differs from most research were so many unanswered questions. So I glucose is the source of energy. Every day, on evolution because we’re watching evo- went to grad school at the University of someone takes 1% of the volume from each lution in action. Most evolutionary biolo- North Carolina to study ecology. I began flask and transfers it to a new flask with gists study fossils or use the comparative to see the deep connections between ecol- fresh medium. The bacteria grow and, approach—that is, quantifying similari- ogy and evolution. Many ecologists have after some hours, deplete the glucose, ties and differences in phenotypes and lifelong interests in particular organ- so it’s a “feast or famine” existence. The genomes of living organisms—in order isms—birds, snakes, butterflies, or what- dilution and regrowth allows about seven to infer the characteristics of organ- ever. But I didn’t have any special skills bacterial generations per day. I started the isms that lived in the past. In this E. coli in that respect; I was more interested in experiment in 1988, and the bacteria have experiment, we can observe changes as the general questions. I remembered now been evolving for well over 50,000 the generations go by, and we can directly the elegance of the genetics experiments with bacteria that I had learned about as an undergraduate. So I decided that, for my postdoctoral work, I should find a lab where I could learn how to work with microbes. I found a superb mentor, Bruce Levin, who was interested in evolution. Why did you perform your long-term experimental evolution study with Escherichia coli? What makes it different from previous studies of evolution? I started the experiment to ask one main question: How repeatable is evolution? Mutations occur at random, but popula- tions become more fit over time if some of the mutants survive and reproduce bet- ter than their ancestors—that’s natural selection. In essence, I wanted to know OF RICHARD LENSKI COURTESY how many different ways there were One E. coli population evolved the novel capacity to consume citrate for energy (clouded flask). 2 002-004_SFMB3e_Part01.inddW. W. 2 Norton & Company, Inc. • Independent and Employee-owned • wwnorton.com • page 1 9/6/13 3:52 PM PART 1 The Microbial Cell compare the evolving bacteria with their cose. At first I thought we had a contami- use other natural processes, such as grav- ancestors. We’ve stored the ancestral nant—some other species—in this flask, ity and the action of water, to do work via strain and samples from every 500 genera- but genetic analyses showed it really was mill wheels and hydroelectric plants. In tions in a freezer, and with E. coli we can a descendant of the E. coli strain used fact, the selective breeding and domesti- revive the frozen cells. It’s like bringing to start the experiment. So here’s a case cation of farm animals, crop plants, and fossils back to life. where one population evolved to be very even microbes (like baker’s yeast) show Over the 25 years of this experi- different from all the other populations. that our ancestors employed evolution ment, the research has involved dozens Zack Blount, a postdoc in the lab, is ana- for practical purposes long before the of dedicated people. I have an excellent lyzing the mutations that allow the bac- mechanisms of evolution were under- technician, Neerja Hajela, who either teria to grow on citrate. Caroline Turner, stood. More recently, scientists have been does the transfers herself or makes sure a grad student, is studying how this new pursuing genetic engineering to modify someone else does them. Mike Travisano ability changes the ecological interac- microbes for new purposes, like biofuels. was the first student to base his disserta- tions between different genotypes in the Experimental evolution—where scientists tion research on this experiment, and population. construct environments that select for he’s now a professor at the University of organisms with the desired properties— Minnesota. What new technologies have made offers a valuable complement to genetic it possible to take full advantage engineering. What results have you obtained? of your study? Have any results surprised you? When I started this experiment in 1988, How does your family relate One result is that the average fitness in I couldn’t imagine the amazing tech- to your work? each population increases over time. We nologies that would come along and I sometimes joke that I have two fami- measure fitness by competing bacteria allow us to analyze the evolution that lies: my biological family with my wife from different generations against the has taken place. The ability to sequence and kids, and my lab family, with all the common ancestor. This result is not sur- entire genomes is the most important students and postdocs who’ve been a part prising, since the environment has been advance. By sequencing the genomes of of it over the years. As much as I love my constant over time, but it’s a concrete evolved bacteria and comparing them to work—and I can’t imagine a better job demonstration of adaptation by natural the ancestor’s genome, we’re finding the than being a biology professor—there’s selection, the same process that Darwin mutations that led to improved fitness always more research to be done. So discovered. and other phenotypic changes. I’m grateful that my wife and kids have Another finding is that evolution can been supportive of my work. Now I have be quite repeatable; that is, we’ve seen Does experimental evolution have a granddaughter, and she reminds me many examples of parallel changes in the industrial applications? just how fortunate I am to see another replicate lines. For example, all 12 popu- Yes, it does. Humans can apply evolu- generation in the great evolutionary lations evolved to produce larger indi- tion for practical purposes, just like we tree of life. vidual cells than the ancestor produced. And when we look at their mutations, we Cell size increased in all 12 evolving 1.2 see many cases in which some or even all populations of bacteria. Source: of the lines have mutations in the same Modified from Richard Lenski and Michael genes. 1.0 Travisano. Dynamics of adaptation and diversi- The most dramatic change we’ve fication: a 10,000-generation experiment with bacterial populations. 1994. PNAS 91:6808. seen happened in only one population. liter) Glucose was the source of energy for —15 0.8 the bacteria, but there’s been another resource—citrate—in the medium all along. E. coli cells can’t use the citrate, 0.6 however, because they’re unable to take Cell volume (10 up citrate in the presence of oxygen. In 0.4 fact, the inability to grow on citrate is a key feature of E. coli as a species. But after about 30,000 generations, a mutant 0.2 0 2,000 4,000 6,000 8,000 10,000 For further details on Lenski’s ex- in one population discovered there was perimental evolution of E. coli, see Time (generations) something else to eat besides the glu- Chapter 17 Origins and Evolutions. 3 002-004_SFMB3e_Part01.indd 3 9/6/13 3:52 PM W. W. Norton & Company, Inc. • Independent and Employee-owned • wwnorton.com • page 2.