E. coli long-term evolution experiment

The "E. coli" long-term evolution experiment (LTEE) is an ongoing study in experimental evolution led by Richard Lenski that has been tracking genetic changes in 12 initially nearly identical populations of asexual "Escherichia coli" bacteria since February 15, 1988.Richard E. Lenski, [https://myxo.css.msu.edu/ecoli/strainsource.html Source of founding strain] , 2000. Accessed June 18, 2008.] Since the experiment's inception, Lenski and his colleagues have reported a wide array of genetic changes; some evolutionary adaptations have occurred in all 12 populations, while others have only appeared in one or a few populations.

Experimental approach

The long-term evolution experiment was intended to provide experimental evidence for several of the central problems of evolutionary biology: how rates of evolution vary over time; the extent to which evolutionary changes are repeatable in separate populations with identical environments; and the relationship between evolution at the phenotypic and genomic levels.Cite journal| volume = 24| issue = 2| pages = 225–265| last = Lenski| first = Richard E. |title = Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli| journal = Plant Breeding Reviews| accessdate = 2008-06-18| date = 2004|url=http://myxo.css.msu.edu/lenski/pdf/2004,%20Plant%20Breeding%20Reviews,%20Lenski.pdf]

The use of "E. coli" as the experimental organism has allowed many generations and large populations to be studied in a relatively short period of time, and has made experimental procedures (refined over decades of "E. coli" use in molecular biology) fairly simple. The bacteria can also be frozen and preserved, creating what Lenski has described as a "frozen fossil record" that can be revived at any time (and can be used to restart recent populations in cases of contamination or other disruption of the experiment). Lenski chose an "E. coli" strain that reproduces only asexually, without bacterial conjugation; this limits the study to evolution based on new mutations and also allows genetic markers to persist without spreading except by common descent.

Methods

Each of the 12 populations is kept in Lenski's laboratory at Michigan State University in a minimal growth medium and transferred daily into a flask of fresh nutrients, with samples of each population preserved at 500-generation (75 day) intervals. The populations are also regularly screened for changes in mean fitness, and supplemental experiments are regularly performed to study interesting developments in the populations. [Richard E. Lenski, [https://myxo.css.msu.edu/ecoli/overview.html Overview of the "E. coli" long-term evolution experiment] , 2000. Accessed June 18, 2008.] As of 2008, the "E. coli" populations have been under study for over 40,000 generations, and are thought to have undergone enough spontaneous mutations that every possible single point mutation in the "E. coli" genome should have occurred multiple times.Cite journal| doi = 10.1073/pnas.0803151105| volume = 105| issue = 23| pages = 7899–7906| last = Blount| first = Zachary D.| coauthors = Christina Z. Borland, Richard E. Lenski| title = Inaugural Article: Historical contingency and the evolution of a key innovation in an experimental population of "Escherichia coli"| journal = Proceedings of the National Academy of Sciences| accessdate = 2008-06-18| date = 2008-06-10| url = http://www.pnas.org/cgi/content/abstract/105/23/7899. This pdflink| [http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf article is available in PDF form] from Richard Lenski's website.]

The initial strain of "E. coli" for Lenski's long-term evolution experiment came from "strain Bc251", as described in a 1966 paper by Seymour Lederberg, via Bruce Levin (who used it in a bacterial ecology experiment in 1972). The defining genetics traits of this strain were: T6^r, Str^r, r⁻m⁻, Ara⁻ (unable to grow on arabinose). Before the beginning of the experiment Lenski prepared a Ara⁺ variant (a point mutation in the "ara" operon that enables growth on arabinose) of the strain; the initial populations consisted of 6 Ara⁻ colonies and 6 Ara⁺ colonies, which allowed the two sets of strains to be differentiated and tested for fitness against each other. Unique genetic markers have since evolved to allow identification of each strain.

Results

In the early years of the experiment, there were several common evolutionary developments shared by the populations. The mean fitness of each population, as measured against the ancestor strain, increased—rapidly at first, but leveling off after close to 20,000 generations (at which point they grew about 70% faster than the ancestor strain). All populations evolved larger cell volumes and lower maximum population densities, and all became specialized for living on glucose (with declines in fitness relative to the ancestor strain when grown in dissimilar nutrients). 4 of the 12 populations developed defects in their ability to repair DNA, greatly increasing the rate of additional mutations in those strains. Although the bacteria in each population are thought to have generated hundreds of millions of mutations over the first 20,000 generations, Lenski has estimated that only 10 to 20 beneficial mutations achieved fixation in each population, with less than 100 total point mutations (including neutral mutations) reaching fixation in each population.

In 2008, Lenski and his collaborators reported on a particularly important adaptation that occurred in one of the twelve populations: the bacteria evolved the ability to utilize citrate as a source of energy. Normally, "E. coli" cannot transport citrate from outside the cell to the cell interior (where it could be incorporated into the citric acid cycle); the lack of citrate transport is considered a defining characteristic of the species. Around generation 33,127, the experimenters noticed a dramatically expanded population-size in one of the samples; they found that this population could grow on the excess citrate in the growth medium. They found that the ability to use citrate could spontaneously (although rarely) appear in cultures replicated from earlier frozen samples of that population, from before the citrate mutation appeared, but not in the other 11 populations or in samples before generation 20,000. According to the authors of the study, this suggests that the mutation depends on an earlier, perhaps non-adaptive, change—and more generally (following the argument of Stephen Jay Gould) "that historical contingency can have a profound and lasting impact" on the course of evolution.

Notes

External links

* [http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html Bacteria make major evolutionary shift in the lab] Bob Holmes "New Scientist" 09 June 2008
* [https://myxo.css.msu.edu/ecoli/ "E. coli" Long-term Experimental Evolution Project Site]
* [http://myxo.css.msu.edu/cgi-bin/lenski/prefman.pl?group=aad List of publications on the experiment]