Ecology and evolution are typically viewed as separate microbiome processes interacting over short scales. To study these dynamics in a natural setting, scientists conducted a new study in which they gathered a two-decade-long, 471-metagenome time series from Lake Mendota in Wisconsin, USA.
Researchers discovered that bacterial species in Lake Mendota evolved rapidly throughout the year, likely in response to seasonal shifts. Gene variants fluctuated across generations, but many species reverted genetically to their original state after approximately a thousand generations of evolutionary pressures.
Since individual microbes have lifespans of only a few days, the scientists tracked genetic changes across seasons by comparing bacterial genomes. The study revealed a cyclical pattern where evolution resets yearly as if replaying the same sequence without significant long-term change.
Robin Rohwer, a postdoctoral researcher at The University of Texas at Austin in the lab of co-author Brett Baker, said, “I was surprised that such a large portion of the bacterial community was undergoing this type of change. I hoped to observe just a couple of cool examples, but there were hundreds.”
Lake Mendota experiences dramatic seasonal changes, with ice covering the water in winter and algae dominating in summer. Different strains within the same bacterial species are better suited to these varying conditions, causing them to outcompete each other depending on the season.
The research team used a unique archive of 471 water samples collected over 20 years from Lake Mendota as part of long-term National Science Foundation-funded monitoring projects to explore these dynamics. They constructed a metagenome for each sample, analyzing the genetic sequences from DNA fragments left behind by bacteria and other organisms. This created the longest metagenome time series ever gathered from a natural system.
The study represents a groundbreaking shift in our understanding of how microbial communities evolve and adapt over time, marking just the beginning of what these data can reveal about microbial ecology and evolution in the natural world.
The archive also uncovered longer-lasting genetic changes in the microbial community. In 2012, Lake Mendota experienced atypical conditions: early ice melt, a hotter and drier summer, reduced river flow, and a shortage of algae, typically providing organic nitrogen for bacteria. As a result, Rohwer and the team found that many bacteria in the lake underwent significant genetic changes related to nitrogen metabolism, likely in response to the algae scarcity.
Rohwer said, “I thought, out of hundreds of bacteria, I might find one or two with a long-term shift. But instead, 1 in 5 had big sequence changes that played out over the years. We could only dig deep into one species, but some of those other species probably also had major gene changes.”
Climate scientists predict more extreme weather events—like the hot, dry summer experienced at Lake Mendota in 2012—for the midwestern U.S. in the coming years.
“Climate change is slowly shifting the seasons and average temperatures, but also causing more abrupt, extreme weather events,” Rohwer said. “We don’t know exactly how microbes will respond to climate change, but our study suggests they will evolve in response to both these gradual and abrupt changes.”
Unlike the famous Long-Term Evolution Experiment at the University of Texas, which focuses on bacterial evolution in a controlled environment, Rohwer and Baker’s study examined bacterial evolution in the complex and ever-changing natural conditions of Lake Mendota.
The researchers utilized supercomputing resources at the Texas Advanced Computing Center (TACC) to reconstruct bacterial genomes from the short DNA sequences in water samples. Rohwer estimated that the same analysis, which took a few months at TACC, would have taken 34 years using a standard laptop. The study involved over 30,000 genomes from about 2,800 species.
Rohwer likened the process to piecing together a puzzle: “Imagine each species’ genome is a book, and each little DNA fragment is a sentence. Each sample has hundreds of books, all cut up into these sentences. To reassemble each book, you have to figure out which sentences belong to which book and put them back in order.”
Journal Reference:
- Rohwer, R.R., Kirkpatrick, M., Garcia, S.L. et al. Two decades of bacterial ecology and evolution in a freshwater lake. Nat Microbiol (2025). DOI: 10.1038/s41564-024-01888-3