E. coli long-term evolution experiment

For example, all 12 populations showed a similar pattern of rapid improvement in fitness that decelerated over time, faster growth rates, and increased cell size.

The most notable adaptation reported so far is the evolution of aerobic growth on citrate, which is unusual in E. coli, in one population at some point between generations 31,000 and 31,500.

[12][11] On May 4, 2020, Lenski announced a five-year renewal of the grant through the National Science Foundation's Long-Term Research in Environmental Biology (LTREB) Program that supports the LTEE.

[13] He also announced that Dr. Jeffrey Barrick, an associate professor of Molecular Biosciences at The University of Texas at Austin, would take over supervision of the experiment within the five-year funding period.

[16] 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.

Moreover, due to the long use of E. coli as a principal model organism in molecular biology, a wide array of tools, protocols, and procedures were available for studying changes at the genetic, phenotypic, and physiological levels.

This has permitted the creation of what Lenski describes as a "frozen fossil record" of samples of evolving populations that can be revived at any time.

This frozen fossil record allows populations to be restarted in cases of contamination or other disruption in the experiment, and permits the isolation and comparison of living exemplars of ancestral and evolved clones.

Lenski chose an E. coli strain that reproduces only asexually, lacks any plasmids that could permit bacterial conjugation, and has no viable prophage.

As a consequence, evolution in the experiment occurs only by the core evolutionary processes of mutation, genetic drift, and natural selection.

This strict asexuality also means that genetic markers persist in lineages and clades by common descent, but cannot otherwise spread in the populations.

[19] DM25 also contains a large amount of citrate (about 11 times the concentration of glucose), which was originally included by Davis because it improved the killing efficiency of penicillin during his experiments, though it is now known to aid in E. coli's acquisition of iron from the medium.

This was first described in 2000, when Cooper and Lenski demonstrated that all populations had experienced decay of unused metabolic functions after 20,000 generations, restricting the range of substances on which the bacteria could grow.

Moreover, they concluded that the metabolic losses were not due to antagonistic pleiotropy, but the neutral accumulation of mutations in unused portions of the genome, suggesting that adaptation to a simple environment might not necessarily lead to specialization.

[36] By analyzing the large collection of whole-genome sequences of E. coli clones sampled from the LTEE populations,[37] a 2024 study discovered several possible instances of gene birth that involved the generation of novel mRNA transcripts and proteins associated with nearby mutations.

[11] However, E. coli has a complete citric acid cycle, and therefore metabolizes citrate as an intermediate during aerobic growth on other substances, including glucose.

Although Cit+ strains of E. coli have been isolated from environmental and agricultural samples, in every such case, the trait was found to be due to the presence of a plasmid that carries a foreign citrate transporter.

This metabolic capacity permitted the population to grow several-fold larger than it had previously, due to the large amount of citrate present in the medium.

More generally, the authors suggest these results indicate, following the argument of Stephen Jay Gould, "that historical contingency can have a profound and lasting impact" on the course of evolution.

This new configuration placed a copy of the previously silent, unexpressed citT under the control of the adjacent rnk gene's promoter, which directs expression when oxygen is present.

The researchers found that the number of copies of the rnk-citT module had to be increased to strengthen the Cit+ trait sufficiently to permit the bacteria to grow well on the citrate.

In 2015 paleontologist Douglas Erwin suggested a modification to a four-step model to better reflect a possible distinction between evolutionary novelty and evolutionary innovation, and to highlight the importance of environmental conditions: potentiation, generation of novel phenotypes (actualization), adaptive refinement, and exploitation (conversion of a novelty to an innovation as it becomes important for the ecological establishment of possessing organisms).

[48] In 2014, a research team led by Eric Quandt in the lab of Jeffrey Barrick at the University of Texas at Austin described the application of a new technique called Recursive Genomewide Recombination and Sequencing (REGRES) to identify potentiating mutations among the 70 present in the Ara-3 lineage that evolved Cit+.

This increased DctA expression, they found, permitted Cit+ cells to re-uptake succinate, malate, and fumarate released into the medium by the CitT transporter during import of citrate.

[50] This mutation was in the gltA gene, which encodes citrate synthase, an enzyme involved in the flow of carbon into the citric acid cycle.

The Cit− cells had rapidly evolved the ability to grow on these substances due to a mutation that restored expression of an appropriate transporter protein that was silent in the ancestor.

[53] Barry Hall had already isolated a mutant strain of aerobic citrate-utilizing E. coli in 1982 and he attributed it to two mutations in genes citA and citB, which are linked to the gal operon.

Dustin Van Hofwegen et al. were able to isolate 46 independent citrate-utilizing mutants of E. coli in just 12 to 100 generations using highly prolonged selection under starvation, during which the bacteria would sample more mutations more rapidly.

They concluded that the rarity of the citrate-utilizing mutant in Lenski's research was likely a result of the selective experimental conditions used by his team rather than being a unique evolutionary speciation event.

[56] In contrast, Van Hofwegen's team allowed for a continuous selection period of 7 days, which yielded a more rapid development of citrate-using E. coli.