Witnessing Natural Selection at Warp Speed
Look at a petri dish or a drop of pond water, and you're looking at a bustling metropolis where a relentless, invisible war is being waged. The combatants are trillions of bacteria and viruses, locked in a battle for survival that has been raging for billions of years. For scientists, this microscopic battlefield is not just a subject of study; it's a perfect, high-speed laboratory for observing the principles of natural selection in real-time. While Darwin studied finches over centuries, modern biologists can watch evolution unfold in days, with profound implications for our health, our medicines, and our understanding of life itself.
At its heart, evolution by natural selection is an elegant and simple concept, built on three key principles:
Individuals in a population are not identical. They possess variations in their traits. In the microbial world, this could be a random genetic mutation that makes one bacterium slightly better at pumping out a toxin or one virus with a protein coat that's harder for an immune system to recognize.
These variations are heritable, passed from parent to offspring. Bacteria reproduce by dividing, creating perfect clones, but mutations during replication introduce new variations. Viruses hijack host cells to create copies of themselves, and errors in this process do the same.
Individuals with traits that give them a survival or reproductive advantage in a specific environment will, on average, leave more offspring. Over time, these advantageous traits become more common in the population.
In the microbial world, the "environment" is a brutal and ever-changing landscape. It can be a sudden dose of antibiotic, a shift in temperature, a lack of nutrients, or the constant threat of a predatory virus. The organisms that can survive these challenges are the ones that pass their genes to the next generation. This is evolution in its purest, fastest form.
To truly see this process in action, we turn to one of the most famous long-term experiments in biology: the E. coli Long-Term Evolution Experiment (LTEE) started by Dr. Richard Lenski in 1988.
To directly observe the process of evolution by tracking genetic changes in populations of the bacterium Escherichia coli over thousands of generations.
The beauty of the LTEE lies in its simplicity. Here's how it works, step-by-step:
Lenski started 12 genetically identical populations (flasks) from a single E. coli bacterium.
Every day, a small sample (1%) from each flask is transferred to a new flask containing fresh, but limited, glucose. This is the bacteria's only food source.
The transfer creates a "population bottleneck." Only a tiny fraction of the bacteria get to found the next day's population.
The new flask has abundant food, but only for a short time. The bacteria that can reproduce the fastest and most efficiently in this environment will outcompete their slower neighbors and come to dominate the population.
Every 500 generations (about 75 days), samples of bacteria from each population are frozen, creating a "frozen fossil record" that allows scientists to go back in time and compare ancestors with their modern descendants.
This cycle has been repeated for over 75,000 generations and counting—the equivalent of over 1.5 million years of human evolution!
The results have been a spectacular confirmation of evolutionary theory. All 12 populations have evolved to become much better at reproducing in their specific environment. Their fitness, measured as their growth rate relative to their ancestor, has increased significantly.
But the most stunning discovery came around generation 33,000 in one of the 12 populations. The bacteria in this flask suddenly experienced a massive population boom. Lenski and his team discovered that these E. coli had evolved a game-changing new ability: they could now eat citrate.
E. coli cannot normally use citrate as a food source in the presence of oxygen. This is a defining trait of the species. Yet, this one population had overcome a fundamental metabolic limitation. It was a rare, monumental evolutionary event—the origin of a new function—witnessed in real-time.
The LTEE provides direct, observable evidence that evolution is not a theoretical historical process but an ongoing, powerful force. It shows that evolution is:
All 12 lines improved, though in different ways.
It depends on random mutations, but selection acts predictably.
It can produce complex new traits, like citrate metabolism, from accumulated mutations.
| Generation | Population A | Population B | Population C (Citrate+) |
|---|---|---|---|
| 0 (Ancestor) | 1.00 | 1.00 | 1.00 |
| 2,000 | 1.15 | 1.22 | 1.18 |
| 10,000 | 1.31 | 1.45 | 1.40 |
| 50,000 | 1.52 | 1.61 | 1.85 |
Caption: Over time, all populations evolved larger cell sizes, a common adaptation in this environment. The citrate-using population (C) shows a distinct trajectory after it gained access to a second food source.
| Population | Fitness at 10,000 gens | Fitness at 50,000 gens |
|---|---|---|
| 1 | 1.45 | 1.68 |
| 2 | 1.48 | 1.71 |
| 3 (Citrate+) | 1.42 | 3.05 |
| ... | ... | ... |
| Average | 1.46 | 1.85 |
Caption: The dramatic fitness jump in the citrate-using population (3) after generation 33,000 demonstrates how a key innovation can provide a massive selective advantage.
Some populations evolved higher mutation rates (became "mutators"), which can accelerate adaptation.
About half of the LTEE populations evolved defects in their DNA repair machinery, making them mutators. This is a risky strategy (more harmful mutations) but can be beneficial in a stable environment by generating more beneficial mutations.
To run experiments like the LTEE, scientists rely on a suite of specialized tools and reagents.
A simple growth broth with glucose as the sole food source. This creates a controlled, defined environment where competition for limited resources drives natural selection.
Petri dishes filled with a nutrient-infused jelly. Used to grow isolated bacterial colonies, count the number of living cells, and test for new abilities (e.g., plating on citrate agar to detect citrate-users).
A device that measures the cloudiness (optical density) of a liquid bacterial culture. This provides a quick, non-invasive way to estimate bacterial population density and growth rate.
The ultimate tool for tracking evolution. By sequencing the genomes of ancestral and evolved bacteria, scientists can pinpoint the exact genetic mutations responsible for new traits.
Used as selective pressures. Adding a low dose of antibiotic or a virus (bacteriophage) to the environment directly tests the population's ability to evolve resistance.
The "time machine" of the LTEE. Preserving frozen samples creates a living fossil record, allowing researchers to resurrect ancestors and directly compete them against their evolved descendants.
The rapid evolution of bacteria and viruses is more than an academic curiosity; it is a force that intimately affects our lives. It is the reason we face the looming crisis of antibiotic resistance and the constant challenge of new flu strains every year. By studying evolution in these tiny, fast-reproducing organisms, we gain the predictive power to understand how a pathogen might evolve to escape a drug or a vaccine.
The flasks in Richard Lenski's lab are a humbling reminder. They show us that evolution is not a slow, ponderous force of the distant past. It is happening here and now, all around us and within us, driving an unseen arms race of astounding complexity. In studying these microscopic worlds, we hold a mirror to the process that shaped all life on Earth.